High-Throughput Identification of Bacteria and Yeast by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry in Conventional Medical Microbiology Laboratories ▿

PubMed Central

van Veen, S. Q.; Claas, E. C. J.; Kuijper, Ed J.

2010-01-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory. PMID:20053859

High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories.

PubMed

van Veen, S Q; Claas, E C J; Kuijper, Ed J

2010-03-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory.

Evaluation of two matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems for the identification of Candida species.

PubMed

Lacroix, C; Gicquel, A; Sendid, B; Meyer, J; Accoceberry, I; François, N; Morio, F; Desoubeaux, G; Chandenier, J; Kauffmann-Lacroix, C; Hennequin, C; Guitard, J; Nassif, X; Bougnoux, M-E

2014-02-01

Candida spp. are responsible for severe infections in immunocompromised patients and those undergoing invasive procedures. The accurate identification of Candida species is important because emerging species can be associated with various antifungal susceptibility spectra. Conventional methods have been developed to identify the most common pathogens, but have often failed to identify uncommon species. Several studies have reported the efficiency of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the identification of clinically relevant Candida species. In this study, we evaluated two commercially available MALDI-TOF systems, Andromas™ and Bruker Biotyper™, for Candida identification in routine diagnosis. For this purpose, we investigated 1383 Candida isolates prospectively collected in eight hospital laboratories during routine practice. MALDI-TOF MS results were compared with those obtained using conventional phenotypic methods. Analysis of rDNA gene sequences with internal transcribed regions or D1-D2 regions is considered the reference standard for identification. Both MALDI-TOF MS systems could accurately identify 98.3% of the isolates at the species level (1359/1383 for Andromas™; 1360/1383 for Bruker Biotyper™) vs. 96.5% for conventional techniques. Furthermore, whereas conventional methods failed to identify rare or emerging species, these were correctly identified by MALDI-TOF MS. Both MALDI-TOF MS systems are accurate and cost-effective alternatives to conventional methods for mycological identification of clinically relevant Candida species and should improve the diagnosis of fungal infections as well as patient management. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Application of polymerase chain reaction for detection of Vibrio parahaemolyticus associated with tropical seafoods and coastal environment.

PubMed

Dileep, V; Kumar, H S; Kumar, Y; Nishibuchi, M; Karunasagar, Indrani; Karunasagar, Iddya

2003-01-01

To study the incidence of Vibrio parahaemolyticus in seafoods, water and sediment by molecular techniques vs conventional microbiological methods. Of 86 samples analysed, 28 recorded positive for V. parahaemolyticus by conventional microbiological method, while 53 were positive by the toxR-targeted PCR, performed directly on enrichment broth lysates. While one sample of molluscan shellfish was positive for tdh gene, trh gene was detected in three enrichment broths of molluscan shellfish. Direct application of PCR to enrichment broths will be useful for the rapid and sensitive detection of potentially pathogenic strains of V. parahemolyticus in seafoods. Vibrio parahaemolyticus is an important human pathogen responsible for food-borne gastroenteritis world-wide. As, both pathogenic and non-pathogenic strains of V. parahaemolyticus exist in the seafood, application of PCR specific for the virulence genes (tdh & trh) will help in detection of pathogenic strains of V. parahaemolyticus and consequently reduce the risk of food-borne illness.

Cost Savings Realized by Implementation of Routine Microbiological Identification by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

PubMed

Tran, Anthony; Alby, Kevin; Kerr, Alan; Jones, Melissa; Gilligan, Peter H

2015-08-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is an emerging technology for rapid identification of bacterial and fungal isolates. In comparison to conventional methods, this technology is much less labor intensive and can provide accurate and reliable results in minutes from a single isolated colony. We compared the cost of performing the bioMérieux Vitek MALDI-TOF MS with conventional microbiological methods to determine the amount saved by the laboratory by converting to the new technology. Identification costs for 21,930 isolates collected between April 1, 2013, and March 31, 2014, were directly compared for MALDI-TOF MS and conventional methodologies. These isolates were composed of commonly isolated organisms, including commonly encountered aerobic and facultative bacteria and yeast but excluding anaerobes and filamentous fungi. Mycobacterium tuberculosis complex and rapidly growing mycobacteria were also evaluated for a 5-month period during the study. Reagent costs and a total cost analysis that included technologist time in addition to reagent expenses and maintenance service agreement costs were analyzed as part of this study. The use of MALDI-TOF MS equated to a net savings of $69,108.61, or 87.8%, in reagent costs annually compared to traditional methods. When total costs are calculated to include technologist time and maintenance costs, traditional identification would have cost $142,532.69, versus $68,886.51 with the MALDI-TOF MS method, resulting in a laboratory savings of $73,646.18, or 51.7%, annually by adopting the new technology. The initial cost of the instrument at our usage level would be offset in about 3 years. MALDI-TOF MS not only represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates, it also provides a significant cost savings for the laboratory. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Evaluation of the microbiological quality of conventional and organic leafy greens at the time of purchase from retail markets in Alexandria, Egypt.

PubMed

Khalil, Rowaida; Gomaa, Mohamed

2014-01-01

This is a pioneer study in Egypt that provides some assessment of the microbiological quality of conventional and organic leafy green vegetables that constitute an essential component of the Egyptians' daily diet. A total of 380 samples of unpackaged whole conventional and 84 packaged whole organic leafy greens were collected from retail markets in Alexandria, and analyzed for total aerobic mesophilic count (AMC) and total E. coli count (ECC) using the standard spread plate method. Mean AMC values for organic samples were statistically less (p < 0.05) than those of the corresponding conventional samples. Conventional radish and organic parsley samples had the highest AMC of 7.17 and 7.68 log CFU/g respectively, while conventional green cabbage and organic basil had the lowest AMC of 3.63 and 3.23 log CFU/g respectively. The presence of E. coli in 100% of the studied leafy greens was indicative of potential fecal contamination, in view of open and unhygienic environmental and unsanitary handling conditions, as leafy green items are available for sale by street-vendors. Unsatisfactory AMC and ECC levels encountered in the studied samples, warrant future investigations to determine the potential prevalence of foodborne pathogens, and to identify sources of dominating microorganisms, which could make a contribution to the field of food safety

A field study evaluation of Petrifilm™ plates as a 24-h rapid diagnostic test for clinical mastitis on a dairy farm.

PubMed

Mansion-de Vries, Elisabeth Maria; Knorr, Nicole; Paduch, Jan-Hendrik; Zinke, Claudia; Hoedemaker, Martina; Krömker, Volker

2014-03-01

Clinical mastitis is one of the most common and expensive diseases of dairy cattle. To make an informed treatment decision, it is important to know the causative pathogen. However, no detection of bacterial growth can be made in approximately 30% of all clinical cases of mastitis. Before selecting the treatment regimen, it is important to know whether the mastitis-causing pathogen (MCP) is Gram-positive or Gram-negative. The aim of this field study was to investigate whether using two 3M Petrifilm™ products on-farm (which conveys a higher degree of sample freshness but also bears a higher risk for contamination than working in a lab) as 24-h rapid diagnostic of clinical mastitis achieved results that were comparable to the conventional microbiological diagnostic method. AerobicCount (AC)-Petrifilm™ and ColiformCount (CC)-Petrifilm™ were used to identify the total bacterial counts and Gram-negative bacteria in samples from clinical mastitis cases, respectively. Missing growth on both plates was classified as no bacterial detection. Growth only on the AC-Petrifilm™ was assessed as Gram-positive, and growth on both Petrifilm™ plates was assessed as Gram-negative bacterial growth. Additionally, milk samples were analysed by conventional microbiological diagnostic method on aesculin blood agar as a reference method. Overall, 616 samples from clinical mastitis cases were analysed. Using the reference method, Gram-positive and Gram-negative bacteria, mixed bacterial growth, contaminated samples and yeast were determined in 32.6%, 20.0%, 2.5%, 14.1% and 1.1% of the samples, respectively. In 29.7% of the samples, microbiological growth could not be identified. Using the Petrifilm™ concept, bacterial growth was detected in 59% of the culture-negative samples. The sensitivity of the Petrifilm™ for Gram-positive and Gram-negative MCP was 85.2% and 89.9%, respectively. The specificity was 75.4% for Gram-positive and 88.4% for Gram-negative MCP. For the culture-negative samples, sensitivity was 41.0% and specificity was 91.0%. The results indicate that the Petrifilm™ concept is suitable for therapeutic decision-making at the farm level or in veterinary practice. As this concept does not allow any statement about the genus or species of microorganisms, relevant MCP should be assessed periodically at the herd level with conventional microbiological diagnostics. Copyright © 2014 Elsevier B.V. All rights reserved.

The effect of a cannula milk sampling technique on the microbiological diagnosis of bovine mastitis.

PubMed

Friman, M; Hiitiö, H; Niemi, M; Holopainen, J; Pyörälä, S; Simojoki, H

2017-08-01

Two methods of collecting milk samples from mastitic bovine mammary quarters were compared. Samples were taken in a consistent order in which standard aseptic technique sampling was done first, followed by insertion of a sterile cannula through the teat canal and collection of a second sample. Microbiological results of those two sampling techniques were compared. Milk samples were analysed using multiplex real-time polymerase chain reaction (PCR). The cannula technique produced a reduced number of microbial species or groups of species per sample compared with conventional sampling. Staphylococcus spp. were the most common species identified and were detected more often during conventional sampling than with cannula sampling. Staphylococcus spp. identified in milk samples could also have originated from the teat canal without being present in the milk. The number of samples positive for Trueperella pyogenes or yeasts in the conventional samples was twice as high as in the cannula samples, indicating that the presence of Trueperella pyogenes and yeast species should not necessarily be interpreted as being the causative agents of bovine intra-mammary infections (IMI). Copyright © 2017 Elsevier Ltd. All rights reserved.

Application of MALDI-TOF mass spectrometry in clinical diagnostic microbiology.

PubMed

De Carolis, Elena; Vella, Antonietta; Vaccaro, Luisa; Torelli, Riccardo; Spanu, Teresa; Fiori, Barbara; Posteraro, Brunella; Sanguinetti, Maurizio

2014-09-12

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently emerged as a powerful technique for identification of microorganisms, changing the workflow of well-established laboratories so that its impact on microbiological diagnostics has been unparalleled. In comparison with conventional identification methods that rely on biochemical tests and require long incubation procedures, MALDI-TOF MS has the advantage of identifying bacteria and fungi directly from colonies grown on culture plates in a few minutes and with simple procedures. Numerous studies on different systems available demonstrate the reliability and accuracy of the method, and new frontiers have been explored besides microbial species level identification, such as direct identification of pathogens from positive blood cultures, subtyping, and drug susceptibility detection.

Efficacy of the FilmArray blood culture identification panel for direct molecular diagnosis of infectious diseases from samples other than blood.

PubMed

Micó, Miquel; Navarro, Ferran; de Miniac, Daniela; González, Yésica; Brell, Albert; López, Cristina; Sánchez-Reus, Ferran; Mirelis, Beatriz; Coll, Pere

2015-12-01

Molecular-based techniques reduce the delay in diagnosing infectious diseases and therefore contribute to better patient outcomes. We assessed the FilmArray blood culture identification (BCID) panel (Biofire Diagnostics/bioMérieux) directly on clinical specimens other than blood: cerebrospinal, joint, pleural and ascitic fluids, bronchoscopy samples and abscesses. We compared the results from 88 samples obtained by culture-based techniques. The percentage of agreement between the two methods was 75 % with a Cohen κ value of 0.51. Global sensitivity and specificity using the FilmArray BCID panel were 71 and 97 %, respectively. Sensitivity was poorer in samples with a low bacterial load, such as ascitic and pleural fluids (25 %), whereas the sensitivity for abscess samples was high (89 %). These findings suggest that the FilmArray BCID panel could be useful to perform microbiological diagnosis directly from samples other than positive blood cultures, as it offers acceptable sensitivity and moderate agreement with conventional microbiological methods. Nevertheless, cost-benefit studies should be performed before introducing this method into algorithms for microbiological diagnostics.

Future of diagnostic microbiology.

PubMed

Khardori, N

2014-01-01

Diagnostic Microbiology is the tool that makes it possible to identify the exact etiology of infectious diseases and the most optimal therapy at the level of individual patients as well as communities. Conventional methods require time to grow the microbes in vitro under specific conditions and not all microbes are easily cultivable. This is followed by biochemical methods for identification which also require hours and sometimes days. Transport of the specimens under less than ideal conditions, prior use of antibiotics and small number of organisms are among the factors that render culture-based methods less reliable. Newer methods depend on amplification of nucleic acids followed by use of probes for identification. This mitigates the need for higher microbial load, presence of metabolically active viable organisms and shortens the time to reporting. These methods can be used to detect antibiotic resistance genes directly from the specimen and help direct targeted therapy. Since these methods will not fulfill all the diagnostic needs, a second approach is being used to shorten the time to identification after the organism has already grown. Mass spectrometry and bioinformatics are the tools making this possible. This review gives a historical perspective on diagnostic microbiology, discusses the pitfalls of current methodology and provides an overview of newer and future methods.

Comparison of sensory, microbiological, and biochemical parameters of microwave versus indirect UHT fluid skim milk during storage.

PubMed

Clare, D A; Bang, W S; Cartwright, G; Drake, M A; Coronel, P; Simunovic, J

2005-12-01

Shelf-stable milk could benefit from sensory quality improvement. Current methods of heating cause flavor and nutrient degradation through exposure to overheated thermal exchange surfaces. Rapid heating with microwaves followed by sudden cooling could reduce or eliminate this problem. The objectives for this study were focused on designing and implementing continuous microwave thermal processing of skim fluid milks (white and chocolate) to compare sensory, microbiological, and biochemical parameters with conventionally prepared, indirect UHT milks. All test products were aseptically packaged and stored at ambient temperature for 12 mo. Every 3 mo, samples were taken for microbiological testing, reactive sulfhydryl determinations, active enzyme analysis, instrumental viscosity readings, color measurements, and descriptive sensory evaluation. Microbiological plate counts were negative on all milks at each time point. Enzymatic assays showed that plasmin was inactivated by both heat treatments. 5,5'-dithio-bis(2-nitrobenzoic acid) analysis, a measure of reactive sulfhydryl (-SH-) groups, showed that the initial thiol content was not significantly different between the microwave-processed and UHT-treated milks. However, both heating methods resulted in an increased thiol level compared with conventionally pasteurized milk samples due to the higher temperatures attained. Sulfhydryl oxidase, a milk enzyme that catalyzes disulfide bond formation using a variety of protein substrates, retained activity following microwave processing, and decreased during storage. Viscosity values were essentially equivalent in microwave- and UHT-heated white skim milks. Sensory analyses established that UHT-treated milks were visibly darker, and exhibited higher caramelized and stale/fatty flavors with increased astringency compared with the microwave samples. Sweet aromatic flavor and sweet taste decreased during storage in both UHT and microwave milk products, whereas stale/fatty flavors increased over time. Sensory effects were more apparent in white milks than in chocolate varieties. These studies suggest that microwave technology may provide a useful alternative processing method for delivery of aseptic milk products that retain a long shelf life.

Treatment of complicated urinary tract infection and acute pyelonephritis by short-course intravenous levofloxacin (750 mg/day) or conventional intravenous/oral levofloxacin (500 mg/day): prospective, open-label, randomized, controlled, multicenter, non-inferiority clinical trial.

PubMed

Ren, Hong; Li, Xiao; Ni, Zhao-Hui; Niu, Jian-Ying; Cao, Bin; Xu, Jie; Cheng, Hong; Tu, Xiao-Wen; Ren, Ai-Min; Hu, Ying; Xing, Chang-Ying; Liu, Ying-Hong; Li, Yan-Feng; Cen, Jun; Zhou, Rong; Xu, Xu-Dong; Qiu, Xiao-Hui; Chen, Nan

2017-03-01

To compare the efficacy and safety of short-course intravenous levofloxacin (LVFX) 750 mg with a conventional intravenous/oral regimen of LVFX 500 mg in patients from China with complicated urinary tract infections (cUTIs) and acute pyelonephritis (APN). This was a prospective, open-label, randomized, controlled, multicenter, non-inferiority clinical trial. Patients with cUTI and APN were randomly assigned to a short-course therapy group (intravenous LVFX at750 mg/day for 5 days) or a conventional therapy group (intravenous/oral regimen of LVFX at 500 mg/day for 7-14 days). The clinical, laboratory, and microbiological results were evaluated for efficacy and safety. The median dose of LVFX was 3555.4 mg in the short-course therapy group and 4874.2 mg in the conventional therapy group. Intention-to-treat analysis indicated the clinical effectiveness in the short-course therapy group (89.87%, 142/158) was non-inferior to that in the conventional therapy group (89.31%, 142/159). The microbiological effectiveness rates were also similar (short-course therapy: 89.55%, 60/67; conventional therapy: 86.30%, 63/73; p > 0.05). There were no significant differences in other parameters, including clinical and microbiological recurrence rates. The incidence of adverse effects and drug-related adverse effects were also similar for the short-course therapy group (21.95%, 36/164; 18.90%, 31/164) and the conventional therapy group (23.03%, 38/165; 15.76%, 26/165). Patients with cUTIs and APN who were given short-course LVFX therapy and conventional LVFX therapy had similar outcomes in clinical and microbiological efficacy, tolerance, and safety. The short-course therapy described here is a more convenient alternative to the conventional regimen with potential implication in anti-resistance and cost saving.

Comparison of the lysis centrifugation method with the conventional blood culture method in cases of sepsis in a tertiary care hospital.

PubMed

Parikh, Harshal R; De, Anuradha S; Baveja, Sujata M

2012-07-01

Physicians and microbiologists have long recognized that the presence of living microorganisms in the blood of a patient carries with it considerable morbidity and mortality. Hence, blood cultures have become critically important and frequently performed test in clinical microbiology laboratories for diagnosis of sepsis. To compare the conventional blood culture method with the lysis centrifugation method in cases of sepsis. Two hundred nonduplicate blood cultures from cases of sepsis were analyzed using two blood culture methods concurrently for recovery of bacteria from patients diagnosed clinically with sepsis - the conventional blood culture method using trypticase soy broth and the lysis centrifugation method using saponin by centrifuging at 3000 g for 30 minutes. Overall bacteria recovered from 200 blood cultures were 17.5%. The conventional blood culture method had a higher yield of organisms, especially Gram positive cocci. The lysis centrifugation method was comparable with the former method with respect to Gram negative bacilli. The sensitivity of lysis centrifugation method in comparison to conventional blood culture method was 49.75% in this study, specificity was 98.21% and diagnostic accuracy was 89.5%. In almost every instance, the time required for detection of the growth was earlier by lysis centrifugation method, which was statistically significant. Contamination by lysis centrifugation was minimal, while that by conventional method was high. Time to growth by the lysis centrifugation method was highly significant (P value 0.000) as compared to time to growth by the conventional blood culture method. For the diagnosis of sepsis, combination of the lysis centrifugation method and the conventional blood culture method with trypticase soy broth or biphasic media is advocable, in order to achieve faster recovery and a better yield of microorganisms.

A quick and effective method of limb preparation with health, safety and efficiency benefits.

PubMed

Naderi, N; Maw, K; Thomas, M; Boyce, D E; Shokrollahi, K

2012-03-01

Pre-operative limb preparation (PLP) usually involves lifting the limb and holding it in a fixed 'static' posture for several minutes. This is hazardous to theatre staff. Furthermore, 'painting' the limb can be time consuming and difficult areas such as between toes and fingers may remain unsterile. We demonstrate the time efficiency and asepsis achieved using the 'sterile bag' preparation technique. An additional advantage is the ability to prepare and anaesthetise a limb prior to theatre, increasing efficiency substantially for units with a large throughput of cases, such as day-case hand surgery lists. We monitored the duration of PLP in 20 patients using the 'sterile bag' technique compared to 20 patients using a conventional 'painting' method. Additionally, microbiology samples acquired from prepared upper limbs of 27 sequential patients operated on by a single surgeon over a two-month period were sent for culture immediately prior to commencement of surgery. The mean duration of the 'sterile bag' PLP was significantly lower than that of the conventional method (24 seconds vs 85 seconds, p=0.045). The technique can take as little as ten seconds (n=1). Final microbiology reports showed no growth for any of the 27 patients from whom a culture sample was taken. The sterile bag technique is effective in achieving asepsis, has the potential to increase theatre efficiency and reduces manual handling hazards compared to the conventional method. It is now taught to all theatre staff in our hospital during manual handling training. It can be undertaken in approximately ten seconds with practice for the upper limb.

The potential of high resolution melting analysis (hrma) to streamline, facilitate and enrich routine diagnostics in medical microbiology.

PubMed

Ruskova, Lenka; Raclavsky, Vladislav

2011-09-01

Routine medical microbiology diagnostics relies on conventional cultivation followed by phenotypic techniques for identification of pathogenic bacteria and fungi. This is not only due to tradition and economy but also because it provides pure culture needed for antibiotic susceptibility testing. This review focuses on the potential of High Resolution Melting Analysis (HRMA) of double-stranded DNA for future routine medical microbiology. Search of MEDLINE database for publications showing the advantages of HRMA in routine medical microbiology for identification, strain typing and further characterization of pathogenic bacteria and fungi in particular. The results show increasing numbers of newly-developed and more tailor-made assays in this field. For microbiologists unfamiliar with technical aspects of HRMA, we also provide insight into the technique from the perspective of microbial characterization. We can anticipate that the routine availability of HRMA in medical microbiology laboratories will provide a strong stimulus to this field. This is already envisioned by the growing number of medical microbiology applications published recently. The speed, power, convenience and cost effectiveness of this technology virtually predestine that it will advance genetic characterization of microbes and streamline, facilitate and enrich diagnostics in routine medical microbiology without interfering with the proven advantages of conventional cultivation.

[Microbiological diagnosis of viral respiratory infections].

PubMed

Eiros, José M; Ortiz de Lejarazu, Raúl; Tenorio, Alberto; Casas, Inmaculada; Pozo, Francisco; Ruiz, Guillermo; Pérez-Breña, Pilar

2009-03-01

Acute respiratory infection is the most common disease occurring over a person's lifetime, with etiological variations determined mainly by age, environmental circumstances, the healthcare setting, and the underlying pathology. More than 200 different viruses distributed in six viral families have been implicated in the pathogenesis of respiratory tract infection. These facts are generating an increasing diagnostic demand that should be incorporated into the healthcare setting without delay. To meet this demand, the Spanish Society of Infectious Diseases and Clinical Microbiology has updated its Standard Procedure for the microbiological diagnosis of viral respiratory infection. This document contains an update primarily of infections caused by influenza viruses, and secondarily, infections due to other conventional and emerging respiratory viruses. In all cases, the methods for direct virological diagnosis (cell culture, and detection of antigens and nucleic acid) are reviewed, with special reference to techniques for molecular detection and genetic characterization.

Real-time quantitative PCR of Staphylococcus aureus and application in restaurant meals.

PubMed

Berrada, H; Soriano, J M; Mañes, J; Picó, Y

2006-01-01

Staphylococcus aureus is considered the second most common pathogen to cause outbreaks of food poisoning, exceeded only by Campylobacter. Consumption of foods containing this microorganism is often identified as the cause of illness. In this study, a rapid, reliable, and sensitive real-time quantitative PCR was developed and compared with conventional culture methods. Real-time quantitative PCR was carried out by purifying DNA extracts of S. aureus with a Staphylococcus sample preparation kit and quantifying it in the LightCycler system with hybridization probes. The assay was linear from a range of 10 to 10(6) S. aureus cells (r2 > 0.997). The PCR reaction presented an efficiency of >85%. Accuracy of the PCR-based assay, expressed as percent bias, was around 13%, and the precision, expressed as a percentage of the coefficient of variation, was 7 to 10%. Intraday and interday variability were studied at 10(2) CFU/g and was 12 and 14%, respectively. The proposed method was applied to the analysis of 77 samples of restaurant meals in Valencia (Spain). In 11.6% of samples S. aureus was detected by real-time quantitative PCR, as well as by the conventional microbiological method. An excellent correspondence between real-time quantitative PCR and microbiological numbers (CFU/g) was observed with deviations of < 28%.

Evaluation of a Parchment Document, the 13th Century Incorporation Charter for the City of Krakow, Poland, for Microbial Hazards.

PubMed

Lech, Tomasz

2016-05-01

The literature of environmental microbiology broadly discusses issues associated with microbial hazards in archives, but these publications are mainly devoted to paper documents. There are few articles on historical parchment documents, which used to be very important for the development of literature and the art of writing. These studies present a broad spectrum of methods for the assessment of biodeterioration hazards of the parchment document in question. They are based on both conventional microbiological methods and advanced techniques of molecular biology. Here, a qualitative analysis was conducted, based on genetic identification of bacteria and fungi present on the document as well as denaturing gradient gel electrophoresis profiling and examining the destructive potential of isolated microbes. Moreover, the study involved a quantitative and qualitative microbiological assessment of the indoor air in the room where the parchment was kept. The microbes with the highest destructive potential that were isolated from the investigated item were Bacillus cereus and Acinetobacter lwoffii bacteria and Penicillium chrysogenum,Chaetomium globosum, and Trichoderma longibrachiatum fungi. The presence of the B. cereuss train was particularly interesting since, under appropriate conditions, it leads to complete parchment degradation within several days. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Classification of shiga toxin-producing escherichia coli (STEC) serotypes with hyperspectral microscope imagery

USDA-ARS?s Scientific Manuscript database

Non-O157:H7 Shiga toxin-producing Escherichia coli (STEC) strains such as O26, O45, O103, O111, O121 and O145 are recognized as serious outbreak to cause human illness due to their toxicity. Since a conventional microbiological method for cell counting is laborious and time-consuming process, optica...

Classification of non-O157 shiga toxin-producing escherichia coli(STEC) serotypes with hyperspectral microscope imaging

USDA-ARS?s Scientific Manuscript database

Non-O157 Shiga toxin-producing Escherichia coli (STEC) strains such as O26, O45, O103, O111, O121 and O145 are recognized as serious outbreak to cause human illness due to their toxicity. A conventional microbiological method for cell counting is laborious and needs long time for the results. Since ...

Agricultural reuse of municipal wastewater through an integral water reclamation management.

PubMed

Intriago, Juan Carlo; López-Gálvez, Francisco; Allende, Ana; Vivaldi, Gaetano Alessandro; Camposeo, Salvatore; Nicolás Nicolás, Emilio; Alarcón, Juan José; Pedrero Salcedo, Francisco

2018-05-01

The DESERT-prototype, a state-of-the-art compact combination of water treatment technologies based on filtration and solar-based renewable energy, was employed to reclaim water for agricultural irrigation. Water reclaimed through the DESERT-prototype (PW) from a secondary effluent of a wastewater treatment plant, as well as conventional irrigation water (CW) and the secondary effluent (SW) itself, were employed to cultivate baby romaine lettuces in a greenhouse in Murcia (Spain), by means of drip and sprinkler irrigation methods, thus establishing six treatments. Assessments of physicochemical and microbiological quality of irrigation water, as well as agronomic and microbiological quality of crops from all treatments, showed that results associated to PW complied in all cases with relevant standards and guidelines. In contrast, results linked to SW and CW presented certain non-compliance cases of water and crop microbiological quality. These assessments lead to conclude that the DESERT-prototype is an appropriate technology for safe water reclamation oriented to agricultural production, that can be complemented by a proper irrigation method in reaching safety targets. Copyright © 2018 Elsevier Ltd. All rights reserved.

Controlling organic chemical hazards in food manufacturing: a hazard analysis critical control points (HACCP) approach.

PubMed

Ropkins, K; Beck, A J

2002-08-01

Hazard analysis by critical control points (HACCP) is a systematic approach to the identification, assessment and control of hazards. Effective HACCP requires the consideration of all hazards, i.e., chemical, microbiological and physical. However, to-date most 'in-place' HACCP procedures have tended to focus on the control of microbiological and physical food hazards. In general, the chemical component of HACCP procedures is either ignored or limited to applied chemicals, e.g., food additives and pesticides. In this paper we discuss the application of HACCP to a broader range of chemical hazards, using organic chemical contaminants as examples, and the problems that are likely to arise in the food manufacturing sector. Chemical HACCP procedures are likely to result in many of the advantages previously identified for microbiological HACCP procedures: more effective, efficient and economical than conventional end-point-testing methods. However, the high costs of analytical monitoring of chemical contaminants and a limited understanding of formulation and process optimisation as means of controlling chemical contamination of foods are likely to prevent chemical HACCP becoming as effective as microbiological HACCP.

Blood culture bottles are superior to conventional media for vitreous culture.

PubMed

Thariya, Patsuda; Yospaiboon, Yosanan; Sinawat, Suthasinee; Sanguansak, Thuss; Bhoomibunchoo, Chavakij; Laovirojjanakul, Wipada

2016-08-01

To compare blood culture bottles and conventional media for the vitreous culture in patients with clinically suspected infectious endophthalmitis. Retrospective comparative study at KKU Eye Center, Khon Kaen University. There were 342 patients with clinically suspected infectious endophthalmitis participated in the study. The vitreous specimens were inoculated in both blood culture bottles and on conventional culture media (blood agar, MacConkey agar, chocolate agar, Sabouraud dextrose agar and thioglycolate broth). The number of positive culture yields in both blood culture bottles and conventional media. Positive culture yields in both methods were found in 151 eyes (49.5%). There were 136 of 151 eyes (90.1%) with positive culture in blood culture bottles, whereas 99 of 151 eyes (65.6%) yielded positive cultures in conventional media. These findings were different with a statistical significance (P < 0.00001) and an odds ratio of 3.47 (95% confidence interval 1.92, 6.63). A combination of blood culture bottles and conventional media improved the yield. Blood culture bottles are superior to conventional media for vitreous culture in clinically suspected infectious endophthalmitis. Vitreous culture using blood culture bottles should be recommended as the primary method for microbiological diagnosis. A combination of both methods further improves the positive culture yield. © 2016 Royal Australian and New Zealand College of Ophthalmologists.

The application of uniplex, duplex, and multiplex PCR for the absence of specified microorganism testing of pharmaceutical excipients and drug products.

PubMed

Ragheb, Suzan M; Yassin, Aymen S; Amin, Magdy A

2012-01-01

Notable progress has been made in methods that encourage the use of polymerase chain reaction (PCR) as a rapid and accurate tool in microbiological testing of pharmaceuticals. In this study, the detection of the four main specified microorganisms according to the pharmacopeial recommendations, Salmonella spp, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus, was optimized in different pharmaceutical dosage forms and raw materials. Uniplex PCR was performed for the detection of each microorganism individually targeting the conserved region in each bacterial genome. Further optimizations were done to perform duplex and multiplex PCR assays considering relative concentrations of competitor primers used in the reaction. The uniplex PCR amplicons were successfully sequenced, confirming the conservation of used primers. Other validation parameters such as specificity, sensitivity, and robustness were examined closely. The method provides a high-throughput screening method to test different pharmaceutical preparations for specified microorganisms for the detection of microbiological contamination. Strict regulations govern the production of pharmaceutical products whether they are sterile or nonsterile. Certain official tests are carried out in microbiology testing laboratory in any pharmaceutical production facility to ensure the pharmaceuticals microbiological quality according to the standard pharmacopeial recommendations. Nonsterile products must be free of specified microorganisms that are used as a check for their quality. Topical preparations must be free of Pseudomonas aeruginosa and Staphylococcus aureus, and oral preparations must be free of Salmonella spp and Escherichia coli. Conventional microbiological methods are time-consuming, labor-intensive, and require long incubation times, resulting in delaying the release of the products. In this study, we tested and validated a polymerase chain reaction identification approach to detect indicator bacteria in pharmaceutical preparations. The method depends on amplification of certain conserved genes located in the four specified bacteria. The method is optimized to be carried out individually or collectively to detect all indicator bacteria in a single reaction in different forms of pharmaceutical products.

Algorithm for Automatic Segmentation of Nuclear Boundaries in Cancer Cells in Three-Channel Luminescent Images

NASA Astrophysics Data System (ADS)

Lisitsa, Y. V.; Yatskou, M. M.; Apanasovich, V. V.; Apanasovich, T. V.

2015-09-01

We have developed an algorithm for segmentation of cancer cell nuclei in three-channel luminescent images of microbiological specimens. The algorithm is based on using a correlation between fluorescence signals in the detection channels for object segmentation, which permits complete automation of the data analysis procedure. We have carried out a comparative analysis of the proposed method and conventional algorithms implemented in the CellProfiler and ImageJ software packages. Our algorithm has an object localization uncertainty which is 2-3 times smaller than for the conventional algorithms, with comparable segmentation accuracy.

Development of a micromanipulation method for single cell isolation of prokaryotes and its application in food safety.

PubMed

Hohnadel, Marisa; Maumy, Myriam; Chollet, Renaud

2018-01-01

For nearly a century, conventional microbiological methods have been standard practice for detecting and identifying pathogens in food. Nevertheless, the microbiological safety of food has improved and various rapid methods have been developed to overcome the limitations of conventional methods. Alternative methods are expected to detect low cell numbers, since the presence in food of even a single cell of a pathogenic organism may be infectious. With respect to low population levels, the performance of a detection method is assessed by producing serial dilutions of a pure bacterial suspension to inoculate representative food matrices with highly diluted bacterial cells (fewer than 10 CFU/ml). The accuracy of data obtained by multiple dilution techniques is not certain and does not exclude some colonies arising from clumps of cells. Micromanipulation techniques to capture and isolate single cells from environmental samples were introduced more than 40 years ago. The main limitation of the current micromanipulation technique is still the low recovery rate for the growth of a single cell in culture medium. In this study, we describe a new single cell isolation method and demonstrate that it can be used successfully to grow various types of microorganism from picked individual cells. Tests with Gram-positive and Gram-negative organisms, including cocci, rods, aerobes, anaerobes, yeasts and molds showed growth recovery rates from 60% to 100% after micromanipulation. We also highlight the use of our method to evaluate and challenge the detection limits of standard detection methods in food samples contaminated by a single cell of Salmonella enterica.

A modified Elek test for detection of toxigenic corynebacteria in the diagnostic laboratory.

PubMed

Engler, K H; Glushkevich, T; Mazurova, I K; George, R C; Efstratiou, A

1997-02-01

The detection of toxigenicity among Corynebacterium diphtheriae and Corynebacterium ulcerans strains is the most important test for the microbiological diagnosis of diphtheria. Difficulties with current methods, in particular the Elek test, are well documented. We therefore describe a modified Elek test which provides an accurate result after only 16 h of incubation, in contrast to 48 h for the conventional test.

Validation Study of Rapid Assays of Bioburden, Endotoxins and Other Contamination.

PubMed

Shintani, Hideharu

2016-01-01

Microbial testing performed in support of pharmaceutical and biopharmaceutical production falls into three main categories: detection (qualitative), enumeration (quantitative), and characterization/identification. Traditional microbiological methods are listed in the compendia and discussed by using the conventional growth-based techniques, which are labor intensive and time consuming. In general, such tests require several days of incubation for microbial contamination (bioburden) to be detected, and therefore management seldom is able to take proactive corrective measures. In addition, microbial growth is limited by the growth medium used and incubation conditions, thus impacting testing sensitivity, accuracy, and reproducibility. 　For more than 20 years various technology platforms for rapid microbiological methods (RMM) have been developed, and many have been readily adopted by the food industry and clinical microbiology laboratories. Their use would certainly offer drug companies faster test turnaround times to accommodate the aggressive deadlines for manufacturing processes and product release. Some rapid methods also offer the possibility for real-time microbial analyses, enabling management to respond to microbial contamination events in a more timely fashion, and can provide cost savings and higher efficiencies in quality control testing laboratories. Despite the many proven business and quality benefits and the fact that the FDA's initiative to promote the use of process analytical technology (PAT) includes rapid microbial methods, pharmaceutical and biopharmaceutical industries have been somewhat slow to embrace alternative microbial methodologies for several reasons. The major reason is that the bioburden counts detected by the incubation method and rapid assay are greatly divergent. 　The use of rapid methods is a dynamic field in applied microbiology and one that has gained increased attention nationally and internationally over time. This topic has been extensively addressed at conferences and in published documents around the world. More recently, the use of alternative methods for control of the microbiological quality of pharmaceutical products and materials used in pharmaceutical production has been addressed by the compendia in an attempt to facilitate implementation of these technologies by pharmaceutical companies. The author presents some of the rapid method technologies under evaluation or in use by pharmaceutical microbiologists and the current status of the implementation of alternative microbial methods.

[Applications of MALDI-TOF-MS in clinical microbiology laboratory].

PubMed

Carbonnelle, Etienne; Nassif, Xavier

2011-10-01

For twenty years, mass spectrometry (MS) has emerged as a particularly powerful tool for analysis and characterization of proteins in research. It is only recently that this technology, especially MALDI-TOF-MS (Matrix Assisted Laser Desorption Ionization Time-Of-Flight) has entered the field of routine microbiology. This method has proven to be reliable and safe for the identification of bacteria, yeasts, filamentous fungi and dermatophytes. MALDI-TOF-MS is a rapid, precise and cost-effective method for identification, compared to conventional phenotypic techniques or molecular biology. Its ability to analyse whole microorganisms with few sample preparation has greatly reduced the time to identification (1-2 min). Furthermore, this technology can be used to identify bacteria directly from clinical samples as blood culture bottles or urines. Future applications will be developed in order to provide direct information concerning virulence or resistance protein markers. © 2011 médecine/sciences – Inserm / SRMS.

MALDI-TOF-mass spectrometry applications in clinical microbiology.

PubMed

Seng, Piseth; Rolain, Jean-Marc; Fournier, Pierre Edouard; La Scola, Bernard; Drancourt, Michel; Raoult, Didier

2010-11-01

MALDI-TOF-mass spectrometry (MS) has been successfully adapted for the routine identification of microorganisms in clinical microbiology laboratories in the past 10 years. This revolutionary technique allows for easier and faster diagnosis of human pathogens than conventional phenotypic and molecular identification methods, with unquestionable reliability and cost-effectiveness. This article will review the application of MALDI-TOF-MS tools in routine clinical diagnosis, including the identification of bacteria at the species, subspecies, strain and lineage levels, and the identification of bacterial toxins and antibiotic-resistance type. We will also discuss the application of MALDI-TOF-MS tools in the identification of Archaea, eukaryotes and viruses. Pathogenic identification from colony-cultured, blood-cultured, urine and environmental samples is also reviewed.

Gnotobiotic pigs-derivation and rearing.

PubMed

Miniats, O P; Jol, D

1978-10-01

The procurement, rearing, nutrition and microbiological monitoring of gnotobiotic pigs and a method for conditioning of primary, colostrum-deprived, specific pathogen free pigs is described. As compared to the established hysterectomy and closed hysterotomy methods for the derivation of gnotobiotic piglets an alternative approach, open caesarian section with the sow maintained under general halothane-nitrous oxide anaesthesia and the introduction of each fetus into the sterile isolator via a liquid germicidal trap, was found to be more efficient and equally successful in providing viable and microbiologically sterile piglets. Two sterile commercially available milk diets, a special formula for orphan animals and condensed cow's milk, when the latter was supplemented with injectable vitamin E, selenium and iron, proved adequate for satisfactory health of the animals. Two types of pelleted starter rations, sterilized by 4.5 megarads of gamma irradiation, provided adequately for the nutritional needs of older gnotobiotic pigs. Results of microbiological monitoring indicated that the surgical and rearing methods employed were capable of preventing contamination of the animals with bacteria, mycoplasma, yeasts, molds, protozoa and helminths but probably could not exclude occasional vertically transmitted viral infections. Exposure of the animals for four weeks to selected strains of lactobacilli, fecal streptococci and Escherichia coli did not result in visible disease while they were maintained in isolators and conditioned them for transfer into a conventional microbial environment.

Evaluation of a Parchment Document, the 13th Century Incorporation Charter for the City of Krakow, Poland, for Microbial Hazards

PubMed Central

2016-01-01

The literature of environmental microbiology broadly discusses issues associated with microbial hazards in archives, but these publications are mainly devoted to paper documents. There are few articles on historical parchment documents, which used to be very important for the development of literature and the art of writing. These studies present a broad spectrum of methods for the assessment of biodeterioration hazards of the parchment document in question. They are based on both conventional microbiological methods and advanced techniques of molecular biology. Here, a qualitative analysis was conducted, based on genetic identification of bacteria and fungi present on the document as well as denaturing gradient gel electrophoresis profiling and examining the destructive potential of isolated microbes. Moreover, the study involved a quantitative and qualitative microbiological assessment of the indoor air in the room where the parchment was kept. The microbes with the highest destructive potential that were isolated from the investigated item were Bacillus cereus and Acinetobacter lwoffii bacteria and Penicillium chrysogenum, Chaetomium globosum, and Trichoderma longibrachiatum fungi. The presence of the B. cereus strain was particularly interesting since, under appropriate conditions, it leads to complete parchment degradation within several days. PMID:26896133

Economic impact of rapid diagnostic methods in Clinical Microbiology: Price of the test or overall clinical impact.

PubMed

Cantón, Rafael; Gómez G de la Pedrosa, Elia

2017-12-01

The need to reduce the time it takes to establish a microbiological diagnosis and the emergence of new molecular microbiology and proteomic technologies has fuelled the development of rapid and point-of-care techniques, as well as the so-called point-of-care laboratories. These laboratories are responsible for conducting both techniques partially to response to the outsourcing of the conventional hospital laboratories. Their introduction has not always been accompanied with economic studies that address their cost-effectiveness, cost-benefit and cost-utility, but rather tend to be limited to the unit price of the test. The latter, influenced by the purchase procedure, does not usually have a regulated reference value in the same way that medicines do. The cost-effectiveness studies that have recently been conducted on mass spectrometry in the diagnosis of bacteraemia and the use of antimicrobials have had the greatest clinical impact and may act as a model for future economic studies on rapid and point-of-care tests. Copyright © 2017 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Comparison of Real-Time PCR, Reverse Transcriptase Real-Time PCR, Loop-Mediated Isothermal Amplification, and the FDA Conventional Microbiological Method for the Detection of Salmonella spp. in Produce ▿ †

PubMed Central

Zhang, Guodong; Brown, Eric W.; González-Escalona, Narjol

2011-01-01

Contamination of foods, especially produce, with Salmonella spp. is a major concern for public health. Several methods are available for the detection of Salmonella in produce, but their relative efficiency for detecting Salmonella in commonly consumed vegetables, often associated with outbreaks of food poisoning, needs to be confirmed. In this study, the effectiveness of three molecular methods for detection of Salmonella in six produce matrices was evaluated and compared to the FDA microbiological detection method. Samples of cilantro (coriander leaves), lettuce, parsley, spinach, tomato, and jalapeno pepper were inoculated with Salmonella serovars at two different levels (105 and <101 CFU/25 g of produce). The inoculated produce was assayed by the FDA Salmonella culture method (Bacteriological Analytical Manual) and by three molecular methods: quantitative real-time PCR (qPCR), quantitative reverse transcriptase real-time PCR (RT-qPCR), and loop-mediated isothermal amplification (LAMP). Comparable results were obtained by these four methods, which all detected as little as 2 CFU of Salmonella cells/25 g of produce. All control samples (not inoculated) were negative by the four methods. RT-qPCR detects only live Salmonella cells, obviating the danger of false-positive results from nonviable cells. False negatives (inhibition of either qPCR or RT-qPCR) were avoided by the use of either a DNA or an RNA amplification internal control (IAC). Compared to the conventional culture method, the qPCR, RT-qPCR, and LAMP assays allowed faster and equally accurate detection of Salmonella spp. in six high-risk produce commodities. PMID:21803916

Direct identification of pathogens from positive blood cultures using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry.

PubMed

Rodríguez-Sánchez, B; Sánchez-Carrillo, C; Ruiz, A; Marín, M; Cercenado, E; Rodríguez-Créixems, M; Bouza, E

2014-07-01

In recent years, matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has proved a rapid and reliable method for the identification of bacteria and yeasts that have already been isolated. The objective of this study was to evaluate this technology as a routine method for the identification of microorganisms directly from blood culture bottles (BCBs), before isolation, in a large collection of samples. For this purpose, 1000 positive BCBs containing 1085 microorganisms have been analysed by conventional phenotypic methods and by MALDI-TOF MS. Discrepancies have been resolved using molecular methods: the amplification and sequencing of the 16S rRNA gene or the Superoxide Dismutase gene (sodA) for streptococcal isolates. MALDI-TOF predicted a species- or genus-level identification of 81.4% of the analysed microorganisms. The analysis by episode yielded a complete identification of 814 out of 1000 analysed episodes (81.4%). MALDI-TOF identification is available for clinicians within hours of a working shift, as oppose to 18 h later when conventional identification methods are performed. Moreover, although further improvement of sample preparation for polymicrobial BCBs is required, the identification of more than one pathogen in the same BCB provides a valuable indication of unexpected pathogens when their presence may remain undetected in Gram staining. Implementation of MALDI-TOF identification directly from the BCB provides a rapid and reliable identification of the causal pathogen within hours. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

An Investigation of the Effectiveness of Radiotracer Techniques for Instruction in Microbiology.

ERIC Educational Resources Information Center

Hurlburt, Evelyn McClelland

Students in a junior college microbiology course were randomly assigned to one of two laboratory treatments: one using radiotracer techniques to investigate aspects of microbial metabolism, and the other using conventional techniques to investigate the same metabolic features. An achievement test administered at the completion of the unit and six…

Identification of a novel 16S rRNA gene variant of Actinomyces funkei from six patients with purulent infections.

PubMed

Hinić, V; Straub, C; Schultheiss, E; Kaempfer, P; Frei, R; Goldenberger, D

2013-07-01

Little is known about the clinical significance and laboratory diagnosis of Actinomyces funkei. In this report we describe six clinical cases where A. funkei was isolated from purulent, polymicrobial infections. Conventional identification procedures were compared with molecular methods including matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technique. Analysis of the full 16S rRNA gene sequence of the six investigated strains revealed differences from the A. funkei type strain. DNA-DNA hybridization showed that the clinical strains represent a novel 16S rRNA gene variant within the species of A. funkei. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Microbiological Analysis of Surfaces of Leonardo Da Vinci's Atlantic Codex: Biodeterioration Risk.

PubMed

Tarsitani, Gianfranco; Moroni, Catia; Cappitelli, Francesca; Pasquariello, Giovanna; Maggi, Oriana

2014-01-01

Following the discovery of discoloration on some pages of the Atlantic Codex (AC) of Leonardo da Vinci kept in the Biblioteca Ambrosiana in Milan, some investigations have been carried out to verify the presence of microorganisms, such as bacteria and fungi. To verify the presence of microorganisms a noninvasive method of sampling has been used that was efficient and allowed us to highlight the microbial facies of the material that was examined using conventional microbiological techniques. The microclimatic conditions in the storage room as well as the water content of the volume were also assessed. The combined observations allowed the conclusion that the discoloration of suspected biological origin on some pages of AC is not related to the presence or current attack of microbial agents.

Microbiological Analysis of Surfaces of Leonardo Da Vinci's Atlantic Codex: Biodeterioration Risk

PubMed Central

Moroni, Catia; Pasquariello, Giovanna; Maggi, Oriana

2014-01-01

Following the discovery of discoloration on some pages of the Atlantic Codex (AC) of Leonardo da Vinci kept in the Biblioteca Ambrosiana in Milan, some investigations have been carried out to verify the presence of microorganisms, such as bacteria and fungi. To verify the presence of microorganisms a noninvasive method of sampling has been used that was efficient and allowed us to highlight the microbial facies of the material that was examined using conventional microbiological techniques. The microclimatic conditions in the storage room as well as the water content of the volume were also assessed. The combined observations allowed the conclusion that the discoloration of suspected biological origin on some pages of AC is not related to the presence or current attack of microbial agents. PMID:25574171

Individuality, phenotypic differentiation, dormancy and ‘persistence’ in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology

PubMed Central

Kell, Douglas; Potgieter, Marnie; Pretorius, Etheresia

2015-01-01

For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically ‘nonculturable’ on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as ‘persisters’. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one’s bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit. PMID:26629334

Bacterial meningitis in children under 15 years of age in Nepal.

PubMed

Shrestha, Rajani Ghaju; Tandukar, Sarmila; Ansari, Shamshul; Subedi, Akriti; Shrestha, Anisha; Poudel, Rekha; Adhikari, Nabaraj; Basnyat, Shital Raj; Sherchand, Jeevan Bahadur

2015-08-19

Bacterial meningitis in children is a life-threatening problem resulting in severe morbidity and mortality. For the prompt initiation of antibacterial therapy, rapid and reliable diagnostic methods are of utmost importance. Therefore, this study was designed to find out the rate of bacterial pathogens of meningitis from suspected cases by performing conventional methods and latex agglutination. A descriptive type of study was carried out from May 2012 to April 2013. Cerebrospinal fluid (CSF) specimens from 252 suspected cases of meningitis were subjected for Gram staining, bacterial culture and latex agglutination test. The identification of growth of bacteria was done following standard microbiological methods recommended by American Society for Microbiology. Antibiotic sensitivity testing was done by modified Kirby-Bauer disk diffusion method. From the total 252 suspected cases, 7.2 % bacterial meningitis was revealed by Gram staining and culture methods whereas latex agglutination method detected 5.6 %. Gram-negative organisms contributed the majority of the cases (72.2 %) with Haemophilus influenzae as the leading pathogen for meningitis. Overall, 33.3 % mortality rate was found. In conclusion, a significant rate of bacterial meningitis was found in this study prompting concern for national wide surveillance.

The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults

PubMed Central

Lewis, Debbie A.; Brown, Richard; Williams, Jon; White, Paul; Jacobson, S. Kim; Marchesi, Julian R.; Drake, Marcus J.

2013-01-01

The urinary microbiome of healthy individuals and the way it alters with ageing have not been characterized and may influence disease processes. Conventional microbiological methods have limited scope to capture the full spectrum of urinary bacterial species. We studied the urinary microbiota from a population of healthy individuals, ranging from 26 to 90 years of age, by amplification of the 16S rRNA gene, with resulting amplicons analyzed by 454 pyrosequencing. Mid-stream urine (MSU) was collected by the “clean-catch” method. Quantitative PCR of 16S rRNA genes in urine samples, allowed relative enumeration of the bacterial loads. Analysis of the samples indicates that females had a more heterogeneous mix of bacterial genera compared to the male samples and generally had representative members of the phyla Actinobacteria and Bacteroidetes. Analysis of the data leads us to conclude that a “core” urinary microbiome could potentially exist, when samples are grouped by age with fluctuation in abundance between age groups. The study also revealed age-specific genera Jonquetella, Parvimonas, Proteiniphilum, and Saccharofermentans. In conclusion, conventional microbiological methods are inadequate to fully identify around two-thirds of the bacteria identified in this study. Whilst this proof-of-principle study has limitations due to the sample size, the discoveries evident in this sample data are strongly suggestive that a larger study on the urinary microbiome should be encouraged and that the identification of specific genera at particular ages may be relevant to pathogenesis of clinical conditions. PMID:23967406

The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults.

PubMed

Lewis, Debbie A; Brown, Richard; Williams, Jon; White, Paul; Jacobson, S Kim; Marchesi, Julian R; Drake, Marcus J

2013-01-01

The urinary microbiome of healthy individuals and the way it alters with ageing have not been characterized and may influence disease processes. Conventional microbiological methods have limited scope to capture the full spectrum of urinary bacterial species. We studied the urinary microbiota from a population of healthy individuals, ranging from 26 to 90 years of age, by amplification of the 16S rRNA gene, with resulting amplicons analyzed by 454 pyrosequencing. Mid-stream urine (MSU) was collected by the "clean-catch" method. Quantitative PCR of 16S rRNA genes in urine samples, allowed relative enumeration of the bacterial loads. Analysis of the samples indicates that females had a more heterogeneous mix of bacterial genera compared to the male samples and generally had representative members of the phyla Actinobacteria and Bacteroidetes. Analysis of the data leads us to conclude that a "core" urinary microbiome could potentially exist, when samples are grouped by age with fluctuation in abundance between age groups. The study also revealed age-specific genera Jonquetella, Parvimonas, Proteiniphilum, and Saccharofermentans. In conclusion, conventional microbiological methods are inadequate to fully identify around two-thirds of the bacteria identified in this study. Whilst this proof-of-principle study has limitations due to the sample size, the discoveries evident in this sample data are strongly suggestive that a larger study on the urinary microbiome should be encouraged and that the identification of specific genera at particular ages may be relevant to pathogenesis of clinical conditions.

Cost Savings Realized by Implementation of Routine Microbiological Identification by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

PubMed Central

Alby, Kevin; Kerr, Alan; Jones, Melissa; Gilligan, Peter H.

2015-01-01

Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) is an emerging technology for rapid identification of bacterial and fungal isolates. In comparison to conventional methods, this technology is much less labor intensive and can provide accurate and reliable results in minutes from a single isolated colony. We compared the cost of performing the bioMérieux Vitek MALDI-TOF MS with conventional microbiological methods to determine the amount saved by the laboratory by converting to the new technology. Identification costs for 21,930 isolates collected between April 1, 2013, and March 31, 2014, were directly compared for MALDI-TOF MS and conventional methodologies. These isolates were composed of commonly isolated organisms, including commonly encountered aerobic and facultative bacteria and yeast but excluding anaerobes and filamentous fungi. Mycobacterium tuberculosis complex and rapidly growing mycobacteria were also evaluated for a 5-month period during the study. Reagent costs and a total cost analysis that included technologist time in addition to reagent expenses and maintenance service agreement costs were analyzed as part of this study. The use of MALDI-TOF MS equated to a net savings of $69,108.61, or 87.8%, in reagent costs annually compared to traditional methods. When total costs are calculated to include technologist time and maintenance costs, traditional identification would have cost $142,532.69, versus $68,886.51 with the MALDI-TOF MS method, resulting in a laboratory savings of $73,646.18, or 51.7%, annually by adopting the new technology. The initial cost of the instrument at our usage level would be offset in about 3 years. MALDI-TOF MS not only represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates, it also provides a significant cost savings for the laboratory. PMID:25994167

Microorganisms direct identification from blood culture by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Ferreira, L; Sánchez-Juanes, F; Porras-Guerra, I; García-García, M I; García-Sánchez, J E; González-Buitrago, J M; Muñoz-Bellido, J L

2011-04-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows a fast and reliable bacterial identification from culture plates. Direct analysis of clinical samples may increase its usefulness in samples in which a fast identification of microorganisms can guide empirical treatment, such as blood cultures (BC). Three hundred and thirty BC, reported as positive by the automated BC incubation device, were processed by conventional methods for BC processing, and by a fast method based on direct MALDI-TOF MS. Three hundred and eighteen of them yield growth on culture plates, and 12 were false positive. The MALDI-TOF MS-based method reported that no peaks were found, or the absence of a reliable identification profile, in all these false positive BC. No mixed cultures were found. Among these 318 BC, we isolated 61 Gram-negatives (GN), 239 Gram-positives (GP) and 18 fungi. Microorganism identifications in GN were coincident with conventional identification, at the species level, in 83.3% of BC and, at the genus level, in 96.6%. In GP, identifications were coincident with conventional identification in 31.8% of BC at the species level, and in 64.8% at the genus level. Fungaemia was not reliably detected by MALDI-TOF. In 18 BC positive for Candida species (eight C. albicans, nine C. parapsilosis and one C. tropicalis), no microorganisms were identified at the species level, and only one (5.6%) was detected at the genus level. The results of the present study show that this fast, MALDI-TOF MS-based method allows bacterial identification directly from presumptively positive BC in a short time (<30 min), with a high accuracy, especially when GN bacteria are involved. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

Mycoplasma testing of cell substrates and biologics: Review of alternative non-microbiological techniques.

PubMed

Volokhov, Dmitriy V; Graham, Laurie J; Brorson, Kurt A; Chizhikov, Vladimir E

2011-01-01

Mycoplasmas, particularly species of the genera Mycoplasma and Acholeplasma, are known to be occasional microbial contaminants of cell cultures that produce biologics. This presents a serious concern regarding the risk of mycoplasma contamination for research laboratories and commercial facilities developing and manufacturing cell-derived biological and biopharmaceutical products for therapeutic use. Potential undetected contamination of these products or process intermediates with mycoplasmas represents a potential safety risk for patients and a business risk for producers of biopharmaceuticals. To minimize these risks, monitoring for adventitious agents, such as viruses and mycoplasmas, is performed during the manufacture of biologics produced in cell culture substrates. The "gold standard" microbiological assay, currently recommended by the USP, EP, JP and the US FDA, for the mycoplasma testing of biologics, involves the culture of viable mycoplasmas in broth, agar plates and indicator cells. Although the procedure enables highly efficient mycoplasma detection in cell substrates and cell-derived products, the overall testing strategy is time consuming (a minimum of 28 days) and requires skilled interpretation of the results. The long time period required for these conventional assays does not permit their use for products with short shelf-lives or for timely 'go/no-go' decisions during routine in-process testing. PCR methodology has existed for decades, however PCR based and other alternative methods for mycoplasma detection have only recently been considered for application to biologics manufacture. The application of alternative nucleic acid-based, enzyme-based and/or recombinant cell-culture methods, particularly in combination with efficient sample preparation procedures, could provide advantages over conventional microbiological methods in terms of analytical throughput, simplicity, and turnaround time. However, a challenge to the application of alternative methods for detection of mycoplasmas remains whether these alternative methods can provide a limit of detection comparable or superior to those of the culture methods. An additional challenge is that nucleic acid amplification technique (NAT) methods do not allow for accurate discrimination between viable and non-viable mycoplasma contaminants, which might lead to false-positive results (e.g. from inactivated raw materials, etc.). Our review provides an overview of these alternative methods and discusses the pros and cons of their application for the testing of mycoplasmas in biologics and cell substrates. Published by Elsevier Ltd.

Superresolution microscopy for microbiology

PubMed Central

Coltharp, Carla; Xiao, Jie

2014-01-01

Summary This review provides a practical introduction to superresolution microscopy from the perspective of microbiological research. Because of the small sizes of bacterial cells, superresolution methods are particularly powerful and suitable for revealing details of cellular structures that are not resolvable under conventional fluorescence light microscopy. Here we describe the methodological concepts behind three major categories of super-resolution light microscopy: photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) and stimulated emission-depletion (STED) microscopy. We then present recent applications of each of these techniques to microbial systems, which have revealed novel conformations of cellular structures and described new properties of in vivo protein function and interactions. Finally, we discuss the unique issues related to implementing each of these superresolution techniques with bacterial specimens and suggest avenues for future development. The goal of this review is to provide the necessary technical background for interested microbiologists to choose the appropriate super-resolution method for their biological systems, and to introduce the practical considerations required for designing and analysing superresolution imaging experiments. PMID:22947061

[Invasive pulmonary aspergillosis].

PubMed

Blanchard, E; Gabriel, F; Jeanne-Leroyer, C; Servant, V; Dumas, P-Y

2018-02-01

Invasive pulmonary aspergillosis (IPA) is an important cause of morbidity and mortality in a wide range of patients. Early recognition and diagnosis have become a major focus in improving the management and outcomes of this life-threatening disease. IPA typically occurs during a period of severe and prolonged neutropenia. However, solid organ transplant recipients, patients under immunosuppressive therapy or hospitalized in intensive care units are also at risk. The diagnosis is suspected in the presence of a combination of clinical, biological and CT scan evidence. The microbiological diagnostic strategy should be adapted to the patient's profile. Conventional methods with culture and species identification remain the standard but early diagnosis has been improved by the use of biomarkers such as galactomannan antigen in serum or in bronchoalveolar lavage. The epidemiology of IPA should change with the increased use of antifungal prophylactic regimens and the arrival of targeted therapies. Other microbiological tools, such as PCR and other biomarkers, are currently being assessed. IPA must be considered in a wide range of patients. Its prognosis remains poor despite progress in the microbiological diagnosis and therapeutic management. Copyright © 2018 SPLF. Published by Elsevier Masson SAS. All rights reserved.

Differentiation between Staphylococcus aureus and coagulase-negative Staphylococcus species by real-time PCR including detection of methicillin resistants in comparison to conventional microbiology testing.

PubMed

Klaschik, Sven; Lehmann, Lutz E; Steinhagen, Folkert; Book, Malte; Molitor, Ernst; Hoeft, Andreas; Stueber, Frank

2015-03-01

Staphylococcus aureus has long been recognized as a major pathogen. Methicillin-resistant strains of S. aureus (MRSA) and methicillin-resistant strains of S. epidermidis (MRSE) are among the most prevalent multiresistant pathogens worldwide, frequently causing nosocomial and community-acquired infections. In the present pilot study, we tested a polymerase chain reaction (PCR) method to quickly differentiate Staphylococci and identify the mecA gene in a clinical setting. Compared to the conventional microbiology testing the real-time PCR assay had a higher detection rate for both S. aureus and coagulase-negative Staphylococci (CoNS; 55 vs. 32 for S. aureus and 63 vs. 24 for CoNS). Hands-on time preparing DNA, carrying out the PCR, and evaluating results was less than 5 h. The assay is largely automated, easy to adapt, and has been shown to be rapid and reliable. Fast detection and differentiation of S. aureus, CoNS, and the mecA gene by means of this real-time PCR protocol may help expedite therapeutic decision-making and enable earlier adequate antibiotic treatment. © 2014 Wiley Periodicals, Inc.

Adventures in the Environmental World and Environmental Microbiology Sampling of Air for Pharmaceutical Sterile Compounding.

PubMed

Ligugnana, Roberto

2017-01-01

Chapter <797> issued by the United States Pharmacopeial Convention, Inc. is the standard for sterile compounding. It is designed to reduce the number of patient infections due to contaminated pharmaceutical preparation. This regulation applies to all staff who prepare compounded sterile preparations and all places where they are produced, including hospitals, clinics, pharmacies, and physician's offices. This article provides the history of environmental microbiology and provides a discussion on environmental microbiology sampling of air for pharmaceutical sterile compounding. Copyright© by International Journal of Pharmaceutical Compounding, Inc.

[Microbiological testing of the artificial gingival margin in dentures].

PubMed

Hermann, Péter; Klein, Ildikó; Barna, Zsuzsanna; Kaán, Miklós; Fejérdy, Pál

2004-06-01

In everyday practice dental laboratories try to reproduce the natural form of sulcus gingivae at the transitional area between artificial teeth and gingiva of removable dentures, even on esthetically less important areas. Aim of these investigations were to examine how artificial recreation of the sulcus gingivae influences plaque retention, and what is the microbiological relevance of these. Investigations were carried out on the vestibular side of removable dentures of 32 randomly selected patients treated at the Department of Prosthodontics at the Faculty of Dentistry, Semmelweis University. Microbiological samples were taken from each patient using the same method. Samples were taken from the left upper first molars' artificial gingival margin using sterile paper points. Paper points were then transported in Eppendorf-tubes, in 2 ml of physiological saline solution, and processed within a two-hour period of time. Series dilutions were made of the sample solutions, then surface-streaked on Subaraud and Gentamycin, blood-agar, eosin-methylene blue and Mitis Salivarius culture enriched with Bacitracin. Subaraud culture was induced under aerob conditions, at room temperature for two days, then the total amount of fungi quantified. After pure-culturing Candida albicans ID-culture was used for identification, and BioMerieux ATB automatic equipment to identify different Candida species. From pure cultures identification was carried out with Gram-staining, Neisser-staining, catalase, oxidase and also with other biochemical reactions. Blood-agar was used to determine total germ count, and normal commensal pharyngeal and oral bacteria. After collecting the microbiological samples, the conventional shape of the dental margin of gingiva was abolished on one side of the dentures and a smooth transition was created between denture teeth and the artificial gingiva in the molar and premolar region. During our investigations only blastomycetes were found. Besides most common Candida albicans, Candida glabrata, tropicallis, spherica and lambica were also identified. Our patients did not miss artificial sulcus gingivae, had no aesthetic complaints about smooth transition between artificial teeth and gingiva. Microbiological investigations of the samples and the comparative analysis showed, that on the smooth transitional areas compared to conventionally shaped sulci significantly less gram-negative, gram-positive bacteria and oral fungi were found, and there was no plaque formation.

Microbiological stabilization of tiger nuts' milk beverage using ultra-high pressure homogenization. A preliminary study on microbial shelf-life extension.

PubMed

Codina-Torrella, I; Guamis, B; Zamora, A; Quevedo, J M; Trujillo, A J

2018-02-01

Tiger nuts' milk beverages are highly perishable products. For this reason, the interest of food industry for their commercialization makes necessary the application of preservation treatments to prolong their shelf-life. In the current study, the effect of ultra-high pressure homogenization (UHPH) on the microbiological and sensory qualities of tiger nuts' milk beverage was evaluated. Characteristics of UHPH-treated products (at 200 and 300 MPa, with inlet temperature of 40 °C) were compared with those of raw (RP) and conventionally homogenized-pasteurized (H-P) beverages, after treatment and during cold storage at 4 °C. Microbiological quality of beverages was studied by enumerating total counts, psychrotrophic bacteria, lactobacilli, enterobacteria, molds and yeasts, and mesophilic spores. Evolution of color and sensory characteristics of beverages were also determined. Microbiological shelf-life of the tiger nuts' milk beverages was extended from 3 to 25, 30 and 57 days by applying H-P and UHPH treatments at 200 and 300 MPa, respectively. Color of beverages was the only attribute that differentiated UHPH samples from the others, with greater luminosity and whiteness. Hence, UHPH treatments showed to be an alternative to the conventional H-P for obtaining tiger nuts' milk beverages with an improved microbiological shelf-life and good sensorial characteristics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of Conventional and Real-Time Reverse Transcription Polymerase Chain Reaction Assays to Detect Tembusu Virus in Culex tarsalis Mosquitoes

DTIC Science & Technology

2014-08-11

methods for determining potential human health hazards , especially in field environment set- tings. We described the development of sensitive and specific...Smith, Department of Microbiology , Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort...2012. Adapted Tembusu-like virus in chickens and geese in China. J Clin Microbiol 50: 2807–2809. 7. Yun T, Ye W, Ni Z, Zhang D, Zhang C, 2012

Comparison between nasopharyngeal swab and nasal wash, using culture and PCR, in the detection of potential respiratory pathogens.

PubMed

Gritzfeld, Jenna F; Roberts, Paul; Roche, Lorna; El Batrawy, Sherouk; Gordon, Stephen B

2011-04-13

Nasopharyngeal carriage of potential pathogens is important as it is both the major source of transmission and the prerequisite of invasive disease. New methods for detecting carriage could improve comfort, accuracy and laboratory utility. The aims of this study were to compare the sensitivities of a nasopharyngeal swab (NPS) and a nasal wash (NW) in detecting potential respiratory pathogens in healthy adults using microbiological culture and PCR. Healthy volunteers attended for nasal washing and brushing of the posterior nasopharynx. Conventional and real-time PCR were used to detect pneumococcus and meningococcus. Statistical differences between the two nasal sampling methods were determined using a nonparametric Mann-Whitney U test; differences between culture and PCR methods were determined using the McNemar test.Nasal washing was more comfortable for volunteers than swabbing (n = 24). In detection by culture, the NW was significantly more likely to detect pathogens than the NPS (p < 0.00001). Overall, there was a low carriage rate of pathogens in this sample; no significant difference was seen in the detection of bacteria between culture and PCR methods. Nasal washing and PCR may provide effective alternatives to nasopharyngeal swabbing and classical microbiology, respectively.

Molecular Methods for the Detection of Mycoplasma and Ureaplasma Infections in Humans

PubMed Central

Waites, Ken B.; Xiao, Li; Paralanov, Vanya; Viscardi, Rose M.; Glass, John I.

2012-01-01

Mycoplasma and Ureaplasma species are well-known human pathogens responsible for a broad array of inflammatory conditions involving the respiratory and urogenital tracts of neonates, children, and adults. Greater attention is being given to these organisms in diagnostic microbiology, largely as a result of improved methods for their laboratory detection, made possible by powerful molecular-based techniques that can be used for primary detection in clinical specimens. For slow-growing species, such as Mycoplasma pneumoniae and Mycoplasma genitalium, molecular-based detection is the only practical means for rapid microbiological diagnosis. Most molecular-based methods used for detection and characterization of conventional bacteria have been applied to these organisms. A complete genome sequence is available for one or more strains of all of the important human pathogens in the Mycoplasma and Ureaplasma genera. Information gained from genome analyses and improvements in efficiency of DNA sequencing are expected to significantly advance the field of molecular detection and genotyping during the next few years. This review provides a summary and critical review of methods suitable for detection and characterization of mycoplasmas and ureaplasmas of humans, with emphasis on molecular genotypic techniques. PMID:22819362

Principles and applications of polymerase chain reaction in medical diagnostic fields: a review

PubMed Central

Valones, Marcela Agne Alves; Guimarães, Rafael Lima; Brandão, Lucas André Cavalcanti; de Souza, Paulo Roberto Eleutério; de Albuquerque Tavares Carvalho, Alessandra; Crovela, Sergio

2009-01-01

Recent developments in molecular methods have revolutionized the detection and characterization of microorganisms in a broad range of medical diagnostic fields, including virology, mycology, parasitology, microbiology and dentistry. Among these methods, Polymerase Chain Reaction (PCR) has generated great benefits and allowed scientific advancements. PCR is an excellent technique for the rapid detection of pathogens, including those difficult to culture. Along with conventional PCR techniques, Real-Time PCR has emerged as a technological innovation and is playing an ever-increasing role in clinical diagnostics and research laboratories. Due to its capacity to generate both qualitative and quantitative results, Real-Time PCR is considered a fast and accurate platform. The aim of the present literature review is to explore the clinical usefulness and potential of both conventional PCR and Real-Time PCR assays in diverse medical fields, addressing its main uses and advances. PMID:24031310

Microbiological Surveillance of Operation Theatres: Five Year Retrospective Analysis from a Tertiary Care Hospital in North India

PubMed Central

Najotra, Dipender Kaur; Malhotra, Aneeta Singh; Slathia, Poonam; Raina, Shivani; Dhar, Ashok

2017-01-01

Introduction: Microbiological contamination of air and environment in the operation theaters (OTs) are major risk factor for surgical site and other hospital-associated infections. Objectives: The aim was to identify bacterial colonization of surfaces and equipment and to determine the microbial contamination of air in the OTs of a tertiary care hospital. Materials and Methods: Five years (January 2010–December 2014) retrospective analysis of the data obtained from routine microbiological surveillance of the five OTs of the hospital was done. Surface samples were taken with wet swabs from different sites and equipment. Bacterial species were isolated and identified by conventional methods. Air quality surveillance of OTs was done by settle plate method. Results: A total of 4387 samples were collected from surfaces and articles of various OTs. Out of these only 195 (4.4%), samples showed bacterial growth and yielded 210 isolates. The predominant species isolated was Bacillus with 184 (87.6%) isolates followed by coagulase-negative Staphylococcus 17 (8.1%), Staphylococcus aureus 6 (2.9%), and Enteroccoccus spp. 3 (1.4%). Analysis of the OT air samples showed least colony forming unit (cfu) rate of air (27 cfu/m3) in ophthalmology OT and highest rate of 133 cfu/m3 in general surgery OT. Conclusion: The study shows that OTs of our hospital showed a very low bacterial contamination rate on surface swabbing and a cfu count per m3 of air well within permissible limits. PMID:28904915

Multiplex molecular testing for management of infectious gastroenteritis in a hospital setting: a comparative diagnostic and clinical utility study.

PubMed

Halligan, E; Edgeworth, J; Bisnauthsing, K; Bible, J; Cliff, P; Aarons, E; Klein, J; Patel, A; Goldenberg, S

2014-08-01

Laboratory diagnosis and clinical management of inpatients with diarrhoea is complex and time consuming. Tests are often requested sequentially and undertaken in different laboratories. This causes prolonged unnecessary presumptive isolation of patients, because most cases are non-infectious. A molecular multiplex test (Luminex(®) Gastrointestinal Pathogen Panel (GPP)) was compared with conventional testing over 8 months to determine diagnostic accuracy, turnaround times, laboratory costs, use of isolation facilities and user acceptability. A total of 262 (12%) patients had a pathogen detected by conventional methods compared with 483 (22.1%) by GPP. Most additional cases were detected in patients developing symptoms in the first 4 days of admission. Additional cases were detected because of presumed improved diagnostic sensitivity but also because clinicians had not requested the correct pathogen. Turnaround time (41.8 h) was faster than bacterial culture (66.5 h) and parasite investigation (66.5 h) but slower than conventional testing for Clostridium difficile (17.3 h) and viruses (27 h). The test could allow simplified requesting by clinicians and a consolidated laboratory workflow, reducing the overall number of specimens received by the laboratory. A total of 154 isolation days were saved at an estimated cost of £30 800. Consumables and labour were estimated at £150 641 compared with £63 431 for conventional testing. Multiplex molecular testing using a panel of targets allowed enhanced detection and a consolidated laboratory workflow. This is likely to be of greater benefit to cases that present within the first 4 days of hospital admission. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

A Focus on the Death Kinetics in Predictive Microbiology: Benefits and Limits of the Most Important Models and Some Tools Dealing with Their Application in Foods

PubMed Central

Bevilacqua, Antonio; Speranza, Barbara; Sinigaglia, Milena; Corbo, Maria Rosaria

2015-01-01

Predictive Microbiology (PM) deals with the mathematical modeling of microorganisms in foods for different applications (challenge test, evaluation of microbiological shelf life, prediction of the microbiological hazards connected with foods, etc.). An interesting and important part of PM focuses on the use of primary functions to fit data of death kinetics of spoilage, pathogenic, and useful microorganisms following thermal or non-conventional treatments and can also be used to model survivors throughout storage. The main topic of this review is a focus on the most important death models (negative Gompertz, log-linear, shoulder/tail, Weibull, Weibull+tail, re-parameterized Weibull, biphasic approach, etc.) to pinpoint the benefits and the limits of each model; in addition, the last section addresses the most important tools for the use of death kinetics and predictive microbiology in a user-friendly way. PMID:28231222

A commentary on the role of molecular technology and automation in clinical diagnostics

PubMed Central

O’Connor, Ciara; Fitzgibbon, Marie; Powell, James; Barron, Denis; O’Mahony, Jim; Power, Lorraine; O’Connell, Nuala H; Dunne, Colum

2014-01-01

Historically, the identification of bacterial or yeast isolates has been based on phenotypic characteristics such as growth on defined media, colony morphology, Gram stain, and various biochemical reactions, with significant delay in diagnosis. Clinical microbiology as a medical specialty has embraced advances in molecular technology for rapid species identification with broad-range 16S rDNA polymerase chain reaction (PCR) and matrix-assisted laser desorption and/or ionization time of flight (MALDI-TOF) mass spectrometry demonstrated as accurate, rapid, and cost-effective methods for the identification of most, but not all, bacteria and yeasts. Protracted conventional incubation times previously necessary to identify certain species have been mitigated, affording patients quicker diagnosis with associated reduction in exposure to empiric broad-spectrum antimicrobial therapy and shortened hospital stay. This short commentary details such molecular advances and their implications in the clinical microbiology setting. PMID:24658184

A commentary on the role of molecular technology and automation in clinical diagnostics.

PubMed

O'Connor, Ciara; Fitzgibbon, Marie; Powell, James; Barron, Denis; O'Mahony, Jim; Power, Lorraine; O'Connell, Nuala H; Dunne, Colum

2014-01-01

Historically, the identification of bacterial or yeast isolates has been based on phenotypic characteristics such as growth on defined media, colony morphology, Gram stain, and various biochemical reactions, with significant delay in diagnosis. Clinical microbiology as a medical specialty has embraced advances in molecular technology for rapid species identification with broad-range 16S rDNA polymerase chain reaction (PCR) and matrix-assisted laser desorption and/or ionization time of flight (MALDI-TOF) mass spectrometry demonstrated as accurate, rapid, and cost-effective methods for the identification of most, but not all, bacteria and yeasts. Protracted conventional incubation times previously necessary to identify certain species have been mitigated, affording patients quicker diagnosis with associated reduction in exposure to empiric broad-spectrum antimicrobial therapy and shortened hospital stay. This short commentary details such molecular advances and their implications in the clinical microbiology setting.

Microbiological testing of pharmaceuticals and cosmetics in Egypt.

PubMed

Zeitoun, Hend; Kassem, Mervat; Raafat, Dina; AbouShlieb, Hamida; Fanaki, Nourhan

2015-12-09

Microbial contamination of pharmaceuticals poses a great problem to the pharmaceutical manufacturing process, especially from a medical as well as an economic point of view. Depending upon the product and its intended use, the identification of isolates should not merely be limited to the United States Pharmacopeia (USP) indicator organisms. Eighty-five pre-used non-sterile pharmaceuticals collected from random consumers in Egypt were examined for the eventual presence of bacterial contaminants. Forty-one bacterial contaminants were isolated from 31 of the tested preparations. These isolates were subjected to biochemical identification by both conventional tests as well as API kits, which were sufficient for the accurate identification of only 11 out of the 41 bacterial contaminants (26.8%) to the species level. The remaining isolates were inconclusively identified or showed contradictory results after using both biochemical methods. Using molecular methods, 24 isolates (58.5%) were successfully identified to the species level. Moreover, polymerase chain reaction (PCR) assays were compared to standard biochemical methods in the detection of pharmacopoeial bacterial indicators in artificially-contaminated pharmaceutical samples. PCR-based methods proved to be superior regarding speed, cost-effectiveness and sensitivity. Therefore, pharmaceutical manufacturers would be advised to adopt PCR-based methods in the microbiological quality testing of pharmaceuticals in the future.

Microbial indicators, pathogens and methods for their monitoring in water environment.

PubMed

Saxena, Gaurav; Bharagava, Ram Naresh; Kaithwas, Gaurav; Raj, Abhay

2015-06-01

Water is critical for life, but many people do not have access to clean and safe drinking water and die because of waterborne diseases. The analysis of drinking water for the presence of indicator microorganisms is key to determining microbiological quality and public health safety. However, drinking water-related illness outbreaks are still occurring worldwide. Moreover, different indicator microorganisms are being used in different countries as a tool for the microbiological examination of drinking water. Therefore, it becomes very important to understand the potentials and limitations of indicator microorganisms before implementing the guidelines and regulations designed by various regulatory agencies. This review provides updated information on traditional and alternative indicator microorganisms with merits and demerits in view of their role in managing the waterborne health risks as well as conventional and molecular methods proposed for monitoring of indicator and pathogenic microorganisms in the water environment. Further, the World Health Organization (WHO) water safety plan is emphasized in order to develop the better approaches designed to meet the requirements of safe drinking water supply for all mankind, which is one of the major challenges of the 21st century.

Monitoring chicken flock behaviour provides early warning of infection by human pathogen Campylobacter

PubMed Central

Colles, Frances M.; Cain, Russell J.; Nickson, Thomas; Smith, Adrian L.; Roberts, Stephen J.; Maiden, Martin C. J.; Lunn, Daniel; Dawkins, Marian Stamp

2016-01-01

Campylobacter is the commonest bacterial cause of gastrointestinal infection in humans, and chicken meat is the major source of infection throughout the world. Strict and expensive on-farm biosecurity measures have been largely unsuccessful in controlling infection and are hampered by the time needed to analyse faecal samples, with the result that Campylobacter status is often known only after a flock has been processed. Our data demonstrate an alternative approach that monitors the behaviour of live chickens with cameras and analyses the ‘optical flow’ patterns made by flock movements. Campylobacter-free chicken flocks have higher mean and lower kurtosis of optical flow than those testing positive for Campylobacter by microbiological methods. We show that by monitoring behaviour in this way, flocks likely to become positive can be identified within the first 7–10 days of life, much earlier than conventional on-farm microbiological methods. This early warning has the potential to lead to a more targeted approach to Campylobacter control and also provides new insights into possible sources of infection that could transform the control of this globally important food-borne pathogen. PMID:26740618

[Evaluation of the quality of poultry meat and its processing for vacuum packaging].

PubMed

Swiderski, F; Russel, S; Waszkiewicz-Robak, B; Cholewińska, E

1997-01-01

The aim of study was to evaluate the quality of poultry meat, roasted and smoked chicken and poultry pie packing under low and high vacuum. All investigated products were stored at +4 degrees C and evaluated by microbiological analysis. It was showed that packing under low and high vacuum inhibited development of aerobic microorganisms, proteolytic bacteria, yeasts and moulds. Vacuum-packaged storage of poultry meat and its products stimulated activity of anaerobic, nonsporeforming bacteria. The fast spoilage of fresh poultry meat was observed both under vacuum and conventional storage. The microbiology quality of poultry products depended on technology of production and microbiological quality of raw material.

Rapid Detection of Escherichia coli O157:H7 in Fresh Lettuce Based on Localized Surface Plasmon Resonance Combined with Immunomagnetic Separation.

PubMed

Lee, Nari; Choi, Sung-Wook; Chang, Hyun-Joo; Chun, Hyang Sook

2018-05-01

This study presents a method for rapid detection of Escherichia coli O157:H7 in fresh lettuce based on the properties of target separation and localized surface plasmon resonance of immunomagnetic nanoparticles. The multifunctional immunomagnetic nanoparticles enabling simultaneous separation and detection were prepared by synthesizing magnetic nanoparticles (ca. 10 nm in diameter) composed of an iron oxide (Fe 3 O 4 ) core and gold shell and then conjugating these nanoparticles with the anti- E. coli O157:H7 antibodies. The application of multifunctional immunomagnetic nanoparticles for detecting E. coli O157:H7 in a lettuce matrix allowed detection of the presence of <1 log CFU mL -1 without prior enrichment. In contrast, the detection limit of the conventional plating method was 2.74 log CFU mL -1 . The method, which requires no preenrichment, provides an alternative to conventional microbiological detection methods and can be used as a rapid screening tool for a large number of food samples.

[A rarely isolated bacterium in microbiology laboratories: Streptococcus uberis].

PubMed

Eryıldız, Canan; Bukavaz, Şebnem; Gürcan, Şaban; Hatipoğlu, Osman

2017-04-01

Streptococcus uberis is a gram-positive bacterium that is mostly responsible for mastitis in cattle. The bacterium rarely has been associated with human infections. Conventional phenotyphic methods can be inadequate for the identification of S.uberis; and in microbiology laboratories S.uberis is confused with the other streptococci and enterococci isolates. Recently, molecular methods are recommended for the accurate identification of S.uberis isolates. The aim of this report is to present a lower respiratory tract infection case caused by S.uberis and the microbiological methods for identification of this bacterium. A 66-year-old male patient with squamous cell lung cancer who received radiotherapy was admitted in our hospital for the control. According to the chest X-Ray, patient was hospitalized with the prediagnosis of ''cavitary tumor, pulmonary abscess''. In the first day of the hospitalization, blood and sputum cultures were drawn. Blood culture was negative, however, Candida albicans was isolated in the sputum culture and it was estimated to be due to oral lesions. After two weeks from the hospitalization, sputum sample was taken from the patient since he had abnormal respiratory sounds and cough complaint. In the Gram stained smear of the sputum there were abundant leucocytes and gram-positive cocci, and S.uberis was isolated in both 5% sheep blood and chocolate agar media. Bacterial identification and antibiotic susceptibility tests were performed by VITEK 2 (Biomerieux, France) and also, the bacterium was identified by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) based VITEK MS system as S.uberis. The isolate was determined susceptible to ampicillin, erythromycin, clindamycin, levofloxacin, linezolid, penicillin, cefotaxime, ceftriaxone, tetracycline and vancomycin. 16S, 23S ribosomal RNA and 16S-23S intergenic spacer gene regions were amplified with specific primers and partial DNA sequence analysis of 16S rRNA polymerase chain reaction (PCR) products were performed by 3500xL Genetic Analyzer (Applied Biosystems, USA). According to the partial 16S rRNA gene sequencing results, bacterium was confirmed as S.uberis. This report makes a significant contribution to the number of case reports of human infections caused by S.uberis as the identification was performed by current microbiological methods in our case. In conclusion, S.uberis should be evaluated as an opportunistic pathogen among the immunosuppressed patients and in addition to phenotypic bacteriological methods, the other recent microbiological methods should also be utilized for the identification.

Five-year comparative study on conventional and laser-assisted therapy of periimplantitis and periodontitis

NASA Astrophysics Data System (ADS)

Bach, Georg; Neckel, Claus P.

2000-03-01

Numerous groups have recommended the use of the diode laser to decontaminate infected root and implant surfaces. The aim of this study was to show the outcome after laser assisted and conventional therapy of periimplantitis and periodontitis administering approved treatment protocols. Between 1994 and 1999 a total of 50 patients with periimplantitis (20) and periodontitis (30) were treated in two groups each. Clinical, microbiological and radiographic evaluation was performed before and 6, 12, 24, 36, 48 and 60 months after treatment. In addition to the conventional treatment protocol, flap surgery, the tooth or implant surface was decontaminated with a 810 nm diode laser using 1 Watt output for 20 sec (CW mode). All accessible surfaces were decontaminated at the follow up dates. In the periimplantitis group recurrence of the marker bacteria was higher and faster over time for the conventionally operated patients. Also the clinical and radiographic reevaluation showed significantly better results. The laser group of the periodontitis patients also showed significantly better outcome in terms of clinical evaluation, microbiological counts, radiographic evaluation and tooth loss. In comparison to other long term studies our results for the conventional therapy were adequate, the laser assisted therapy brought up significantly better and reproducible results.

[Agrobacterium rubi strains from blueberry plants are highly diverse].

PubMed

Abrahamovich, Eliana; López, Ana C; Alippi, Adriana M

2014-01-01

The diversity of a collection of Agrobacterium rubi strains isolated from blueberries from different regions of Argentina was studied by conventional microbiological tests and molecular techniques. Results from biochemical and physiological reactions, as well as from rep-PCR and RFLP analysis of PCR-amplified 23S rDNA showed high phenotypic and genotypic intraspecific variation. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España. All rights reserved.

Identification of active fluorescence stained bacteria by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Krause, Mario; Beyer, Beatrice; Pietsch, Christian; Radt, Benno; Harz, Michaela; Rösch, Petra; Popp, Jürgen

2008-04-01

Microorganisms can be found everywhere e.g. in food both as useful ingredients or harmful contaminations causing food spoilage. Therefore, a fast and easy to handle analysis method is needed to detect bacteria in different kinds of samples like meat, juice or air to decide if the sample is contaminated by harmful microorganisms. Conventional identification methods in microbiology require always cultivation and therefore are time consuming. In this contribution we present an analysis approach to identify fluorescence stained bacteria on strain level by means of Raman spectroscopy. The stained bacteria are highlighted and can be localized easier against a complex sample environment e.g. in food. The use of Raman spectroscopy in combination with chemometrical methods allows the identification of single bacteria within minutes.

Analysis of total microbiota in dentin after mechanical or papain-based chemomechanical caries removal.

PubMed

de Almeida, Sandro Marco Steanini; Franca, Fabiana Mantovani Gomes; Florio, Flavia Martao; Ambrosano, Glaucia Maria Bovi; Basting, Roberta Tarkany

2013-07-01

Chemomechanical caries removal, when compared with removal using conventional rotary instruments, seems to preserve healthy tooth structure with less trauma to the patient. This study performed in vivo analysis of the total number of microorganisms in dentin after the use of conventional or chemomechanical (papain gel) caries removal methods. Analyses were performed before caries removal (baseline), immediately after caries removal, and 45 days after caries removal and temporary cavity sealing. Sixty patients were selected for this study, each with two mandibular molars (one on each side) with occlusal caries of moderate depth, for a total of 120 teeth. For each patient, the carious lesion of one tooth was removed by conventional methods using low speed drills (Group 1). For the other tooth, a chemomechanical method was used (Group 2). Dentin samples were collected at the three intervals and subjected to microbiological culture in blood agar. For the total number of microorganisms in both groups, ANOVA and Tukey tests (which considered the baseline values as a covariable) showed a higher microbial count immediately after the preparation of the cavity compared to the count at 45 days (P < 0.05). For both groups, the total count of microorganisms in dentin decreased 45 days after placing the temporary cavity sealing.

The urinary microbiome and its contribution to lower urinary tract symptoms; ICI-RS 2015.

PubMed

Drake, Marcus J; Morris, Nicola; Apostolidis, Apostolos; Rahnama'i, Mohammad S; Marchesi, Julian R

2017-04-01

The microbiome is the term used for the symbiotic microbial colonisation of healthy organs. Studies have found bacterial identifiers within voided urine which is apparently sterile on conventional laboratory culture, and accordingly there may be health and disease implications. The International Consultation on Incontinence Research Society (ICI-RS) established a literature review and expert consensus discussion focussed on the increasing awareness of the urinary microbiome, and potential research priorities. The consensus considered the discrepancy between findings of conventional clinical microbiology methods, which generally rely on culture parameters predisposed towards certain "expected" organisms. Discrepancy between selective culture and RNA sequencing to study species-specific 16S ribosomal RNA is increasingly clear, and highlights the possibility that protective or harmful bacteria may be overlooked where microbiological methods are selective. There are now strong signals of the existence of a "core" urinary microbiome for the human urinary tract, particularly emerging with ageing. The consensus reviewed the potential relationship between a patient's microbiome and lower urinary tract dysfunction, whether low-count bacteriuria may be clinically significant and mechanisms which could associate micro-organisms with lower urinary tract symptoms. Key research priorities identified include the need to establish the scope of microbiome across the range of normality and clinical presentations, and gain consensus on testing protocols. Proteomics to study enzymatic and other functions may be necessary, since different bacteria may have overlapping phenotype. Longitudinal studies into risk factors for exposure, cumulative risk, and emergence of disease need to undertaken. Neurourol. Urodynam. 36:850-853, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Direct ultrafiltration performance and membrane integrity monitoring by microbiological analysis.

PubMed

Ferrer, O; Casas, S; Galvañ, C; Lucena, F; Bosch, A; Galofré, B; Mesa, J; Jofre, J; Bernat, X

2015-10-15

The feasibility of substituting a conventional pre-treatment, consisting of dioxi-chlorination, coagulation/flocculation, settling and sand filtration, of a drinking water treatment plant (DWTP) by direct ultrafiltration (UF) has been assessed from a microbiological standpoint. Bacterial indicators, viral indicators and human viruses have been monitored in raw river, ultrafiltered and conventionally pre-treated water samples during two years. Direct UF has proven to remove bacterial indicators quite efficiently and to a greater extent than the conventional process does. Nevertheless, the removal of small viruses such as some small bacteriophages and human viruses (e.g. enteroviruses and noroviruses) is lower than the current conventional pre-treatment. Membrane integrity has been assessed during two years by means of tailored tests based on bacteriophages with different properties (MS-2, GA and PDR-1) and bacterial spores (Bacillus spores). Membrane integrity has not been compromised despite the challenging conditions faced by directly treating raw river water. Bacteriophage PDR-1 appears as a suitable microbe to test membrane integrity, as its size is slightly larger than the considered membrane pore size. However, its implementation at full scale plant is still challenging due to difficulties in obtaining enough phages for its seeding. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evaluation of an electricity-free, culture-based approach for detecting typhoidal Salmonella bacteremia during enteric fever in a high burden, resource-limited setting.

PubMed

Andrews, Jason R; Prajapati, Krishna G; Eypper, Elizabeth; Shrestha, Poojan; Shakya, Mila; Pathak, Kamal R; Joshi, Niva; Tiwari, Priyanka; Risal, Manisha; Koirala, Samir; Karkey, Abhilasha; Dongol, Sabina; Wen, Shawn; Smith, Amy B; Maru, Duncan; Basnyat, Buddha; Baker, Stephen; Farrar, Jeremy; Ryan, Edward T; Hohmann, Elizabeth; Arjyal, Amit

2013-01-01

In many rural areas at risk for enteric fever, there are few data on Salmonella enterica serotypes Typhi (S. Typhi) and Paratyphi (S. Paratyphi) incidence, due to limited laboratory capacity for microbiologic culture. Here, we describe an approach that permits recovery of the causative agents of enteric fever in such settings. This approach involves the use of an electricity-free incubator based upon use of phase-change materials. We compared this against conventional blood culture for detection of typhoidal Salmonella. Three hundred and four patients with undifferentiated fever attending the outpatient and emergency departments of a public hospital in the Kathmandu Valley of Nepal were recruited. Conventional blood culture was compared against an electricity-free culture approach. Blood from 66 (21.7%) patients tested positive for a Gram-negative bacterium by at least one of the two methods. Sixty-five (21.4%) patients tested blood culture positive for S. Typhi (30; 9.9%) or S. Paratyphi A (35; 11.5%). From the 65 individuals with culture-confirmed enteric fever, 55 (84.6%) were identified by the conventional blood culture and 60 (92.3%) were identified by the experimental method. Median time-to-positivity was 2 days for both procedures. The experimental approach was falsely positive due to probable skin contaminants in 2 of 239 individuals (0.8%). The percentages of positive and negative agreement for diagnosis of enteric fever were 90.9% (95% CI: 80.0%-97.0%) and 96.0% (92.7%-98.1%), respectively. After initial incubation, Salmonella isolates could be readily recovered from blood culture bottles maintained at room temperature for six months. A simple culture approach based upon a phase-change incubator can be used to isolate agents of enteric fever. This approach could be used as a surveillance tool to assess incidence and drug resistance of the etiologic agents of enteric fever in settings without reliable local access to electricity or local diagnostic microbiology laboratories.

[Utility of MALDI-TOF MS for the identification of anaerobic bacteria].

PubMed

Zárate, Mariela S; Romano, Vanesa; Nievas, Jimena; Smayevsky, Jorgelina

2014-01-01

The analysis by MALDI-TOF MS (Matrix-assited laser desorption/ionization time-of-flight mass spectrometry) has become a reference method for the identification of microorganisms in Clinical Microbiology. However, data on some groups of microorganisms are still controversial. The aim of this study is to determine the utility of MALDI-TOF MS for the identification of clinical isolates of anaerobic bacteria. One-hundred and six anaerobic bacteria isolates were analyzed by MALDI-TOF MS and by conventional biochemical tests. In those cases where identification by conventional methodology was not applicable or in the face of discordance between sequencing methodologies, 16 S rRNA gene sequence analysis was performed. The conventional method and MALDI-TOF MS agreed at genus and species level by 95.3 %. Concordance in gram-negative bacilli was 91.4% and 100% among gram-positive bacilli; there was also concordance both in the 8 isolates studied in gram-positive cocci and in the single gram-negative cocci included. The data obtained in this study demonstrate that MALDI-TOF MS offers the possibility of adequate identification of anaerobic bacteria. Copyright © 2014 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Prevalence and Comparing of Some Microbiological Properties, Somatic Cell Count and Antibiotic Residue of Organic and Conventional Raw Milk Produced in Turkey

PubMed Central

Şengül, Mustafa; Erkaya, Tuba; Aksakal, Vecihi

2017-01-01

The aim of this study was to investigate the effects of production systems and milk collection periods on the somatic cell count (SCC), some microbiological properties, total aerobic mesophilic bacteria (TAMB), coliform, Staphylococcus aureus (S. aureus), yeast and mould) and antibiotic residue of milk; in Turkey. Milk samples were collected from 9 conventional farms and 9 organic farms during one year time, at six different months (December 2013 to October 2014), and all farms were selected from the same geographical locations. All organically managed farms had organic production certificates given by the Republic of Turkey Ministry of Food, Agriculture and Livestock. The count of TAMB, coliform, and coagulase positive S. aureus were affected by production systems at the level of p<0.01; yeast and mold, and somatic cell count (SCC) were affected at the level of p<0.05. But, differences according to months were statistically significant only on TAMB (p<0.01) and coliform (p<0.05) counts. The general means of TAMB, coliform and yeast and mould counts of the organic milk (OM) were significantly lower (p<0.05), while the general means of SCC and coagulase positive S. aureus count of the OM was significantly higher (p<0.05) compared to conventional milk (CM). Antibiotic residue was determined in one of the CM sample and in two of the OM samples. Our study is the first research that compared conventional and organic milk in Turkey. This study indicated that the microbiological quality of OM was the higher in terms of TAMB, coliform and yeast and mould, whereas was the lower in relation to SCC and coagulase positive S. aureus counts. But, the quality of both milk types should be improved. PMID:28515650

A rapid, efficient and sensitive plate assay for detection and screening of l-asparaginase-producing microorganisms.

PubMed

Mahajan, Richi V; Saran, Saurabh; Saxena, Rajendra K; Srivastava, Ayush K

2013-04-01

l-Asparaginase-producing microbes are conventionally screened on phenol red l-asparagine-containing plates. However, sometimes the contrast of the zone obtained (between yellow and pink) is not very sharp and distinct. In the present investigation, an improved method for screening of the microorganisms producing extracellular l-asparaginase is reported wherein bromothymol blue (BTB) is incorporated as pH indicator in l-asparagine-containing medium instead of phenol red. Plates containing BTB at acidic pH are yellow and turn dark blue at alkaline pH. Thus, a dense dark blue zone is formed around microbial colonies producing l-asparaginase, differentiating between enzyme producers and non-producers. The present method is more sensitive and accurate than the conventional method for screening of both fungi and bacteria producing extracellular l-asparaginase. Furthermore, BTB gives a transient green colour at neutral pH (7.0) and dark blue colour at higher pH 8.0-9.0, indicating the potency of the microorganism for l-asparaginase production. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Rapid Antimicrobial Susceptibility Testing of Bacillus anthracis, Yersinia pestis, and Burkholderia pseudomallei by Use of Laser Light Scattering Technology.

PubMed

Bugrysheva, Julia V; Lascols, Christine; Sue, David; Weigel, Linda M

2016-06-01

Rapid methods to determine antimicrobial susceptibility would assist in the timely distribution of effective treatment or postexposure prophylaxis in the aftermath of the release of bacterial biothreat agents such as Bacillus anthracis, Yersinia pestis, or Burkholderia pseudomallei Conventional susceptibility tests require 16 to 48 h of incubation, depending on the bacterial species. We evaluated a method that is based on laser light scattering technology that measures cell density in real time. We determined that it has the ability to rapidly differentiate between growth (resistant) and no growth (susceptible) of several bacterial threat agents in the presence of clinically relevant antimicrobials. Results were available in <4 h for B. anthracis and <6 h for Y. pestis and B. pseudomallei One exception was B. pseudomallei in the presence of ceftazidime, which required >10 h of incubation. Use of laser scattering technology decreased the time required to determine antimicrobial susceptibility by 50% to 75% for B. anthracis, Y. pestis, and B. pseudomallei compared to conventional methods. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Ultrasonic non invasive techniques for microbiological instrumentation

NASA Astrophysics Data System (ADS)

Elvira, L.; Sierra, C.; Galán, B.; Resa, P.

2010-01-01

Non invasive techniques based on ultrasounds have advantageous features to study, characterize and monitor microbiological and enzymatic reactions. These processes may change the sound speed, viscosity or particle distribution size of the medium where they take place, which makes possible their analysis using ultrasonic techniques. In this work, two different systems for the analysis of microbiological liquid media based on ultrasounds are presented. In first place, an industrial application based on an ultrasonic monitoring technique for microbiological growth detection in milk is shown. Such a system may improve the quality control strategies in food production factories, being able to decrease the time required to detect possible contaminations in packed products. Secondly, a study about the growing of the Escherichia coli DH5 α in different conditions is presented. It is shown that the use of ultrasonic non invasive characterization techniques in combination with other conventional measurements like optical density provides complementary information about the metabolism of these bacteria.

Fungal Rhinosinusitis: Microbiological and Histopathological Perspective

PubMed Central

Singh, Ajay Kumar; Verma, Nitya; Khare, Vineeta; Ahamad, Abrar; Verma, Virendra; Agarwal, S.P

2017-01-01

Introduction On the basis of histopathology Fungal Rhinosinusitis (FRS) is categorized into non-invasive (allergic fungal rhinosinusitis, fungal ball) and invasive (acute invasive, chronic invasive and granulomatous invasive fungal sinusitis). This differentiation helps to decide the treatment. Role of latest molecular methods such as PCR and conventional methods such as KOH microscopy and culture also needs to be evaluated. Therefore, in this study we planned to categorise fungal rhinosinusitis on the basis of histopathology and compare it with other methods such as PCR, culture and KOH microscopy. Aim To analyse fungal rhinosinusitis cases by both histopathologically and microbiologically. Materials and Methods A total of 76 clinically suspected fungal rhinosinusitis cases were included in the study. The tissue of suspected cases were processed and examined by KOH microscopy, histopathologically, culture and PCR. Histopathological examination was done by PAS, GMS and H&E stain. Results FRS was diagnosed in 37 (48.68%) cases out of 76 clinically suspected cases of FRS. In which 17 (22.3%) cases were positive by direct microscopy, 21 (27.6%) by culture, 27 (35.5%) by PCR and 14 (18.42%) by histopathology. Approximately 14 cases of FRS were classified according to histopathology; 10 (71.3%) as non-invasive FRS. Out of these 10, 9 (64.2%) were classified as AFRS and 1 (7.14%) as fungal ball. Only 4 cases (28.5%) were diagnosed with invasive FRS. Out of these 4 cases, 2 (14.2%) were of chronic invasive fungal rhinosinusitis, 1 (7.14%) was of granulomatous invasive fungal rhinosinusitis and 1 (7.14%) was of acute fulminant invasive fungal rhinosinusitis. Allergic Fungal Rhinosinusitis (AFRS) is the most common type of FRS. Aspergillus flavus was found to be the most common fungi causing FRS. Conclusion Diagnosis should not be based on the single method. It should be done by both histopathological and microbiological methods, especially for those cases which are difficult to diagnose. PMID:28892889

Identification of yeasts and evaluation of their distribution in Taiwanese Kefir and Viili starters.

PubMed

Wang, S Y; Chen, H C; Liu, J R; Lin, Y C; Chen, M J

2008-10-01

The objective of the present study was to investigate yeast communities in kefir grains and viili starters in Taiwan through conventional microbiological cultivation and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The DNA sequencing was used as a validity technique to ensure that all isolates within each group belonged to just one species, and to confirm the identified results of PCR-DGGE. Results indicated that a combination of conventional microbiological cultivation with PCR-DGGE and sequencing could successfully identify 4 yeast species from both types of cultures in Taiwan. Kluyveromyces marxianus, Saccharomyces turicensis, and Pichia fermentans were found in Taiwanese kefir grains with a distribution of 76, 22, and 2%, respectively, whereas Klu. marxianus, Saccharomyces unisporus and P. fermentans were identified in viili starters corresponding to 58, 11, and 31% of the total cell counts, respectively. Furthermore, the culture-independent method was applied to identify the yeast species using DGGE. Only 2 yeast species, Klu. marxianus and S. turicensis, were found in kefir grains and 2, Klu. marxianus and P. fermentans, in viili starters. These results suggest that in samples containing multiple species, PCR-DGGE may fail to detect some species. Sequences of yeast isolates reported in this study have been deposited in the GenBank database under accession nos. DQ139802, AF398485, DQ377652, and AY007920.

An appropriately performed conventional blood culture can facilitate choice of therapy in resource-constrained settings-comparison with BACTEC 9050.

PubMed

Surase, P V; Nataraj, G; Pattamadai, K; Mehta, P R; Pazare, A R; Agarwal, M C; Nanavati, R N

2016-01-01

Comparison of conventional blood culture with BACTEC 9050 for rate and time to detection of microorganisms. A prospective study was carried out in a multispecialty tertiary care teaching hospital. A total of 835 paired specimens (797 blood and 38 nonblood specimens) were collected and processed according to standard microbiological procedures by both conventional method as well as by BACTEC 9050 automated culture system. Clinical details of patients were recorded. Data were analyzed for time to detection and isolation rate by the two systems and compared. Overall culture positivity for BACTEC 9050 and the conventional system was 32% and 19.88%, respectively. Eighty-five demonstrated concordant growth, 136 specimens were culture positive by BACTEC only, and 38 specimens were culture positive by conventional only. Twelve contaminants in BACTEC and nine contaminants in conventional system were detected. Using BACTEC 9050, higher isolation was observed for Acinetobacter spp., coagulase negative Staphylococcus spp., Streptococcus spp., and Candida spp. A total of 410 patients were on antimicrobial treatment and culture positivity was significantly higher with BACTEC 9050 (P < 0.0001). There was a significant difference in the mean time to detection with BACTEC 9050 recovering 86.8% of isolates within 48 h (P < 0.0001). Although BACTEC 9050 demonstrated a significantly higher recovery of microorganisms from blood, an appropriately performed conventional blood culture can facilitate the choice of therapy.

Test method development to evaluate hot, humid air decontamination of materials contaminated with Bacillus anthracis ∆Sterne and B. thuringiensis Al Hakam spores.

PubMed

Buhr, T L; Young, A A; Minter, Z A; Wells, C M; McPherson, D C; Hooban, C L; Johnson, C A; Prokop, E J; Crigler, J R

2012-11-01

To develop test methods and evaluate the survival of Bacillus anthracis ∆Sterne and Bacillus thuringiensis Al Hakam spores after exposure to hot, humid air. Spores (>7 logs) of both strains were dried on six different test materials. Response surface methodology was employed to identify the limits of spore survival at optimal test combinations of temperature (60, 68, 77°C), relative humidity (60, 75, 90%) and time (1, 4, 7 days). No spores survived the harshest test run (77°C, 90% r.h., 7 days), while > 6·5 logs of spores survived the mildest test run (60°C, 60% r.h., 1 day). Spores of both strains inoculated on nylon webbing and polypropylene had greater survival rates at 68°C, 75% r.h., 4 days than spores on other materials. Electron microscopy showed no obvious physical damage to spores using hot, humid air, which contrasted with pH-adjusted bleach decontamination. Test methods were developed to show that hot, humid air effectively inactivates B. anthracis ∆Sterne and B. thuringiensis Al Hakam spores with similar kinetics. Hot, humid air is a potential alternative to conventional chemical decontamination. © 2012 The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Direct maldi-tof mass spectrometry assay of blood culture broths for rapid identification of Candida species causing bloodstream infections: an observational study in two large microbiology laboratories.

PubMed

Spanu, Teresa; Posteraro, Brunella; Fiori, Barbara; D'Inzeo, Tiziana; Campoli, Serena; Ruggeri, Alberto; Tumbarello, Mario; Canu, Giulia; Trecarichi, Enrico Maria; Parisi, Gabriella; Tronci, Mirella; Sanguinetti, Maurizio; Fadda, Giovanni

2012-01-01

We evaluated the reliability of the Bruker Daltonik's MALDI Biotyper system in species-level identification of yeasts directly from blood culture bottles. Identification results were concordant with those of the conventional culture-based method for 95.9% of Candida albicans (187/195) and 86.5% of non-albicans Candida species (128/148). Results were available in 30 min (median), suggesting that this approach is a reliable, time-saving tool for routine identification of Candida species causing bloodstream infection.

'Neisseria skkuensis' sp. nov., isolated from the blood of a diabetic patient with a foot ulcer.

PubMed

Lee, Mi Young; Park, Eu Gene; Choi, Ji Young; Cheong, Hae Suk; Chung, Doo Ryeon; Peck, Kyong Ran; Song, Jae-Hoon; Ko, Kwan Soo

2010-07-01

A Gram-negative bacterium was isolated from the blood of a patient with diabetes mellitus. However, it could not be identified by conventional microbiological methods, and so was characterized by phenotypic and genotypic analyses. 16S rRNA gene sequence analysis revealed that the strain belonged to the genus Neisseria. Based on the phenotypic and genotypic characteristics, we propose that strain SMC-A9199(T) (=KCTC 22696(T)=JCM 16127(T)) should be classified as a novel species, 'Neisseria skkuensis' sp. nov. The patient was further treated with amoxicillin-clavulanate and ciprofloxacin for 3 weeks.

Detection of periodontopathogenic bacteria in pregnant women by traditional anaerobic culture method and by a commercial molecular genetic method.

PubMed

Urbán, Edit; Terhes, Gabriella; Radnai, Márta; Gorzó, István; Nagy, Elisabeth

2010-06-01

To culture facultative and strict anaerobic bacteria is a well-established method for analyzing subgingival plaque samples. Micro-IDent and micro-IDent Plus (HAIN Lifescience GmbH, Nehren, Germany) tests are two commercially available rapid PCR-based methods for the identification and quantification of putative periodontopathogen bacteria. In this study, we compared these commercial PCR-based hybridization methods with conventional anaerobic culture technique. A total of 36 subgingival plaque samples were collected from periodontal pockets of pregnant women with chronic localized periodontitis. Aliquots of these samples were evaluated with species-specific probes provided by micro-IDent and micro-IDent Plus tests simultaneously, and from the same samples anaerobic and capnophylic bacteria were cultured on selective media. The overall agreement between both methods was excellent for Eubacterium nodatum, Tannerella forsythia and Porphyromonas gingivalis (97-92%), fair for Capnocytophaga sp, Eikenella corrodens, Actinobacillus actinomycetemcomitans, and Prevotella intermedia (91-89%) and poor for Fusobacterium nucleatum, Parvimonas micra (Micromonas micros), and Campylobacter rectus (86-78%). Discrepancies in the results may be explained by inability of culture method to distinguish between closely related taxa (e.i P. intermedia/Prevotella. nigrescens), and problems of keeping periodontopathogen bacteria viable, which is required for successful detection by standard culture method. Nucleic acid-based methods may replace cultivation method as frequently used methods in microbiological diagnosis of progressive periodontitis, thus micro-IDent and micro-IDent Plus tests can be recommended where culture of periodontopathogenic bacteria is not performed in routine microbiology laboratories to analyze subgingival plaque samples. 2010 Elsevier Ltd. All rights reserved.

Microbial deterioration of vacuum-packaged chilled beef cuts and techniques for microbiota detection and characterization: a review.

PubMed

Hernández-Macedo, Maria Lucila; Barancelli, Giovana Verginia; Contreras-Castillo, Carmen Josefina

2011-01-01

Gas production from microbial deterioration in vacuum-packs of chilled meat leads to pack distension, which is commonly referred as blown pack. This phenomenon is attributed to some psychrophilic and psychrotrophic Clostridium species, as well as Enterobacteria. The ability of these microorganisms to grow at refrigeration temperatures makes the control by the meat industry a challenge. This type of deterioration has been reported in many countries including some plants in the Midwestern and Southeastern regions of Brazil. In addition to causing economic losses, spoilage negatively impacts the commercial product brand, thereby impairing the meat industry. In the case of strict anaerobes species they are difficult to grow and isolate using culture methods in conventional microbiology laboratories. Furthermore, conventional culture methods are sometimes not capable of distinguishing species or genera. DNA-based molecular methods are alternative strategies for detecting viable and non-cultivable microorganisms and strict anaerobic microorganisms that are difficult to cultivate. Here, we review the microorganisms and mechanisms involved in the deterioration of vacuum-packaged chilled meat and address the use of molecular methods for detecting specific strict anaerobic microorganisms and microbial communities in meat samples.

A combined disc method with resazurin agar plate assay for early phenotypic screening of KPC, MBL and OXA-48 carbapenemases among Enterobacteriaceae.

PubMed

Teethaisong, Y; Eumkeb, G; Nakouti, I; Evans, K; Hobbs, G

2016-08-01

To validate a combined disc method along with resazurin chromogenic agar for early screening and differentiation of Klebsiella pneumoniae carbapenemase, metallo-β-lactamase and OXA-48 carbapenemase-producing Enterobacteriaceae. The combined disc test comprising of meropenem alone and with EDTA, phenylboronic acid or both EDTA and phenylboronic acid, and temocillin alone were evaluated with the resazurin chromogenic agar plate assay against a total of 86 molecularly confirmed Enterobacteriaceae clinical isolates (11 metallo-β-lactamases, eight Kl. pneumoniae carbapenemases, 11 OXA-48, 32 AmpC and 15 extended-spectrum-β-lactamase producers and nine co-producers of extended-spectrum-β-lactamase and AmpC). The inhibition zone diameters were measured and interpreted at 7 h for the presence of carbapenemase. All carbapenemase producers were phenotypically distinguished by this assay with 100% sensitivity and specificity. This early phenotypic method is very simple, inexpensive, and reliable in the detection and differentiation of carbapenemase-producing Enterobacteriaceae. It could be exploited in any microbiological laboratory for diagnosis of these recalcitrant bacteria. This assay poses excellent performance in discrimination of Kl. pneumoniae carbapenemase, metallo-β-lactamase and OXA-48 carbapenemases within 7 h, which is much faster than conventional disc diffusion methods. The rapid detection could help clinicians screen patients, control infection and provide epidemiological surveillance. © 2016 The Society for Applied Microbiology.

Evaluation of a Method Using Three Genomic Guided Escherichia coli Markers for Phylogenetic Typing of E. coli Isolates of Various Genetic Backgrounds.

PubMed

Hamamoto, Kouta; Ueda, Shuhei; Yamamoto, Yoshimasa; Hirai, Itaru

2015-06-01

Genotyping and characterization of bacterial isolates are essential steps in the identification and control of antibiotic-resistant bacterial infections. Recently, one novel genotyping method using three genomic guided Escherichia coli markers (GIG-EM), dinG, tonB, and dipeptide permease (DPP), was reported. Because GIG-EM has not been fully evaluated using clinical isolates, we assessed this typing method with 72 E. coli collection of reference (ECOR) environmental E. coli reference strains and 63 E. coli isolates of various genetic backgrounds. In this study, we designated 768 bp of dinG, 745 bp of tonB, and 655 bp of DPP target sequences for use in the typing method. Concatenations of the processed marker sequences were used to draw GIG-EM phylogenetic trees. E. coli isolates with identical sequence types as identified by the conventional multilocus sequence typing (MLST) method were localized to the same branch of the GIG-EM phylogenetic tree. Sixteen clinical E. coli isolates were utilized as test isolates without prior characterization by conventional MLST and phylogenetic grouping before GIG-EM typing. Of these, 14 clinical isolates were assigned to a branch including only isolates of a pandemic clone, E. coli B2-ST131-O25b, and these results were confirmed by conventional typing methods. Our results suggested that the GIG-EM typing method and its application to phylogenetic trees might be useful tools for the molecular characterization and determination of the genetic relationships among E. coli isolates. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Comparison of BacT/Alert FAN and FAN Plus Bottles with Conventional Medium for Culturing Cerebrospinal Fluid.

PubMed

Yoo, In Young; Chun, Sejong; Song, Dong Joon; Huh, Hee Jae; Lee, Nam Yong

2016-11-01

We compared the BacT/Alert system FAN and FAN Plus media to conventional media for culturing cerebrospinal fluid (CSF) with 2,545 samples. FAN/FAN Plus bottles showed better performance for isolating microorganisms in CSF than conventional media (positive rate, 7.2% [182/2,545] versus 3.1% [80/2,545]). The incremental recovery rate of Cryptococcus neoformans from FAN Plus bottles was higher than that from FAN bottles. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Evaluation of PDA Technical Report No 33. Statistical Testing Recommendations for a Rapid Microbiological Method Case Study.

PubMed

Murphy, Thomas; Schwedock, Julie; Nguyen, Kham; Mills, Anna; Jones, David

2015-01-01

New recommendations for the validation of rapid microbiological methods have been included in the revised Technical Report 33 release from the PDA. The changes include a more comprehensive review of the statistical methods to be used to analyze data obtained during validation. This case study applies those statistical methods to accuracy, precision, ruggedness, and equivalence data obtained using a rapid microbiological methods system being evaluated for water bioburden testing. Results presented demonstrate that the statistical methods described in the PDA Technical Report 33 chapter can all be successfully applied to the rapid microbiological method data sets and gave the same interpretation for equivalence to the standard method. The rapid microbiological method was in general able to pass the requirements of PDA Technical Report 33, though the study shows that there can be occasional outlying results and that caution should be used when applying statistical methods to low average colony-forming unit values. Prior to use in a quality-controlled environment, any new method or technology has to be shown to work as designed by the manufacturer for the purpose required. For new rapid microbiological methods that detect and enumerate contaminating microorganisms, additional recommendations have been provided in the revised PDA Technical Report No. 33. The changes include a more comprehensive review of the statistical methods to be used to analyze data obtained during validation. This paper applies those statistical methods to analyze accuracy, precision, ruggedness, and equivalence data obtained using a rapid microbiological method system being validated for water bioburden testing. The case study demonstrates that the statistical methods described in the PDA Technical Report No. 33 chapter can be successfully applied to rapid microbiological method data sets and give the same comparability results for similarity or difference as the standard method. © PDA, Inc. 2015.

A "three-in-one" sample preparation method for simultaneous determination of B-group water-soluble vitamins in infant formula using VitaFast(®) kits.

PubMed

Zhang, Heng; Lan, Fang; Shi, Yupeng; Wan, Zhi-Gang; Yue, Zhen-Feng; Fan, Fang; Lin, Yan-Kui; Tang, Mu-Jin; Lv, Jing-Zhang; Xiao, Tan; Yi, Changqing

2014-06-15

VitaFast(®) test kits designed for the microbiological assay in microtiter plate format can be applied to quantitative determination of B-group water-soluble vitamins such as vitamin B12, folic acid and biotin, et al. Compared to traditional microbiological methods, VitaFast(®) kits significantly reduce sample processing time and provide greater reliability, higher productivity and better accuracy. Recently, simultaneous determination of vitamin B12, folic acid and biotin in one sample is urgently required when evaluating the quality of infant formulae in our practical work. However, the present sample preparation protocols which are developed for individual test systems, are incompatible with simultaneous determination of several analytes. To solve this problem, a novel "three-in-one" sample preparation method is herein developed for simultaneous determination of B-group water-soluble vitamins using VitaFast(®) kits. The performance of this novel "three-in-one" sample preparation method was systematically evaluated through comparing with individual sample preparation protocols. The experimental results of the assays which employed "three-in-one" sample preparation method were in good agreement with those obtained from conventional VitaFast(®) extraction methods, indicating that the proposed "three-in-one" sample preparation method is applicable to the present three VitaFast(®) vitamin test systems, thus offering a promising alternative for the three independent sample preparation methods. The proposed new sample preparation method will significantly improve the efficiency of infant formulae inspection. Copyright © 2013 Elsevier Ltd. All rights reserved.

Microbiological Quality and Food Safety of Plants Grown on ISS Project

NASA Technical Reports Server (NTRS)

Wheeler, Raymond M. (Compiler)

2014-01-01

The goal of this project is to select and advance methods to enable real-time sampling, microbiological analysis, and sanitation of crops grown on the International Space Station (ISS). These methods would validate the microbiological quality of crops grown for consumption to ensure safe and palatable fresh foods. This would be achieved through the development / advancement of microbiological sample collection, rapid pathogen detection and effective sanitation methods that are compatible with a microgravity environment.

[Bacterial identification methods in the microbiology laboratory].

PubMed

Bou, Germán; Fernández-Olmos, Ana; García, Celia; Sáez-Nieto, Juan Antonio; Valdezate, Sylvia

2011-10-01

In order to identify the agent responsible of the infectious process and understanding the pathogenic/pathological implications, clinical course, and to implement an effective antimicrobial therapy, a mainstay in the practice of clinical microbiology is the allocation of species to a microbial isolation. In daily routine practice microbiology laboratory phenotypic techniques are applied to achieve this goal. However, they have some limitations that are seen more clearly for some kinds of microorganism. Molecular methods can circumvent some of these limitations, although its implementation is not universal. This is due to higher costs and the level of expertise required for thei implementation, so molecular methods are often centralized in reference laboratories and centers. Recently, proteomics-based methods made an important breakthrough in the field of diagnostic microbiology and will undoubtedly have a major impact on the future organization of the microbiology services. This paper is a short review of the most noteworthy aspects of the three bacterial identification methods described above used in microbiology laboratories. Copyright © 2011 Elsevier España, S.L. All rights reserved.

Are the Conventional Commercial Yeast Identification Methods Still Helpful in the Era of New Clinical Microbiology Diagnostics? A Meta-Analysis of Their Accuracy.

PubMed

Posteraro, Brunella; Efremov, Ljupcho; Leoncini, Emanuele; Amore, Rosarita; Posteraro, Patrizia; Ricciardi, Walter; Sanguinetti, Maurizio

2015-08-01

Accurate identification of pathogenic species is important for early appropriate patient management, but growing diversity of infectious species/strains makes the identification of clinical yeasts increasingly difficult. Among conventional methods that are commercially available, the API ID32C, AuxaColor, and Vitek 2 systems are currently the most used systems in routine clinical microbiology. We performed a systematic review and meta-analysis to estimate and to compare the accuracy of the three systems, in order to assess whether they are still of value for the species-level identification of medically relevant yeasts. After adopting rigorous selection criteria, we included 26 published studies involving Candida and non-Candida yeasts that were tested with the API ID32C (674 isolates), AuxaColor (1,740 isolates), and Vitek 2 (2,853 isolates) systems. The random-effects pooled identification ratios at the species level were 0.89 (95% confidence interval [CI], 0.80 to 0.95) for the API ID32C system, 0.89 (95% CI, 0.83 to 0.93) for the AuxaColor system, and 0.93 (95% CI, 0.89 to 0.96) for the Vitek 2 system (P for heterogeneity, 0.255). Overall, the accuracy of studies using phenotypic analysis-based comparison methods was comparable to that of studies using molecular analysis-based comparison methods. Subanalysis of studies conducted on Candida yeasts showed that the Vitek 2 system was significantly more accurate (pooled ratio, 0.94 [95% CI, 0.85 to 0.99]) than the API ID32C system (pooled ratio, 0.84 [95% CI, 0.61 to 0.99]) and the AuxaColor system (pooled ratio, 0.76 [95% CI, 0.67 to 0.84]) with respect to uncommon species (P for heterogeneity, <0.05). Subanalysis of studies conducted on non-Candida yeasts (i.e., Cryptococcus, Rhodotorula, Saccharomyces, and Trichosporon) revealed pooled identification accuracies of ≥98% for the Vitek 2, API ID32C (excluding Cryptococcus), and AuxaColor (only Rhodotorula) systems, with significant low or null levels of heterogeneity (P > 0.05). Nonetheless, clinical microbiologists should reconsider the usefulness of these systems, particularly in light of new diagnostic tools such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, which allow for considerably shortened turnaround times and/or avoid the requirement for additional tests for species identity confirmation. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

A manual and an automatic TERS based virus discrimination

NASA Astrophysics Data System (ADS)

Olschewski, Konstanze; Kämmer, Evelyn; Stöckel, Stephan; Bocklitz, Thomas; Deckert-Gaudig, Tanja; Zell, Roland; Cialla-May, Dana; Weber, Karina; Deckert, Volker; Popp, Jürgen

2015-02-01

Rapid techniques for virus identification are more relevant today than ever. Conventional virus detection and identification strategies generally rest upon various microbiological methods and genomic approaches, which are not suited for the analysis of single virus particles. In contrast, the highly sensitive spectroscopic technique tip-enhanced Raman spectroscopy (TERS) allows the characterisation of biological nano-structures like virions on a single-particle level. In this study, the feasibility of TERS in combination with chemometrics to discriminate two pathogenic viruses, Varicella-zoster virus (VZV) and Porcine teschovirus (PTV), was investigated. In a first step, chemometric methods transformed the spectral data in such a way that a rapid visual discrimination of the two examined viruses was enabled. In a further step, these methods were utilised to perform an automatic quality rating of the measured spectra. Spectra that passed this test were eventually used to calculate a classification model, through which a successful discrimination of the two viral species based on TERS spectra of single virus particles was also realised with a classification accuracy of 91%.Rapid techniques for virus identification are more relevant today than ever. Conventional virus detection and identification strategies generally rest upon various microbiological methods and genomic approaches, which are not suited for the analysis of single virus particles. In contrast, the highly sensitive spectroscopic technique tip-enhanced Raman spectroscopy (TERS) allows the characterisation of biological nano-structures like virions on a single-particle level. In this study, the feasibility of TERS in combination with chemometrics to discriminate two pathogenic viruses, Varicella-zoster virus (VZV) and Porcine teschovirus (PTV), was investigated. In a first step, chemometric methods transformed the spectral data in such a way that a rapid visual discrimination of the two examined viruses was enabled. In a further step, these methods were utilised to perform an automatic quality rating of the measured spectra. Spectra that passed this test were eventually used to calculate a classification model, through which a successful discrimination of the two viral species based on TERS spectra of single virus particles was also realised with a classification accuracy of 91%. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07033j

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for rapid identification of fungal rhinosinusitis pathogens.

PubMed

Huang, Yanfei; Wang, Jinglin; Zhang, Mingxin; Zhu, Min; Wang, Mei; Sun, Yufeng; Gu, Haitong; Cao, Jingjing; Li, Xue; Zhang, Shaoya; Lu, Xinxin

2017-03-01

Filamentous fungi are among the most important pathogens, causing fungal rhinosinusitis (FRS). Current laboratory diagnosis of FRS pathogens mainly relies on phenotypic identification by culture and microscopic examination, which is time consuming and expertise dependent. Although matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS has been employed to identify various fungi, its efficacy in the identification of FRS fungi is less clear. A total of 153 FRS isolates obtained from patients were analysed at the Clinical Laboratory at the Beijing Tongren Hospital affiliated to the Capital Medical University, between January 2014 and December 2015. They were identified by traditional phenotypic methods and Bruker MALDI-TOF MS (Bruker, Biotyper version 3.1), respectively. Discrepancies between the two methods were further validated by sequencing. Among the 153 isolates, 151 had correct species identification using MALDI-TOF MS (Bruker, Biot 3.1, score ≥2.0 or 2.3). MALDI-TOF MS enabled identification of some very closely related species that were indistinguishable by conventional phenotypic methods, including 1/10 Aspergillus versicolor, 3/20 Aspergillus flavus, 2/30 Aspergillus fumigatus and 1/20 Aspergillus terreus, which were misidentified by conventional phenotypic methods as Aspergillus nidulans, Aspergillus oryzae, Aspergillus japonicus and Aspergillus nidulans, respectively. In addition, 2/2 Rhizopus oryzae and 1/1 Rhizopus stolonifer that were identified only to the genus level by the phenotypic method were correctly identified by MALDI-TOF MS. MALDI-TOF MS is a rapid and accurate technique, and could replace the conventional phenotypic method for routine identification of FRS fungi in clinical microbiology laboratories.

Recent applications of hyperspectral imaging in microbiology.

PubMed

Gowen, Aoife A; Feng, Yaoze; Gaston, Edurne; Valdramidis, Vasilis

2015-05-01

Hyperspectral chemical imaging (HSI) is a broad term encompassing spatially resolved spectral data obtained through a variety of modalities (e.g. Raman scattering, Fourier transform infrared microscopy, fluorescence and near-infrared chemical imaging). It goes beyond the capabilities of conventional imaging and spectroscopy by obtaining spatially resolved spectra from objects at spatial resolutions varying from the level of single cells up to macroscopic objects (e.g. foods). In tandem with recent developments in instrumentation and sampling protocols, applications of HSI in microbiology have increased rapidly. This article gives a brief overview of the fundamentals of HSI and a comprehensive review of applications of HSI in microbiology over the past 10 years. Technical challenges and future perspectives for these techniques are also discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Pulmonary infections in critical/intensive care - rapid diagnosis and optimizing antimicrobial usage.

PubMed

Douglas, Ivor S

2017-05-01

Diagnosis of pulmonary infection, including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) in the critically ill patient remains a common and therapeutically challenging diagnosis with significant attributable morbidity, mortality, and cost. Current clinical approaches to surveillance, early detection and, conventional culture-based microbiology are inadequate for optimal targeted antibiotic treatment and stewardship. Efforts to enhance diagnosis of HAP and VAP and the impact of these novel approaches on rational antimicrobial selection and stewardship are the focus of recent studies reviewed here. Recent consensus guidelines for diagnosis and management of HAP and VAP are relatively silent on the potential role of novel rapid microbiological techniques and reply heavily on conventional culture strategies of noninvasively obtained (including endotracheal aspirate samples). Novel rapid microbiological diagnostics, including nucleic acid amplification, mass spectrometry, and fluorescence microscopy-based technologies are promising approaches for the future. Exhaled breath biomarkers, including measurement of VOC represent a future approach. Further validation of novel diagnostic technology platforms will be required to evaluate their utility for enhancing diagnosis and guiding treatment of pulmonary infections in the critically ill. However, the integration of novel diagnostics for rapid microbial identification, resistance phenotyping, and antibiotic sensitivity testing into usual care practice could significantly transform the care of patients and potentially inform improved targeted antimicrobial selection, de-escalation, and stewardship.

Comparison of Vitek Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Versus Conventional Methods in Candida Identification.

PubMed

Keçeli, Sema Aşkın; Dündar, Devrim; Tamer, Gülden Sönmez

2016-02-01

Candida species are generally identified by conventional methods such as germ tube or morphological appearance on corn meal agar, biochemical methods using API kits and molecular biological methods. Alternative to these methods, rapid and accurate identification methods of microorganisms called matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDİ-TOF MS) has recently been described. In this study, Candida identification results by API Candida kit, API 20C AUX kit and identifications on corn meal agar (CMA) are compared with the results obtained on Vitek-MS. All results were confirmed by sequencing internal transcribed spacer (ITS) regions of rDNA. Totally, 97 Candida strains were identified by germ tube test, CMA, API and Vitek-MS. Vitek-MS results were compatible with 74.2 % of API 20C AUX and 81.4 % of CMA results. The difference between the results of API Candida and API 20C AUX was detected. The ratio of discrepancy between Vitek-MS and API 20C AUX was 25.8 %. Candida species mostly identified as C. famata or C. tropicalis by and not compatible with API kits were identified as C. albicans by Vitek-MS. Sixteen Candida species having discrepant results with Vitek-MS, API or CMA were randomly chosen, and ITS sequence analysis was performed. The results of sequencing were compatible 56.2 % with API 20C AUX, 50 % with CMA and 93.7 % with Vitek-MS. When compared with conventional identification methods, MS results are more reliable and rapid for Candida identification. MS system may be used as routine identification method in clinical microbiology laboratories.

Electricity generation from synthesis gas by microbial processes: CO fermentation and microbial fuel cell technology.

PubMed

Kim, Daehee; Chang, In Seop

2009-10-01

A microbiological process was established to harvest electricity from the carbon monoxide (CO). A CO fermenter was enriched with CO as the sole carbon source. The DGGE/DNA sequencing results showed that Acetobacterium spp. were enriched from the anaerobic digester fluid. After the fermenter was operated under continuous mode, the products were then continuously fed to the microbial fuel cell (MFC) to generate electricity. Even though the conversion yield was quite low, this study proved that synthesis gas (syn-gas) can be converted to electricity with the aid of microbes that do not possess the drawbacks of metal catalysts of conventional methods.

Sonication technique improves microbiological diagnosis in patients treated with antibiotics before surgery for prosthetic joint infections.

PubMed

Scorzolini, Laura; Lichtner, Miriam; Iannetta, Marco; Mengoni, Fabio; Russo, Gianluca; Panni, Alfredo Schiavone; Vasso, Michele; Vasto, Michele; Bove, Marco; Villani, Ciro; Mastroianni, Claudio M; Vullo, Vincenzo

2014-07-01

Microbiological diagnosis is crucial for the appropriate management of implant-associated orthopedic infections (IAOIs). Sonication of biomaterials for microbiological diagnosis has not yet been introduced in routine clinical practice. Aim of this study was to describe the advantages and feasibility of this procedure in the clinical setting. We prospectively studied 56 consecutive patients undergoing revision because of IAOI and compared the sensitivity of sonication of explanted orthopedic implants with standard cultures. Patients were divided into two groups: those with foreign body infection (FBI, 15 patients) and those with prosthetic joint infection (PJI, 41 patients). Clinical, radiological and microbiological features were recorded. In the PJI group the sensitivity of sonication in detecting bacterial growth was higher than conventional culture (77% vs 34.1% respectively, p<0.002), while no difference was observed in the FBI group (85.7% vs 86% respectively, p>0.05). Coagulase-negative Staphylococci accounted for 90% of the bacteria detected by sonication. Moreover, we found that in the PJI group the sensitivity of sonication was not affected by the timing of antibiotic interruption before surgery. Sonication remains an important tool to improve microbiological diagnosis in PJIs, especially in patients who received previous antimicrobial treatment.

Do aggregate stability and soil organic matter content increase following organic inputs?

NASA Astrophysics Data System (ADS)

Lehtinen, Taru; Gísladóttir, Guðrún; van Leeuwen, Jeroen P.; Bloem, Jaap; Steffens, Markus; Vala Ragnarsdóttir, Kristin

2014-05-01

Agriculture is facing several challenges such as loss of soil organic matter (SOM); thus, sustainable farming management practices are needed. Organic farming is growing as an alternative to conventional farming; in Iceland approximately 1% and in Austria 16% of utilized agricultural area is under organic farming practice. We analyzed the effect of different farming practices (organic, and conventional) on soil physicochemical and microbiological properties in grassland soils in Iceland and cropland soils in Austria. Organic farms differed from conventional farms by absence of chemical fertilizers and pesticide use. At these farms, we investigated soil physicochemical (e.g. soil texture, pH, CAL-extractable P and K) and microbiological properties (fungal and bacterial biomass and activity). The effects of farming practices on soil macroaggregate stability and SOM quantity, quality and distribution between different fractions were studied following a density fractionation. In Iceland, we sampled six grassland sites on Brown (BA) and Histic (HA) Andosols; two sites on extensively managed grasslands, two sites under organic and two sites under conventional farming practice. In Austria, we sampled four cropland sites on Haplic Chernozems; two sites under organic and two sites under conventional farming practice. We found significantly higher macroaggregate stability in the organic compared to the conventional grasslands in Iceland. In contrast, slightly higher macroaggregation in conventional compared to the organic farming practice was found in croplands in Austria, although the difference was not significant. Macroaggregates were positively correlated with fungal biomass in Iceland, and with Feo and fungal activity in Austria. In Austria, SOM content and nutrient status (except for lower CAL-extractable P at one site) were similar between organic and conventional farms. Our results show that the organic inputs may have enhanced macroaggregation in organic farming practice compared to conventional in the permanent grassland soils in Iceland but were only enough to maintain the SOM content and macroaggregation in the cropland soils in Austria.

The effects of a pulsed Nd:YAG laser on subgingival bacterial flora and on cementum: an in vivo study.

PubMed

Ben Hatit, Y; Blum, R; Severin, C; Maquin, M; Jabro, M H

1996-06-01

The purpose of this study was to compare the effects of scaling and Nd:YAG laser treatments with that of scaling alone on cementum and levels of Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Porphyromonas gingivalis, and Treponema denticola. Study samples consisted of 14 patients, age 30 to 75 years, 8 females and 6 males, with a total of 150 periodontally involved sites with probing depth > or = 5 mm. Group A consisted of 100 pockets that were subdivided into 4 equal groups that were treated with conventional scaling and pulsed Nd:YAG laser using an optic fiber of 300 microns and 4 different power levels as follows: Group 1: P = 0.8 W, f = 10 Hz, E = 100 mJ/pulse; Group 2: P = 1.0 W, f = 1.0 Hz, E = 100 mJ/pulse; Group 3: P = 1.2 W, f = 12 Hz, E = 100 mJ/purse; and Group 4: P = 1.5 W, f = 15 Hz, E = 100 mJ/pulse. The time of each treatment was 60 sec per pocket in all 4 groups. Group B consisted of 50 pockets that were treated by conventional scaling alone and served as a control group. Microbiological samples from group A were collected before scaling; after scaling = before laser, just after laser, 2 weeks later, 6 weeks later, and 10 weeks later. Microbiological samples from group B were collected before scaling, after scaling, 6 weeks later, and 10 weeks later. Microbiological analysis of all samples was done by the Institute Für Angewandte Immunologie (IAI) method. The effects of laser on root surfaces were assessed by SEM examination and the sample consisted of 13 teeth from 5 different patients. Four sets of 3 teeth each were treated with Nd:YAG laser using 0.8, 1.0, 1.2, and 1.5 W, respectively. One tooth was just scaled and not treated with laser to serve as a control. Microbiological analysis of Group A samples indicated posttreatment reduction in levels of all 4 bacterial types tested compared to pretreatment levels and Group B controls. SEM examination of the specimens treated with Nd:YAG laser at different levels exhibited different features of root surface alterations.

Comparison of methods for the identification of microorganisms isolated from blood cultures.

PubMed

Monteiro, Aydir Cecília Marinho; Fortaleza, Carlos Magno Castelo Branco; Ferreira, Adriano Martison; Cavalcante, Ricardo de Souza; Mondelli, Alessandro Lia; Bagagli, Eduardo; da Cunha, Maria de Lourdes Ribeiro de Souza

2016-08-05

Bloodstream infections are responsible for thousands of deaths each year. The rapid identification of the microorganisms causing these infections permits correct therapeutic management that will improve the prognosis of the patient. In an attempt to reduce the time spent on this step, microorganism identification devices have been developed, including the VITEK(®) 2 system, which is currently used in routine clinical microbiology laboratories. This study evaluated the accuracy of the VITEK(®) 2 system in the identification of 400 microorganisms isolated from blood cultures and compared the results to those obtained with conventional phenotypic and genotypic methods. In parallel to the phenotypic identification methods, the DNA of these microorganisms was extracted directly from the blood culture bottles for genotypic identification by the polymerase chain reaction (PCR) and DNA sequencing. The automated VITEK(®) 2 system correctly identified 94.7 % (379/400) of the isolates. The YST and GN cards resulted in 100 % correct identifications of yeasts (15/15) and Gram-negative bacilli (165/165), respectively. The GP card correctly identified 92.6 % (199/215) of Gram-positive cocci, while the ANC card was unable to correctly identify any Gram-positive bacilli (0/5). The performance of the VITEK(®) 2 system was considered acceptable and statistical analysis showed that the system is a suitable option for routine clinical microbiology laboratories to identify different microorganisms.

A six-month Serratia marcescens outbreak in a Neonatal Intensive Care Unit.

PubMed

Morillo, Áurea; González, Verónica; Aguayo, Josefa; Carreño, Concepción; Torres, María José; Jarana, Daniel; Artacho, María José; Jiménez, Francisco; Conde, Manuel; Aznar, Javier

2016-12-01

To investigate a Serratia marcescens (S. marcescens) outbreak in a Neonatal Unit in a tertiary university hospital. Descriptive study of children admitted to the Unit with S. marcescens infection from November 2012 to March 2013. Conventional microbiological methods for clinical and environmental samples were used. The clonal relationship between all available isolates was established by molecular methods. A multidisciplinary team was formed, and preventive measures were taken. S. marcescens was isolated from 18 children. The overall attack rate was 12%, and the case fatality rate in the Intensive Care Unit was 23.5%. The most prevalent types of infections were pneumonia (6), conjunctivitis (6), and bloodstream infection (5). Clinical isolates and environmental isolates obtained from an incubator belonged to a unique clone. The clonal relationship between all S. marcescens strains helped us to identify the possible source of the outbreak. Isolation of S. marcescens from stored water in a container, and from the surface of an incubator after cleaning, suggests a possible environmental source as the outbreak origin, which has been perpetuated due to a failure of cleaning methods in the Unit. The strict hygiene and cleaning measures were the main factors that contributed to the end of the outbreak. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Microbiological community analysis of vermicompost tea and its influence on the growth of vegetables and cereals.

PubMed

Fritz, J I; Franke-Whittle, I H; Haindl, S; Insam, H; Braun, R

2012-07-01

Vermicompost, the digestion product of organic material by earthworms, has been widely reported to have a more positive effect on plant growth and plant health than conventional compost. A study was conducted to investigate the effects of different vermicompost elutriates (aerated compost teas) on soils and plant growth. The teas were analyzed by chemical, microbiological, and molecular methods accompanied by plant growth tests at laboratory and field scale. The number of microorganisms in the teas increased during the extraction process and was affected by substrate addition. The vermicompost tea found to increase plant growth best under laboratory tests was applied to cereals (wheat and barley) and vegetables (Raphanus sativus, Rucola selvatica, and Pisum sativum) in a field study. The results revealed no effects of tea application on plant yield; however, sensoric tests indicated an improvement in crop quality. The soils from laboratory and field studies were investigated to detect possible microbial or chemical changes. The results indicated that minor changes to the soil microbial community occurred following tea application by foliar spray in both the laboratory-scale and field-scale experiments.

New diagnostic methods for pneumonia in the ICU.

PubMed

Douglas, Ivor S

2016-04-01

Pneumonia leading to severe sepsis and critical illness including respiratory failure remains a common and therapeutically challenging diagnosis. Current clinical approaches to surveillance, early detection, and conventional culture-based microbiology are inadequate for optimal targeted antibiotic treatment and stewardship. Efforts to enhance diagnosis of community-acquired and health care-acquired pneumonia, including ventilator-associated pneumonia (VAP), are the focus of recent studies reviewed here. Newer surveillance definitions are sensitive for pneumonia in the ICU including VAP but consistently underdetect patients that are clinically shown to have bacterial VAP based on clinical diagnostic criteria and response to antibiotic treatment. Routinely measured plasma biomarkers, including procalcitonin and C-reactive protein, lack sufficient precision and predictive accuracy to inform diagnosis. Novel rapid microbiological diagnostics, including nucleic-acid amplification, mass spectrometry, and fluorescence microscopy-based technologies are promising approaches for the future. Exhaled breath biomarkers, including measurement of volatile organic compounds, represent a future approach. The integration of novel diagnostics for rapid microbial identification, resistance phenotyping, and antibiotic sensitivity testing into usual care practice could significantly transform the care of patients and potentially inform significantly improved targeted antimicrobial selection, de-escalation, and stewardship.

Comparative study on the microbiological features of angular cheilitis in HIV seropositive and HIV seronegative patients from South India

PubMed Central

Krishnan, P Anitha; Kannan, Ranganathan

2013-01-01

Objective: This study was designed to compare the microbiological features of angular cheilitis (AC) in human immunodeficiency virus (HIV) seropositive and HIV seronegative individuals, in a group of south Indians. Materials and Methods: Swabs from oral commissures of 46 patients were obtained and inoculated on to Sabouraud's dextrose agar (SDA) supplemented with chloramphenicol, blood agar (BA) and MacConkey's agar (MCA) plates and cultured. α-hemolytic Streptococci, Staphylococcus albus, Staphylococcus aureus, Candida species, Klebsiella species and Pseudomonas species were cultured. Candidal colonies were further speciated by the conventional biotyping technique. Results: In AC of HIV seropositive patients Candida albicans and Staphylococcus aureus were more prevalent than that in HIV seronegative patients. Incidentally in patients with CD4 cell count less than 200 there was an increase in the incidence of Candidal and Staphylococcus aureus colonization when compared to patients with CD4 cell count higher than 200. Conclusion: The present study suggests a definite difference in the microbial flora of AC in HIV seropositive patients than that of HIV seronegative population. PMID:24574650

Microbioligical Hazard Contamination in Fermented Vegetables Sold in Local Markets in Cambodia.

PubMed

Chrun, Rithy; Hosotani, Yukie; Kawasaki, Susumu; Inatsu, Yasuhiro

2017-01-01

　Fermented vegetables are common part of Cambodian diet. The food safety status for these foods has not been investigated. This study was conducted to evaluate the microbiological hazards that contaminated fermented vegetables. A total of 68 samples of fermented vegetables were purchased randomly from five wet markets in Phnom Penh. The conventional culture methods for microbiological analysis were used. Coliform bacteria (Escherichia coli, Cronobactersakazakii, and Enterobacter spp.), opportunistic non-Entrobacteriaceae, Enterococcus spp., Staphylococcus spp., and Listeria spp. were found in these fermented foods. The highest contamination rate of Enterococcus spp. was 34% of total fermented vegetable samples, followed by Bacillus spp. coliform bacteria and E. coli (31%, 24% and 10%, respectively). The potential foodborne pathogen, C. sakazakii, was identified in one sample. Fermented mixed vegetables showed higher contamination rate of coliform bacteria (50%) than fermented single-type vegetables (13%). The results showed that fermented vegetables sold in wet market are poor in hygiene. The stage in the processing chain where contamination occurred should be identified and basic sanitary practice should be enforced to improve the food safety of fermented vegetables in Cambodia.

A preliminary microbiological assessment of process hygiene of traditional outdoor camel slaughter in Sahrawi refugee camps.

PubMed

Corrò, M; Saleh-Mohamed-Lamin, S; Jatri-Hamdi, S; Slut-Ahmed, B; Mohamed-Lejlifa, S; Di Lello, S; Rossi, D; Broglia, A; Vivas-Alegre, L

2012-10-01

The aim of this study was to investigate the hygiene performance of a camel (Camelus dromedarius) slaughtering process as carried out with the traditional method in the Sahrawi refugee camps located in southwestern Algeria. The camel slaughtering process in this region differs significantly from that carried out in commercial abattoirs. Slaughtering is performed outdoors in desert areas, and dehiding of the carcass is approached via the dorsoventral route rather than the classic ventrodorsal route. Samples were taken from 10 camel carcasses from three different areas: the hide, the carcass meat immediately after dehiding, and the meat after final cutting. Enterobacteriaceae counts (EC) were enumerated employing conventional laboratory techniques. Carcass meat samples resulted in EC below the detection limit more frequently if the hide samples from the same carcass had also EC counts below the detection limit. Because of the low number of trials, the calculation of statistical significance of the results was not possible. Further experimental research is needed in order to validate the results presented in this study. The comparison of the microbiological hygiene performance between dorsal dehiding and traditional ventral dehiding of slaughtered animals could serve to validate the hypothesis of the potential positive impact of the dorsal dehiding method in carcass meat hygiene.

Comparison of the Antibacterial Effect of 810 nm Diode Laser and Photodynamic Therapy in Reducing the Microbial Flora of Root Canal in Endodontic Retreatment in Patients With Periradicular Lesions

PubMed Central

Asnaashari, Mohammad; Godiny, Mostafa; Azari-Marhabi, Saranaz; Tabatabaei, Fahimeh Sadat; Barati, Maryam

2016-01-01

Introduction: The aim of this study was to compare the antibacterial efficacy of diode laser 810nm and photodynamic therapy (PDT) in reducing bacterial microflora in endodontic retreatment of teeth with periradicular lesion. Methods: In this in vivo clinical trial, 20 patients who needed endodontic retreatment were selected. After conventional chemo mechanical preparation of root canals, microbiological samples were taken with sterile paper point (PP), held in thioglycollate broth, and then were transferred to the microbiological lab. In the first group, PDT with methylene blue (MB) and diode laser (810 nm, 0.2 W, 40 seconds) was performed and in the second group diode laser (810 nm, 1.2 W, 30 seconds) was irradiated. Then second samples were taken from all canals. Results: CFU/ml amounts showed statistically significant reduction in both groups (P < 0.001). CFU/ml amounts were compared between the two groups and there was no statistical difference. Conclusion: PDT and diode laser 810 nm irradiation are effective methods for root canal disinfection. PDT is a suitable alternative for diode laser 810 nm irradiation, because of lower thermal risk on root dentin. PMID:27330705

Evaluation of an Electricity-free, Culture-based Approach for Detecting Typhoidal Salmonella Bacteremia during Enteric Fever in a High Burden, Resource-limited Setting

PubMed Central

Andrews, Jason R.; Prajapati, Krishna G.; Eypper, Elizabeth; Shrestha, Poojan; Shakya, Mila; Pathak, Kamal R.; Joshi, Niva; Tiwari, Priyanka; Risal, Manisha; Koirala, Samir; Karkey, Abhilasha; Dongol, Sabina; Wen, Shawn; Smith, Amy B.; Maru, Duncan; Basnyat, Buddha; Baker, Stephen; Farrar, Jeremy; Ryan, Edward T.; Hohmann, Elizabeth; Arjyal, Amit

2013-01-01

Background In many rural areas at risk for enteric fever, there are few data on Salmonella enterica serotypes Typhi (S. Typhi) and Paratyphi (S. Paratyphi) incidence, due to limited laboratory capacity for microbiologic culture. Here, we describe an approach that permits recovery of the causative agents of enteric fever in such settings. This approach involves the use of an electricity-free incubator based upon use of phase-change materials. We compared this against conventional blood culture for detection of typhoidal Salmonella. Methodology/Principal Findings Three hundred and four patients with undifferentiated fever attending the outpatient and emergency departments of a public hospital in the Kathmandu Valley of Nepal were recruited. Conventional blood culture was compared against an electricity-free culture approach. Blood from 66 (21.7%) patients tested positive for a Gram-negative bacterium by at least one of the two methods. Sixty-five (21.4%) patients tested blood culture positive for S. Typhi (30; 9.9%) or S. Paratyphi A (35; 11.5%). From the 65 individuals with culture-confirmed enteric fever, 55 (84.6%) were identified by the conventional blood culture and 60 (92.3%) were identified by the experimental method. Median time-to-positivity was 2 days for both procedures. The experimental approach was falsely positive due to probable skin contaminants in 2 of 239 individuals (0.8%). The percentages of positive and negative agreement for diagnosis of enteric fever were 90.9% (95% CI: 80.0%–97.0%) and 96.0% (92.7%–98.1%), respectively. After initial incubation, Salmonella isolates could be readily recovered from blood culture bottles maintained at room temperature for six months. Conclusions/Significance A simple culture approach based upon a phase-change incubator can be used to isolate agents of enteric fever. This approach could be used as a surveillance tool to assess incidence and drug resistance of the etiologic agents of enteric fever in settings without reliable local access to electricity or local diagnostic microbiology laboratories. PMID:23853696

Isolation of bacteriophages from air using vacuum filtration technique: an improved and novel method.

PubMed

Magare, B; Nair, A; Khairnar, K

2017-10-01

Development of a simple and economical air sampler for isolation and enrichment of bacteriophages from air samples. A vacuum filtration unit with simple modifications was used for isolation of bacteriophages from air sampled in the lavatory. Air was sampled at the rate of 62 l min -1 by bubbling into Mcllvaine buffer for 30 min, which was used as bacteriophage solution for enrichment and plaque assessment against individual hosts. Alternatively, the aforementioned phage solution was enriched using a host consortium before plaque assessment. Phages were isolated in the range of 1-12 PFU per ml by the first method, whereas enrichment with host consortium gave phages around 10- to 1000-folds higher in number. Combining with established enrichment method, an improvement of about 10 times in phage isolation efficiency was attained. The method is very useful for studying the natural bacteriophages of air, requiring only a basic microbiological laboratory setup making it simple and economical. This study brings out a simple, economical air sampler for assessing air bacteriophages that can be employed by any microbial laboratory. Although various methods are available for studying bacteriophages in water and soil, very limited are available for air. To the best of our knowledge, the method developed in this study is unique in its design and concept for studying bacteriophages in air. The sampler is sterilizable by autoclaving and maintains a healthy rate of airflow provided by conventional vacuum pumps. The use of a nonspecific 'trapping solution' allows for the qualitative and quantitative study of air bacteriophages. © 2017 The Society for Applied Microbiology.

Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories.

PubMed

Gargis, Amy S; Kalman, Lisa; Lubin, Ira M

2016-12-01

Clinical microbiology and public health laboratories are beginning to utilize next-generation sequencing (NGS) for a range of applications. This technology has the potential to transform the field by providing approaches that will complement, or even replace, many conventional laboratory tests. While the benefits of NGS are significant, the complexities of these assays require an evolving set of standards to ensure testing quality. Regulatory and accreditation requirements, professional guidelines, and best practices that help ensure the quality of NGS-based tests are emerging. This review highlights currently available standards and guidelines for the implementation of NGS in the clinical and public health laboratory setting, and it includes considerations for NGS test validation, quality control procedures, proficiency testing, and reference materials. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Distribution of different yeasts isolates among trauma patients and comparison of accuracy in identification of yeasts by automated method versus conventional methods for better use in low resource countries.

PubMed

Rajkumari, N; Mathur, P; Xess, I; Misra, M C

2014-01-01

As most trauma patients require long-term hospital stay and long-term antibiotic therapy, the risk of fungal infections in such patients is steadily increasing. Early diagnosis and rapid treatment is life saving in such critically ill trauma patients. To see the distribution of various species of Candida among trauma patients and compare the accuracy, rapid identification and cost effectiveness between VITEK 2, CHROMagar and conventional methods. Retrospective laboratory-based surveillance study performed over a period of 52 months (January 2009 to April 2013) at a level I trauma centre in New Delhi, India. All microbiological samples positive for Candida were processed for microbial identification using standard methods. Identification of Candida was done using chromogenic medium and by automated VITEK 2 Compact system and later confirmed using the conventional method. Time to identification in both was noted and accuracy compared with conventional method. Performed using the SPSS software for Windows (SPSS Inc. Chicago, IL, version 15.0). P values calculated using χ2 test for categorical variables. A P<0.05 was considered significant. Out of 445 yeasts isolates, Candida tropicalis (217, 49%) was the species that was maximally isolated. VITEK 2 was able to correctly identify 354 (79.5%) isolates but could not identify 48 (10.7%) isolates and wrongly identified or showed low discrimination in 43 (9.6%) isolates but CHROM agar correctly identified 381 (85.6%) isolates with 64 (14.4%) misidentification. Highest rate of misidentification was seen in C. tropicalis and C. glabrata (13, 27.1% each) by VITEK 2 and among C. albicans (9, 14%) by CHROMagar. Though CHROMagar gives identification at a lower cost compared with VITEK 2 and are more accurate, which is useful in low resource countries, its main drawback is the long duration taken for complete identification.

Phenotypic Identification of Actinomyces and Related Species Isolated from Human Sources

PubMed Central

Sarkonen, Nanna; Könönen, Eija; Summanen, Paula; Könönen, Mauno; Jousimies-Somer, Hannele

2001-01-01

Recent advancements in chemotaxonomic and molecular biology-based identification methods have clarified the taxonomy of the genus Actinomyces and have led to the recognition of several new Actinomyces and related species. Actinomyces-like gram-positive rods have increasingly been isolated from various clinical specimens. Thus, an easily accessible scheme for reliable differentiation at the species level is needed in clinical and oral microbiology laboratories, where bacterial identification is mainly based on conventional biochemical methods. In the present study we designed a two-step protocol that consists of a flowchart that describes rapid, cost-efficient tests for preliminary identification of Actinomyces and closely related species and an updated more comprehensive scheme that also uses fermentation reactions for accurate differentiation of Actinomyces and closely related species. PMID:11682514

Unexpected Listeria monocytogenes detection with a dithiothreitol-based device during an aseptic hip revision.

PubMed

Banche, Giuliana; Bistolfi, Alessandro; Allizond, Valeria; Galletta, Claudia; Iannantuoni, Maria Rita; Marra, Elisa Simona; Merlino, Chiara; Massè, Alessandro; Cuffini, Anna Maria

2018-06-18

Prosthetic joint infection diagnosis is often difficult since biofilm-embedded microorganisms attach well to the prosthetic surfaces and resist their detection by conventional methods. DL-dithiothreitol has been described as a valid method for biofilm detachment on orthopedic devices. We report the case of an occasional detection of Listeria monocytogenes in a non immuno-compromised patient with a preoperative diagnosis of aseptic loosening. The infection diagnosis due to such rare bacteria was made postoperatively, thanks to a DL-dithiothreitol-based device. This may be considered a feasible approach for the microbiological analysis of prosthetic joint infection, considering that a prompt diagnosis of such biofilm-associated infections could bring some advantages, such as an early and appropriate antibiotic therapy administration and a reduction of undiagnosed infections.

Microbial Ecology: Where are we now?

PubMed

Boughner, Lisa A; Singh, Pallavi

2016-11-01

Conventional microbiological methods have been readily taken over by newer molecular techniques due to the ease of use, reproducibility, sensitivity and speed of working with nucleic acids. These tools allow high throughput analysis of complex and diverse microbial communities, such as those in soil, freshwater, saltwater, or the microbiota living in collaboration with a host organism (plant, mouse, human, etc). For instance, these methods have been robustly used for characterizing the plant (rhizosphere), animal and human microbiome specifically the complex intestinal microbiota. The human body has been referred to as the Superorganism since microbial genes are more numerous than the number of human genes and are essential to the health of the host. In this review we provide an overview of the Next Generation tools currently available to study microbial ecology, along with their limitations and advantages.

A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill.

PubMed

Zhang, Shuangfei; Hu, Zhong; Wang, Hui

2018-01-01

The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico in 2010 resulted in serious damage to local marine and coastal environments. In addition to the physical removal and chemical dispersion of spilled oil, biodegradation by indigenous microorganisms was regarded as the most effective way for cleaning up residual oil. Different microbiological methods were applied to investigate the changes and responses of bacterial communities after the DWH oil spills. By summarizing and analyzing these microbiological methods, giving recommendations and proposing some methods that have not been used, this review aims to provide constructive guidelines for microbiological studies after environmental disasters, especially those involving organic pollutants.

A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill

PubMed Central

Zhang, Shuangfei; Hu, Zhong; Wang, Hui

2018-01-01

The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico in 2010 resulted in serious damage to local marine and coastal environments. In addition to the physical removal and chemical dispersion of spilled oil, biodegradation by indigenous microorganisms was regarded as the most effective way for cleaning up residual oil. Different microbiological methods were applied to investigate the changes and responses of bacterial communities after the DWH oil spills. By summarizing and analyzing these microbiological methods, giving recommendations and proposing some methods that have not been used, this review aims to provide constructive guidelines for microbiological studies after environmental disasters, especially those involving organic pollutants. PMID:29628913

Evaluation of Two Surface Sampling Methods for Microbiological and Chemical Analyses To Assess the Presence of Biofilms in Food Companies.

PubMed

Maes, Sharon; Huu, Son Nguyen; Heyndrickx, Marc; Weyenberg, Stephanie van; Steenackers, Hans; Verplaetse, Alex; Vackier, Thijs; Sampers, Imca; Raes, Katleen; Reu, Koen De

2017-12-01

Biofilms are an important source of contamination in food companies, yet the composition of biofilms in practice is still mostly unknown. The chemical and microbiological characterization of surface samples taken after cleaning and disinfection is very important to distinguish free-living bacteria from the attached bacteria in biofilms. In this study, sampling methods that are potentially useful for both chemical and microbiological analyses of surface samples were evaluated. In the manufacturing facilities of eight Belgian food companies, surfaces were sampled after cleaning and disinfection using two sampling methods: the scraper-flocked swab method and the sponge stick method. Microbiological and chemical analyses were performed on these samples to evaluate the suitability of the sampling methods for the quantification of extracellular polymeric substance components and microorganisms originating from biofilms in these facilities. The scraper-flocked swab method was most suitable for chemical analyses of the samples because the material in these swabs did not interfere with determination of the chemical components. For microbiological enumerations, the sponge stick method was slightly but not significantly more effective than the scraper-flocked swab method. In all but one of the facilities, at least 20% of the sampled surfaces had more than 10 2 CFU/100 cm 2 . Proteins were found in 20% of the chemically analyzed surface samples, and carbohydrates and uronic acids were found in 15 and 8% of the samples, respectively. When chemical and microbiological results were combined, 17% of the sampled surfaces were contaminated with both microorganisms and at least one of the analyzed chemical components; thus, these surfaces were characterized as carrying biofilm. Overall, microbiological contamination in the food industry is highly variable by food sector and even within a facility at various sampling points and sampling times.

Pathogen Prevalence From Traditional Cage and Free Range Production

USDA-ARS?s Scientific Manuscript database

Overview: A study was conducted to determine if differences in pathogen prevalence occurred between a sister flock of conventional cage and free range laying hens. Both environmental and egg microbiology was monitored throughout 20 – 79 weeks of age. Salmonella, Campylobacter, and Listeria preval...

Microbiology of organic and conventionally grown fresh produce.

PubMed

Maffei, Daniele F; Batalha, Erika Y; Landgraf, Mariza; Schaffner, Donald W; Franco, Bernadette D G M

2016-12-01

Fresh produce is a generalized term for a group of farm-produced crops, including fruits and vegetables. Organic agriculture has been on the rise and attracting the attention of the food production sector, since it uses eco-agricultural principles that are ostensibly environmentally-friendly and provides products potentially free from the residues of agrochemicals. Organic farming practices such as the use of animal manure can however increase the risk of contamination by enteric pathogenic microorganisms and may consequently pose health risks. A number of scientific studies conducted in different countries have compared the microbiological quality of produce samples from organic and conventional production and results are contradictory. While some have reported greater microbial counts in fresh produce from organic production, other studies do not. This manuscript provides a brief review of the current knowledge and summarizes data on the occurrence of pathogenic microorganisms in vegetables from organic production. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Salmonella enterica isolates from pasture-raised poultry exhibit antimicrobial resistance and class I integrons.

PubMed

Melendez, S N; Hanning, I; Han, J; Nayak, R; Clement, A R; Wooming, A; Hererra, P; Jones, F T; Foley, S L; Ricke, S C

2010-12-01

While considerable foodborne pathogen research has been conducted on conventionally produced broilers and turkeys, few studies have focused on free-range (organic) or pastured poultry. The current surveillance study was designed to isolate, identify and genetically characterize Salmonella from pastured poultry farm environment and from retail samples. In this study, 59 isolates were collected from two pastured poultry farms (n = 164; pens, feed, water and insect traps) and retail carcasses (n = 36) from a local natural foods store and a local processing plant. All isolates were serotyped and analysed phenotypically (antimicrobial resistance profiles) and genotypically (DNA fingerprints, plasmid profiles and integron analysis). Salmonella enterica was detected using standard microbiological methods. Salmonella Kentucky was the most prevalent serotype detected from the sampled sources (53%), followed by Salmonella Enteritidis (24%), Bareilly (10%), Mbandaka (7%), Montevideo (5%) or Newport (2%). All isolates were resistant to sulfisoxazole and novobiocin, and the majority (40/59) possessed class I integrons shown by PCR detection. Each Salmonella serotype elicited a distinct pulsed-field gel electrophoresis fingerprint profile, and unique differences were observed among the serotypes.  The findings of this study show that Salmonella serotypes isolated from pasture-raised poultry exhibit antimicrobial resistance and class I integrons.  This study demonstrates that despite the cessation of antibiotic usage in poultry production, antibiotic resistant Salmonella may still be recovered from the environment and poultry products. © 2010 The Authors. Journal of Applied Microbiology © 2010 The Society for Applied Microbiology.

Case-based Learning in Microbiology: Observations from a North West Indian Medical College.

PubMed

Singhal, Anita

2017-12-01

Microbiology is usually taught by conventional lectures, and its retention and application is observed to be poor among medical graduates/practitioners. Introduction of case-based learning (CBL) in microbiology for second-year professional MBBS students. Students were divided into two groups of fifty each. Four clinical cases were used for CBL. One group had two CBL sessions whereas the other had didactic lectures (DLs) and then the groups were crossed over. Case scenario handouts were given to students a week before the session, and smaller groups were formed for discussions and presentations in CBL sessions. Posttest, in multiple choice questions format, was conducted in two phases: First, immediately after the completion of the four CBL and DL sessions, and second, 6 weeks after the first posttest. Student and faculty feedback was taken about CBL sessions. Hundred MBBS students of the fourth semester voluntarily participated in the CBL study. The CBL scores were significantly higher than DL session scores ( P = 0.015). This difference was more marked in scoring done after 6 weeks of session completion ( P < 0.001). Student reported satisfaction in being taught by CBL method in 5-point Likert scale feedback form. Faculty feedback was positive for CBL. CBL helped in retention of knowledge and its application better than DL in our observation. More sessions on commonly encountered case scenarios will be useful for students in recalling basic science knowledge in their later years as practitioners.

Power Ultrasound to Process Dairy Products

NASA Astrophysics Data System (ADS)

Bermúdez-Aguirre, Daniela; Barbosa-Cánovas, Gustavo V.

Conventional methods of pasteurizing milk involve the use of heat regardless of treatment (batch, high temperature short time - HTST or ultra high temperature - UHT sterilization), and the quality of the milk is affected because of the use of high temperatures. Consequences of thermal treatment are a decrease in nutritional properties through the destruction of vitamins or denaturation of proteins, and sometimes the flavor of milk is undesirably changed. These changes are produced at the same time that the goal of the pasteurization process is achieved, which is to have a microbiological safe product, free of pathogenic bacteria, and to reduce the load of deteriorative microorganisms and enzymes, resulting in a product with a longer storage life.

Glycogen with short average chain length enhances bacterial durability

NASA Astrophysics Data System (ADS)

Wang, Liang; Wise, Michael J.

2011-09-01

Glycogen is conventionally viewed as an energy reserve that can be rapidly mobilized for ATP production in higher organisms. However, several studies have noted that glycogen with short average chain length in some bacteria is degraded very slowly. In addition, slow utilization of glycogen is correlated with bacterial viability, that is, the slower the glycogen breakdown rate, the longer the bacterial survival time in the external environment under starvation conditions. We call that a durable energy storage mechanism (DESM). In this review, evidence from microbiology, biochemistry, and molecular biology will be assembled to support the hypothesis of glycogen as a durable energy storage compound. One method for testing the DESM hypothesis is proposed.

Pulmonary toxoplasmosis in immunocompromised patients with interstitial pneumonia: a single-centre prospective study assessing PCR-based diagnosis.

PubMed

Desoubeaux, Guillaume; Cabanne, Églantine; Franck-Martel, Claire; Gombert, Martin; Gyan, Emmanuel; Lissandre, Séverine; Renaud, Marc; Monjanel, Hélène; Dartigeas, Caroline; Bailly, Éric; Van Langendonck, Nathalie; Chandenier, Jacques

2016-08-01

Pulmonary toxoplasmosis has become a very rare parasitic infection since the advent of highly active antiretroviral therapies. It is generally diagnosed by the direct microscopic observation of Toxoplasma gondii tachyzoites in bronchoalveolar lavage fluid (BALF). The aim of this study was to assess possible improvements in diagnostic performance associated with the use of real-time PCR. This prospective study was carried out on BALFs obtained from immunocompromised patients over a 2-year period. We systematically compared the results of conventional staining with those of molecular detection. Two cases of pulmonary toxoplasmosis were diagnosed for a total of 336 samples. PCR did not detect any additional cases and was more time-consuming than conventional staining. Conventional staining is a reliable technique and is probably the most appropriate method for experienced microbiology laboratories, whereas T. gondii-specific PCR may be useful for laboratories with less experience in parasitology. 2015_030, May 27th 2015. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Simple method for quantifying microbiologically assisted chloramine decay in drinking water.

PubMed

Sathasivan, Arumugam; Fisher, Ian; Kastl, George

2005-07-15

In a chloraminated drinking water distribution system, monochloramine decays due to chemical and microbiological reactions. For modeling and operational control purposes, it is necessary to know the relative contribution of each type of reaction, but there was no method to quantify these contributions separately. A simple method was developed to do so. It compares monochloramine decay rates of processed (0.2 microm filtered or microbiologically inhibited by adding 100 microg of silver/L as silver nitrate) and unprocessed samples under controlled temperature conditions. The term microbial decay factor (Fm) was defined and derived from this method, to characterize the relative contribution of microbiologically assisted monochloramine decay to the total monochloramine decay observed in bulk water. Fm is the ratio between microbiologically assisted monochloramine decay and chemical decay of a given water sample measured at 20 degrees C. One possible use of the method is illustrated, where a service reservoir's bulk and inlet waters were sampled twice and analyzed for both the traditional indicators and the microbial decay factor. The microbial decay factor values alone indicated that more microbiologically assisted monochloramine decay was occurring in one bulk water than the other. In contrast, traditional nitrification indicators failed to show any difference. Further analysis showed that the microbial decay factor is more sensitive and that it alone can provide an early warning.

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 3 2012-01-01 2012-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 3 2011-01-01 2011-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 3 2013-01-01 2013-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

7 CFR 58.644 - Test methods.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 3 2014-01-01 2014-01-01 false Test methods. 58.644 Section 58.644 Agriculture... Procedures § 58.644 Test methods. (a) Microbiological. Microbiological determinations shall be made in accordance with the methods described in the latest edition of Standard Methods for the Examination of Dairy...

The diagnosis of chronic endometritis in infertile asymptomatic women: a comparative study of histology, microbial cultures, hysteroscopy, and molecular microbiology.

PubMed

Moreno, Inmaculada; Cicinelli, Ettore; Garcia-Grau, Iolanda; Gonzalez-Monfort, Marta; Bau, Davide; Vilella, Felipe; De Ziegler, Dominique; Resta, Leonardo; Valbuena, Diana; Simon, Carlos

2018-06-01

Chronic endometritis is a persistent inflammation of the endometrial mucosa caused by bacterial pathogens such as Enterobacteriaceae, Enterococcus, Streptococcus, Staphylococcus, Mycoplasma, and Ureaplasma. Although chronic endometritis can be asymptomatic, it is found in up to 40% of infertile patients and is responsible for repeated implantation failure and recurrent miscarriage. Diagnosis of chronic endometritis is based on hysteroscopy of the uterine cavity, endometrial biopsy with plasma cells being identified histologically, while specific treatment is determined based on microbial culture. However, not all microorganisms implicated are easily or readily culturable needing a turnaround time of up to 1 week. We sought to develop a molecular diagnostic tool for chronic endometritis based on real-time polymerase chain reaction equivalent to using the 3 classic methods together, overcoming the bias of using any of them alone. Endometrial samples from patients assessed for chronic endometritis (n = 113) using at least 1 or several conventional diagnostic methods namely histology, hysteroscopy, and/or microbial culture, were blindly evaluated by real-time polymerase chain reaction for the presence of 9 chronic endometritis pathogens: Chlamydia trachomatis, Enterococcus, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Mycoplasma hominis, Neisseria gonorrhoeae, Staphylococcus, and Streptococcus. The sensitivity and specificity of the molecular analysis vs the classic diagnostic techniques were compared in the 65 patients assessed by all 3 recognized classic methods. The molecular method showed concordant results with histological diagnosis in 30 samples (14 double positive and 16 double negative) with a matching accuracy of 46.15%. Concordance of molecular and hysteroscopic diagnosis was observed in 38 samples (37 double positive and 1 double negative), with an accuracy of 58.46%. When the molecular method was compared to microbial culture, concordance was present in 37 samples (22 double positive and 15 double negative), a matching rate of 56.92%. When cases of potential contamination and/or noncultivable bacteria were considered, the accuracy increased to 66.15%. Of these 65 patients, only 27 patients had consistent histological + hysteroscopic diagnosis, revealing 58.64% of nonconcordant results. Only 13 of 65 patients (20%) had consistent histology + hysteroscopy + microbial culture results. In these cases, the molecular microbiology matched in 10 cases showing a diagnostic accuracy of 76.92%. Interestingly, the molecular microbiology confirmed over half of the isolated pathogens and provided additional detection of nonculturable microorganisms. These results were confirmed by the microbiome assessed by next-generation sequencing. In the endometrial samples with concordant histology + hysteroscopy + microbial culture results, the molecular microbiology diagnosis demonstrates 75% sensitivity, 100% specificity, 100% positive and 25% negative predictive values, and 0% false-positive and 25% false-negative rates. The molecular microbiology method describe herein is a fast and inexpensive diagnostic tool that allows for the identification of culturable and nonculturable endometrial pathogens associated with chronic endometritis. The results obtained were similar to all 3 classic diagnostic methods together with a degree of concordance of 76.92% providing an opportunity to improve the clinical management of infertile patients with a risk of experiencing this ghost endometrial pathology. Copyright © 2018 Elsevier Inc. All rights reserved.

Lessons learned from implementing a wet laboratory molecular training workshop for beach water quality monitoring.

PubMed

Verhougstraete, Marc Paul; Brothers, Sydney; Litaker, Wayne; Blackwood, A Denene; Noble, Rachel

2015-01-01

Rapid molecular testing methods are poised to replace many of the conventional, culture-based tests currently used in fields such as water quality and food science. Rapid qPCR methods have the benefit of being faster than conventional methods and provide a means to more accurately protect public health. However, many scientists and technicians in water and food quality microbiology laboratories have limited experience using these molecular tests. To ensure that practitioners can use and implement qPCR techniques successfully, we developed a week long workshop to provide hands-on training and exposure to rapid molecular methods for water quality management. This workshop trained academic professors, government employees, private industry representatives, and graduate students in rapid qPCR methods for monitoring recreational water quality. Attendees were immersed in these new methods with hands-on laboratory sessions, lectures, and one-on-one training. Upon completion, the attendees gained sufficient knowledge and practice to teach and share these new molecular techniques with colleagues at their respective laboratories. Key findings from this workshop demonstrated: 1) participants with no prior experience could be effectively trained to conduct highly repeatable qPCR analysis in one week; 2) participants with different desirable outcomes required exposure to a range of different platforms and sample processing approaches; and 3) the collaborative interaction amongst newly trained practitioners, workshop leaders, and members of the water quality community helped foster a cohesive cohort of individuals which can advocate powerful cohort for proper implementation of molecular methods.

Lessons Learned from Implementing a Wet Laboratory Molecular Training Workshop for Beach Water Quality Monitoring

PubMed Central

Verhougstraete, Marc Paul; Brothers, Sydney; Litaker, Wayne; Blackwood, A. Denene; Noble, Rachel

2015-01-01

Rapid molecular testing methods are poised to replace many of the conventional, culture-based tests currently used in fields such as water quality and food science. Rapid qPCR methods have the benefit of being faster than conventional methods and provide a means to more accurately protect public health. However, many scientists and technicians in water and food quality microbiology laboratories have limited experience using these molecular tests. To ensure that practitioners can use and implement qPCR techniques successfully, we developed a week long workshop to provide hands-on training and exposure to rapid molecular methods for water quality management. This workshop trained academic professors, government employees, private industry representatives, and graduate students in rapid qPCR methods for monitoring recreational water quality. Attendees were immersed in these new methods with hands-on laboratory sessions, lectures, and one-on-one training. Upon completion, the attendees gained sufficient knowledge and practice to teach and share these new molecular techniques with colleagues at their respective laboratories. Key findings from this workshop demonstrated: 1) participants with no prior experience could be effectively trained to conduct highly repeatable qPCR analysis in one week; 2) participants with different desirable outcomes required exposure to a range of different platforms and sample processing approaches; and 3) the collaborative interaction amongst newly trained practitioners, workshop leaders, and members of the water quality community helped foster a cohesive cohort of individuals which can advocate powerful cohort for proper implementation of molecular methods. PMID:25822486

MODELING CHLORINE DECAY AND THE FORMATION OF DISINFECTION BY-PRODUCTS (DBPS) IN DRINKING WATER

EPA Science Inventory

A major objective of drinking water treatment is to provide microbiologically safe drinking water. The combination of conventional drinking water treatment and disinfection has proved to be one of the major public health advances in modern times. In the US, chlorine is most often...

Microbial Ecology: Where are we now?

PubMed Central

2016-01-01

Conventional microbiological methods have been readily taken over by newer molecular techniques due to the ease of use, reproducibility, sensitivity and speed of working with nucleic acids. These tools allow high throughput analysis of complex and diverse microbial communities, such as those in soil, freshwater, saltwater, or the microbiota living in collaboration with a host organism (plant, mouse, human, etc). For instance, these methods have been robustly used for characterizing the plant (rhizosphere), animal and human microbiome specifically the complex intestinal microbiota. The human body has been referred to as the Superorganism since microbial genes are more numerous than the number of human genes and are essential to the health of the host. In this review we provide an overview of the Next Generation tools currently available to study microbial ecology, along with their limitations and advantages. PMID:27975077

Numerical approach to reference identification of Staphylococcus, Stomatococcus, and Micrococcus spp.

PubMed

Rhoden, D L; Hancock, G A; Miller, J M

1993-03-01

A numerical-code system for the reference identification of Staphylococcus species, Stomatococcus mucilaginosus, and Micrococcus species was established by using a selected panel of conventional biochemicals. Results from 824 cultures (289 eye isolate cultures, 147 reference strains, and 388 known control strains) were used to generate a list of 354 identification code numbers. Each six-digit code number was based on results from 18 conventional biochemical reactions. Seven milliliters of purple agar base with 1% sterile carbohydrate solution added was poured into 60-mm-diameter agar plates. All biochemical tests were inoculated with 1 drop of a heavy broth suspension, incubated at 35 degrees C, and read daily for 3 days. All reactions were read and interpreted by the method of Kloos et al. (G. A. Hebert, C. G. Crowder, G. A. Hancock, W. R. Jarvis, and C. Thornsberry, J. Clin. Microbiol. 26:1939-1949, 1988; W. E. Kloos and D. W. Lambe, Jr., P. 222-237, in A. Balows, W. J. Hansler, Jr., K. L. Herrmann, H. D. Isenberg, and H. J. Shadomy, ed., Manual of Clinical Microbiology, 5th ed., 1991). This modified reference identification method was 96 to 98% accurate and could have value in reference and public health laboratory settings.

Development of a specific immunomagnetic capture-PCR for rapid detection of viable Mycoplasma agalactiae in sheep milk samples.

PubMed

Sanna, G; Lecca, V; Foddai, A; Tola, S

2014-12-01

To develop an immunomagnetic capture (IMC) to detect viable Mycoplasma agalactiae in routine ovine milk samples. Polyclonal antibodies against two M. agalactiae membrane surface proteins (P80 and P55) were covalently conjugated to magnetic beads (MBs) to form MB-Ab80 and MB-Ab55. Mycoplasma agalactiae cells were captured by a specific antigen-antibody reaction and magnetic separation. Immunomagnetic capture (IMC) was used to isolate and concentrate M. agalactiae in serial decimal dilutions and in artificially contaminated milk to facilitate subsequent detection by PCR. A 375-bp fragment of M. agalactiae was amplified using a pair of M. agalactiae-specific primers in PCR. The limit of detection of IMC-PCR method ranged from 10 to 10(2)  CCU ml(-1) when mycoplasmas were resuspended in PBS and from 10(2) to 10(3)  CCU ml(-1) when mycoplasmas were resuspended in uncontaminated ovine milk. This study also describes the application of IMC-PCR method to test for M. agalactiae in 516 milk samples collected from sheep with suspected contagious agalactia. Its performance was evaluated relative to culture. This report has demonstrated for the first time, the effective use of rapid and reliable IMC combined with PCR assay for the detection of viable M. agalactiae. The method IMC-PCR provides an alternative to conventional microbiological detection, method and it could be applied to quick detection of M. agalactiae in routine sheep milk samples. © 2014 The Authors published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.

Performance of Kiestra Total Laboratory Automation Combined with MS in Clinical Microbiology Practice

PubMed Central

Hodiamont, Caspar J.; de Jong, Menno D.; Overmeijer, Hendri P. J.; van den Boogaard, Mandy; Visser, Caroline E.

2014-01-01

Background Microbiological laboratories seek technologically innovative solutions to cope with large numbers of samples and limited personnel and financial resources. One platform that has recently become available is the Kiestra Total Laboratory Automation (TLA) system (BD Kiestra B.V., the Netherlands). This fully automated sample processing system, equipped with digital imaging technology, allows superior detection of microbial growth. Combining this approach with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MS) (Bruker Daltonik, Germany) is expected to enable more rapid identification of pathogens. Methods Early growth detection by digital imaging using Kiestra TLA combined with MS was compared to conventional methods (CM) of detection. Accuracy and time taken for microbial identification were evaluated for the two methods in 219 clinical blood culture isolates. The possible clinical impact of earlier microbial identification was assessed according to antibiotic treatment prescription. Results Pathogen identification using Kiestra TLA combined with MS resulted in a 30.6 hr time gain per isolate compared to CM. Pathogens were successfully identified in 98.4% (249/253) of all tested isolates. Early microbial identification without susceptibility testing led to an adjustment of antibiotic regimen in 12% (24/200) of patients. Conclusions The requisite 24 hr incubation time for microbial pathogens to reach sufficient growth for susceptibility testing and identification would be shortened by the implementation of Kiestra TLA in combination with MS, compared to the use of CM. Not only can this method optimize workflow and reduce costs, but it can allow potentially life-saving switches in antibiotic regimen to be initiated sooner. PMID:24624346

Successful Application of Active Learning Techniques to Introductory Microbiology.

ERIC Educational Resources Information Center

Hoffman, Elizabeth A.

2001-01-01

Points out the low student achievement in microbiology courses and presents an active learning method applied in an introductory microbiology course which features daily quizzes, cooperative learning activities, and group projects. (Contains 30 references.) (YDS)

Comparison of Diagnostic Accuracy of Periprosthetic Tissue Culture in Blood Culture Bottles to That of Prosthesis Sonication Fluid Culture for Diagnosis of Prosthetic Joint Infection (PJI) by Use of Bayesian Latent Class Modeling and IDSA PJI Criteria for Classification.

PubMed

Yan, Qun; Karau, Melissa J; Greenwood-Quaintance, Kerryl E; Mandrekar, Jayawant N; Osmon, Douglas R; Abdel, Matthew P; Patel, Robin

2018-06-01

We have previously demonstrated that culturing periprosthetic tissue in blood culture bottles (BCBs) improves sensitivity compared to conventional agar and broth culture methods for diagnosis of prosthetic joint infection (PJI). We have also shown that prosthesis sonication culture improves sensitivity compared to periprosthetic tissue culture using conventional agar and broth methods. The purpose of this study was to compare the diagnostic accuracy of tissue culture in BCBs (subsequently referred to as tissue culture) to prosthesis sonication culture (subsequently referred to as sonicate fluid culture). We studied 229 subjects who underwent arthroplasty revision or resection surgery between March 2016 and October 2017 at Mayo Clinic in Rochester, Minnesota. Using the Infectious Diseases Society of America (IDSA) PJI diagnostic criteria (omitting culture criteria) as the gold standard, the sensitivity of tissue culture was similar to that of the sonicate fluid culture (66.4% versus 73.1%, P = 0.07) but was significantly lower than that of the two tests combined (66.4% versus 76.9%, P < 0.001). Using Bayesian latent class modeling, which assumes no gold standard for PJI diagnosis, the sensitivity of tissue culture was slightly lower than that of sonicate fluid culture (86.3% versus 88.7%) and much lower than that of the two tests combined (86.3% versus 99.1%). In conclusion, tissue culture in BCBs reached sensitivity similar to that of prosthesis sonicate fluid culture for diagnosis of PJI, but the two tests combined had the highest sensitivity without compromising specificity. The combination of tissue culture in BCBs and sonicate fluid culture is recommended to achieve the highest level of microbiological diagnosis of PJI. Copyright © 2018 American Society for Microbiology.

Sterilization validation for medical devices at IRASM microbiological laboratory—Practical approaches

NASA Astrophysics Data System (ADS)

Trandafir, Laura; Alexandru, Mioara; Constantin, Mihai; Ioniţă, Anca; Zorilă, Florina; Moise, Valentin

2012-09-01

EN ISO 11137 established regulations for setting or substantiating the dose for achieving the desired sterility assurance level. The validation studies can be designed in particular for different types of products. Each product needs distinct protocols for bioburden determination and sterility testing. The Microbiological Laboratory from Irradiation Processing Center (IRASM) deals with different types of products, mainly for the VDmax25 method. When it comes to microbiological evaluation the most challenging was cotton gauze. A special situation for establishing the sterilization validation method appears in cases of cotton packed in large quantities. The VDmax25 method cannot be applied for items with average bioburden more than 1000 CFU/pack, irrespective of the weight of the package. This is a method limitation and implies increased costs for the manufacturer when choosing other methods. For microbiological tests, culture condition should be selected in both cases of the bioburden and sterility testing. Details about choosing criteria are given.

Comparison of the Antibacterial Effect of 810 nm Diode Laser and Photodynamic Therapy in Reducing the Microbial Flora of Root Canal in Endodontic Retreatment in Patients With Periradicular Lesions.

PubMed

Asnaashari, Mohammad; Godiny, Mostafa; Azari-Marhabi, Saranaz; Tabatabaei, Fahimeh Sadat; Barati, Maryam

2016-01-01

The aim of this study was to compare the antibacterial efficacy of diode laser 810nm and photodynamic therapy (PDT) in reducing bacterial microflora in endodontic retreatment of teeth with periradicular lesion. In this in vivo clinical trial, 20 patients who needed endodontic retreatment were selected. After conventional chemo mechanical preparation of root canals, microbiological samples were taken with sterile paper point (PP), held in thioglycollate broth, and then were transferred to the microbiological lab. In the first group, PDT with methylene blue (MB) and diode laser (810 nm, 0.2 W, 40 seconds) was performed and in the second group diode laser (810 nm, 1.2 W, 30 seconds) was irradiated. Then second samples were taken from all canals. CFU/ml amounts showed statistically significant reduction in both groups (P < 0.001). CFU/ml amounts were compared between the two groups and there was no statistical difference. PDT and diode laser 810 nm irradiation are effective methods for root canal disinfection. PDT is a suitable alternative for diode laser 810 nm irradiation, because of lower thermal risk on root dentin.

Isolation and Identification of Campylobacter spp. from Poultry and Poultry By-Products in Tunisia by Conventional Culture Method and Multiplex Real-Time PCR.

PubMed

Jribi, Hela; Sellami, Hanen; Mariam, Siala; Smaoui, Salma; Ghorbel, Asma; Hachicha, Salma; Benejat, Lucie; Messadi-Akrout, Feriel; Mégraud, Francis; Gdoura, Radhouane

2017-10-01

Thermophilic Campylobacter spp. are one of the primary causes of bacterial human diarrhea. The consumption of poultry meats, by-products, or both is suspected to be a major cause of human campylobacteriosis. The aims of this study were to determine the prevalence of thermophilic Campylobacter spp. in fresh poultry meat and poultry by-products by conventional culture methods and to confirm Campylobacter jejuni and Campylobacter coli isolates by using the multiplex PCR assay. Two hundred fifty fresh poultry samples were collected from a variety of supermarkets and slaughterhouses located in Sfax, Tunisia, including chicken (n =149) and turkey (n =101). The samples were analyzed using conventional microbiological examinations according to the 2006 International Organization for Standardization method (ISO 10272-1) for Campylobacter spp. Concurrently, a real-time PCR was used for identification of C. jejuni and C. coli . Of the 250 samples of poultry meat and poultry by-products, 25.6% (n = 64) were contaminated with Campylobacter spp. The highest prevalence of Campylobacter spp. was found in chicken meat (26.8%) followed by turkey meat (23.7%). Among the different products, poultry breasts showed the highest contamination (36.6%) followed by poultry by-products (30%), poultry wings (28%) and poultry legs (26%) showed the lowest contamination, and no contamination was found on neck skin. Of the 64 thermophilic Campylobacter isolates, C. jejuni (59.7%) was the most frequently isolated species and 10.9% of the isolates were identified as C. coli . All of the 64 Campylobacter isolates identified by the conventional culture methods were further confirmed by PCR. The seasonal peak of Campylobacter spp. contamination was in the warm seasons (spring and summer). The study concluded that high proportions of poultry meat and poultry by-products marketed in Tunisia are contaminated by Campylobacter spp. Furthermore, to ensure food safety, poultry meats must be properly cooked before consuming.

Analysing attitude data through ridit schemes.

PubMed

El-rouby, M G

1994-12-02

The attitudes of individuals and populations on various issues are usually assessed through sample surveys. Responses to survey questions are then scaled and combined into a meaningful whole which defines the measured attitude. The applied scales may be of nominal, ordinal, interval, or ratio nature depending upon the degree of sophistication the researcher wants to introduce into the measurement. This paper discusses methods of analysis for categorical variables of the type used in attitude and human behavior research, and recommends adoption of ridit analysis, a technique which has been successfully applied to epidemiological, clinical investigation, laboratory, and microbiological data. The ridit methodology is described after reviewing some general attitude scaling methods and problems of analysis related to them. The ridit method is then applied to a recent study conducted to assess health care service quality in North Carolina. This technique is conceptually and computationally more simple than other conventional statistical methods, and is also distribution-free. Basic requirements and limitations on its use are indicated.

Molecular Characterization of Clostridium botulinum Isolates from Foodborne Outbreaks in Thailand, 2010

PubMed Central

Wangroongsarb, Piyada; Kohda, Tomoko; Jittaprasartsin, Chutima; Suthivarakom, Karun; Kamthalang, Thanitchi; Umeda, Kaoru; Sawanpanyalert, Pathom; Kozaki, Shunji; Ikuta, Kazuyoshi

2014-01-01

Background Thailand has had several foodborne outbreaks of botulism, one of the biggest being in 2006 when laboratory investigations identified the etiologic agent as Clostridium botulinum type A. Identification of the etiologic agent from outbreak samples is laborious using conventional microbiological methods and the neurotoxin mouse bioassay. Advances in molecular techniques have added enormous information regarding the etiology of outbreaks and characterization of isolates. We applied these methods in three outbreaks of botulism in Thailand in 2010. Methodology/Principal Findings A total of 19 cases were involved (seven each in Lampang and Saraburi and five in Maehongson provinces). The first outbreak in Lampang province in April 2010 was associated with C. botulinum type F, which was detected by conventional methods. Outbreaks in Saraburi and Maehongson provinces occurred in May and December were due to C. botulinum type A1(B) and B that were identified by conventional methods and molecular techniques, respectively. The result of phylogenetic sequence analysis showed that C. botulinum type A1(B) strain Saraburi 2010 was close to strain Iwate 2007. Molecular analysis of the third outbreak in Maehongson province showed C. botulinum type B8, which was different from B1–B7 subtype. The nontoxic component genes of strain Maehongson 2010 revealed that ha33, ha17 and botR genes were close to strain Okra (B1) while ha70 and ntnh genes were close to strain 111 (B2). Conclusion/Significance This study demonstrates the utility of molecular genotyping of C. botulinum and how it contributes to our understanding the epidemiology and variation of boNT gene. Thus, the recent botulism outbreaks in Thailand were induced by various C. botulinum types. PMID:24475015

Molecular characterization of Clostridium botulinum isolates from foodborne outbreaks in Thailand, 2010.

PubMed

Wangroongsarb, Piyada; Kohda, Tomoko; Jittaprasartsin, Chutima; Suthivarakom, Karun; Kamthalang, Thanitchi; Umeda, Kaoru; Sawanpanyalert, Pathom; Kozaki, Shunji; Ikuta, Kazuyoshi

2014-01-01

Thailand has had several foodborne outbreaks of botulism, one of the biggest being in 2006 when laboratory investigations identified the etiologic agent as Clostridium botulinum type A. Identification of the etiologic agent from outbreak samples is laborious using conventional microbiological methods and the neurotoxin mouse bioassay. Advances in molecular techniques have added enormous information regarding the etiology of outbreaks and characterization of isolates. We applied these methods in three outbreaks of botulism in Thailand in 2010. A total of 19 cases were involved (seven each in Lampang and Saraburi and five in Maehongson provinces). The first outbreak in Lampang province in April 2010 was associated with C. botulinum type F, which was detected by conventional methods. Outbreaks in Saraburi and Maehongson provinces occurred in May and December were due to C. botulinum type A1(B) and B that were identified by conventional methods and molecular techniques, respectively. The result of phylogenetic sequence analysis showed that C. botulinum type A1(B) strain Saraburi 2010 was close to strain Iwate 2007. Molecular analysis of the third outbreak in Maehongson province showed C. botulinum type B8, which was different from B1-B7 subtype. The nontoxic component genes of strain Maehongson 2010 revealed that ha33, ha17 and botR genes were close to strain Okra (B1) while ha70 and ntnh genes were close to strain 111 (B2). This study demonstrates the utility of molecular genotyping of C. botulinum and how it contributes to our understanding the epidemiology and variation of boNT gene. Thus, the recent botulism outbreaks in Thailand were induced by various C. botulinum types.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Britton, L.J.; Greeson, P.E.

1988-01-01

Chapter A4, methods for collection and analyses of aquatic biological and microbiological samples, contains methods used by the U.S. Geological Survey to collect, preserve, and analyze waters to determine their biological and microbiological properties. Part 1 consists of detailed descriptions of more than 45 individual methods, including those for bacteria, phytoplankton, zooplankton, seston, periphyton, macrophytes, benthic invertebrates, fish and other vertebrates, cellular contents, productivity and bioassay. Each method is summarized, and the applications, interferences, apparatus, reagents, analyses, calculations, reporting of results, precisions, and references are given. Part 2 consists of a glossary. Part 3 is a list of taxonomic references. (USGS)

Rapid method for direct identification of bacteria in urine and blood culture samples by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: intact cell vs. extraction method.

PubMed

Ferreira, L; Sánchez-Juanes, F; Muñoz-Bellido, J L; González-Buitrago, J M

2011-07-01

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a fast and reliable technology for the identification of microorganisms with proteomics approaches. Here, we compare an intact cell method and a protein extraction method before application on the MALDI plate for the direct identification of microorganisms in both urine and blood culture samples from clinical microbiology laboratories. The results show that the intact cell method provides excellent results for urine and is a good initial method for blood cultures. The extraction method complements the intact cell method, improving microorganism identification from blood culture. Thus, we consider that MALDI-TOF MS performed directly on urine and blood culture samples, with the protocols that we propose, is a suitable technique for microorganism identification, as compared with the routine methods used in the clinical microbiology laboratory. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

Diagnostic microbiology in veterinary dermatology: present and future.

PubMed

Guardabassi, Luca; Damborg, Peter; Stamm, Ivonne; Kopp, Peter A; Broens, Els M; Toutain, Pierre-Louis

2017-02-01

The microbiology laboratory can be perceived as a service provider rather than an integral part of the healthcare team. The aim of this review is to discuss the current challenges of providing a state-of-the-art diagnostic veterinary microbiology service including the identification (ID) and antimicrobial susceptibility testing (AST) of key pathogens in veterinary dermatology. The Study Group for Veterinary Microbiology (ESGVM) of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) identified scientific, technological, educational and regulatory issues impacting the predictive value of AST and the quality of the service offered by microbiology laboratories. The advent of mass spectrometry has significantly reduced the time required for ID of key pathogens such as Staphylococcus pseudintermedius. However, the turnaround time for validated AST methods has remained unchanged for many years. Beyond scientific and technological constraints, AST methods are not harmonized and clinical breakpoints for some antimicrobial drugs are either missing or inadequate. Small laboratories, including in-clinic laboratories, are usually not adequately equipped to run up-to-date clinical microbiologic diagnostic tests. ESGVM recommends the use of laboratories employing mass spectrometry for ID and broth micro-dilution for AST, and offering assistance by expert microbiologists on pre- and post-analytical issues. Setting general standards for veterinary clinical microbiology, promoting antimicrobial stewardship, and the development of new, validated and rapid diagnostic methods, especially for AST, are among the missions of ESGVM. © 2017 The Authors. Veterinary Dermatology published by John Wiley & Sons Ltd on behalf of the ESVD and ACVD.

Case report: Infrapatellar bursitis caused by Prototheca wickerhamii

PubMed Central

Van den Bossche, Dorien; de Haan, Roel; Van der Werff ten Bosch, Jutte; Van Hecke, Wim; Symoens, Françoise; Van den Borre, Ina; Allard, Sabine; De Bel, Annelies

2012-01-01

A 54-year-old immunocompetent man presented with an infrapatellar bursitis caused by Prototheca wickerhamii. Because of clinical and microbiological relapse two weeks after bursectomy, six weekly injections of 5 mg of conventional amphotericin B were chosen for intrabursal treatment. Four months after completion of the treatment, the patient remains cured. PMID:24371726

Effect of Changing Treatment Disinfectants on the Microbiology of Distributed Water and Pipe Biofilm Communities using Conventional and Metagenomic Approaches

EPA Science Inventory

The purpose of this research was to add to our knowledge of chlorine and monochloramine disinfectants, with regards to effects on the microbial communities in distribution systems. A whole metagenome-based approach using sophisticated molecular tools (e.g., next generation sequen...

Comparison of environmental and egg microbiology associated with conventional and free range laying hen management

USDA-ARS?s Scientific Manuscript database

Eggs from alternative production practices are a growing niche in the market. Meeting consumer requests for greater diversity in retail egg options has resulted in some unique challenges such as understanding the food safety implications of eggs from alternative production practices. A study was c...

Microbiological differences between laying hen strains housed in various production systems.

USDA-ARS?s Scientific Manuscript database

Sister flocks of three strains of laying hens were housed in conventional cage, free range, and cage free production systems. All flocks were located on a single, commercial-style research facility and provided the same dietary and lighting regimens. Once a season, a sample of shell eggs was asept...

Microbiological Surveillance and State of the Art Technological Strategies for the Prevention of Dialysis Water Pollution

PubMed Central

Bolasco, Piergiorgio; Contu, Antonio; Meloni, Patrizia; Vacca, Dorio; Galfrè, Andrea

2012-01-01

Methods: The present report attempts to illustrate the positive impact on the microbiological quality of dialysis patients over a 15-year period through the progressive implementation of state-of-the-art technological strategies and the optimization of microbiological surveillance procedures in five dialysis units in Sardinia. Results: Following on better microbiological, quality controls of dialysis water and improvement of procedures and equipment, a drastic improvement of microbiological water quality was observed in a total of 945 samples. The main aim was to introduce the use of microbiological culture methods as recommended by the most important guidelines. The microbiological results obtained have led to a progressive refining of controls and introduction of new materials and equipment, including two-stage osmosis and piping distribution rings featuring a greater capacity to prevent biofilm adhesion. The actions undertaken have resulted in unexpected quality improvements. Conclusions: Dialysis water should be viewed by the nephrologist as a medicinal product exerting a demonstrable positive impact on microinflammation in dialysis patients. A synergic effort between nephrologists and microbiologists undoubtedly constitutes the most effective means of preventing dialysis infections. PMID:23066395

Application of MALDI-TOF MS for the Identification of Food Borne Bacteria

PubMed Central

Pavlovic, Melanie; Huber, Ingrid; Konrad, Regina; Busch, Ulrich

2013-01-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently emerged as a powerful tool for the routine identification of clinical isolates. MALDI-TOF MS based identification of bacteria has been shown to be more rapid, accurate and cost-efficient than conventional phenotypic techniques or molecular methods. Rapid and reliable identification of food-associated bacteria is also of crucial importance for food processing and product quality. This review is concerned with the applicability of MALDI-TOF MS for routine identification of foodborne bacteria taking the specific requirements of food microbiological laboratories and the food industry into account. The current state of knowledge including recent findings and new approaches are discussed. PMID:24358065

A new Microbacterium species isolated from the blood of a patient with fever: Microbacterium pyrexiae sp. nov.

PubMed

Ko, Kwan Soo; Oh, Won Sup; Lee, Mi Young; Peck, Kyong Ran; Lee, Nam Yong; Song, Jae-Hoon

2007-04-01

A Gram-positive bacterium, SMC-A8265(T), which was isolated from the blood of a patient with fever but could not be identified by a conventional microbiologic method, was finally characterized by performing phenotypic and genotypic analyses. 16S rRNA gene sequence analysis revealed that the strain SMC-A8265(T) belonged to the genus Microbacterium, but it did not correspond to any of the previously described Microbacterium spp. Biochemical tests and cellular fatty acid composition analysis also confirmed that this bacterium is distinct from other Microbacterium spp. Based on the phenotypic and genotypic characteristics, we propose that the strain SMC-A8265(T) should be classified as a new species, namely, Microbacterium pyrexiae sp. nov.

Improvement of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification of difficult-to-identify bacteria and its impact in the workflow of a clinical microbiology laboratory.

PubMed

Rodríguez-Sánchez, Belén; Marín, Mercedes; Sánchez-Carrillo, Carlos; Cercenado, Emilia; Ruiz, Adrián; Rodríguez-Créixems, Marta; Bouza, Emilio

2014-05-01

This study evaluates matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) capability for the identification of difficult-to-identify microorganisms. A total of 150 bacterial isolates inconclusively identified with conventional phenotypic tests were further assessed by 16S rRNA sequencing and by MALDI-TOF MS following 2 methods: a) a simplified formic acid-based, on-plate extraction and b) performing a tube-based extraction step. Using the simplified method, 29 isolates could not be identified. For the remaining 121 isolates (80.7%), we obtained a reliable identification by MALDI-TOF: in 103 isolates, the identification by 16S rRNA sequencing and MALDI TOF coincided at the species level (68.7% from the total 150 analyzed isolates and 85.1% from the samples with MALDI-TOF result), and in 18 isolates, the identification by both methods coincided at the genus level (12% from the total and 14.9% from the samples with MALDI-TOF results). No discordant results were observed. The performance of the tube-based extraction step allowed the identification at the species level of 6 of the 29 unidentified isolates by the simplified method. In summary, MALDI-TOF can be used for the rapid identification of many bacterial isolates inconclusively identified by conventional methods. Copyright © 2014 Elsevier Inc. All rights reserved.

Can the design of glove dispensing boxes influence glove contamination?

PubMed

Assadian, O; Leaper, D J; Kramer, A; Ousey, K J

2016-11-01

Few studies have explored the microbial contamination of glove boxes in clinical settings. The objective of this observational study was to investigate whether a new glove packaging system in which single gloves are dispensed vertically, cuff end first, has lower levels of contamination on the gloves and on the surface around the box aperture compared with conventional glove boxes. Seven participating sites were provided with vertical glove dispensing systems (modified boxes) and conventional boxes. Before opening glove boxes, the surface around the aperture was sampled microbiologically to establish baseline levels of superficial contamination. Once the glove boxes were opened, the first pair of gloves in each box was sampled for viable bacteria. Thereafter, testing sites were visited on a weekly basis over a period of six weeks and the same microbiological assessments were made. The surface near the aperture of the modified boxes became significantly less contaminated over time compared with the conventional boxes (P<0.001), with an average of 46.7% less contamination around the aperture. Overall, gloves from modified boxes showed significantly less colony-forming unit contamination than gloves from conventional boxes (P<0.001). Comparing all sites over the entire six-week period, gloves from modified boxes had 88.9% less bacterial contamination. This simple improvement to glove box design reduces contamination of unused gloves. Such modifications could decrease the risk of microbial cross-transmission in settings that use gloves. However, such advantages do not substitute for strict hand hygiene compliance and appropriate use of non-sterile, single-use gloves. Copyright © 2016 The Healthcare Infection Society. All rights reserved.

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota

PubMed Central

Roach, David J.; Burton, Joshua N.; Lee, Choli; Stackhouse, Bethany; Butler-Wu, Susan M.; Cookson, Brad T.

2015-01-01

Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology, but it has not yet been applied systematically or comprehensively within a clinical context. Here, over the course of one year, we performed prospective collection and whole genome sequencing of nearly all bacterial isolates obtained from a tertiary care hospital’s intensive care units (ICUs). This unbiased collection of 1,229 bacterial genomes from 391 patients enables detailed exploration of several features of clinical pathogens. A sizable fraction of isolates identified as clinically relevant corresponded to previously undescribed species: 12% of isolates assigned a species-level classification by conventional methods actually qualified as distinct, novel genomospecies on the basis of genomic similarity. Pan-genome analysis of the most frequently encountered pathogens in the collection revealed substantial variation in pan-genome size (1,420 to 20,432 genes) and the rate of gene discovery (1 to 152 genes per isolate sequenced). Surprisingly, although potential nosocomial transmission of actively surveilled pathogens was rare, 8.7% of isolates belonged to genomically related clonal lineages that were present among multiple patients, usually with overlapping hospital admissions, and were associated with clinically significant infection in 62% of patients from which they were recovered. Multi-patient clonal lineages were particularly evident in the neonatal care unit, where seven separate Staphylococcus epidermidis clonal lineages were identified, including one lineage associated with bacteremia in 5/9 neonates. Our study highlights key differences in the information made available by conventional microbiological practices versus whole genome sequencing, and motivates the further integration of microbial genome sequencing into routine clinical care. PMID:26230489

Antimicrobial susceptibility patterns of enterobacteriaceae isolated from HIV-infected patients in Kinshasa.

PubMed

Iyamba, Jean-Marie Liesse; Wambale, José Mulwahali; Takaisi-Kikuni, Ntondo Za Balega

2014-01-01

People infected by Human Immunodeficiency Virus (HIV) are susceptible to develop severe bacterial infections. We set out to determine the frequency and the sensitivity to antibiotics of enterobaceriaceae isolated from urine and feces of HIV-infected persons. Urine and feces samples were collected from HIV-infected patients of the Centre de Traitement Ambulatoire de Kabinda (CTA/Kabinda, Kinshasa) and analyzed at the Reference National Laboratory for HIV/AIDS and Sexually Transmitted Infections. The isolated enterobacteriaceae strains were identified by conventional microbiological methods. Antibiotic sensitivity pattern was carried out by disc diffusion method. THE FOLLOWING BACTERIA PATHOGENS WERE ISOLATED: Escherichia coli, Klebsiella, Enterobacter, Proteus, and Providencia. Most species were sensitive to cefotaxim, ceftriaxon, and gentamicin and resistant to chloramphenicol, cotrimoxazole, tetracycline, and norfloxacin. The results of the present study show that the most frequently bacteria isolated were Esherichia coli and cefotaxim, ceftriaxon, and gentamicin were the most active antibiotics.

Photobacteriosis: Prevention and Diagnosis

PubMed Central

2014-01-01

Photobacteriosis or fish pasteurellosis is a bacterial disease affecting wild and farm fish. Its etiological agent, the gram negative bacterium Photobacterium damselae subsp. piscicida, is responsible for important economic losses in cultured fish worldwide, in particular in Mediterranean countries and Japan. Efforts have been focused on gaining a better understanding of the biology of the pathogenic microorganism and its natural hosts with the aim of developing effective vaccination strategies and diagnostic tools to control the disease. Conventional vaccinology has thus far yielded unsatisfactory results, and recombinant technology has been applied to identify new antigen candidates for the development of subunit vaccines. Furthermore, molecular methods represent an improvement over classical microbiological techniques for the identification of P. damselae subsp. piscicida and the diagnosis of the disease. The complete sequencing, annotation, and analysis of the pathogen genome will provide insights into the pathogen laying the groundwork for the development of vaccines and diagnostic methods. PMID:24982922

Detection of pathogenic gram negative bacteria using infrared thermography

NASA Astrophysics Data System (ADS)

Lahiri, B. B.; Divya, M. P.; Bagavathiappan, S.; Thomas, Sabu; Philip, John

2012-11-01

Detection of viable bacteria is of prime importance in all fields of microbiology and biotechnology. Conventional methods of enumerating bacteria are often time consuming and labor-intensive. All living organisms generate heat due to metabolic activities and hence, measurement of heat energy is a viable tool for detection and quantification of bacteria. In this article, we employ a non-contact and real time method - infrared thermography (IRT) for measurement of temperature variations in four clinically significant gram negative pathogenic bacteria, viz. Vibrio cholerae, Vibrio mimicus, Proteus mirabilis and Pseudomonas aeruginosa. We observe that, the energy content, defined as the ratio of heat generated by bacterial metabolic activities to the heat lost from the liquid medium to the surrounding, vary linearly with the bacterial concentration in all the four pathogenic bacteria. The amount of energy content observed in different species is attributed to their metabolisms and morphologies that affect the convection velocity and hence heat transport in the medium.

Housing system and laying hen strain impacts on egg microbiology.

PubMed

Jones, D R; Anderson, K E

2013-08-01

Alternative hen housing is becoming more commonplace in the egg market. However, a complete understanding of the implications for alternative housing systems on egg safety has not been achieved. The current study examines the impact of housing Hy-Line Brown, Hy-Line Silver Brown, and Barred Plymouth Rock hens in conventional cage, cage-free, and free range egg production systems on shell microbiology. Eggs were collected at 4 sampling periods. Egg shell emulsion pools were formed and enumerated for total aerobic organisms, Enterobacteriaceae, and yeast and mold counts. Hy-Line Brown and Hy-Line Silver Brown hens produced eggs with significantly (P < 0.05 and 0.001, respectively) different levels of aerobic organisms dependent on housing system. Eggs from conventional cages had significantly different (P < 0.05) levels of aerobic contamination in relation to hen strain with Hy-Line Silver Brown having the greatest (4.57 log cfu/mL). Hy-Line Brown and Barred Plymouth Rock hens produced eggs with significantly different (P < 0.01) levels of Enterobacteriaceae among housing systems with conventional caged eggs having the lowest level of contamination for the hen strains. There were no differences within each strain among housing systems for yeast and mold contamination. The study shows that hen strain has an effect on egg microbial levels for various housing systems, and egg safety should be considered when making hen strain selections for each housing system.

Field Evidence Supporting Conventional Onion Curing Practices as a Strategy To Mitigate Escherichia coli Contamination from Irrigation Water.

PubMed

Wright, Daniel; Feibert, Erik; Reitz, Stuart; Shock, Clint; Waite-Cusic, Joy

2018-03-01

The Produce Safety Rule of the U.S. Food Safety Modernization Act includes restrictions on the use of agricultural water of poor microbiological quality. Mitigation options for poor water quality include the application of an irrigation-to-harvest interval of <4 days; however, dry bulb onion production includes an extended irrigation-to-harvest interval (<30 days). This study evaluated conventional curing practices for mitigating Escherichia coli contamination in a field setting. Well water inoculated with rifampin-resistant E. coli (1, 2, or 3 log CFU/mL) was applied to onion fields (randomized block design; n = 5) via drip tape on the final day of irrigation. Onions remained undisturbed for 7 days and were then lifted to the surface to cure for an additional 21 days before harvest. Water, onions, and soil were tested for presence of rifampin-resistant E. coli. One day after irrigation, 13.3% of onions (20 of 150) receiving the poorest quality water (3 log CFU/mL) tested positive for E. coli; this prevalence was reduced to 4% (6 of 150 onions) after 7 days. Regardless of inoculum level, E. coli was not detected on any onions beyond 15 days postirrigation. These results support conventional dry bulb onion curing practices as an effective strategy to mitigate microbiological concerns associated with poor quality irrigation water.

Comparing different methods for fast screening of microbiological quality of beach sand aimed at rapid-response remediation.

PubMed

Testolin, Renan C; Almeida, Tito C M; Polette, Marcus; Branco, Joaquim O; Fischer, Larissa L; Niero, Guilherme; Poyer-Radetski, Gabriel; Silva, Valéria C; Somensi, Cleder A; Corrêa, Albertina X R; Corrêa, Rogério; Rörig, Leonardo R; Itokazu, Ana Gabriela; Férard, Jean-François; Cotelle, Sylvie; Radetski, Claudemir M

2017-05-15

There is scientific evidence that beach sands are a significant contributor to the pathogen load to which visitors are exposed. To develop beach quality guidelines all beach zones must be included in microbiological evaluations, but monitoring methods for beach sand quality are relatively longstanding, expensive, laborious and require moderate laboratory infrastructure. This paper aimed to evaluate the microorganism activity in different beach zones applying and comparing a classical method of membrane filtration (MF) with two colorimetric screening methods based on fluorescein (FDA) and tetrazolium (TTC) salt biotransformation to evaluate a new rapid and low-cost method for beach sand microbiological contamination assessments. The colorimetric results can help beach managers to evaluate rapidly and at low cost the microbiological quality of different beach zones in order to decide whether remedial actions need to be adopted to prevent exposure of the public to microbes due to beach sand and/or water contamination. Copyright © 2017. Published by Elsevier Ltd.

Preventive effect of ginsenoid on chronic bacterial prostatitis.

PubMed

Kim, Sang Hoon; Ha, U-Syn; Sohn, Dong Wan; Lee, Seung-Ju; Kim, Hyun Woo; Han, Chang Hee; Cho, Yong-Hyun

2012-10-01

Empirical antibiotic therapy is the preferred primary treatment modality for chronic bacterial prostatitis (CBP). However, this method of treatment has a low success rate and long-term therapy may result in complications and the appearance of resistant strains. Therefore a new alternative method for the prevention of CBP is necessary. There are several reports that ginsenoid has a preventive effect on urinary tract infection (UTI). To evaluate the preventive effect of ginsenoid on CBP compared to conventional antibiotics, we carried out an experiment in a rat model of the disease. Four groups of adult male Wistar rats were treated with the following medications: (1) control (no medication), (2) ciprofloxacin, (3) ginsenoid, and (4) ciprofloxacin/ginsenoid. All medications were given for 4 weeks, and then we created a CBP model in the animals by injecting an Escherichia coli Z17 (O2:K1;H(-)) suspension into the prostatic urethra. After 4 weeks, results of microbiological cultures of prostate and urine samples, as well as histological findings of the prostate in each group were analyzed. The microbiological cultures of the prostate samples demonstrated reduced bacterial growth in all experimental groups compared with the control group. Histopathological examination showed a significantly decreased rate of infiltration of inflammatory cells into prostatic tissue and decreased interstitial fibrosis in the ginsenoid group compared with the control group. Inhibition of prostate infection was greater in the group receiving both ginsenoid and antibiotic than in the single-medication groups. Although the findings of this study suggest a preventive effect of ginsenoid, preventive methods for CBP are still controversial.

The influence of plant protection by effective microorganisms on the content of bioactive phytochemicals in apples.

PubMed

Kusznierewicz, Barbara; Lewandowska, Anna; Martysiak-Żurowska, Dorota; Bartoszek, Agnieszka

2017-09-01

The phytochemicals of two apple cultivars (Yellow Transparent and Early Geneva) protected in two ways, conventionally with chemical pesticides or by effective microorganisms (EM), were compared. Two types of components were determined: lipids synthesised constitutively and generated via inducible pathways polyphenols along with antioxidant activity and profiles. The antioxidant activities assessed with ABTS, DPPH and Folin-Ciocalteu reagents were about two-fold higher in the case of microbiologically protected apples. The qualitative composition of phenolics determined by LC-DAD-MS varied between cultivars and the part of apples studied, while the method of protection caused mainly differences in concentration of some groups of polyphenols (hydroxycinnamates, flavanols, dihydrochalcones, flavonols, anthocyanins). The apples from biological cultivation contained about 34-54% more phenolics than these from a conventional orchard. In contrast, lipid composition did not differ significantly between apples originating from conventional and bio-crops. The results indicate that the advantage of using the EM technology in agriculture may not only be the reduction of consumption of chemical fertilisers and synthetic pesticides, but also, at least in the case of apples, may lead to the production of crops with improved health quality due to the higher content of bioactive phytochemicals. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Geospatial Hydrochemical and Microbiological Implications on the Occurrence of Crude Oil Biodegradation and Methanogenesis

NASA Astrophysics Data System (ADS)

Shelton, J.; McIntosh, J. C.; Warwick, P.; McCray, J. E.

2014-12-01

Technologies that serve as a bridge between renewable energy and fossil fuels are needed to meet growing energy demands and to mitigate climate change. Many reservoirs contain difficult to produce residual and/or heavily biodegraded (i.e., geochemically altered) crude oil, which remains a relatively untapped resource. Production of this residual crude oil via unconventional methods, such as enhanced oil recovery (EOR), has offset some of the decline in conventional oil production. EOR is not efficient enough to recover all of the original oil in place, and some methods are not effective for very heavy crude oils. Stimulation of in-situ microorganisms to convert the residual crude oil to natural gas (i.e., microbial methane) is one promising strategy to "extract" residual and /or heavy crude oil. Although the hydrogeochemical conditions necessary for the occurrence of both crude oil biodegradation and microbial methanogenesis in various reservoirs have been studied, there are still gaps in research. Many hydrogeochemical factors have been researched individually (not as part of a multifactor or lithologically similar system) and little work has assessed the microbiological limitations of both processes. Our goal is to determine the hydrogeochemical and microbiological conditions required for maximum crude oil biodegradation and microbial methanogenesis across a lithologically similar unit. Produced water, oil, gas, and microbial biomass samples were collected from wells completed in the Paleocene—Eocene Wilcox Group in central Louisiana. Initial results indicate potential relationships between the amount of crude oil biodegradation, indicators of microbial methanogenesis, and aqueous geochemistry. For example, produced waters with the lowest salinity had the highest crude oil biodegradation, and wells exhibiting the most microbial methane generation produce waters with hydrogeochemical conditions most fit for methanogenesis to occur. In sampled wells displaying similar hydrogeochemical conditions (e.g., similar temperatures), indicators of methanogenesis, such as δ13C dissolved inorganic carbon values, are more pronounced in wells displaying oils that are more biodegraded, suggesting methanogenesis may be accelerated with greater amounts of crude oil biodegradation.

Microbial sensor for drug susceptibility testing of Mycobacterium tuberculosis.

PubMed

Zhang, Z-T; Wang, D-B; Li, C-Y; Deng, J-Y; Zhang, J-B; Bi, L-J; Zhang, X-E

2018-01-01

Drug susceptibility testing (DST) of clinical isolates of Mycobacterium tuberculosis is critical in treating tuberculosis. We demonstrate the possibility of using a microbial sensor to perform DST of M. tuberculosis and shorten the time required for DST. The sensor is made of an oxygen electrode with M. tuberculosis cells attached to its surface. This sensor monitors the residual oxygen consumption of M. tuberculosis cells after treatment with anti-TB drugs with glycerine as a carbon source. In principle, after drug pretreatment for 4-5 days, the response differences between the sensors made of drug-sensitive isolates are distinguishable from the sensors made of drug-resistant isolates. The susceptibility of the M. tuberculosis H37Ra strain, its mutants and 35 clinical isolates to six common anti-TB drugs: rifampicin, isoniazid, streptomycin, ethambutol, levofloxacin and para-aminosalicylic acid were tested using the proposed method. The results agreed well with the gold standard method (LJ) and were determined in significantly less time. The whole procedure takes approximately 11 days and therefore has the potential to inform clinical decisions. To our knowledge, this is the first study that demonstrates the possible application of a dissolved oxygen electrode-based microbial sensor in M. tuberculosis drug resistance testing. This study used the microbial sensor to perform DST of M. tuberculosis and shorten the time required for DST. The overall detection result of the microbial sensor agreed well with that of the conventional LJ proportion method and takes less time than the existing phenotypic methods. In future studies, we will build an O 2 electrode array microbial sensor reactor to enable a high-throughput drug resistance analysis. © 2017 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of The Society for Applied Microbiology.

Microbiologically Influenced Corrosion

DTIC Science & Technology

2009-01-01

related directly to the biomineralized deposits on the surface. Ennoble- ment in marine waters has been attributed to depolarization of the oxygen... abiotic ally oxi- dized metal precipitates, and still others that derive energy by oxidizing metals. Manganese. Manganese oxidation is coupled to cell...circumstances, pitting involves the conventional features of differential aeration, a large cathode: anode surface area, and the development of

Storage Test on Apple Juice After Ultrasound Treatment

PubMed Central

Fasolato, Luca; Balzan, Stefania; De Nardi, Roberta; Marchesini, Giorgio; Cardazzo, Barbara; Novelli, Enrico

2014-01-01

Apple juice, for its sensory and nutritional qualities, is consumed by people of all ages. Apples are an excellent source of several phenolic compounds and the presence of polyphenols is recognized for their health promoting antioxidant properties. Thermal pasteurization of fruit juices is the conventional method used for their preservation. Therefore, this constitutes the most extensively available methods for the inactivation of microorganisms in fruit juices but it causes side effects on their flavour and nutritional quality. Consumers tend to prefer recently extracted juices with fresh taste and minimal flavor or vitamin losses. To meet consumers’ demand, among the novel technologies that involve non-thermal processes, power ultrasound have been investigated as an alternative to conventional heat treatments. Objective of this study was to evaluate the effectiveness of the use of ultrasound in an attempt to maintain the organoleptic characteristics typical of a natural apple juice. In particular, it was evaluated the action on the microflora residing and shelf life of the product through microbiological and sensory analyses. Juice treated with ultrasound highlighted a reduction of aerobic mesophilic counts and psychrophilic bacteria respectively about 3 and 5 log CFU/mL and an enhanced yeast growth. The general opinion expressed by the panelist was in favour of the sonicated juice. This preliminary study showed that non-thermal methods such as power ultrasound technology may give new opportunities to develop fresh-like apple juice. PMID:27800306

Comparative study of Gram stain, potassium hydroxide smear, culture and nested PCR in the diagnosis of fungal keratitis.

PubMed

Badiee, Parisa; Nejabat, Mahmood; Alborzi, Abdolvahab; Keshavarz, Fatemeh; Shakiba, Elaheh

2010-01-01

This study seeks to evaluate the efficacy and practicality of the molecular method, compared to the standard microbiological techniques for diagnosing fungal keratitis (FK). Patients with eye findings suspected of FK were enrolled for cornea sampling. Scrapings from the affected areas of the infected corneas were obtained and were divided into two parts: one for smears and cultures, and the other for nested PCR analysis. Of the 38 eyes, 28 were judged to have fungal infections based on clinical and positive findings in the culture, smear and responses to antifungal treatment. Potassium hydroxide, Gram staining, culture and nested PCR results (either positive or negative) matched in 76.3, 42.1, 68.4 and 81.6%, respectively. PCR is a sensitive method but due to the lack of sophisticated facilities in routine laboratory procedures, it can serve only complementarily and cannot replace conventional methods. Copyright © 2010 S. Karger AG, Basel.

Bacillus "next generation" diagnostics: moving from detection toward subtyping and risk-related strain profiling.

PubMed

Ehling-Schulz, Monika; Messelhäusser, Ute

2013-01-01

The highly heterogeneous genus Bacillus comprises the largest species group of endospore forming bacteria. Because of their ubiquitous nature, Bacillus spores can enter food production at several stages resulting in significant economic losses and posing a potential risk to consumers due the capacity of certain Bacillus strains for toxin production. In the past, food microbiological diagnostics was focused on the determination of species using conventional culture-based methods, which are still widely used. However, due to the extreme intra-species diversity found in the genus Bacillus, DNA-based identification and typing methods are gaining increasing importance in routine diagnostics. Several studies showed that certain characteristics are rather strain-dependent than species-specific. Therefore, the challenge for current and future Bacillus diagnostics is not only the efficient and accurate identification on species level but also the development of rapid methods to identify strains with specific characteristics (such as stress resistance or spoilage potential), trace contamination sources, and last but not least discriminate potential hazardous strains from non-toxic strains.

Bacteriological quality of vegetables from organic and conventional production in different areas of Korea.

PubMed

Tango, Charles Nkufi; Choi, Na-Jung; Chung, Myung-Sub; Oh, Deog Hwan

2014-08-01

Foods grown in organic production systems have been described as representing an increased risk to public health compared with foods from conventional production. Leafy vegetables (spinach, romaine lettuce, and green sesame leaves) grown in organic and conventional systems were collected from various areas in Korea and examined using standard culture methods to compare the microbiological quality of the produce grown in the two agricultural systems. The 354 samples of these leafy vegetables were analyzed for levels of indicator bacteria (aerobic bacteria, coliforms, and Escherichia coli) and the prevalence of the pathogens Staphylococcus aureus, E. coli O157:H7, Listeria monocytogenes, Bacillus cereus, and Salmonella. Aerobic bacteria and coliforms were detected in all vegetable types, but nonpathogenic E. coli was below the limit of detection in all samples. B. cereus was the most prevalent pathogen, found on 7 (11.1%) of the 63 organic spinach samples. The prevalence of S. aureus was highest in organic sesame leaves; it was found on 5 (8.0%) of the 63 samples. The prevalence of L. monocytogenes was highest on organic romaine lettuce and spinach; it was found in 4 (6.4%) of 63 samples of each type of vegetable. E. coli O157:H7 found on only 1 (1.58%) of 55 conventional spinach samples. These results suggest that farming type at most only slightly affects the hygienic quality of leafy vegetables, and no effect was found for sample collection area. Salmonella was not isolated from any of the conventional or organic leafy vegetables. These results do not support the hypothesis that organic produce poses a substantially greater risk of pathogen contamination than does conventional produce.

[Evaluation of common commercial systems for the identification of yeast isolates in microbiology laboratories: a multicenter study].

PubMed

Karabıçak, Nilgün; Uludağ Altun, Hatice; Karatuna, Onur; Hazırolan, Gülşen; Aksu, Neriman; Adiloğlu, Ali; Akyar, Işın

2015-04-01

Accurate and rapid identification of yeast isolates have become important in recent years for not only antifungal susceptibility testing due to the species-specific clinical resistance breakpoints but also early initiation of appropriate antifungal therapy. In clinical microbiology laboratories species identification of yeasts is often performed with several commercial systems based on biochemical properties and rarely according to the physiological and morphological characteristics. The aim of this study was to compare the two common commercial systems, VITEK 2 YST ID Card (Vitek; bioMérieux, France) and API 20C AUX (API; bioMérieux, France) with conventional mycological methods. A total of 473 clinical yeast strains isolated from clinical specimens in different university and training/research hospitals and identified by Vitek system were included in the study. The isolates were re-identified with API and conventional methods including morphological identification in the Mycology Reference Laboratory of the Public Health Institute of Turkey. Candida dubliniensis MYA 583, Candida krusei ATCC 6258, Candida parapsilosis ATCC 22019, Candida albicans ATCC 10231 and Cryptococcus neoformans ATCC 32268 were used as quality control strains and those standard strains were studied consecutively 10 days with both of the methods. The results of identification by Vitek and API were compared with the results of conventional methods for those 473 yeast isolates [6 genus (Candida, Cryptococcus, Blastoshizomyces, Rhodotorula, Saccharomyces, Trichosporon), 17 species (5 common and 12 rarely isolated)]. The performances of the systems were better (Vitek: 95%; API: 96%) for the commonly detected species (C.albicans, C.parapsilosis, C.glabrata, C.tropicalis and C.krusei) than those for rarely detected species (Vitek: 78.4%; API: 71.6%) (p= 0.155). Misidentification or unidentification were mostly detected for C.parapsilosis (Vitek: 6/87; API: 7/87) and C.glabrata (Vitek: 9/104; API: 3/104) by both of the systems. For rarely detected yeast isolates, misidentification or unidentification were most frequently observed in species of C.pelliculosa (Vitek: 3/11; API: 6/11) and C.dubliniensis (API and Vitek: 2/5) isolates. Candida guilliermondii (API: 2/5) isolates had lower rate of identification with API compared to other species. Blastoschizomyces capitatus and Saccharomyces cerevisiae isolates could not be identified by both of the systems. As a result, the accurate diagnosis of Vitek and API systems were similar in terms of consistency (86.3%). Two systems performed well in correct identification of common clinical yeast species (at least 95%), while the identification of rare species was more challenging indicating that they require further morphological and physiological testing. The addition of morphological identification to commercial systems will be useful for accurate diagnosis and treatment of mixed infections.

Development and use of a real-time polymerase chain reaction assay for the detection of Ophidiomyces ophiodiicola in snakes.

PubMed

Allender, Matthew C; Bunick, David; Dzhaman, Elena; Burrus, Lucienne; Maddox, Carol

2015-03-01

Fungal pathogens threatening the conservation of wildlife are becoming increasingly common. Since 2008, free-ranging snakes across North America have been experiencing a marked increase in the prevalence of snake fungal disease associated with Ophidiomyces ophiodiicola. Diagnosis has historically relied on histology, microbiology, and conventional polymerase chain reaction (PCR). More sensitive methods are needed to adequately characterize the epidemiology. The current study describes the development of a real-time PCR (qPCR) assay for detecting a segment of the internal transcribed spacer 1 region between the 18S and 5.8S ribosomal RNA gene. The assay was able to detect as few as 1.05 × 10(1) gene copies per reaction. An additional 4 positive cases were detected when comparing a conventional PCR (n = 3) and the qPCR (n = 7) when used on swab samples from 47 eastern massasauga rattlesnakes. The newly developed assay is a sensitive and specific tool for surveillance and monitoring in the conservation of free-ranging snakes. © 2015 The Author(s).

Determination of water-soluble vitamins using a colorimetric microbial viability assay based on the reduction of water-soluble tetrazolium salts.

PubMed

Tsukatani, Tadayuki; Suenaga, Hikaru; Ishiyama, Munetaka; Ezoe, Takatoshi; Matsumoto, Kiyoshi

2011-07-15

A method for the determination of water-soluble vitamins using a colorimetric microbial viability assay based on the reduction of the tetrazolium salt {2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium, monosodium salt (WST-8)} via 2-methyl-1,4-napthoquinone (NQ) was developed. Measurement conditions were optimized for the microbiological determination of water-soluble vitamins, such as vitamin B(6), biotin, folic acid, niacin, and pantothenic acid, using microorganisms that have a water-soluble vitamin requirement. A linear relationship between absorbance and water-soluble vitamin concentration was obtained. The proposed method was applied to determine the concentration of vitamin B(6) in various foodstuffs. There was good agreement between vitamin B(6) concentrations determined after 24h using the WST-8 colorimetric method and those obtained after 48h using a conventional method. The results suggest that the WST-8 colorimetric assay is a useful method for the rapid determination of water-soluble vitamins in a 96-well microtiter plate. Copyright © 2011 Elsevier Ltd. All rights reserved.

[Authorized Qualifications of Staff Conducting Examinations in the Field of Clinical Microbiology].

PubMed

Nishiyama, Hiroyuki

2015-04-01

Because of the increase in healthcare-associated infections, appearance of highly resistant bacteria, and that of emerging/re-emerging infectious diseases, it is necessary for the skills of clinical microbiological technologists and the associated technology to be improved. Technologist in Microbiology (4,717 certified) and Specialist in Microbiology (58 certified) are authorized qualifications in the field of examination for clinical microbiology, with a history of 60 years, and Clinical Microbiological Technologist (670 certified) and Infection Control Microbiological Technologist (ICMT) (528 certified) are necessary qualifications to become a member of an infection control team. As problems to be resolved, clarifying the relationships among the authorized qualifications, reconsidering the fairness of evaluating written examinations, and further consideration of the administration method for an increasing number of examinees need to be tackled.

Microbial Biotechnology 2020; microbiology of fossil fuel resources.

PubMed

Head, Ian M; Gray, Neil D

2016-09-01

This roadmap examines the future of microbiology research and technology in fossil fuel energy recovery. Globally, the human population will be reliant on fossil fuels for energy and chemical feedstocks for at least the medium term. Microbiology is already important in many areas relevant to both upstream and downstream activities in the oil industry. However, the discipline has struggled for recognition in a world dominated by geophysicists and engineers despite widely known but still poorly understood microbially mediated processes e.g. reservoir biodegradation, reservoir souring and control, microbial enhanced oil recovery. The role of microbiology is even less understood in developing industries such as shale gas recovery by fracking or carbon capture by geological storage. In the future, innovative biotechnologies may offer new routes to reduced emissions pathways especially when applied to the vast unconventional heavy oil resources formed, paradoxically, from microbial activities in the geological past. However, despite this potential, recent low oil prices may make industry funding hard to come by and recruitment of microbiologists by the oil and gas industry may not be a high priority. With regards to public funded research and the imperative for cheap secure energy for economic growth in a growing world population, there are signs of inherent conflicts between policies aimed at a low carbon future using renewable technologies and policies which encourage technologies which maximize recovery from our conventional and unconventional fossil fuel assets. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

An assessment of alternative diesel fuels: microbiological contamination and corrosion under storage conditions.

PubMed

Lee, Jason S; Ray, Richard I; Little, Brenda J

2010-08-01

Experiments were designed to evaluate the nature and extent of microbial contamination and the potential for microbiologically influenced corrosion of alloys exposed in a conventional high sulfur diesel (L100) and alternative fuels, including 100% biodiesel (B100), ultra-low sulfur diesel (ULSD) and blends of ULSD and B100 (B5 and B20). In experiments with additions of distilled water, all fuels supported biofilm formation. Changes in the water pH did not correlate with observations related to corrosion. In all exposures, aluminum 5052 was susceptible to pitting while stainless steel 304L exhibited passive behavior. Carbon steel exhibited uniform corrosion in ULSD and L100, and passive behavior in B5, B20, and B100.

A review of current and future molecular diagnostic tests for use in the microbiology laboratory.

PubMed

Jannes, Geert; De Vos, Daniel

2006-01-01

Nucleic acid-based diagnostics gradually are replacing or complementing culture-based, biochemical, and immunological assays in routine microbiology laboratories. Similar to conventional tests, the first-generation deoxyribonucleic acid assays determined only a single analyte. Recent improvements in detection technologies have paved the way for the development of multiparameter assays using macroarrays or micro-arrays, while the introduction of closed-tube real-time polymerase chain reaction systems has resulted in the development of rapid microbial diagnostics with a reduced contamination risk. The use of these new molecular technologies is not restricted to detection and identification of microbial pathogens but also can be used for genotyping, allowing one to determine antibiotic resistance or to perform microbial fingerprinting.

Comparison of Real-Time PCR and Conventional Biochemical Methods for Identification of Staphylococcus lugdunensis▿

PubMed Central

Pinsky, Benjamin A.; Samson, Divinia; Ghafghaichi, Laleh; Baron, Ellen J.; Banaei, Niaz

2009-01-01

Staphylococcus lugdunensis is an aggressive, virulent member of the coagulase-negative staphylococci (CoNS) that is responsible for severe, rapidly progressive skin and soft tissue infections and native valve endocarditis. To facilitate prompt identification and appropriate therapy, we describe here a rapid and robust multiplex real-time PCR assay that is able to definitively distinguish S. lugdunensis from other staphylococci. Using melting curve analysis, the assay also identifies Staphylococcus aureus and CoNS other than S. lugdunensis and determines MecA-dependent resistance to methicillin (meticillin). When applied to a panel of well-characterized staphylococcal reference strains, as well as 165 clinical isolates previously identified by conventional methods, the assay was both sensitive and specific for S. lugdunensis, correctly identifying the reference strain and all 47 S. lugdunensis isolates without inappropriate amplification of other staphylococci. Furthermore, rapid biochemical identification using the WEE-TAB system to detect ornithine decarboxylase activity was found to be unsuitable as an alternative to PCR identification, displaying just 31% sensitivity and 77% specificity when tested on a subset (90 isolates) of the clinical strains. We therefore propose that this simple, accurate PCR approach will allow for the routine and timely identification of S. lugdunensis in the clinical microbiology laboratory. PMID:19741081

Do biological-based strategies hold promise to biofouling control in MBRs?

PubMed

Malaeb, Lilian; Le-Clech, Pierre; Vrouwenvelder, Johannes S; Ayoub, George M; Saikaly, Pascal E

2013-10-01

Biofouling in membrane bioreactors (MBRs) remains a primary challenge for their wider application, despite the growing acceptance of MBRs worldwide. Research studies on membrane fouling are extensive in the literature, with more than 200 publications on MBR fouling in the last 3 years; yet, improvements in practice on biofouling control and management have been remarkably slow. Commonly applied cleaning methods are only partially effective and membrane replacement often becomes frequent. The reason for the slow advancement in successful control of biofouling is largely attributed to the complex interactions of involved biological compounds and the lack of representative-for-practice experimental approaches to evaluate potential effective control strategies. Biofouling is driven by microorganisms and their associated extra-cellular polymeric substances (EPS) and microbial products. Microorganisms and their products convene together to form matrices that are commonly treated as a black box in conventional control approaches. Biological-based antifouling strategies seem to be a promising constituent of an effective integrated control approach since they target the essence of biofouling problems. However, biological-based strategies are in their developmental phase and several questions should be addressed to set a roadmap for translating existing and new information into sustainable and effective control techniques. This paper investigates membrane biofouling in MBRs from the microbiological perspective to evaluate the potential of biological-based strategies in offering viable control alternatives. Limitations of available control methods highlight the importance of an integrated anti-fouling approach including biological strategies. Successful development of these strategies requires detailed characterization of microorganisms and EPS through the proper selection of analytical tools and assembly of results. Existing microbiological/EPS studies reveal a number of implications as well as knowledge gaps, warranting future targeted research. Systematic and representative microbiological studies, complementary utilization of molecular and biofilm characterization tools, standardized experimental methods and validation of successful biological-based antifouling strategies for MBR applications are needed. Specifically, in addition, linking these studies to relevant operational conditions in MBRs is an essential step to ultimately develop a better understanding and more effective and directed control strategy for biofouling. Copyright © 2013 Elsevier Ltd. All rights reserved.

A microbiological method for determining serum levels of broad spectrum β-lactam antibiotics in critically ill patients.

PubMed

Fridlund, Jimmy; Woksepp, Hanna; Schön, Thomas

2016-10-01

Recent studies show that suboptimal blood levels of β-lactam antibiotics are present in intensive care unit (ICU) patients. A common reference method for assessing drug concentrations is liquid chromatography coupled with mass-spectrometry (LC-MS) which is highly accurate but rarely available outside reference centres. Thus, our aim was to develop a microbiological method for monitoring β-lactam antibiotic serum levels which could be used at any hospital with a microbiological laboratory. The method was developed as a 96-well broth microdilution format to assess the concentrations of cefotaxime (CTX), meropenem (MER), and piperacillin (PIP). Patient serum containing antibiotics were diluted in suspensions of bacteria with known minimal inhibitory concentrations (MICs). Serum antibiotic concentrations were calculated by dividing the MIC with the dilution factor at which the serum inhibited growth of the bacterial suspension. Serum (n=88) from ICU patients at four hospitals in south-east Sweden were analysed and compared to LC-MS analysis. The overall accuracy and precision for spiked samples and patient samples was within the pre-set target of ±20.0% for all drugs. There was a significant correlation between the microbiological assay and LC-MS for the patient samples (CTX: r=0.86, n=31; MER: r=0.96, n=11; PIP: r=0.88, n=39) and the agreement around the clinical cut-off for CTX (4.0mg/l), MER (2.0mg/l) and PIP (16.0mg/l) was 90%, 100% and 87%, respectively. The microbiological method has a performance for determination of serum levels of meropenem, piperacillin and cefotaxime suitable for clinical use. It is an inexpensive method applicable in any microbiology laboratory. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbiological effects and recolonization patterns after adjunctive subgingival debridement with Er:YAG laser.

PubMed

Sanz-Sánchez, Ignacio; Ortiz-Vigón, Alberto; Herrera, David; Sanz, Mariano

2016-07-01

The objective of this study was to assess the microbiological effects and recolonization patterns after non-surgical periodontal treatment protocol based on the adjunctive use of erbium-doped yttrium aluminium garnet (Er:YAG) laser. Patients diagnosed with chronic periodontitis were randomly assigned to two different treatment protocols: test, full-mouth subgingival ultrasonic instrumentation followed by Er-YAG laser application 1 week later to sites with initial probing pocket depth ≥4.5 mm; and control, full-mouth ultrasonic subgingival instrumentation within 1 week. Clinical (at sampled sites) and microbiological (culture-based) parameters were recorded at baseline and 3 and 12 months. Microbiological variables included total counts, frequency of detection, proportions and counts of target species. Results from 19 test and 21 control patients were compared. Minor changes were observed for total colony-forming units, with no differences between groups. For the frequency of detection, a limited and similar impact in both groups was observed for the most prevalent (over 80 %) periodontal pathogens (Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum). For proportions, reductions in P. gingivalis occurred at 3 months, both in the test and control groups (from 16.3 to 10 % and 16 to 14.8 %, respectively), although these differences were not statistically significant. At 12 months, the test group showed a statistically significant greater reduction in probing depth for the sampled sites. The adjunctive use of Er:YAG laser when compared with conventional ultrasonic debridement did not provide a microbiological added benefit. Even though some clinical benefits with the adjunctive laser application were identified when comparing both treatment protocols, there were no differences in microbiological outcomes or in the bacterial recolonization patterns.

Monitoring of Gasoline-ethanol Degradation In Undisturbed Soil

NASA Astrophysics Data System (ADS)

Österreicher-Cunha, P.; Nunes, C. M. F.; Vargas, E. A.; Guimarães, J. R. D.; Costa, A.

Environmental contamination problems are greatly emphasised nowadays because of the direct threat they represent for human health. Traditional remediation methods fre- quently present low efficiency and high costs; therefore, biological treatment is being considered as an accessible and efficient alternative for soil and water remediation. Bioventing, commonly used to remediate petroleum hydrocarbon spills, stimulates the degradation capacity of indigenous microorganisms by providing better subsur- face oxygenation. In Brazil, gasoline and ethanol are mixed (78:22 v/v); some authors indicate that despite gasoline high degradability, its degradation in subsurface is hin- dered by the presence of much more rapidly degrading ethanol. Contaminant distribu- tion and degradation in the subsurface can be monitored by several physical, chemical and microbiological methodologies. This study aims to evaluate and follow the degra- dation of a gasoline-ethanol mixture in a residual undisturbed tropical soil from Rio de Janeiro. Bioventing was used to enhance microbial degradation. Shifts in bacte- rial culturable populations due to contamination and treatment effects were followed by conventional microbiology methods. Ground Penetrating Radar (GPR) measure- ments, which consist of the emission of electro-magnetic waves into the soil, yield a visualisation of contaminant degradation because of changes in soil conductivity due to microbial action on the pollutants. Chemical analyses will measure contaminant residue in soil. Our results disclosed contamination impact as well as bioventing stim- ulation on soil culturable heterotrophic bacterial populations. This multidisciplinary approach allows for a wider evaluation of processes occurring in soil.

Antimicrobial effect and shelf-life extension by combined thermal and pulsed electric field treatment of milk.

PubMed

Walkling-Ribeiro, M; Noci, F; Cronin, D A; Lyng, J G; Morgan, D J

2009-01-01

The impact of a combined hurdle treatment of heat and pulsed electric fields (PEF) was studied on native microbiota used for the inoculation of low-fat ultra-high temperature (UHT) milk and whole raw milk. Microbiological shelf-life of the latter following hurdle treatment or thermal pasteurization was also investigated. UHT milk was preheated to 30 degrees C, 40 degrees C or 50 degrees C over a 60-s period, pulsed for 50 micros or 60 micros at a field strength of 40 kV cm(-1) or for 33 micros at 50 kV cm(-1). Heat and PEF reduced the microbial count by a maximum of 6.4 log in UHT milk (50 degrees C; 50 kV cm(-1), 33 micros) compared to 6.0 log (P > or = 0.05) obtained by thermal pasteurization (26 s, 72 degrees C). When raw milk was treated with a combination of hurdles (50 degrees C; 40 kV cm(-1), 60 micros) a 6.0 log inactivation of microbiota was achieved and microbiological milk shelf-life was extended to 21 days under refrigeration (4 degrees C) vs 14 days in thermally pasteurized milk. Native microbiota was decreased by 6.7 log following conventional pasteurization. The findings suggest that heat and PEF achieved similar inactivation of native microbiota in milk and longer stabilization of microbiological shelf-life than thermal pasteurization. A hurdle approach of heat and PEF could represent a valid milk processing alternative to conventional pasteurization. Hurdle treatment might also preserve native milk quality better due to less thermal exposure.

[Validation and verfication of microbiology methods].

PubMed

Camaró-Sala, María Luisa; Martínez-García, Rosana; Olmos-Martínez, Piedad; Catalá-Cuenca, Vicente; Ocete-Mochón, María Dolores; Gimeno-Cardona, Concepción

2015-01-01

Clinical microbiologists should ensure, to the maximum level allowed by the scientific and technical development, the reliability of the results. This implies that, in addition to meeting the technical criteria to ensure their validity, they must be performed with a number of conditions that allows comparable results to be obtained, regardless of the laboratory that performs the test. In this sense, the use of recognized and accepted reference methodsis the most effective tool for these guarantees. The activities related to verification and validation of analytical methods has become very important, as there is continuous development, as well as updating techniques and increasingly complex analytical equipment, and an interest of professionals to ensure quality processes and results. The definitions of validation and verification are described, along with the different types of validation/verification, and the types of methods, and the level of validation necessary depending on the degree of standardization. The situations in which validation/verification is mandatory and/or recommended is discussed, including those particularly related to validation in Microbiology. It stresses the importance of promoting the use of reference strains as controls in Microbiology and the use of standard controls, as well as the importance of participation in External Quality Assessment programs to demonstrate technical competence. The emphasis is on how to calculate some of the parameters required for validation/verification, such as the accuracy and precision. The development of these concepts can be found in the microbiological process SEIMC number 48: «Validation and verification of microbiological methods» www.seimc.org/protocols/microbiology. Copyright © 2013 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolution in clinical microbial identification.

PubMed

Bizzini, A; Greub, G

2010-11-01

Until recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) techniques for the identification of microorganisms remained confined to research laboratories. In the last 2 years, the availability of relatively simple to use MALDI-TOF MS devices, which can be utilized in clinical microbiology laboratories, has changed the laboratory workflows for the identification of pathogens. Recently, the first prospective studies regarding the performance in routine bacterial identification showed that MALDI-TOF MS is a fast, reliable and cost-effective technique that has the potential to replace and/or complement conventional phenotypic identification for most bacterial strains isolated in clinical microbiology laboratories. For routine bacterial isolates, correct identification by MALDI-TOF MS at the species level was obtained in 84.1-93.6% of instances. In one of these studies, a protein extraction step clearly improved the overall valid identification yield, from 70.3% to 93.2%. This review focuses on the current state of use of MALDI-TOF MS for the identification of routine bacterial isolates and on the main difficulties that may lead to erroneous or doubtful identifications. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

[Reliable microbiological diagnosis of vulvovaginal candidiasis].

PubMed

Baykushev, R; Ouzounova-Raykova, V; Stoykova, V; Mitov, I

2014-01-01

Vulvovaginal candidiasis is common infection among those affecting the vulva and vagina. Is caused by the perpesentatives from the genus Candida, in most cases C. albicans (85-90%). An increase in the percentage of the so-called non-albicans agents is seen and these pathgogens are often resistant to the most commonly used in the practice antifungals. Faulty diagnosis, incorrect use of azoles, and self-treatment lead to selection of resistant strains and recurrent infections. Identification of Candida species associated with vulvovaginal candidiasis by conventional and PCR techniques. For six months a total number of 213 vaginal secretions were tested applying Gram stain and cultivation on ChromAgar. API Candida fermentation tests and API 20CAUX assimilation tests were performed for the identification of the bacteria. Extraction of DNA of all the smears with subsequent PCR detection of different Candida species were done. 80.7% materials showed presence of blastospores and/or hyphae. Positive culture results were detected in 60 (28.2%) samples. The species specific identification revealed presence of C. albicans in 51 (85%) smears, C. glabrata--in 8 (13.3%), C. krusei--in 2 (3.3%), and S. cervisie--in 1 (2.1%). The PCR technique confirmed the results of the conventional methods. It is worth to mention that 51 of the tested smears were positive for G. vaginalis using additional PCR. The correct diagnosis of the cause of vulvovaginal candidiasis helps in the correct choice of appropriate antifungal therapy and prevents development of recurrent infections and consequences. The PCR based method is rapid, specific and sensitive. It perfectly correlates with the results from the conventional diagnostic tests so it could be selected as a method of choice for the diagnosis of vulvovaginal candidiasis.

Studying bacteria in respiratory specimens by using conventional and molecular microbiological approaches

PubMed Central

Rogers, Geraint B; Daniels, Thomas WV; Tuck, Andrew; Carroll, Mary P; Connett, Gary J; David, Gondi JP; Bruce, Kenneth D

2009-01-01

Background Drawing from previous studies, the traditional routine diagnostic microbiology evaluation of samples from chronic respiratory conditions may provide an incomplete picture of the bacteria present in airways disease. Here, the aim was to determine the extent to which routine diagnostic microbiology gave a different assessment of the species present in sputa when analysed by using culture-independent assessment. Methods Six different media used in routine diagnostic microbiology were inoculated with sputum from twelve patients. Bacterial growth on these plates was harvested and both RNA and DNA extracted. DNA and RNA were also extracted directly from the same sample of sputum. All nucleic acids served as templates for PCR and reverse transcriptase-PCR amplification of "broad range" bacterial 16S rRNA gene regions. The regions amplified were separated by Terminal Restriction Fragment Length Polymorphism (T-RFLP) profiling and compared to assess the degree of overlap between approaches. Results A mean of 16.3 (SD 10.0) separate T-RF band lengths in the profiles from each sputum sample by Direct Molecular Analysis, with a mean of 8.8 (SD 5.8) resolved by DNA profiling and 13.3 (SD 8.0) resolved by RNA profiling. In comparison, 8.8 (SD 4.4) T-RF bands were resolved in profiles generated by Culture-derived Molecular Analysis. There were a total of 184 instances of T-RF bands detected in the direct sputum profiles but not in the corresponding culture-derived profiles, representing 83 different T-RF band lengths. Amongst these were fifteen instances where the T-RF band represented more than 10% of the total band volume (with a mean value of 23.6%). Eight different T-RF band lengths were resolved as the dominant band in profiles generated directly from sputum. Of these, only three were detected in profiles generated from the corresponding set of cultures. Conclusion Due to their focus on isolation of a small group of recognised pathogens, the use of culture-dependent methods to analyse samples from chronic respiratory infections can provide a restricted understanding of the bacterial species present. The use of a culture-independent molecular approach here identifies that there are many bacterial species in samples from CF and COPD patients that may be clinically relevant. PMID:19368727

Preface: 5th International Symposium on the Interface between Analytical Chemistry and Microbiology - April 19th to 21st, 2004: Hosted at Pacific Northwest National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allmaier, Guenter; Wunschel, David S.; Wahl, Karen L.

2004-04-19

This is an introduction to a special issue of the Journal of microbiological Methods based on a recent meeting held at PNNL: the 5th International Symposium on the Interface between Analytical Chemistry and Microbiology.

Conventional curing practices reduce generic Escherichia coli and Salmonella spp. on dry bulb onions produced with contaminated irrigation water.

PubMed

Emch, Alexander W; Waite-Cusic, Joy G

2016-02-01

Food Safety Modernization Act (FSMA) has emphasized microbial risks associated with irrigation water. Treasure Valley (eastern Oregon/western Idaho) has the highest yield of dry bulb onions in the country; however, their irrigation water is often non-compliant with current industry and proposed federal standards for fresh produce. Conventional curing practices may provide a mechanism to mitigate irrigation water quality to comply with FSMA regulations. Dry bulb onions were grown in Owyhee silt loam and Semiahmoo muck soils in greenhouses and irrigated with water containing a cocktail of rifampicin-resistant generic Escherichia coli and Salmonella spp. (4.80 log CFU/ml). To mimic conventional practices, mature onions remained undisturbed in soil without irrigation for 12 days prior to being lifted and cured for 16 additional days. Surviving generic E. coli and Salmonella spp. were selectively enumerated on using standard plating (Hektoen Enteric Agar with rifampicin; HE + rif) or most probable number (lactose broth with rifampicin; HE + rif) methods. Generic E. coli and Salmonella spp. on onions decreased 0.19-0.26 log CFU/g·d during the initial 12 days of finishing. At lifting, generic E. coli and Salmonella spp. had been reduced to <1 CFU/g and persisted through the end of curing. This study demonstrates conventional curing practices as an effective mitigation strategy for dry bulb onions produced with water of poor microbiological quality. Copyright © 2015 Elsevier Ltd. All rights reserved.

A comparison between effect of photodynamic therapy by LED and calcium hydroxide therapy for root canal disinfection against Enterococcus faecalis: A randomized controlled trial.

PubMed

Asnaashari, Mohammad; Ashraf, Hengameh; Rahmati, Afsaneh; Amini, Neda

2017-03-01

Insufficient root canal disinfection is one of the main reasons for persistent periapical pathology. Photodynamic therapy (PDT) has been proven effective in disinfecting infected root canals. The aim of this study was to evaluate the antimicrobial effect of photo activated disinfection (PAD) when using toluidine blue as photosensitizer and a LED lamp after the conventional treatment, and comparing it with calcium hydroxide therapy in vivo. This clinical trial includes 20 patients with molars requiring endodontic retreatment. After the conventional treatment, first microbiological samples were obtained using sterile rotary ProTaper F2 file and 3 paper points and transferred to a microbiology laboratory. Group 1 (n=10) specimens underwent PAD with photosensitizer (PS) solution (0.1mg/mL TB) and irradiation with Fotosan light emitting diode (LED) lamp (635nm, 200mW/cm2) for 60s. Creamy Ca(OH)2 paste was used in group 2 (n=10) for two weeks. A second sample was then obtained. The samples were cultured and then bacterial colonies were counted. Data included number of colony forming units (CFUs) before and after treatments, analyzed by t-test and analysis of covariance (ANCOVA) using SPSS vs.18. A significant difference between results of before and after treatment of both groups (calcium hydroxide therapy p=0.02<0.05, PAD p<0.0001) indicated the efficacy of both treatments. The mean numbers for log 10CFUs/mL before calcium hydroxide therapy and PAD with LED irradiation was 10.1968 and 11.3773. After treatment, the mean numbers were 9.4202 and 8.3772, respectively. The difference in results after treatment between groups was significant (p=0.01<0.05) and indicate that PAD was more effective. PAD and calcium hydroxide therapy, as auxiliary methods adjunct to conventional root canal therapy, are both effective in root canal disinfection. In comparison with calcium hydroxide therapy, PAD leads to a greater reduction in enterococcus faecalis number in the infected root canals. Copyright © 2016 Elsevier B.V. All rights reserved.

A validation of the Danish microbiology database (MiBa) and incidence rate of Actinotignum schaalii (Actinobaculum schaalii) bacteraemia in Denmark.

PubMed

Bank, S; Søby, K M; Kristensen, L H; Voldstedlund, M; Prag, J

2015-12-01

Actinotignum schaalii (former named Actinobaculum schaalii) can cause urinary tract infections (UTIs) and bacteraemia, mainly in the elderly. A. schaalii is difficult to identify with conventional biochemical tests, and it is often overlooked if the urine is only cultured in ambient air. The aim of this study was to validate data from the nationwide Danish microbiology database (MiBa) with data from the laboratory information system (LIS) at the local department of microbiology in Viborg-Herning, and to evaluate the incidence rate of bacteraemia caused by A. schaalii in Denmark by using data from the MiBa. All departments of microbiology in Denmark report data to the MiBa. All microbiological samples with A. schaalii in Denmark were extracted for a period of 5 years from the MiBa and from the local LISs. All data obtained from our local LIS were also found in the MiBa, except for data on real-time PCR, which were not registered, owing to missing ID codes in the MiBa. From 2010 to 2014, there was a significant increase in the incidence rate of blood cultures with A. schaalii, from 1.8 to 6.8 cases per million, which was probably due to coincident implementation of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) in routine diagnostics. We found that A. schaalii caused bacteraemia and UTIs mainly in the elderly. In conclusion, the MiBa can be a useful source of nationwide microbiological data in Denmark. Our results suggest that the incidence rate of A. schaalii as a cause of bacteraemia has been underestimated, and that culture of urine in CO2 can improve the detection of A. schaalii. Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Streptococcus pyogenes and re-emergence of scarlet fever as a public health problem.

PubMed

Wong, Samson Sy; Yuen, Kwok-Yung

2012-07-01

Explosive outbreaks of infectious diseases occasionally occur without immediately obvious epidemiological or microbiological explanations. Plague, cholera and Streptococcus pyogenes infection are some of the epidemic-prone bacterial infections. Besides epidemiological and conventional microbiological methods, the next-generation gene sequencing technology permits prompt detection of genomic and transcriptomic profiles associated with invasive phenotypes. Horizontal gene transfer due to mobile genetic elements carrying virulence factors and antimicrobial resistance, or mutations associated with the two component CovRS operon are important bacterial factors conferring survival advantage or invasiveness. The high incidence of scarlet fever in children less than 10 years old suggests that the lack of protective immunity is an important host factor. A high population density, overcrowded living environment and a low yearly rainfall are environmental factors contributing to outbreak development. Inappropriate antibiotic use is not only ineffective for treatment, but may actually drive an epidemic caused by drug-resistant strains and worsen patient outcomes by increasing the bacterial density at the site of infection and inducing toxin production. Surveillance of severe S. pyogenes infection is important because it can complicate concurrent chickenpox and influenza. Concomitant outbreaks of these two latter infections with a highly virulent and drug-resistant S. pyogenes strain can be disastrous.

Streptococcus pyogenes and re-emergence of scarlet fever as a public health problem

PubMed Central

Wong, Samson SY; Yuen, Kwok-Yung

2012-01-01

Explosive outbreaks of infectious diseases occasionally occur without immediately obvious epidemiological or microbiological explanations. Plague, cholera and Streptococcus pyogenes infection are some of the epidemic-prone bacterial infections. Besides epidemiological and conventional microbiological methods, the next-generation gene sequencing technology permits prompt detection of genomic and transcriptomic profiles associated with invasive phenotypes. Horizontal gene transfer due to mobile genetic elements carrying virulence factors and antimicrobial resistance, or mutations associated with the two component CovRS operon are important bacterial factors conferring survival advantage or invasiveness. The high incidence of scarlet fever in children less than 10 years old suggests that the lack of protective immunity is an important host factor. A high population density, overcrowded living environment and a low yearly rainfall are environmental factors contributing to outbreak development. Inappropriate antibiotic use is not only ineffective for treatment, but may actually drive an epidemic caused by drug-resistant strains and worsen patient outcomes by increasing the bacterial density at the site of infection and inducing toxin production. Surveillance of severe S. pyogenes infection is important because it can complicate concurrent chickenpox and influenza. Concomitant outbreaks of these two latter infections with a highly virulent and drug-resistant S. pyogenes strain can be disastrous. PMID:26038416

Effects of ultrasound energy density on the non-thermal pasteurization of chocolate milk beverage.

PubMed

Monteiro, Sara H M C; Silva, Eric Keven; Alvarenga, Verônica O; Moraes, Jeremias; Freitas, Mônica Q; Silva, Márcia C; Raices, Renata S L; Sant'Ana, Anderson S; Meireles, M Angela A; Cruz, Adriano G

2018-04-01

This study presents the emerging high-intensity ultrasound (HIUS) processing as a non-thermal alternative to high-temperature short-time pasteurization (HTST). Chocolate milk beverage (CMB) was subjected to different ultrasound energy densities (0.3-3.0 kJ/cm 3 ), as compared to HTST pasteurization (72 °C/15 s) aimed to verify the effect of the HIUS processing on the microbiological and physicochemical characteristics of the beverage. The application of HIUS at an energy density of 3.0 kJ/cm 3 was able to reduce 3.56 ± 0.02 logarithmic cycles in the total aerobic counts. In addition, the ultrasound energy density affected the physical properties of the beverage as the size distribution of fat globule and rheological behavior, as well as the chemical properties such as antioxidant activity, ACE inhibitory activity, fatty acid profile, and volatile profile. In general, the different energetic densities used as a non-thermal method of pasteurization of CMB were more effective when compared to the conventional pasteurization by HTST, since they improved the microbiological and physicochemical quality, besides preserving the bioactive compounds and the nutritional quality of the product. Copyright © 2017 Elsevier B.V. All rights reserved.

Exploring performance issues for a clinical database organized using an entity-attribute-value representation.

PubMed

Chen, R S; Nadkarni, P; Marenco, L; Levin, F; Erdos, J; Miller, P L

2000-01-01

The entity-attribute-value representation with classes and relationships (EAV/CR) provides a flexible and simple database schema to store heterogeneous biomedical data. In certain circumstances, however, the EAV/CR model is known to retrieve data less efficiently than conventionally based database schemas. To perform a pilot study that systematically quantifies performance differences for database queries directed at real-world microbiology data modeled with EAV/CR and conventional representations, and to explore the relative merits of different EAV/CR query implementation strategies. Clinical microbiology data obtained over a ten-year period were stored using both database models. Query execution times were compared for four clinically oriented attribute-centered and entity-centered queries operating under varying conditions of database size and system memory. The performance characteristics of three different EAV/CR query strategies were also examined. Performance was similar for entity-centered queries in the two database models. Performance in the EAV/CR model was approximately three to five times less efficient than its conventional counterpart for attribute-centered queries. The differences in query efficiency became slightly greater as database size increased, although they were reduced with the addition of system memory. The authors found that EAV/CR queries formulated using multiple, simple SQL statements executed in batch were more efficient than single, large SQL statements. This paper describes a pilot project to explore issues in and compare query performance for EAV/CR and conventional database representations. Although attribute-centered queries were less efficient in the EAV/CR model, these inefficiencies may be addressable, at least in part, by the use of more powerful hardware or more memory, or both.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Britton, L.J.; Greeson, P.E.

1989-01-01

The series of chapters on techniques describes methods used by the U.S. Geological Survey for planning and conducting water-resources investigations. The material is arranged under major subject headings called books and is further subdivided into sections and chapters. Book 5 is on laboratory analysis. Section A is on water. The unit of publication, the chapter, is limited to a narrow field of subject matter. "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" is the fourth chapter to be published under Section A of Book 5. The chapter number includes the letter of the section.This chapter was prepared by several aquatic biologists and microbiologists of the U.S. Geological Survey to provide accurate and precise methods for the collection and analysis of aquatic biological and microbiological samples.Use of brand, firm, and trade names in this chapter is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey.This chapter supersedes "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" edited by P.E. Greeson, T.A. Ehlke, G.A. Irwin, B.W. Lium, and K.V. Slack (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4, 1977) and also supersedes "A Supplement to-Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" by P.E. Greeson (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4), Open-File Report 79-1279, 1979.

Detection of Pneumonia Associated Pathogens Using a Prototype Multiplexed Pneumonia Test in Hospitalized Patients with Severe Pneumonia

PubMed Central

Schulte, Berit; Eickmeyer, Holm; Heininger, Alexandra; Juretzek, Stephanie; Karrasch, Matthias; Denis, Olivier; Roisin, Sandrine; Pletz, Mathias W.; Klein, Matthias; Barth, Sandra; Lüdke, Gerd H.; Thews, Anne; Torres, Antoni; Cillóniz, Catia; Straube, Eberhard; Autenrieth, Ingo B.; Keller, Peter M.

2014-01-01

Severe pneumonia remains an important cause of morbidity and mortality. Polymerase chain reaction (PCR) has been shown to be more sensitive than current standard microbiological methods – particularly in patients with prior antibiotic treatment – and therefore, may improve the accuracy of microbiological diagnosis for hospitalized patients with pneumonia. Conventional detection techniques and multiplex PCR for 14 typical bacterial pneumonia-associated pathogens were performed on respiratory samples collected from adult hospitalized patients enrolled in a prospective multi-center study. Patients were enrolled from March until September 2012. A total of 739 fresh, native samples were eligible for analysis, of which 75 were sputa, 421 aspirates, and 234 bronchial lavages. 276 pathogens were detected by microbiology for which a valid PCR result was generated (positive or negative detection result by Curetis prototype system). Among these, 120 were identified by the prototype assay, 50 pathogens were not detected. Overall performance of the prototype for pathogen identification was 70.6% sensitivity (95% confidence interval (CI) lower bound: 63.3%, upper bound: 76.9%) and 95.2% specificity (95% CI lower bound: 94.6%, upper bound: 95.7%). Based on the study results, device cut-off settings were adjusted for future series production. The overall performance with the settings of the CE series production devices was 78.7% sensitivity (95% CI lower bound: 72.1%) and 96.6% specificity (95% CI lower bound: 96.1%). Time to result was 5.2 hours (median) for the prototype test and 43.5 h for standard-of-care. The Pneumonia Application provides a rapid and moderately sensitive assay for the detection of pneumonia-causing pathogens with minimal hands-on time. Trial Registration Deutsches Register Klinischer Studien (DRKS) DRKS00005684 PMID:25397673

High-performance liquid chromatographic method for potency determination of amoxicillin in commercial preparations and for stability studies.

PubMed Central

Hsu, M C; Hsu, P W

1992-01-01

A reversed-phase column liquid chromatographic method was developed for the assay of amoxicillin and its preparations. The linear calibration range was 0.2 to 2.0 mg/ml (r = 0.9998), and recoveries were generally greater than 99%. The high-performance liquid chromatographic assay results were compared with those obtained from a microbiological assay of bulk drug substance and capsule, injection, and granule formulations containing amoxicillin and degraded amoxicillin. At the 99% confidence level, no significant intermethod differences were noted for the paired results. Commercial formulations were also analyzed, and the results obtained by the proposed method closely agreed with those found by the microbiological method. The results indicated that the proposed method is a suitable substitute for the microbiological method for assays and stability studies of amoxicillin preparations. PMID:1416827

Vitamin B12 assays compared by use of patients sera with low vitamin B12 content

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheridan, B.L.; Pearce, L.C.

1985-05-01

The authors compared four radioisotope dilution (RD) methods and a microbiological assay for measuring concentrations of vitamin B12 in a selected panel of serum samples from patients known to be deficient in the vitamin. Low (less than 100 ng/L) and borderline (100-180 ng/L) results were similar between methods, but use of the manufacturers recommended ranges for borderline results would have changed the diagnostic classifications for 22 of 38 samples. Results of all the RD methods inter-correlated well, but less so with the microbiological assay. Borderline, nondiagnostic results were common to all methods, and no apparent advantage was gained from usingmore » the microbiological assay.« less

Molecular diagnostic methods for invasive fungal disease: the horizon draws nearer?

PubMed

Halliday, C L; Kidd, S E; Sorrell, T C; Chen, S C-A

2015-04-01

Rapid, accurate diagnostic laboratory tests are needed to improve clinical outcomes of invasive fungal disease (IFD). Traditional direct microscopy, culture and histological techniques constitute the 'gold standard' against which newer tests are judged. Molecular diagnostic methods, whether broad-range or fungal-specific, have great potential to enhance sensitivity and speed of IFD diagnosis, but have varying specificities. The use of PCR-based assays, DNA sequencing, and other molecular methods including those incorporating proteomic approaches such as matrix-assisted laser desorption ionisation-time of flight mass spectroscopy (MALDI-TOF MS) have shown promising results. These are used mainly to complement conventional methods since they require standardisation before widespread implementation can be recommended. None are incorporated into diagnostic criteria for defining IFD. Commercial assays may assist standardisation. This review provides an update of molecular-based diagnostic approaches applicable to biological specimens and fungal cultures in microbiology laboratories. We focus on the most common pathogens, Candida and Aspergillus, and the mucormycetes. The position of molecular-based approaches in the detection of azole and echinocandin antifungal resistance is also discussed.

[Etiologic diagnosis in meningitis and encephalitis molecular biology techniques].

PubMed

Conca, Natalia; Santolaya, María Elena; Farfan, Mauricio J; Cofré, Fernanda; Vergara, Alejandra; Salazar, Liliana; Torres, Juan Pablo

2016-01-01

The aetiological study of infections of the central nervous system has traditionally been performed using bacterial cultures and, more recently, using polymerase chain reaction (PCR) for herpes simplex virus (HSV). Bacterial cultures may not have good performance, especially in the context of patients who have received antibiotics prior to sampling, and a request for HSV only by PCR reduces the information to only one aetiological agent. The aim of this study is to determine the infectious causes of meningitis and encephalitis, using traditional microbiology and molecular biology to improve the aetiological diagnosis of these diseases. A prospective study was conducted on 19 patients with suspected meningitis, admitted to the Luis Calvo Mackenna Hospital in Santiago, Chile, from March 1, 2011 to March 30, 2012. After obtaining informed consent, the CSF samples underwent cytochemical study, conventional culture, multiplex PCR for the major producing bacterial meningitis (N. meningitidis, S. pneumoniae, H. influenzae), real-time single PCR for HSV-1 and 2, VZV, EBV, CMV, HHV-6 and enterovirus. Clinical and epidemiological data were also collected from the clinical records. Of the 19 patients analysed, 2 were diagnosed by conventional methods and 7 by adding molecular biology (increase to 37%). Three patients had meningitis due to S. pneumoniae, one due to Enterobacter cloacae, 2 patients meningoencephalitis HSV-1, and one VZV meningitis. The addition of PCR to conventional diagnostic methods in CNS infections increases the probability of finding the causal agent. This allows a more adequate, timely and rational management of the disease. Copyright © 2014. Publicado por Elsevier España, S.L.U.

Experiments with Writing to Teach Microbiology.

ERIC Educational Resources Information Center

Cannon, Robert E.

1990-01-01

Described are the experiences of one teacher with the teaching of writing in college level microbiology, virology, and immunology courses. Assignments, methods, evaluation, and student responses are discussed. (CW)

Assessment of the microbiological safety of dried spices and herbs commercialized in Spain.

PubMed

Sospedra, Isabel; Soriano, Jose M; Mañes, Jordi

2010-12-01

Spices and herbs are natural products or their blends that must be free of extraneous matter content. Conventional production of these products implicates a number of hygienic problems so spices and herbs may be exposed to a wide range of microbial contamination during pre- and post-harvest and they can present high microbial counts. In this study, we have analyzed the microbial quality of 53 samples of spices and dry herbs collected from Spanish markets detecting a contamination of samples of spices with mesophilic aerobic counts (10%) and Enterobacteriaceae (20%). The analysis from herbs showed that the percentage of contamination was 26% in both microbiological values. Pathogenic microorganisms like Staphylococcus aureus, Yersinia intermedia, Shigella spp., Enterobacter spp., Acinetobacter calcoaceticus and Hafni alvei were also isolated from spices and herbs. These unsatisfactory results showed a poor microbiological quality. Spices and dry herbs are used as ingredients in a variety of products prepared in different ways, this fact suggests the need to provide a control system to improve the quality of herbs and spices.

The periodontal abscess (I). Clinical and microbiological findings.

PubMed

Herrera, D; Roldán, S; González, I; Sanz, M

2000-06-01

Little information is available regarding the diagnosis and microbiology of periodontal abscesses. The aim of this descriptive clinical and microbiological study was to provide more information in order to help in the characterisation of the periodontal abscess associated to periodontitis. 29 consecutive patients with a periodontal abscess were studied by the assessment of clinical variables, including both subjective (pain, edema, redness and swelling) and objective (bleeding on probing, suppuration, probing pocket depth, tooth mobility and cervical lymphadenopathy) parameters. Microbiological samples were taken for anaerobic microbiology and processed by means of culture. Systemic involvement was also studied through the analysis of blood and urine samples using conventional laboratory standards. 62% of the abscesses affected untreated periodontitis patients, and 69% were associated with a molar tooth. More than 75% of the abscesses had moderate-severe scores related to edema, redness and swelling, and 90% of the patients reported pain. Bleeding occurred in all abscesses, while suppuration on sampling was detected in 66%. Mean associated pocket depth was 7.28 mm, and 79% of teeth presented some degree of mobility. Cervical lymphadenopathy was seen in 10% of patients, while elevated leucocyte counts were observed in 31.6%. The absolute number of neutrophils was elevated in 42% of the patients. High prevalences of putative periodontal pathogens were found, including Fusobacterium nucleatum, Peptostreptococcus micros, Porphyromonas gingivalis, Prevotella intermedia and Bacteroides forsythus. The periodontal abscess has clear clinical characteristics and is usually associated with severe periodontal destruction. This condition may cause systemic involvement and the lesion generally has a large bacterial mass with a high prevalence of well-recognised periodontal pathogens.

Microbiological Sampling Methods and Sanitation of Edible Plants Grown on ISS

NASA Technical Reports Server (NTRS)

Parrish, Charles H. II; Khodadad, Christina L.; Garland, Nathaniel T.; Larson, Brian D.; Hummreick, Mary E.

2013-01-01

Pathogenic microbes on the surfaces of salad crops and growth chambers pose a threat to the health of crew on International Space Station. For astronauts to safely consume spacegrown vegetables produced in NASA's new vegetable production unit, VEGGIE, three technical challenges must be overcome: real-time sampling, microbiological analysis, and sanitation. Raphanus sativus cultivar Cherry Bomb II and Latuca sativa cultivar Outredgeous, two saled crops to be grown in VEGGIE, were inoculated with Salmonella enterica serovar Typhimurium (S. Typhimurium), a bacterium known to cause food-borne illness Tape- and swab-based sampling techniques were optimized for use in microgravity and assessed for effectiveness in recovery of bacteria from crop surfaces: Rapid pathogen detection and molecular analyses were performed via quantitative real-time polymerase chain reactiop using LightCycler® 480 and RAZOR® EX, a scaled-down instrument that is undergoing evaluation and testing for future flight hardware. These methods were compared with conventional, culture-based methods for the recovery of S. Typhimurium colonies. A sterile wipe saturated with a citric acid-based, food-grade sanitizer was applied to two different surface materials used in VEGGIE flight hardware that had been contaminated with the bacterium Pseudomonas aeruginosa,. another known human pathogen. To sanitize surfaces, wipes were saturated with either the sanitizer or sterile deionized water and applied to each surface. Colony forming units of P. aeruginosa grown on tryptic soy agar plates were enumerated from surface samples after sanitization treatments. Depending on the VEGGIE hardware material, 2- to 4.5-log10 reductions in colony-forming units were observed after sanitization. The difference in recovery of S. Typhimurium between tape- and swab- based sampling techniques was insignificant. RAZOR® EX rapidly detected S. Typhimurium present in both raw culture and extracted DNA samples.

Field Application of the Micro Biological Survey Method for a Simple and Effective Assessment of the Microbiological Quality of Water Sources in Developing Countries

PubMed Central

Arienzo, Alyexandra; Sobze, Martin Sanou; Wadoum, Raoul Emeric Guetiya; Losito, Francesca; Colizzi, Vittorio; Antonini, Giovanni

2015-01-01

According to the World Health Organization (WHO) guidelines, “safe drinking-water must not represent any significant risk to health over a lifetime of consumption, including different sensitivities that may occur between life stages”. Traditional methods of water analysis are usually complex, time consuming and require an appropriately equipped laboratory, specialized personnel and expensive instrumentation. The aim of this work was to apply an alternative method, the Micro Biological Survey (MBS), to analyse for contaminants in drinking water. Preliminary experiments were carried out to demonstrate the linearity and accuracy of the MBS method and to verify the possibility of using the evaluation of total coliforms in 1 mL of water as a sufficient parameter to roughly though accurately determine water microbiological quality. The MBS method was then tested “on field” to assess the microbiological quality of water sources in the city of Douala (Cameroon, Central Africa). Analyses were performed on both dug and drilled wells in different periods of the year. Results confirm that the MBS method appears to be a valid and accurate method to evaluate the microbiological quality of many water sources and it can be of valuable aid in developing countries. PMID:26308038

Microbiological water methods: quality control measures for Federal Clean Water Act and Safe Drinking Water Act regulatory compliance.

PubMed

Root, Patsy; Hunt, Margo; Fjeld, Karla; Kundrat, Laurie

2014-01-01

Quality assurance (QA) and quality control (QC) data are required in order to have confidence in the results from analytical tests and the equipment used to produce those results. Some AOAC water methods include specific QA/QC procedures, frequencies, and acceptance criteria, but these are considered to be the minimum controls needed to perform a microbiological method successfully. Some regulatory programs, such as those at Code of Federal Regulations (CFR), Title 40, Part 136.7 for chemistry methods, require additional QA/QC measures beyond those listed in the method, which can also apply to microbiological methods. Essential QA/QC measures include sterility checks, reagent specificity and sensitivity checks, assessment of each analyst's capabilities, analysis of blind check samples, and evaluation of the presence of laboratory contamination and instrument calibration and checks. The details of these procedures, their performance frequency, and expected results are set out in this report as they apply to microbiological methods. The specific regulatory requirements of CFR Title 40 Part 136.7 for the Clean Water Act, the laboratory certification requirements of CFR Title 40 Part 141 for the Safe Drinking Water Act, and the International Organization for Standardization 17025 accreditation requirements under The NELAC Institute are also discussed.

Field Application of the Micro Biological Survey Method for a Simple and Effective Assessment of the Microbiological Quality of Water Sources in Developing Countries.

PubMed

Arienzo, Alyexandra; Sobze, Martin Sanou; Wadoum, Raoul Emeric Guetiya; Losito, Francesca; Colizzi, Vittorio; Antonini, Giovanni

2015-08-25

According to the World Health Organization (WHO) guidelines, "safe drinking-water must not represent any significant risk to health over a lifetime of consumption, including different sensitivities that may occur between life stages". Traditional methods of water analysis are usually complex, time consuming and require an appropriately equipped laboratory, specialized personnel and expensive instrumentation. The aim of this work was to apply an alternative method, the Micro Biological Survey (MBS), to analyse for contaminants in drinking water. Preliminary experiments were carried out to demonstrate the linearity and accuracy of the MBS method and to verify the possibility of using the evaluation of total coliforms in 1 mL of water as a sufficient parameter to roughly though accurately determine water microbiological quality. The MBS method was then tested "on field" to assess the microbiological quality of water sources in the city of Douala (Cameroon, Central Africa). Analyses were performed on both dug and drilled wells in different periods of the year. Results confirm that the MBS method appears to be a valid and accurate method to evaluate the microbiological quality of many water sources and it can be of valuable aid in developing countries.

Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

PubMed

Gunar, O V; Sakhno, N G

2015-12-30

The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods. Copyright © 2015 Elsevier B.V. All rights reserved.

Er:YAG laser in the treatment of periodontal sites with recurring chronic inflammation: a 12-month randomized, controlled clinical trial.

PubMed

Krohn-Dale, Ivar; Bøe, Olav E; Enersen, Morten; Leknes, Knut N

2012-08-01

The objective of this randomized, controlled clinical trial was to compare the clinical and microbiological effects of pocket debridement using erbium-doped: yttrium, aluminium and garnet (Er:YAG) laser with conventional debridement in maintenance patients. Fifteen patients, all smokers, having at least four teeth with residual probing depth (PD) ≥ 5 mm were recruited. Two pockets in two jaw quadrants were randomly assigned to subgingival debridement using an Er:YAG laser (test) or ultrasonic scaler/curette (control) at 3-month intervals. Relative attachment level (RAL), PD, bleeding on probing and dental plaque were recorded at baseline and at 6 and 12 months. Microbiological subgingival samples were taken at the same time points and analysed using a checkerboard DNA-DNA hybridization technique. A significant decrease in PD took place in both treatments from baseline to 12 months (p < 0.01). In the control, the mean initial PD decreased from 5.4 to 4.0 mm at 12 months. For the test, a similar decrease occurred. No significant between-treatment differences were shown at any time point. The mean RAL showed no overall significant inter- or intra-treatment differences (p > 0.05). No significant between-treatment differences were observed in subgingival microbiological composition or total pathogens. The results failed to support that an Er:YAG laser may be superior to conventional debridement in the treatment of smokers with recurring chronic inflammation. This appears to be the first time that repeated Er-YAG laser instrumentation has been compared with mechanical instrumentation of periodontal sites with recurring chronic inflammation over a clinically relevant time period. © 2012 John Wiley & Sons A/S.

Optimising the diagnostic strategy for onychomycosis from sample collection to FUNGAL identification evaluation of a diagnostic kit for real-time PCR.

PubMed

Petinataud, Dimitri; Berger, Sibel; Ferdynus, Cyril; Debourgogne, Anne; Contet-Audonneau, Nelly; Machouart, Marie

2016-05-01

Onychomycosis is a common nail disorder mainly due to dermatophytes for which the conventional diagnosis requires direct microscopic observation and culture of a biological sample. Nevertheless, antifungal treatments are commonly prescribed without a mycological examination having been performed, partly because of the slow growth of dermatophytes. Therefore, molecular biology has been applied to this pathology, to support a quick and accurate distinction between onychomycosis and other nail damage. Commercial kits are now available from several companies for improving traditional microbiological diagnosis. In this paper, we present the first evaluation of the real-time PCR kit marketed by Bio Evolution for the diagnosis of dermatophytosis. Secondly, we compare the efficacy of the kit on optimal and non-optimal samples. This study was conducted on 180 nails samples, processed by conventional methods and retrospectively analysed using this kit. According to our results, this molecular kit has shown high specificity and sensitivity in detecting dermatophytes, regardless of sample quality. On the other hand, and as expected, optimal samples allowed the identification of a higher number of dermatophytes by conventional mycological diagnosis, compared to non-optimal samples. Finally, we have suggested several strategies for the practical use of such a kit in a medical laboratory for quick pathogen detection. © 2016 Blackwell Verlag GmbH.

Effect of Oregano Essential Oil and Aqueous Oregano Infusion Application on Microbiological Properties of Samarella (Tsamarella), a Traditional Meat Product of Cyprus.

PubMed

Ulusoy, Beyza; Hecer, Canan; Kaynarca, Doruk; Berkan, Şifa

2018-03-21

Different types of dried meat products manufactured by different drying and curing methods are very common and well-known with a long history all over the world. Samarella (tsamarella) is one of these products and is famous among traditionally produced meat products in Cypriot gastronomy. The aim of this study was to investigate the effect of oregano essential oil (OEO) and aqueous oregano infusion (AOI) applications on the microbiological properties of samarella. In order to carry out this study, traditional methods were followed for experimental production of samarella. As a result of this study, five percent OEO application was found to be more effective to reduce microbiological counts but this ratio of OEO application was not accepted by panelists. According to all microbiological results correlated with the sensorial scores, it is concluded that one percent OEO application can be used for samarella production as an alternative preservative method.

Effect of Oregano Essential Oil and Aqueous Oregano Infusion Application on Microbiological Properties of Samarella (Tsamarella), a Traditional Meat Product of Cyprus

PubMed Central

Hecer, Canan; Kaynarca, Doruk; Berkan, Şifa

2018-01-01

Different types of dried meat products manufactured by different drying and curing methods are very common and well-known with a long history all over the world. Samarella (tsamarella) is one of these products and is famous among traditionally produced meat products in Cypriot gastronomy. The aim of this study was to investigate the effect of oregano essential oil (OEO) and aqueous oregano infusion (AOI) applications on the microbiological properties of samarella. In order to carry out this study, traditional methods were followed for experimental production of samarella. As a result of this study, five percent OEO application was found to be more effective to reduce microbiological counts but this ratio of OEO application was not accepted by panelists. According to all microbiological results correlated with the sensorial scores, it is concluded that one percent OEO application can be used for samarella production as an alternative preservative method. PMID:29561804

Experimental methods for studying microbial survival in extraterrestrial environments.

PubMed

Olsson-Francis, Karen; Cockell, Charles S

2010-01-01

Microorganisms can be used as model systems for studying biological responses to extraterrestrial conditions; however, the methods for studying their response are extremely challenging. Since the first high altitude microbiological experiment in 1935 a large number of facilities have been developed for short- and long-term microbial exposure experiments. Examples are the BIOPAN facility, used for short-term exposure, and the EXPOSE facility aboard the International Space Station, used for long-term exposure. Furthermore, simulation facilities have been developed to conduct microbiological experiments in the laboratory environment. A large number of microorganisms have been used for exposure experiments; these include pure cultures and microbial communities. Analyses of these experiments have involved both culture-dependent and independent methods. This review highlights and discusses the facilities available for microbiology experiments, both in space and in simulation environments. A description of the microorganisms and the techniques used to analyse survival is included. Finally we discuss the implications of microbiological studies for future missions and for space applications. Copyright 2009 Elsevier B.V. All rights reserved.

Broad-Range Detection of Microorganisms Directly from Bronchoalveolar Lavage Specimens by PCR/Electrospray Ionization-Mass Spectrometry

PubMed Central

Ullberg, Måns; Lüthje, Petra; Mölling, Paula; Strålin, Kristoffer

2017-01-01

The clinical demand on rapid microbiological diagnostic is constantly increasing. PCR coupled to electrospray ionization-mass spectrometry, PCR/ESI-MS, offers detection and identification of over 750 bacteria and Candida species directly from clinical specimens within 6 hours. In this study, we investigated the clinical performance of the IRIDICA BAC LRT Assay for detection of bacterial pathogens in 121 bronchoalveolar lavage (BAL) samples that were received consecutively at our bacterial laboratory for BAL culture. Commensal or pathogenic microorganisms were detected in 118/121 (98%) BAL samples by PCR/ESI-MS, while in 104/121 (86%) samples by routine culture (P<0.01). Detection of potentially pathogenic microorganisms by PCR/ESI-MS was evaluated in comparison with conventional culture-based or molecular methods. The agreement between positive findings was overall good. Most Staphylococcus aureus-positive PCR/ESI-MS results were confirmed by culture or species-specific PCR (27/33, 82%). The identity of Streptococcus pneumoniae could however be confirmed for only 6/17 (35%) PCR/ESI-MS-positive samples. Non-cultivable and fastidious pathogens, which were not covered by standard culture procedures were readily detected by PCR/ESI-MS, including Legionella pneumophila, Bordetella pertussis, Norcadia species and Mycoplasma pneumoniae. In conclusion, PCR/ESI-MS detected a broad range of potential pathogens with equal or superior sensitivity compared to conventional methods within few hours directly from BAL samples. This novel method might thus provide a relevant tool for diagnostics in critically ill patients. PMID:28085931

Response to the Questions Posed by the Food Safety and Inspection Service Regarding Determination of the Most Appropriate Technologies to Adopt for FSIS Routine and Baseline Microbiological Analysis

USDA-ARS?s Scientific Manuscript database

The National Advisory Committee on Microbiological Criteria for Foods (NACMCF) should provide guidance to assist with the United States Department of Agriculture, Food Safety and Inspection Service (USDA/FSIS) Agency’s goal of moving into the next generation of microbiological testing methods. To do...

A rapid detection method of Escherichia coli by surface enhanced Raman scattering

NASA Astrophysics Data System (ADS)

Tao, Feifei; Peng, Yankun; Xu, Tianfeng

2015-05-01

Conventional microbiological detection and enumeration methods are time-consuming, labor-intensive, and giving retrospective information. The objectives of the present work are to study the capability of surface enhanced Raman scattering (SERS) to detect Escherichia coli (E. coli) using the presented silver colloidal substrate. The obtained results showed that the adaptive iteratively reweighed Penalized Least Squares (airPLS) algorithm could effectively remove the fluorescent background from original Raman spectra, and Raman characteristic peaks of 558, 682, 726, 1128, 1210 and 1328 cm-1 could be observed stably in the baseline corrected SERS spectra of all studied bacterial concentrations. The detection limit of SERS could be determined to be as low as 0.73 log CFU/ml for E. coli with the prepared silver colloidal substrate. The quantitative prediction results using the intensity values of characteristic peaks were not good, with the correlation coefficients of calibration set and cross validation set of 0.99 and 0.64, respectively.

Culture-independent Profiling of the Fecal Microbiome to Identify Microbial Species Associated with a Diarrheal Outbreak in Immunocompromised Mice.

PubMed

Misic, Ana M; Miedel, Emily L; Brice, Angela K; Cole, Stephen; Zhang, Grace F; Dyer, Cecilia D; Secreto, Anthony; Smith, Abigail L; Danet-Desnoyers, Gwenn; Beiting, Daniel P

2018-06-13

Immunocompromised mice are used frequently in biomedical research, in part because they accommodate the engraftmentandstudy of primary human cells within a mouse model; however, these animals are susceptible to opportunistic infectionsand require special husbandry considerations. In 2015, an outbreak marked by high morbidity but low mortality swept througha colony of immunocompromised mice; this outbreak rapidly affected 75% of the colony and ultimately required completedepopulation of the barrier suite. Conventional microbiologic and molecular diagnostics were unsuccessful in determiningthe cause; therefore, we explored culture-independent methods to broadly profile the microbial community in the feces of affected animals. This approach identified 4 bacterial taxa-Candidatus Arthromitus, Clostridium celatum, Clostridiales bacterium VE202-01, and Bifidobacterium pseudolongum strain PV8-2- that were significantly enriched in the affected mice. Based on these results, specific changes were made to the animal husbandry procedures for immunocompromised mice. This case report highlights the utility of culture-independent methods in laboratory animal diagnostics.

[Evaluation of mass spectrometry: MALDI-TOF MS for fast and reliable yeast identification].

PubMed

Relloso, María S; Nievas, Jimena; Fares Taie, Santiago; Farquharson, Victoria; Mujica, María T; Romano, Vanesa; Zarate, Mariela S; Smayevsky, Jorgelina

2015-01-01

The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technique known as MALDI-TOF MS is a tool used for the identification of clinical pathogens by generating a protein spectrum that is unique for a given species. In this study we assessed the identification of clinical yeast isolates by MALDI-TOF MS in a university hospital from Argentina and compared two procedures for protein extraction: a rapid method and a procedure based on the manufacturer's recommendations. A short protein extraction procedure was applied in 100 isolates and the rate of correct identification at genus and species level was 98.0%. In addition, we analyzed 201 isolates, previously identified by conventional methods, using the methodology recommended by the manufacturer and there was 95.38% coincidence in the identification at species level. MALDI TOF MS showed to be a fast, simple and reliable tool for yeast identification. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Microscopic quantification of bacterial invasion by a novel antibody-independent staining method.

PubMed

Agerer, Franziska; Waeckerle, Stephanie; Hauck, Christof R

2004-10-01

Microscopic discrimination between extracellular and invasive, intracellular bacteria is a valuable technique in microbiology and immunology. We describe a novel fluorescence staining protocol, called FITC-biotin-avidin (FBA) staining, which allows the differentiation between extracellular and intracellular bacteria and is independent of specific antibodies directed against the microorganisms. FBA staining of eukaryotic cells infected with Gram-negative bacteria of the genus Neisseria or the Gram-positive pathogen Staphylococcus aureus are employed to validate the novel technique. The quantitative evaluation of intracellular pathogens by the FBA staining protocol yields identical results compared to parallel samples stained with conventional, antibody-dependent methods. FBA staining eliminates the need for cell permeabilization resulting in robust and rapid detection of invasive microbes. Taken together, FBA staining provides a reliable and convenient alternative for the differential detection of intracellular and extracellular bacteria and should be a valuable technical tool for the quantitative analysis of the invasive properties of pathogenic bacteria and other microorganisms.

[Methods of identification and assessment of safety of genetically modified microorganisms in manufacture food production].

PubMed

Khovaev, A A; Nesterenko, L N; Naroditskiĭ, B S

2011-01-01

Methods of identification of genetically modified microorganisms (GMM), used in manufacture food on control probes are presented. Results of microbiological and molecular and genetic analyses of food products and their components important in microbiological and genetic expert examination of GMM in foods are considered. Examination of biosafety of GMM are indicated.

Microbiological safety of commercial prime rib preparation methods: thermal inactivation of Salmonella spp. in mechanically tenderized beef roasts

USDA-ARS?s Scientific Manuscript database

A survey of food service operations in a medium-size Midwestern city was conducted to evaluate the microbiological safety of prime rib preparation methods relative to survival of Salmonella spp. in both intact and tenderized (non-intact) product. All six restaurants visited seared rib eye roasts (ai...

Recent development in the application of alternative sterilization technologies to prepared dishes: A review.

PubMed

Huang, Mengsha; Zhang, Min; Bhandari, Bhesh

2018-01-23

Sterilization is one of the most effective food preservation methods. Conventional thermal sterilization commonly used in food industry usually causes the deterioration of food quality. Flavor, aroma, and texture, among other attributes, are significantly affected by thermal sterilization. However, demands of consumers for nutritious and safe dishes with a minimum change in their original textural and sensory properties are growing rapidly. In order to meet these demands, new approaches have been explored in the last few years to extend the shelf-life of dishes. This review discusses advantages and disadvantages of currently available physical sterilization technologies, including irradiation (eg. Gamma rays, X-rays, e-beams), microwave and radio frequency when used in prepared dishes. The preservation effect of these technologies on prepared dishes are normally evaluated by microbiological and sensory analyses.

Clinical and microbiological characteristics of Rhodotorula mucilaginosa infections in a tertiary-care facility.

PubMed

Capoor, M R; Aggarwal, S; Raghvan, C; Gupta, D K; Jain, A K; Chaudhary, R

2014-01-01

Rhodotorula spp. are an emergent opportunistic pathogen, particularly in immunocompromised individuals. The aim of the study was to review reported cases of Rhodotorula infection over a period of 9 years to determine epidemiology, risk factors, treatment and outcome. The Rhodotorula spp. were isolated from cerebrospinal fluid (9) and blood (5). The most common pre-disposing factors were prolonged hospital stay (>1 month) and prolonged usage of broad-spectrum antibiotics (>1 month). All the isolates were identified as R. mucilaginosa by conventional methods. Amphotericin B demonstrated lowest minimum inhibitory concentration (MIC) as compared with other anti-fungal agents (fluconazole, itraconazole and voriconazole). The recognition of unusual yeasts as an agent of life-threatening infection and their intrinsic resistance increases the burden on the mycology laboratory for complete species identification and to determine minimum inhibitory concentration.

Comparative study between the effects of photodynamic therapy and conventional therapy on microbial reduction in ligature-induced peri-implantitis in dogs.

PubMed

Hayek, Ricardo R A; Araújo, Ney S; Gioso, Marco A; Ferreira, Jonathan; Baptista-Sobrinho, Carlos A; Yamada, Aécio M; Ribeiro, Martha S

2005-08-01

Progressive peri-implant bone losses, which are accompanied by inflammatory lesions in the soft tissues, are referred to as peri-implantitis. The aim of this study was to compare the effects of photodynamic therapy (PDT) and conventional technique on microbial reduction in ligature-induced peri-implantitis in dogs. Eighteen third premolars from nine Labrador retriever dogs were extracted and the implants were submerged. After osseointegration, peri-implantitis was induced. After 4 months, ligature was removed and natural bacterial plaque was allowed to form for another 4 months. The animals were then randomly divided into two groups. In the conventional group, they were treated using mucoperiosteal flaps for scaling the implant surface and chlorexidine (conventional) irrigation. In the PDT group, only mucoperiosteal scaling was carried out before photodynamic therapy. Inside the peri-implant pocket, a paste-based azulene photosensitizer was placed and then a GaAlAs low-power laser (lambda=660 nm, P=40 mW, E=7.2 J for 3 minutes) was used. Microbiological samples were obtained before and immediately after treatment. Before treatment, one implant was removed and analyzed by scanning electron microscopy to validate the contamination. The results of this study showed that Prevotella sp., Fusobacterium sp., and S. Beta-haemolyticus were significantly reduced for both groups. After treatment, no significant differences were observed between the groups. These findings suggest that photodynamic therapy is a non-invasive method that could be used to reduce microorganisms in peri-implantitis. J Periodontol 2005;76:1275-1281.

Infrared Drying as a Potential Alternative to Convective Drying for Biltong Production.

PubMed

Cherono, Kipchumba; Mwithiga, Gikuru; Schmidt, Stefan

2016-06-03

Two infrared systems set at an intensity of 4777 W/m 2 with peak emission wavelengths of 2.5 and 3.5 µm were used to produce biltong by drying differently pre-treated meat. In addition to meat texture and colour, the microbial quality of the biltong produced was assessed by quantifying viable heterotrophic microorganisms using a most probable number (MPN) method and by verifying the presence of presumptive Escherichia coli in samples produced using infrared and conventional convective drying. The two infrared drying systems reduced the heterotrophic microbial burden from 5.11 log 10 MPN/g to 2.89 log 10 MPN/g (2.5 µm) and 3.42 log 10 MPN/g (3.5 µm), respectively. The infrared systems achieved an up to one log higher MPN/g reduction than the convective system. In biltong samples produced by short wavelength (2.5 µm) infrared drying, E. coli was not detectable. This study demonstrates that the use of short wavelength infrared drying is a potential alternative to conventional convective drying by improving the microbiological quality of biltong products while at the same time delivering products of satisfactory quality.

Bacillus “next generation” diagnostics: moving from detection toward subtyping and risk-related strain profiling

PubMed Central

Ehling-Schulz, Monika; Messelhäusser, Ute

2013-01-01

The highly heterogeneous genus Bacillus comprises the largest species group of endospore forming bacteria. Because of their ubiquitous nature, Bacillus spores can enter food production at several stages resulting in significant economic losses and posing a potential risk to consumers due the capacity of certain Bacillus strains for toxin production. In the past, food microbiological diagnostics was focused on the determination of species using conventional culture-based methods, which are still widely used. However, due to the extreme intra-species diversity found in the genus Bacillus, DNA-based identification and typing methods are gaining increasing importance in routine diagnostics. Several studies showed that certain characteristics are rather strain-dependent than species-specific. Therefore, the challenge for current and future Bacillus diagnostics is not only the efficient and accurate identification on species level but also the development of rapid methods to identify strains with specific characteristics (such as stress resistance or spoilage potential), trace contamination sources, and last but not least discriminate potential hazardous strains from non-toxic strains. PMID:23440299

High-pressure liquid chromatography analysis of antibiotic susceptibility disks.

PubMed Central

Hagel, R B; Waysek, E H; Cort, W M

1979-01-01

The analysis of antibiotic susceptibility disks by high-pressure liquid chromatography (HPLC) was investigated. Methods are presented for the potency determination of mecillinam, ampicillin, carbenicillin, and cephalothin alone and in various combinations. Good agreement between HPLC and microbiological data is observed for potency determinations with recoveries of greater than 95%. Relative standard deviations of lower than 2% are recorded for each HPLC method. HPLC methods offer improved accuracy and greater precision when compared to the standard microbiological methods of analysis for susceptibility disks. PMID:507793

The advantages of the application of amnion membrane in the treatment of burns.

PubMed

Andonovska, D; Dzokic, Gj; Spasevska, L; Trajkovska, T; Popovska, K; Todorov, I; Petrovski, P; Kondov, G; Sapova, B; Marcikic, G; Atanasova, E; Obocki, E; Ugrinovska, J; Andonovski, D; Andonovski, D; Vasilevska, V; Mircevska-Zogovska, E

2008-07-01

A crucial and important factor for successful treatment of burns is the early covering of the burned area with skin substitutes. The covering of the burn requires material that restores the epidermal function and integrates itself into the process of healing. Biological dressings are the golden standard for the temporary covering of burns. All biological skin substitutes are susceptible to early graft reaction and the only exception is the amnion membrane. The importance of the amnion membrane as a biological dressing for burns amounts to: a barrier to bacterial colonization, hastens the epithelisation, and control of water loss. Amnioplasty is a method of application of amnion membrane on the recipient site. In this comparative study, 60 patients with dermal and sub-dermal burns were included. Research was made on an examination group of 30 patients with burns where the method of amnioplasty was applied, and for this amnion membrane conserved in 76% alcohol was used. The control group was made up of 30 patients with burns treated conventionally, and standard methods for the local treatment of burns were applied: exposition, occlusive dressing and initial excision with skin grafting. Pathohistological and microbiological analyses of the bioptical material were made. The degree of the burns was determined through a pathohistological analysis of the bioptical material taken the third day, and in some of the subjects where re-epithelialization was determined on the seventh day, the further re-epithelialization was observed clinically. Pathohistological examination enabled discrimination between bacterial colonization and the invasive bacterial infection. Furthermore, the type of bacterial colonization and infection was determined, which was confirmed with microbiological analysis. The analysis of the results from the microbiological and pathohistological researches of the bioptical material according to the bacterial colonization and infection showed that, although between the examined and the control group there was no statistically important difference, the value of p = 0.067 is close to the statistically important value of p < 0.05. The results of the pathohistological examination of the bioptical material taken the seventh day and analysed according to the re-epithelialization showed that there was a significant difference between the two groups of p < 0.035. It should be mentioned that, although according to the microbiological examinations of the bioptical material a statistically significant difference was not achieved, clinical significance was achieved. The obtained significance of p < 0.035 compared to the re-epithelialization in both groups approved the application of the method of amnioplasty. The histological analysis of the bioptical material not only determines the degree of the burns specifically, but facilitates the choice of method for further treatment, observes the speed of the re-epithelialization and plays an important part in the correct diagnosis and the early start of the specific therapy, important in preventing sepsis. The application of amnion membrane as a biological dressing speeds the re-epithelialization and prevents invasive bacterial infection. Pathohistological examination of the burns is recommended to be established as a standard method in clinical practice.

Improved control of multiple-antibiotic-resistance-related microbial risk in swine manure wastes by autothermal thermophilic aerobic digestion.

PubMed

Han, Il; Congeevaram, Shankar; Park, Joonhong

2009-01-01

In this study, we microbiologically evaluated antibiotic resistance and pathogenicity in livestock (swine) manure as well as its biologically stabilized products. One of new livestock manure stabilization techniques is ATAD (Autothermal Thermophilic Aerobic Digestion). Because of its high operation temperature (60-65 degrees C), it has been speculated to have effective microbial risk control in livestock manure. This hypothesis was tested by evaluating microbial risk in ATAD-treated swine manure. Antibiotic resistance, multiple antibiotic resistance (MAR), and pathogenicity were microbiologically examined for swine manure as well as its conventionally stabilized (anaerobically fermented) and ATAD-stabilized products. In the swine manure and its conventionally stabilized product, antibiotic resistant (tetracycline-, kanamycine-, ampicillin-, and rifampicin-resistant) bacteria and the pathogen indicator bacteria were detected. Furthermore, approximately 2-5% of the Staphylococcus and Salmonella colonies from their selective culture media were found to exhibit a MAR-phenotypes, suggesting a serious level of microbe induced health risk. In contrast, after the swine manure was stabilized with a pilot-scale ATAD treatment for 3 days at 60-65 degrees C, antibiotic resistant bacteria, pathogen indicator bacteria, and MAR-exhibiting pathogens were all undetected. These findings support the improved control of microbial risk in livestock wastes by ATAD treatment.

Can volatile organic metabolites be used to simultaneously assess microbial and mite contamination level in cereal grains and coffee beans?

PubMed

Salvador, Angelo C; Baptista, Inês; Barros, António S; Gomes, Newton C M; Cunha, Angela; Almeida, Adelaide; Rocha, Silvia M

2013-01-01

A novel approach based on headspace solid-phase microextraction (HS-SPME) combined with comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-ToFMS) was developed for the simultaneous screening of microbial and mite contamination level in cereals and coffee beans. The proposed approach emerges as a powerful tool for the rapid assessment of the microbial contamination level (ca. 70 min versus ca. 72 to 120 h for bacteria and fungi, respectively, using conventional plate counts), and mite contamination (ca. 70 min versus ca. 24 h). A full-factorial design was performed for optimization of the SPME experimental parameters. The methodology was applied to three types of rice (rough, brown, and white rice), oat, wheat, and green and roasted coffee beans. Simultaneously, microbiological analysis of the samples (total aerobic microorganisms, moulds, and yeasts) was performed by conventional plate counts. A set of 54 volatile markers was selected among all the compounds detected by GC×GC-ToFMS. Principal Component Analysis (PCA) was applied in order to establish a relationship between potential volatile markers and the level of microbial contamination. Methylbenzene, 3-octanone, 2-nonanone, 2-methyl-3-pentanol, 1-octen-3-ol, and 2-hexanone were associated to samples with higher microbial contamination level, especially in rough rice. Moreover, oat exhibited a high GC peak area of 2-hydroxy-6-methylbenzaldehyde, a sexual and alarm pheromone for adult mites, which in the other matrices appeared as a trace component. The number of mites detected in oat grains was correlated to the GC peak area of the pheromone. The HS-SPME/GC×GC-ToFMS methodology can be regarded as the basis for the development of a rapid and versatile method that can be applied in industry to the simultaneous assessment the level of microbiological contamination and for detection of mites in cereals grains and coffee beans.

Can Volatile Organic Metabolites Be Used to Simultaneously Assess Microbial and Mite Contamination Level in Cereal Grains and Coffee Beans?

PubMed Central

Salvador, Ângelo C.; Baptista, Inês; Barros, António S.; Gomes, Newton C. M.; Cunha, Ângela; Almeida, Adelaide; Rocha, Silvia M.

2013-01-01

A novel approach based on headspace solid-phase microextraction (HS-SPME) combined with comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC×GC–ToFMS) was developed for the simultaneous screening of microbial and mite contamination level in cereals and coffee beans. The proposed approach emerges as a powerful tool for the rapid assessment of the microbial contamination level (ca. 70 min versus ca. 72 to 120 h for bacteria and fungi, respectively, using conventional plate counts), and mite contamination (ca. 70 min versus ca. 24 h). A full-factorial design was performed for optimization of the SPME experimental parameters. The methodology was applied to three types of rice (rough, brown, and white rice), oat, wheat, and green and roasted coffee beans. Simultaneously, microbiological analysis of the samples (total aerobic microorganisms, moulds, and yeasts) was performed by conventional plate counts. A set of 54 volatile markers was selected among all the compounds detected by GC×GC–ToFMS. Principal Component Analysis (PCA) was applied in order to establish a relationship between potential volatile markers and the level of microbial contamination. Methylbenzene, 3-octanone, 2-nonanone, 2-methyl-3-pentanol, 1-octen-3-ol, and 2-hexanone were associated to samples with higher microbial contamination level, especially in rough rice. Moreover, oat exhibited a high GC peak area of 2-hydroxy-6-methylbenzaldehyde, a sexual and alarm pheromone for adult mites, which in the other matrices appeared as a trace component. The number of mites detected in oat grains was correlated to the GC peak area of the pheromone. The HS-SPME/GC×GC–ToFMS methodology can be regarded as the basis for the development of a rapid and versatile method that can be applied in industry to the simultaneous assessment the level of microbiological contamination and for detection of mites in cereals grains and coffee beans. PMID:23613710

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

PubMed Central

Reuter, Sandra; Ellington, Matthew J.; Cartwright, Edward J. P.; Köser, Claudio U.; Török, M. Estée; Gouliouris, Theodore; Harris, Simon R.; Brown, Nicholas M.; Holden, Matthew T. G.; Quail, Mike; Parkhill, Julian; Smith, Geoffrey P.; Bentley, Stephen D.; Peacock, Sharon J.

2014-01-01

IMPORTANCE The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range of bacteria in less than a day. These could be used to more effectively contain the spread of multidrug-resistant pathogens. OBJECTIVE To compare WGS with standard clinical microbiology practice for the investigation of nosocomial outbreaks caused by multidrug-resistant bacteria, the identification of genetic determinants of antimicrobial resistance, and typing of other clinically important pathogens. DESIGN, SETTING, AND PARTICIPANTS A laboratory-based study of hospital inpatients with a range of bacterial infections at Cambridge University Hospitals NHS Foundation Trust, a secondary and tertiary referral center in England, comparing WGS with standard diagnostic microbiology using stored bacterial isolates and clinical information. MAIN OUTCOMES AND MEASURES Specimens were taken and processed as part of routine clinical care, and cultured isolates stored and referred for additional reference laboratory testing as necessary. Isolates underwent DNA extraction and library preparation prior to sequencing on the Illumina MiSeq platform. Bioinformatic analyses were performed by persons blinded to the clinical, epidemiologic, and antimicrobial susceptibility data. RESULTS We investigated 2 putative nosocomial outbreaks, one caused by vancomycin-resistant Enterococcus faecium and the other by carbapenem-resistant Enterobacter cloacae; WGS accurately discriminated between outbreak and nonoutbreak isolates and was superior to conventional typing methods. We compared WGS with standard methods for the identification of the mechanism of carbapenem resistance in a range of gram-negative bacteria (Acinetobacter baumannii, E cloacae, Escherichia coli, and Klebsiella pneumoniae). This demonstrated concordance between phenotypic and genotypic results, and the ability to determine whether resistance was attributable to the presence of carbapenemases or other resistance mechanisms. Whole-genome sequencing was used to recapitulate reference laboratory typing of clinical isolates of Neisseria meningitidis and to provide extended phylogenetic analyses of these. CONCLUSIONS AND RELEVANCE The speed, accuracy, and depth of information provided by WGS platforms to confirm or refute outbreaks in hospitals and the community, and to accurately define transmission of multidrug-resistant and other organisms, represents an important advance. PMID:23857503

Are the Conventional Commercial Yeast Identification Methods Still Helpful in the Era of New Clinical Microbiology Diagnostics? A Meta-Analysis of Their Accuracy

PubMed Central

Efremov, Ljupcho; Leoncini, Emanuele; Amore, Rosarita; Posteraro, Patrizia; Ricciardi, Walter

2015-01-01

Accurate identification of pathogenic species is important for early appropriate patient management, but growing diversity of infectious species/strains makes the identification of clinical yeasts increasingly difficult. Among conventional methods that are commercially available, the API ID32C, AuxaColor, and Vitek 2 systems are currently the most used systems in routine clinical microbiology. We performed a systematic review and meta-analysis to estimate and to compare the accuracy of the three systems, in order to assess whether they are still of value for the species-level identification of medically relevant yeasts. After adopting rigorous selection criteria, we included 26 published studies involving Candida and non-Candida yeasts that were tested with the API ID32C (674 isolates), AuxaColor (1,740 isolates), and Vitek 2 (2,853 isolates) systems. The random-effects pooled identification ratios at the species level were 0.89 (95% confidence interval [CI], 0.80 to 0.95) for the API ID32C system, 0.89 (95% CI, 0.83 to 0.93) for the AuxaColor system, and 0.93 (95% CI, 0.89 to 0.96) for the Vitek 2 system (P for heterogeneity, 0.255). Overall, the accuracy of studies using phenotypic analysis-based comparison methods was comparable to that of studies using molecular analysis-based comparison methods. Subanalysis of studies conducted on Candida yeasts showed that the Vitek 2 system was significantly more accurate (pooled ratio, 0.94 [95% CI, 0.85 to 0.99]) than the API ID32C system (pooled ratio, 0.84 [95% CI, 0.61 to 0.99]) and the AuxaColor system (pooled ratio, 0.76 [95% CI, 0.67 to 0.84]) with respect to uncommon species (P for heterogeneity, <0.05). Subanalysis of studies conducted on non-Candida yeasts (i.e., Cryptococcus, Rhodotorula, Saccharomyces, and Trichosporon) revealed pooled identification accuracies of ≥98% for the Vitek 2, API ID32C (excluding Cryptococcus), and AuxaColor (only Rhodotorula) systems, with significant low or null levels of heterogeneity (P > 0.05). Nonetheless, clinical microbiologists should reconsider the usefulness of these systems, particularly in light of new diagnostic tools such as matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry, which allow for considerably shortened turnaround times and/or avoid the requirement for additional tests for species identity confirmation. PMID:25994160

Improved detection of Burkholderia pseudomallei from non-blood clinical specimens using enrichment culture and PCR: narrowing diagnostic gap in resource-constrained settings.

PubMed

Tellapragada, Chaitanya; Shaw, Tushar; D'Souza, Annet; Eshwara, Vandana Kalwaje; Mukhopadhyay, Chiranjay

2017-07-01

To evaluate the diagnostic utility of enrichment culture and PCR for improved case detection rates of non-bacteraemic form of melioidosis in limited resource settings. Clinical specimens (n = 525) obtained from patients presenting at a tertiary care hospital of South India with clinical symptoms suggestive of community-acquired pneumonia, lower respiratory tract infections, superficial or internal abscesses, chronic skin ulcers and bone or joint infections were tested for the presence of Burkholderia pseudomallei using conventional culture (CC), enrichment culture (EC) and PCR. Sensitivity, specificity, positive and negative predictive values of CC and PCR were initially deduced using EC as the gold standard method. Further, diagnostic accuracies of all the three methods were analysed using Bayesian latent class modelling (BLCM). Detection rates of B. pseudomallei using CC, EC and PCR were 3.8%, 5.3% and 6%, respectively. Diagnostic sensitivities and specificities of CC and PCR were 71.4, 98.4% and 100 and 99.4%, respectively in comparison with EC as the gold standard test. With Bayesian latent class modelling, EC and PCR demonstrated sensitivities of 98.7 and 99.3%, respectively, while CC showed a sensitivity of 70.3% for detection of B. pseudomallei. An increase of 1.6% (95% CI: 1.08-4.32%) in the case detection rate of melioidosis was observed in the study population when EC and/or PCR were used in adjunct to the conventional culture technique. Our study findings underscore the diagnostic superiority of enrichment culture and/or PCR over conventional microbiological culture for improved case detection of melioidosis from non-blood clinical specimens. © 2017 John Wiley & Sons Ltd.

Comparison of the immunogenicity and safety of the conventional subunit, MF59-adjuvanted, and intradermal influenza vaccines in the elderly.

PubMed

Seo, Yu Bin; Choi, Won Suk; Lee, Jacob; Song, Joon Young; Cheong, Hee Jin; Kim, Woo Joo

2014-07-01

The influenza vaccination is known as the most effective method for preventing influenza infection and its complications in the elderly. Conventional subunit (Agrippal S1; Novartis), MF59-adjuvanted (Fluad; Novartis), and intradermal (IDflu15; Sanofi Pasteur) influenza vaccines are widely used throughout South Korea. However, few comparative studies evaluating the safety and immunogenicity of these vaccines are available. Prior to the beginning of the 2011-2012 influenza season, 335 healthy elderly volunteers randomly received one of three seasonal trivalent influenza vaccines, the conventional subunit, MF59-adjuvanted, or intradermal influenza vaccine. Serum hemagglutination-inhibiting antibody levels were measured at the time of vaccination and at 1 and 6 months after vaccination. Adverse events were recorded prospectively. A total of 113 conventional subunit, 111 MF59-adjuvanted, and 111 intradermal influenza vaccine volunteers were followed up during a 6-month postvaccination period. One month after vaccination, all three vaccines satisfied Committee for Medical Products for Human Use (CHMP) immunogenicity criteria for the A/H1N1 and A/H3N2 strains but not for the B strain. Compared with the subunit vaccine, the intradermal vaccine exhibited noninferiority, while the MF59-adjuvanted vaccine exhibited superiority. Furthermore, the MF59-adjuvanted vaccine was more immunogenic against the A/H3N2 strain than was the subunit vaccine up to 6 months postvaccination. The most common local and systemic reactions to the conventional subunit, MF59-adjuvanted, and intradermal influenza vaccines were pain at the injection site (7.1%, 10.8%, and 6.3%, respectively) and generalized myalgia (0.9%, 8.1%, and 5.4%, respectively). Local and systemic reactions were similar among the three vaccine groups. MF59-adjuvanted vaccine exhibited superior immunogenicity compared with a conventional subunit vaccine and had a comparable safety profile. For older adults, the MF59-adjuvanted vaccine is preferable for providing superior immunogenicity. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Microbiology Education in Nursing Practice.

PubMed

Durrant, Robert J; Doig, Alexa K; Buxton, Rebecca L; Fenn, JoAnn P

2017-01-01

Nurses must have sufficient education and training in microbiology to perform many roles within clinical nursing practice (e.g., administering antibiotics, collecting specimens, preparing specimens for transport and delivery, educating patients and families, communicating results to the healthcare team, and developing care plans based on results of microbiology studies and patient immunological status). It is unclear whether the current microbiology courses required of nursing students in the United States focus on the topics that are most relevant to nursing practice. To gauge the relevance of current microbiology education to nursing practice, we created a confidential, web-based survey that asked nurses about their past microbiology education, the types of microbiology specimens they collect, their duties that require knowledge of microbiology, and how frequently they encounter infectious diseases in practice. We used the survey responses to develop data-driven recommendations for educators who teach microbiology to pre-nursing and nursing students. Two hundred ninety-six Registered Nurses (RNs) completed the survey. The topics they deemed most relevant to current practice were infection control, hospital-acquired infections, disease transmission, and collection and handling of patient specimens. Topics deemed least relevant were the Gram stain procedure and microscope use. In addition, RNs expressed little interest in molecular testing methods. This may reflect a gap in their understanding of the uses of these tests, which could be bridged in a microbiology course. We now have data in support of anecdotal evidence that nurses are most engaged when learning about microbiology topics that have the greatest impact on patient care. Information from this survey will be used to shift the focus of microbiology courses at our university to topics more relevant to nursing practice. Further, these findings may also support an effort to evolve national recommendations for microbiology education in pre-nursing and nursing curricula.

Microbiology Education in Nursing Practice†

PubMed Central

Durrant, Robert J.; Doig, Alexa K.; Buxton, Rebecca L.; Fenn, JoAnn P.

2017-01-01

Nurses must have sufficient education and training in microbiology to perform many roles within clinical nursing practice (e.g., administering antibiotics, collecting specimens, preparing specimens for transport and delivery, educating patients and families, communicating results to the healthcare team, and developing care plans based on results of microbiology studies and patient immunological status). It is unclear whether the current microbiology courses required of nursing students in the United States focus on the topics that are most relevant to nursing practice. To gauge the relevance of current microbiology education to nursing practice, we created a confidential, web-based survey that asked nurses about their past microbiology education, the types of microbiology specimens they collect, their duties that require knowledge of microbiology, and how frequently they encounter infectious diseases in practice. We used the survey responses to develop data-driven recommendations for educators who teach microbiology to pre-nursing and nursing students. Two hundred ninety-six Registered Nurses (RNs) completed the survey. The topics they deemed most relevant to current practice were infection control, hospital-acquired infections, disease transmission, and collection and handling of patient specimens. Topics deemed least relevant were the Gram stain procedure and microscope use. In addition, RNs expressed little interest in molecular testing methods. This may reflect a gap in their understanding of the uses of these tests, which could be bridged in a microbiology course. We now have data in support of anecdotal evidence that nurses are most engaged when learning about microbiology topics that have the greatest impact on patient care. Information from this survey will be used to shift the focus of microbiology courses at our university to topics more relevant to nursing practice. Further, these findings may also support an effort to evolve national recommendations for microbiology education in pre-nursing and nursing curricula. PMID:28861140

Proceedings of the U.S. Geological Survey Interdisciplinary Microbiology Workshop, Estes Park, Colorado, October 15-17, 2008

USGS Publications Warehouse

Briggs, Kay Marano

2010-01-01

Preface A U.S. Geological Survey Interdisciplinary Microbiology Workshop was held in Estes Park, Colorado, on October 15-17, 2008. Participants came from all USGS regions and disciplines. This report contains abstracts from 36 presentations and 35 poster sessions and notes from 5 breakout sessions. The seven presentation topics follow: Ecology of wildlife and fish disease Mechanisms of fish and wildlife disease Microbial ecology Geographic patterns/visualization Public health and water quality Geomicrobiology Ecosystem function The six poster session topics follow: Wildlife disease Disease detection methods Water quality Microbial ecology Metabolic processes Tools and techniques Five working groups met in breakout sessions on October 16, 2008. The highlights for each working group are summarized in this report, and their goals are listed below: Working Group I: to plan a Fact Sheet on interdisciplinary microbiology in the USGS Working Group II: to plan a USGS interdisciplinary microbiology Web site Working Group III: to suggest ways to broadcast and publicize the types of microbiology conducted at the USGS Working Group IV: to identify emerging issues in USGS interdisciplinary microbiology research Working Group V: to identify potential opportunities for interdisciplinary microbiology work at the USGS After the workshop, the USGS interdisciplinary microbiology Web site was activated in June 2009 at http://microbiology.usgs.gov/.

Wine microbiology is driven by vineyard and winery anthropogenic factors.

PubMed

Grangeteau, Cédric; Roullier-Gall, Chloé; Rousseaux, Sandrine; Gougeon, Régis D; Schmitt-Kopplin, Philippe; Alexandre, Hervé; Guilloux-Benatier, Michèle

2017-03-01

The effects of different anthropic activities (vineyard: phytosanitary protection; winery: pressing and sulfiting) on the fungal populations of grape berries were studied. The global diversity of fungal populations (moulds and yeasts) was performed by pyrosequencing. The anthropic activities studied modified fungal diversity. Thus, a decrease in biodiversity was measured for three successive vintages for the grapes of the plot cultivated with Organic protection compared to plots treated with Conventional and Ecophyto protections. The fungal populations were then considerably modified by the pressing-clarification step. The addition of sulfur dioxide also modified population dynamics and favoured the domination of the species Saccharomyces cerevisiae during fermentation. The non-targeted chemical analysis of musts and wines by FT-ICR-MS showed that the wines could be discriminated at the end of alcoholic fermentation as a function of adding SO 2 or not, but also and above all as a function of phytosanitary protection, regardless of whether these fermentations took place in the presence of SO 2 or not. Thus, the existence of signatures in wines of chemical diversity and microbiology linked to vineyard protection has been highlighted. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Recent advances in diagnostic microbiology.

PubMed

Bravo, Lulette Tricia C; Procop, Gary W

2009-07-01

The past decade has seen a surge in the development of a variety of molecular diagnostics designed to rapidly identify or characterize medically important microorganisms. We briefly review important advances in molecular microbiology, and then discuss specific assays that have been implemented in clinical microbiology laboratories throughout the country. We also discuss emerging methods and technologies that will soon be more widely used for the prompt and accurate detection of the agents of infectious diseases.

Sampling methods and data generation

USDA-ARS?s Scientific Manuscript database

The study of forensic microbiology is an inherent blend of forensic science and microbiology, and both disciplines have recently been undergoing rapid advancements in technology that are allowing for exciting new research avenues. The integration of two different disciplines poses challenges becaus...

Antimicrobial Testing Methods & Procedures: MB-10-06

EPA Pesticide Factsheets

Describes the procedures used to log-in, prepare, and evaluate the quality of media and reagents used in microbiological assays by the Microbiology Laboratory Branch (MLB), for use in the quality evaluation of media and reagents used by MLB.

Identification of Burkholderia spp. in the Clinical Microbiology Laboratory: Comparison of Conventional and Molecular Methods

PubMed Central

van Pelt, Cindy; Verduin, Cees M.; Goessens, Wil H. F.; Vos, Margreet C.; Tümmler, Burkhard; Segonds, Christine; Reubsaet, Frans; Verbrugh, Henri; van Belkum, Alex

1999-01-01

Cystic fibrosis (CF) predisposes patients to bacterial colonization and infection of the lower airways. Several species belonging to the genus Burkholderia are potential CF-related pathogens, but microbiological identification may be complicated. This situation is not in the least due to the poorly defined taxonomic status of these bacteria, and further validation of the available diagnostic assays is required. A total of 114 geographically diverse bacterial isolates, previously identified in reference laboratories as Burkholderia cepacia (n = 51), B. gladioli (n = 14), Ralstonia pickettii (n = 6), B. multivorans (n = 2), Stenotrophomonas maltophilia (n = 3), and Pseudomonas aeruginosa (n = 11), were collected from environmental, clinical, and reference sources. In addition, 27 clinical isolates putatively identified as Burkholderia spp. were recovered from the sputum of Dutch CF patients. All isolates were used to evaluate the accuracy of two selective growth media, four systems for biochemical identification (API 20NE, Vitek GNI, Vitek NFC, and MicroScan), and three different PCR-based assays. The PCR assays amplify different parts of the ribosomal DNA operon, either alone or in combination with cleavage by various restriction enzymes (PCR-restriction fragment length polymorphism [RFLP] analysis). The best system for the biochemical identification of B. cepacia appeared to be the API 20NE test. None of the biochemical assays successfully grouped the B. gladioli strains. The PCR-RFLP method appeared to be the optimal method for accurate nucleic acid-mediated identification of the different Burkholderia spp. With this method, B. gladioli was also reliably classified in a separate group. For the laboratory diagnosis of B. cepacia, we recommend parallel cultures on blood agar medium and selective agar plates. Further identification of colonies with a Burkholderia phenotype should be performed with the API 20NE test. For final confirmation of species identities, PCR amplification of the small-subunit rRNA gene followed by RFLP analysis with various enzymes is recommended. PMID:10364579

Methods for microbiological and immunological studies of space flight crews

NASA Technical Reports Server (NTRS)

Taylor, G. R. (Editor); Zaloguev, S. N. (Editor)

1978-01-01

Systematic laboratory procedures compiled as an outgrowth of a joint U.S./U.S.S.R. microbiological-immunological experiment performed during the Apollo-Soyuz Test Project space flight are presented. Included are mutually compatible methods for the identification of aerobic and microaerophilic bacteria, yeast and yeastlike microorganisms, and filamentous fungi; methods for the bacteriophage typing of Staphylococcus aureus; and methods for determining the sensitivity of S. aureus to antibiotics. Immunological methods using blood and immunological and biochemical methods using salivary parotid fluid are also described. Formulas for media and laboratory reagents used are listed.

Clinical diagnosis of ventilator associated pneumonia revisited: comparative validation using immediate post-mortem lung biopsies.

PubMed

Fàbregas, N; Ewig, S; Torres, A; El-Ebiary, M; Ramirez, J; de La Bellacasa, J P; Bauer, T; Cabello, H

1999-10-01

A study was undertaken to assess the diagnostic value of different clinical criteria and the impact of microbiological testing on the accuracy of clinical diagnosis of suspected ventilator associated pneumonia (VAP). Twenty five deceased mechanically ventilated patients were studied prospectively. Immediately after death, multiple bilateral lung biopsy specimens (16 specimens/patient) were obtained for histological examination and quantitative lung cultures. The presence of both histological pneumonia and positive lung cultures was used as a reference test. The presence of infiltrates on the chest radiograph and two of three clinical criteria (leucocytosis, purulent secretions, fever) had a sensitivity of 69% and a specificity of 75%; the corresponding numbers for the clinical pulmonary infection score (CPIS) were 77% and 42%. Non-invasive as well as invasive sampling techniques had comparable values. The combination of all techniques achieved a sensitivity of 85% and a specificity of 50%, and these values remained virtually unchanged despite the presence of previous treatment with antibiotics. When microbiological results were added to clinical criteria, adequate diagnoses originating from microbiological results which might have corrected false positive and false negative clinical judgements (n = 5) were countered by a similar proportion of inadequate diagnoses (n = 6). Clinical criteria had reasonable diagnostic values. CPIS was not superior to conventional clinical criteria. Non-invasive and invasive sampling techniques had diagnostic values comparable to clinical criteria. An algorithm guiding antibiotic treatment exclusively by microbiological results does not increase the overall diagnostic accuracy and carries the risk of undertreatment.

Emerging Technologies for the Clinical Microbiology Laboratory

PubMed Central

Buchan, Blake W.

2014-01-01

SUMMARY In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory. PMID:25278575

Resident training in microbiology.

PubMed

Haller, Barbara L

2007-06-01

To meet the challenges of diagnosis and management of infectious diseases, clinical pathology residents must receive comprehensive training in microbiology, learn to think critically, develop problem-solving skills, and take active roles as laboratory consultants. Residents well trained in clinical microbiology become capable laboratory professionals, developing cost-effective testing strategies, decreasing risk for medical errors, and improving patient care. Newer methods for diagnosing infectious disease, such as real-time polymerase chain reaction, microarrays for pathogen detection, and rapid assays for antigen or antibody detection, have become standard. Knowledge of infectious disease principles, drug therapeutic options, and drug resistance is also important. Suggestions for training and for assessing resident competency in clinical microbiology are presented.

Microbiological surveillance and state of the art technological strategies for the prevention of dialysis water pollution.

PubMed

Bolasco, Piergiorgio; Contu, Antonio; Meloni, Patrizia; Vacca, Dorio; Galfrè, Andrea

2012-08-01

The present report attempts to illustrate the positive impact on the microbiological quality of dialysis patients over a 15-year period through the progressive implementation of state-of-the-art technological strategies and the optimization of microbiological surveillance procedures in five dialysis units in Sardinia. Following on better microbiological, quality controls of dialysis water and improvement of procedures and equipment, a drastic improvement of microbiological water quality was observed in a total of 945 samples. The main aim was to introduce the use of microbiological culture methods as recommended by the most important guidelines. The microbiological results obtained have led to a progressive refining of controls and introduction of new materials and equipment, including two-stage osmosis and piping distribution rings featuring a greater capacity to prevent biofilm adhesion. The actions undertaken have resulted in unexpected quality improvements. Dialysis water should be viewed by the nephrologist as a medicinal product exerting a demonstrable positive impact on microinflammation in dialysis patients. A synergic effort between nephrologists and microbiologists undoubtedly constitutes the most effective means of preventing dialysis infections.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology.

PubMed

Clark, Andrew E; Kaleta, Erin J; Arora, Amit; Wolk, Donna M

2013-07-01

Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.

Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: a Fundamental Shift in the Routine Practice of Clinical Microbiology

PubMed Central

Clark, Andrew E.; Kaleta, Erin J.; Arora, Amit

2013-01-01

SUMMARY Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the “nuts and bolts” of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care. PMID:23824373

Use of containers with sterilizing filter in autologous serum eyedrops.

PubMed

López-García, José S; García-Lozano, Isabel

2012-11-01

To assess the effect of the use of containers with an adapted sterilizing filter on the contamination of autologous serum eyedrops. Prospective, consecutive, comparative, and randomized study. Thirty patients with Sjögren syndrome. One hundred seventy-six autologous serum containers used in home therapy were studied; 48 of them included an adapted filter (Hyabak; Thea, Clermont-Ferrand, France), and the other 128 were conventional containers. Containers equipped with a filter were tested at 7, 14, 21, and 28 days of use, whereas conventional containers were studied after 7 days of use. In addition, testing for contamination was carried out in 14 conventional containers used during in-patient therapy every week for 4 weeks. In all cases, the preparation of the autologous serum was similar. Blood agar and chocolate agar were used as regular culture media for the microbiologic studies, whereas Sabouraud agar with chloramphenicol was the medium for fungal studies. Microbiologic contamination of containers with autologous serum eyedrops. Only one of the containers with an adapted sterilizing filter (2.1%) became contaminated with Staphylococcus epidermidis after 1 month of treatment, whereas the contamination rate among conventional containers reached 28.9% after 7 days of treatment. The most frequent germs found in the samples were coagulase-negative Staphylococcus (48.6%). With regard the containers used in the in-patient setting, 2 (14.3%) became contaminated after 2 weeks, 5 (35.7%) became contaminated after 3 weeks, and 5 (50%) became contaminated after 4 weeks, leaving 7 (50%) that did not become contaminated after 1 month of treatment. Using containers with an adapted filter significantly reduces the contamination rates in autologous serum eyedrops, thus extending the use of such container by the patients for up to 4 weeks with virtually no contamination risks. Copyright © 2012 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Farm Management in Organic and Conventional Dairy Production Systems Based on Pasture in Southern Brazil and Its Consequences on Production and Milk Quality

PubMed Central

Kuhnen, Shirley; Stibuski, Rudinei Butka; Honorato, Luciana Aparecida; Pinheiro Machado Filho, Luiz Carlos

2015-01-01

Simple Summary This study provides the characteristics of the conventional high input (C-HI), conventional low input (C-LI), and organic low input (O-LI) pasture-based production systems used in Southern Brazil, and its consequences on production and milk quality. C-HI farms had larger farms and herds, annual pasture with higher inputs and milk yield, whereas O-LI had smaller farms and herds, perennial pastures with lowest input and milk yields; C-LI was in between. O-LI farms may contribute to eco-system services, but low milk yield is a major concern. Hygienic and microbiological milk quality was poor for all farms and needs to be improved. Abstract Pasture-based dairy production is used widely on family dairy farms in Southern Brazil. This study investigates conventional high input (C-HI), conventional low input (C-LI), and organic low input (O-LI) pasture-based systems and their effects on quantity and quality of the milk produced. We conducted technical site visits and interviews monthly over one year on 24 family farms (n = 8 per type). C-HI farms had the greatest total area (28.9 ha), greatest percentage of area with annual pasture (38.7%), largest number of lactating animals (26.2) and greatest milk yield per cow (22.8 kg·day−1). O-LI farms had the largest perennial pasture area (52.3%), with the greatest botanical richness during all seasons. Area of perennial pasture was positively correlated with number of species consumed by the animals (R2 = 0.74). Milk from O-LI farms had higher levels of fat and total solids only during the winter. Hygienic and microbiological quality of the milk was poor for all farms and need to be improved. C-HI farms had high milk yield related to high input, C-LI had intermediate characteristics and O-LI utilized a year round perennial pasture as a strategy to diminish the use of supplements in animal diets, which is an important aspect in ensuring production sustainability. PMID:26479369

Preemptive Isolation Precautions of Patients at High Risk for Methicillin-Resistant Staphylococcus aureus in Combination With Ultrarapid Polymerase Chain Reaction Screening as an Effective Tool for Infection Control.

PubMed

Hallak, Ghias; Neuner, Bruno; Schefold, Joerg C; Gorzelniak, Kerstin; Rapsch, Brigitte; Pfüller, Roland; Stengel, Dirk; Wellmann, Jürgen; Ekkernkamp, Axel; Walter, Michael

2016-12-01

This sequential nonrandomized intervention study investigated the role of preemptive isolation precautions plus ultrarapid polymerase chain reaction screening for methicillin-resistant Staphylococcus aureus (MRSA). Compared with no prophylactic isolation plus conventional microbiology MRSA screening, nosocomial MRSA colonization and total MRSA incidence per 10,000 patient days significantly decreased. Infect Control Hosp Epidemiol 2016;1489-1491.

Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS.

PubMed

Bechy-Loizeau, Anne-Laure; Flandrois, Jean-Pierre; Abaibou, Hafid

2015-07-01

On the ISS, as on Earth, water is an essential element for life and its quality control on a regular basis allows to ensure the health of the crew and the integrity of equipment. Currently, microbial water analysis onboard ISS still relies on the traditional culture-based microbiology methods. Molecular methods based on the amplification of nucleic acids for microbiological analysis of water quality show enormous potential and are considered as the best alternative to culture-based methods. For this reason, the Midass, a fully integrated and automated prototype was designed conjointly by ESA and bioMérieux for a rapid monitoring of the microbiological quality of air. The prototype allows air sampling, sample processing and the amplification/detection of nucleic acids. We describe herein the proof of principle of an analytical approach based on molecular biology that could fulfill the ESA's need for a rapid monitoring of the microbiological quality of recycled water onboard ISS. Both concentration and recovery of microorganisms are the main critical steps when the microfiltration technology is used for water analysis. Among filters recommended standards for monitoring the microbiological quality of the water, the polycarbonate filter was fully in line with the requirements of the ISO 7704-1985 standard in terms of efficacy of capture and recovery of bacteria. Moreover, this filter does not retain nucleic acids on the surface and has no inhibitory effect on their downstream processing steps such as purification and amplification/detection. Although the Midass system was designed for the treatment of air samples, the first results on the integration of PC filters were encouraging. Nevertheless, system modifications are needed to better adapt the Midass system for the monitoring of the microbiological water quality. Copyright © 2015 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

Interpretation of Blood Microbiology Results - Function of the Clinical Microbiologist.

PubMed

Kristóf, Katalin; Pongrácz, Júlia

2016-04-01

The proper use and interpretation of blood microbiology results may be one of the most challenging and one of the most important functions of clinical microbiology laboratories. Effective implementation of this function requires careful consideration of specimen collection and processing, pathogen detection techniques, and prompt and precise reporting of identification and susceptibility results. The responsibility of the treating physician is proper formulation of the analytical request and to provide the laboratory with complete and precise patient information, which are inevitable prerequisites of a proper testing and interpretation. The clinical microbiologist can offer advice concerning the differential diagnosis, sampling techniques and detection methods to facilitate diagnosis. Rapid detection methods are essential, since the sooner a pathogen is detected, the better chance the patient has of getting cured. Besides the gold-standard blood culture technique, microbiologic methods that decrease the time in obtaining a relevant result are more and more utilized today. In the case of certain pathogens, the pathogen can be identified directly from the blood culture bottle after propagation with serological or automated/semi-automated systems or molecular methods or with MALDI-TOF MS (matrix-assisted laser desorption-ionization time of flight mass spectrometry). Molecular biology methods are also suitable for the rapid detection and identification of pathogens from aseptically collected blood samples. Another important duty of the microbiology laboratory is to notify the treating physician immediately about all relevant information if a positive sample is detected. The clinical microbiologist may provide important guidance regarding the clinical significance of blood isolates, since one-third to one-half of blood culture isolates are contaminants or isolates of unknown clinical significance. To fully exploit the benefits of blood culture and other (non- culture based) diagnoses, the microbiologist and the clinician should interact directly.

[Current panorama of the teaching of microbiology and parasitology in Spain].

PubMed

Cantón, Rafael; Sánchez-Romero, María Isabel; Gómez-Mampaso, Enrique

2010-10-01

The training program of residents in microbiology and parasitology in Spain includes clinical skills, ranging from the diagnostic approach to the patient and adequate sample collection for diagnosis of infectious diseases to antimicrobial therapy and infection control measures. Training also includes new challenges in clinical microbiology that ensure residents' participation in infection control programs of health-care associated infections, training in the resolution of public health problems, and application of new molecular microbiology methods. Specialization in clinical microbiology may be undertaken by graduates in Medicine, Biology, Biochemistry and Chemistry. The training is performed in accredited microbiology laboratories at different hospitals (n = 61) across the country through 4-year residency programs. In the last few years, there has been a major imbalance between the number of intended residents (0.17 per 100,000 inhabitants) and those graduating as specialists in clinical microbiology (0.13 per 100,000 inhabitants), with wide variations across the country. The current tendency in Europe is to strengthen the role of clinical microbiologists as key figures in the diagnosis of infectious diseases and in public health microbiology. Training programs have been hampered by the practice of sending samples for microbiological tests to external, centralized multipurpose laboratories with few clinical microbiologists and without a core curriculum. Essential elements in the training of specialists in clinical microbiology are a close relationship between the laboratory and the clinical center and collaboration with other specialists. Copyright © 2010 Elsevier España S.L. All rights reserved.

Candida bloodstream infection: a clinical microbiology laboratory perspective.

PubMed

Pongrácz, Júlia; Kristóf, Katalin

2014-09-01

The incidence of Candida bloodstream infection (BSI) has been on the rise in several countries worldwide. Species distribution is changing; an increase in the percentage of non-albicans species, mainly fluconazole non-susceptible C. glabrata was reported. Existing microbiology diagnostic methods lack sensitivity, and new methods need to be developed or further evaluation for routine application is necessary. Although reliable, standardized methods for antifungal susceptibility testing are available, the determination of clinical breakpoints remains challenging. Correct species identification is important and provides information on the intrinsic susceptibility profile of the isolate. Currently, acquired resistance in clinical Candida isolates is rare, but reports indicate that it could be an issue in the future. The role of the clinical microbiology laboratory is to isolate and correctly identify the infective agent and provide relevant and reliable susceptibility data as soon as possible to guide antifungal therapy.

Wavelength-normalized spectroscopic analysis of Staphylococcus aureus and Pseudomonas aeruginosa growth rates.

PubMed

McBirney, Samantha E; Trinh, Kristy; Wong-Beringer, Annie; Armani, Andrea M

2016-10-01

Optical density (OD) measurements are the standard approach used in microbiology for characterizing bacteria concentrations in culture media. OD is based on measuring the optical absorbance of a sample at a single wavelength, and any error will propagate through all calculations, leading to reproducibility issues. Here, we use the conventional OD technique to measure the growth rates of two different species of bacteria, Pseudomonas aeruginosa and Staphylococcus aureus. The same samples are also analyzed over the entire UV-Vis wavelength spectrum, allowing a distinctly different strategy for data analysis to be performed. Specifically, instead of only analyzing a single wavelength, a multi-wavelength normalization process is implemented. When the OD method is used, the detected signal does not follow the log growth curve. In contrast, the multi-wavelength normalization process minimizes the impact of bacteria byproducts and environmental noise on the signal, thereby accurately quantifying growth rates with high fidelity at low concentrations.

Tepidimonas arfidensis Sp. Nov., a Novel Gram-negative and thermophilic bacterium isolated from the bone marrow of a patient with leukemia in Korea.

PubMed

Ko, Kwan Soo; Lee, Nam Yong; Oh, Won Sup; Lee, Jang Ho; Ki, Hyun Kyun; Peck, Kyong Ran; Song, Jae-Hoon

2005-01-01

A Gram-negative bacillus, SMC-6271(T), which was isolated from the bone marrow of a patient with leukemia but could not be identified by a conventional microbiologic method, was characterized by a genotypic analysis of 16S rRNA gene. Sequences of the 16S rRNA gene revealed that this bacterium was closely related to Tepidimonas ignava and other slightly thermophilic isolates but diverged distinctly from them. Analyses of cellular fatty acid composition and performance of biochemical tests confirmed that this bacterium is a distinct species from the other Tepidimonas species. Based on the evaluated phenotypic and genotypic characteristics, it is proposed that SMC-6271T (=ABB 0301T =KCTC 12412T =JCM 13232T) should be classified as a new species, namely Tepidimonas arfidensis sp. nov.

New species of Bordetella, Bordetella ansorpii sp. nov., isolated from the purulent exudate of an epidermal cyst.

PubMed

Ko, Kwan Soo; Peck, Kyong Ran; Oh, Won Sup; Lee, Nam Yong; Lee, Jang Ho; Song, Jae-Hoon

2005-05-01

A gram-negative bacillus, SMC-8986(T), which was isolated from the purulent exudate of an epidermal cyst but could not be identified by a conventional microbiologic method, was characterized by a variety of phenotypic and genotypic analyses. Sequences of the 16S rRNA gene revealed that this bacterium belongs to the genus Bordetella but diverged distinctly from previously described Bordetella species. Analyses of cellular fatty acid composition and performance of biochemical tests confirmed that this bacterium is distinct from other Bordetella species. Furthermore, the results of comparative sequence analyses of two protein-coding genes (risA and ompA) also showed that this strain represents a new species within the genus Bordetella. Based on the evaluated phenotypic and genotypic characteristics, it is proposed that SMC-8986(T) should be classified as a new species, namely Bordetella ansorpii sp. nov.

Sampling methods for microbiological analysis of red meat and poultry carcasses.

PubMed

Capita, Rosa; Prieto, Miguel; Alonso-Calleja, Carlos

2004-06-01

Microbiological analysis of carcasses at slaughterhouses is required in the European Union for evaluating the hygienic performance of carcass production processes as required for effective hazard analysis critical control point implementation. The European Union microbial performance standards refer exclusively to the excision method, even though swabbing using the wet/dry technique is also permitted when correlation between both destructive and nondestructive methods can be established. For practical and economic reasons, the swab technique is the most extensively used carcass surface-sampling method. The main characteristics, advantages, and limitations of the common excision and swabbing methods are described here.

How to access and exploit natural resources sustainably: petroleum biotechnology.

PubMed

Sherry, Angela; Andrade, Luiza; Velenturf, Anne; Christgen, Beate; Gray, Neil D; Head, Ian M

2017-09-01

As we transition from fossil fuel reliance to a new energy future, innovative microbial biotechnologies may offer new routes to maximize recovery from conventional and unconventional energy assets; as well as contributing to reduced emission pathways and new technologies for carbon capture and utilization. Here we discuss the role of microbiology in petroleum biotechnologies in relation to addressing UN Sustainable Development Goal 12 (ensure sustainable consumption and production patterns), with a focus on microbially-mediated energy recovery from unconventionals (heavy oil to methane), shale gas and fracking, bioelectrochemical systems for the production of electricity from fossil fuel resources, and innovations in synthetic biology. Furthermore, using wastes to support a more sustainable approach to fossil fuel extraction processes is considered as we undertake the move towards a more circular global economy. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Commutability of food microbiology proficiency testing samples.

PubMed

Abdelmassih, M; Polet, M; Goffaux, M-J; Planchon, V; Dierick, K; Mahillon, J

2014-03-01

Food microbiology proficiency testing (PT) is a useful tool to assess the analytical performances among laboratories. PT items should be close to routine samples to accurately evaluate the acceptability of the methods. However, most PT providers distribute exclusively artificial samples such as reference materials or irradiated foods. This raises the issue of the suitability of these samples because the equivalence-or 'commutability'-between results obtained on artificial vs. authentic food samples has not been demonstrated. In the clinical field, the use of noncommutable PT samples has led to erroneous evaluation of the performances when different analytical methods were used. This study aimed to provide a first assessment of the commutability of samples distributed in food microbiology PT. REQUASUD and IPH organized 13 food microbiology PTs including 10-28 participants. Three types of PT items were used: genuine food samples, sterile food samples and reference materials. The commutability of the artificial samples (reference material or sterile samples) was assessed by plotting the distribution of the results on natural and artificial PT samples. This comparison highlighted matrix-correlated issues when nonfood matrices, such as reference materials, were used. Artificially inoculated food samples, on the other hand, raised only isolated commutability issues. In the organization of a PT-scheme, authentic or artificially inoculated food samples are necessary to accurately evaluate the analytical performances. Reference materials, used as PT items because of their convenience, may present commutability issues leading to inaccurate penalizing conclusions for methods that would have provided accurate results on food samples. For the first time, the commutability of food microbiology PT samples was investigated. The nature of the samples provided by the organizer turned out to be an important factor because matrix effects can impact on the analytical results. © 2013 The Society for Applied Microbiology.

Etiology of parapneumonic effusion and pleural empyema in children. The role of conventional and molecular microbiological tests.

PubMed

Krenke, Katarzyna; Sadowy, Ewa; Podsiadły, Edyta; Hryniewicz, Waleria; Demkow, Urszula; Kulus, Marek

2016-07-01

An increasing incidence of parapneumonic effusion and pleural empyema (PPE/PE) has been reported in recent studies. As only few data on etiology of PPE/PE in Central Europe have been reported, we undertook a study on the etiology of PPE/PE in children, using both standard culture and molecular techniques. This prospective study was conducted between June 2011 and December 2013. Consecutive children with PPE/PE complicating community acquired pneumonia, who required diagnostic/therapeutic thoracentesis were included. Blood and pleural fluid samples for microbiological cultures were collected. Molecular methods were applied to identify Streptococcus pneumonia, Haemophilus influenzae, Staphylococcus aureus, Streptococcus pyogenes, Mycoplasma pneumoniae, Chlamydophila pneumoniae, and respiratory viruses in pleural fluid. The study group included 64 children, median age 4 (1-15). Seven of 64 (10.9%) blood cultures and 11 of 64 (17.2%) pleural fluid cultures revealed bacterial growth. The most common bacteria detected was S. pneumoniae (13 blood and pleural fluid samples from 11/64 (17.2%) children). DNA sequences of typical bacteria were found in 29/64 (45.3%) pleural fluid samples. S. pneumoniae was identified in 90% of these samples. The most common serotypes were: serotype 6B in 9/26 (36.6%), 19A in 6/26 (23%), serotype 3 in 3/26 (11.5%), 6A and 23F (both in 2/26 i.e. 7.7%) patients. Molecular methods identified atypical bacteria in 8/58 (13.8%) and respiratory viruses in 12/58 (20.7%) pleural fluid samples. S. pneumoniae, in particular serotype 6B and 19A, is the most common etiologic agent of PPE/PE in Polish children. The use of PCR significantly improves pathogen identification in pleural fluid. Copyright © 2016 Elsevier Ltd. All rights reserved.

Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring.

PubMed

Van Nevel, S; Koetzsch, S; Proctor, C R; Besmer, M D; Prest, E I; Vrouwenvelder, J S; Knezev, A; Boon, N; Hammes, F

2017-04-15

Drinking water utilities and researchers continue to rely on the century-old heterotrophic plate counts (HPC) method for routine assessment of general microbiological water quality. Bacterial cell counting with flow cytometry (FCM) is one of a number of alternative methods that challenge this status quo and provide an opportunity for improved water quality monitoring. After more than a decade of application in drinking water research, FCM methodology is optimised and established for routine application, supported by a considerable amount of data from multiple full-scale studies. Bacterial cell concentrations obtained by FCM enable quantification of the entire bacterial community instead of the minute fraction of cultivable bacteria detected with HPC (typically < 1% of all bacteria). FCM measurements are reproducible with relative standard deviations below 3% and can be available within 15 min of samples arriving in the laboratory. High throughput sample processing and complete automation are feasible and FCM analysis is arguably less expensive than HPC when measuring more than 15 water samples per day, depending on the laboratory and selected staining procedure(s). Moreover, many studies have shown FCM total (TCC) and intact (ICC) cell concentrations to be reliable and robust process variables, responsive to changes in the bacterial abundance and relevant for characterising and monitoring drinking water treatment and distribution systems. The purpose of this critical review is to initiate a constructive discussion on whether FCM could replace HPC in routine water quality monitoring. We argue that FCM provides a faster, more descriptive and more representative quantification of bacterial abundance in drinking water. Copyright © 2017 Elsevier Ltd. All rights reserved.

AN OVERVIEW OF PATHOGEN RESEARCH IN THE MICROBIOLOGICAL AND CHEMICAL EXPOSURE ASSESSMENT RESEARCH DIVISION

EPA Science Inventory

The Microbiological and Chemical Exposure Assessment Research Division of the EPA Office of Research and Development's National Exposure Research Laboratory has a robust in-house research program aimed at developing better occurrence and exposure methods for waterborne pathogens....

[Infection control team (ICT) in cooperation with microbiology laboratories].

PubMed

Okazaki, Mitsuhiro

2012-10-01

Infection control as a medical safety measure is an important issue in all medical facilities. In order to tackle this measure, cooperation between the infection control team (ICT) and microbiological laboratory is indispensable. Multiple drug-resistant bacteria have shifted from Gram-positive bacteria to Gram-negative bacilli within the last ten years. There are also a variety of bacilli, complicating the examination method and test results further. Therefore, cooperation between the ICT and microbiological laboratory has become important to understand examination results and to use them. In order to maintain functional cooperation, explanatory and communicative ability between the microbiological laboratory and ICT is required every day. Such positive information exchange will develop into efficient and functional ICT activity.

Revolutionizing Clinical Microbiology Laboratory Organization in Hospitals with In Situ Point-of-Care

PubMed Central

Cohen-Bacrie, Stéphan; Ninove, Laetitia; Nougairède, Antoine; Charrel, Rémi; Richet, Hervé; Minodier, Philippe; Badiaga, Sékéné; Noël, Guilhem; La Scola, Bernard; de Lamballerie, Xavier; Drancourt, Michel; Raoult, Didier

2011-01-01

Background Clinical microbiology may direct decisions regarding hospitalization, isolation and anti-infective therapy, but it is not effective at the time of early care. Point-of-care (POC) tests have been developed for this purpose. Methods and Findings One pilot POC-lab was located close to the core laboratory and emergency ward to test the proof of concept. A second POC-lab was located inside the emergency ward of a distant hospital without a microbiology laboratory. Twenty-three molecular and immuno-detection tests, which were technically undemanding, were progressively implemented, with results obtained in less than four hours. From 2008 to 2010, 51,179 tests yielded 6,244 diagnoses. The second POC-lab detected contagious pathogens in 982 patients who benefited from targeted isolation measures, including those undertaken during the influenza outbreak. POC tests prevented unnecessary treatment of patients with non-streptococcal tonsillitis (n = 1,844) and pregnant women negative for Streptococcus agalactiae carriage (n = 763). The cerebrospinal fluid culture remained sterile in 50% of the 49 patients with bacterial meningitis, therefore antibiotic treatment was guided by the molecular tests performed in the POC-labs. With regard to enterovirus meningitis, the mean length-of-stay of infected patients over 15 years old significantly decreased from 2008 to 2010 compared with 2005 when the POC was not in place (1.43±1.09 versus 2.91±2.31 days; p = 0.0009). Altogether, patients who received POC tests were immediately discharged nearly thrice as often as patients who underwent a conventional diagnostic procedure. Conclusions The on-site POC-lab met physicians' needs and influenced the management of 8% of the patients that presented to emergency wards. This strategy might represent a major evolution of decision-making regarding the management of infectious diseases and patient care. PMID:21811599

Kinetic microplate bioassays for relative potency of antibiotics improved by partial Least Square (PLS) regression.

PubMed

Francisco, Fabiane Lacerda; Saviano, Alessandro Morais; Almeida, Túlia de Souza Botelho; Lourenço, Felipe Rebello

2016-05-01

Microbiological assays are widely used to estimate the relative potencies of antibiotics in order to guarantee the efficacy, safety, and quality of drug products. Despite of the advantages of turbidimetric bioassays when compared to other methods, it has limitations concerning the linearity and range of the dose-response curve determination. Here, we proposed to use partial least squares (PLS) regression to solve these limitations and to improve the prediction of relative potencies of antibiotics. Kinetic-reading microplate turbidimetric bioassays for apramacyin and vancomycin were performed using Escherichia coli (ATCC 8739) and Bacillus subtilis (ATCC 6633), respectively. Microbial growths were measured as absorbance up to 180 and 300min for apramycin and vancomycin turbidimetric bioassays, respectively. Conventional dose-response curves (absorbances or area under the microbial growth curve vs. log of antibiotic concentration) showed significant regression, however there were significant deviation of linearity. Thus, they could not be used for relative potency estimations. PLS regression allowed us to construct a predictive model for estimating the relative potencies of apramycin and vancomycin without over-fitting and it improved the linear range of turbidimetric bioassay. In addition, PLS regression provided predictions of relative potencies equivalent to those obtained from agar diffusion official methods. Therefore, we conclude that PLS regression may be used to estimate the relative potencies of antibiotics with significant advantages when compared to conventional dose-response curve determination. Copyright © 2016 Elsevier B.V. All rights reserved.

[Cariogenic properties of various snacks in animal experiments].

PubMed

Karle, E J; Gehring, F; Trautner, K

1977-09-01

In a conventional animal experiment with rats, the cariogenic properties of different snacks were studied and compared. Bananas caused the highest caries incidence, apples the lowest. In between ranged the caries values of two other tested sweets, wafers and gum drops. The differences in caries incidence were due to specific chemo-physical properties (stickiness, fat content). In addition to the evaluation of caries incidence, microbiological plaque examinations and sugar analyses of the tested substances were carried out.

Microbiological methods for surveillance of carrier status of multiresistant bacteria.

PubMed

Oteo, Jesús; Bou, Germán; Chaves, Fernando; Oliver, Antonio

2017-12-01

The presence of colonised patients is one of the main routes for the spread of multiresistant bacteria, and its containment is a clinical and public health priority. Surveillance studies are essential for early detection of colonisation by these bacteria. This article discusses the different microbiological methods, both based on culturing and molecular methods, for detection of carriers of multiresistant bacteria. Those species with a high clinical/epidemiological impact or generating therapeutic difficulties are included: Methicillin-resistant Staphylococcus aureus, Enterococcus spp. resistant to glycopeptides, enterobacteriaceae producing extended spectrum β-lactamases and plasmid-mediated AmpC, carbapenemases producing enterobacteriaceae, Acinetobacter baumannii and multiresistant Pseudomonas aeruginosa. The information in this document should be considered as a structure matrix to be tailored to the specific needs of each centre. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Providing a sound habitat for man in space

NASA Astrophysics Data System (ADS)

Stranger-Johannessen, Maria

Microbiological growth on materials in an indoor environment contributes to the well known "sick building syndrome". The inhabitants' health and well-being is affected by injurious vapours and odours given off to the air. This is particularly pronounced in new and better tightened houses with unconventional building materials and wider employment of air conditioning. The European Space Agency has recognized the problems to be expected in a totally closed and self-supported long-term habitat and has induced work on the selection of materials, resistant to microbiological growth, and on other microbial contamination control measures. Requirements and procedures are being established as a basis for the microbiological cleanliness of the manned space environment and for the avoidance of microbiological growth on materials and equipment. Methods are being developed, suitable for testing and predicting the resistivity to microbiological growth of materials to be used in long-term space habitats.

Classification of Shiga toxin-producing escherichia coli (STEC) serotypes with hyperspectral microscope imagery

NASA Astrophysics Data System (ADS)

Park, Bosoon; Windham, William R.; Ladely, Scott R.; Gurram, Prudhvi; Kwon, Heesung; Yoon, Seung-Chul; Lawrence, Kurt C.; Narang, Neelam; Cray, William C.

2012-05-01

Non-O157:H7 Shiga toxin-producing Escherichia coli (STEC) strains such as O26, O45, O103, O111, O121 and O145 are recognized as serious outbreak to cause human illness due to their toxicity. A conventional microbiological method for cell counting is laborious and needs long time for the results. Since optical detection method is promising for realtime, in-situ foodborne pathogen detection, acousto-optical tunable filters (AOTF)-based hyperspectral microscopic imaging (HMI) method has been developed for identifying pathogenic bacteria because of its capability to differentiate both spatial and spectral characteristics of each bacterial cell from microcolony samples. Using the AOTF-based HMI method, 89 contiguous spectral images could be acquired within approximately 30 seconds with 250 ms exposure time. From this study, we have successfully developed the protocol for live-cell immobilization on glass slides to acquire quality spectral images from STEC bacterial cells using the modified dry method. Among the contiguous spectral imagery between 450 and 800 nm, the intensity of spectral images at 458, 498, 522, 546, 570, 586, 670 and 690 nm were distinctive for STEC bacteria. With two different classification algorithms, Support Vector Machine (SVM) and Sparse Kernel-based Ensemble Learning (SKEL), a STEC serotype O45 could be classified with 92% detection accuracy.

Evaluation of two recommended disinfection methods for cleaning cloths used in food services of southern Brazil

PubMed Central

Bartz, Sabrina; Tondo, Eduardo Cesar

2013-01-01

In the State of Rio Grande do Sul (RS), Southern Brazil, a good manufacturing practices regulation was published recommending two disinfection methods for cleaning cloths used in food services. The aim of the present study was to evaluate the efficacy of those methods. Cleaning cloths were sampled without prior notice at food services, on common working days. For the analyses, the cloths were divided in two sub-samples, being one of them microbiologically analyzed. The second sub-sample was further divided in two pieces and submitted to hand washing for two minutes. After that, one piece was boiled in water for 15 min and the other one was soaked in a 200 ppm sodium hypochlorite solution for 15 min. Both pieces of cloth were submitted to microbiological analyses. Cleaning cloths presented total aerobic mean counts of 6.9 ± 6.7 log/cm2. All cleaning cloths presented coliform contamination, and 40% demonstrated mean counts of 6.2 ± 5.6 log/cm2. Presumptive S. aureus mean counts of 5.5 ± 4.9 log/cm2 were found. No statistic correlation was observed among the number of meals served daily in the food services and the microbiological contamination levels. After washing and disinfection, microbiological counts were significantly (p < 0.05) reduced by both methods, achieving an approximately 5 log reduction. The reductions achieved by the sodium hypochlorite soaking method and the boiling method were not significantly different. Thus, it was possible to conclude that both recommended methods were suitable to disinfect cleaning cloths used in food services. PMID:24516443

Evaluation of two recommended disinfection methods for cleaning cloths used in food services of southern Brazil.

PubMed

Bartz, Sabrina; Tondo, Eduardo Cesar

2013-01-01

In the State of Rio Grande do Sul (RS), Southern Brazil, a good manufacturing practices regulation was published recommending two disinfection methods for cleaning cloths used in food services. The aim of the present study was to evaluate the efficacy of those methods. Cleaning cloths were sampled without prior notice at food services, on common working days. For the analyses, the cloths were divided in two sub-samples, being one of them microbiologically analyzed. The second sub-sample was further divided in two pieces and submitted to hand washing for two minutes. After that, one piece was boiled in water for 15 min and the other one was soaked in a 200 ppm sodium hypochlorite solution for 15 min. Both pieces of cloth were submitted to microbiological analyses. Cleaning cloths presented total aerobic mean counts of 6.9 ± 6.7 log/cm(2). All cleaning cloths presented coliform contamination, and 40% demonstrated mean counts of 6.2 ± 5.6 log/cm(2). Presumptive S. aureus mean counts of 5.5 ± 4.9 log/cm(2) were found. No statistic correlation was observed among the number of meals served daily in the food services and the microbiological contamination levels. After washing and disinfection, microbiological counts were significantly (p < 0.05) reduced by both methods, achieving an approximately 5 log reduction. The reductions achieved by the sodium hypochlorite soaking method and the boiling method were not significantly different. Thus, it was possible to conclude that both recommended methods were suitable to disinfect cleaning cloths used in food services.

[Frequency of Candida in root canals of teeth with primary and persistent endodontic infections].

PubMed

Bernal-Treviño, Angel; González-Amaro, Ana María; Méndez González, Verónica; Pozos-Guillen, Amaury

Microbiological identification in endodontic infections has focused mainly on bacteria without giving much attention to yeasts, which, due to their virulence factors, can affect the outcomes of root canal treatment. To determine the frequency of Candida in anaerobic conditions in root canals with primary and persistent endodontic infection, as well as to evaluate a microbiological sampling method using aspiration compared to the traditional absorption method with paper points. Fifty microbiological samples were obtained from teeth of 47 patients requiring endodontic treatments, due to either primary or persistent infections. Two microbiological sampling methods were used: an aspiration method, and the traditional paper point absorption method. In each of these methods, two types of medium were used (M 1 -M 4 ). Samples were cultured under anaerobic conditions until reaching 0.5 McFarland turbidity, and then inoculated on Sabouraud dextrose, as well as on anaerobic enriched blood agar plates. Macroscopic and microscopic observations of the colonies were performed. The germ-tube test, growth on CHROMagar, and biochemical identification were performed on the isolated yeasts. Fungal infection was found in 18 (36%) samples out of the 50 teeth evaluated. In the 18 samples positive for fungal infection, 15 out of 36 (41.6%) teeth were taken from a primary infection, and 3 out of 14 (21.4%) from a persistent infection. The aspiration method using Sabouraud dextrose medium recovered a greater diversity of species. Yeasts frequency was higher in teeth with primary infections compared to teeth with persistent infections. The predominant yeast species was Candida albicans. The aspirating sampling method was more efficient in the recovery of Candida isolates than the traditional absorption method. Copyright © 2018 Asociación Española de Micología. Publicado por Elsevier España, S.L.U. All rights reserved.

A new microbiological risk analysis tool for cryptosporidium to support decision making in drinking water treatment plants

NASA Astrophysics Data System (ADS)

Macián-Cervera, Javier; Escuder-Bueno, Ignacio

2017-04-01

One of the main hazards over the water quality in the water supply systems from surface raw water is cryptosporidium, considered by World Health Organization, as the most dangerous emergent pathogen. Analitycal methods for cryptosporidium are expensive, laborious and they do not have enough precission, on the other hand, labs analyze discretal samples, while drinking water production is a continuous process. In that point, the introduction of risk models in necessary to check the ability of safety of the water produced. The advances in tools able to quantify risk applied to conventional treatment drinking water treatment plants is quite useful for the operators, able to assess about decisions in operation and in investments. The model is applied into a real facility. With the results, it's possible to conclude interesting guidelines and policies about improving plant's operation mode. The main conclusion is that conventional treatment is able to work as effective barrier against cryptosporidium, but it is necessary to assess the risk of the plant while it is operating. Taking into account limitations of knowledge, risk estimation can rise non tolerable levels. In that situation, the plant must make investments in the treatment improving the operation, to get tolerable risk levels.

Performance of the Chromogenic Medium CHROMagar Staph Aureus and the Staphychrom Coagulase Test in the Detection and Identification of Staphylococcus aureus in Clinical Specimens

PubMed Central

Carricajo, Anne; Treny, Axel; Fonsale, Nathalie; Bes, Michele; Reverdy, Marie Elisabeth; Gille, Yves; Aubert, Gerald; Freydiere, Anne Marie

2001-01-01

CHROMagar Staph aureus (CSAM) (CHROMagar Microbiology, Paris, France) is a new chromogenic medium designed to enable detection of colonies of Staphylococcus aureus by their pink color. A total of 775 specimens were cultured in parallel on CHROMagar Staph aureus and conventional media. Among the 267 S. aureus strains recovered on at least one medium, 263 were isolated on CSAM medium (sensitivity, 98.5%), and 245 (sensitivity, 91.8%) were isolated on conventional media. The specificity of presumptive identification of S. aureus on the basis of pink colony color on CSAM medium was 97% (493 of 508). This specificity increased to 100% when coagulase detection with the Staphychrom coagulase test was added and to 98.8% when S. aureus surface components were detected by agglutination in the Pastorex Staph Plus test. Susceptibility testing of 67 S. aureus strains, performed in parallel on pink CSAM colonies and on colonies grown on blood agar, gave similar results. Thus, rapid and accurate recognition and identification of S. aureus isolates were achieved with CSAM as the primary isolation medium, followed by the staphylocoagulase Staphychrom test. Antimicrobial susceptibility testing (disk-diffusion method or ATB STAPH System) can be performed directly on pink CSAM colonies. PMID:11427572

Digital droplet multiple displacement amplification (ddMDA) for whole genome sequencing of limited DNA samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rhee, Minsoung; Light, Yooli K.; Meagher, Robert J.

Here, multiple displacement amplification (MDA) is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples) before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA) technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently,more » the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet), ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli) compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.« less

Digital droplet multiple displacement amplification (ddMDA) for whole genome sequencing of limited DNA samples

DOE PAGES

Rhee, Minsoung; Light, Yooli K.; Meagher, Robert J.; ...

2016-05-04

Here, multiple displacement amplification (MDA) is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples) before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA) technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently,more » the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet), ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli) compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.« less

Microbiological quality of spinach irrigated with reclaimed wastewater and roof-harvest water

USDA-ARS?s Scientific Manuscript database

Aims: The effect of reclaimed wastewater (RCW) and roof-harvest rainwater (RHW) on microbiological quality of irrigated spinach was investigated. Methods and Results: Spinach grown in controlled environment chamber was irrigated by RCW, RHW, or creek water (CW; control water) for four weeks, and th...

Introduction of Molecular Methods into a Food Microbiology Curriculum

ERIC Educational Resources Information Center

Pleitner, Aaron M.; Hammons, Susan R.; McKenzie, Emily; Cho, Young-Hee; Oliver, Haley F.

2014-01-01

Maintaining current, relevant curriculum in undergraduate Food Microbiology courses is essential for training future experts in food quality and safety. Having an understanding of the fundamental techniques (for example, polymerase chain reaction [PCR]) that are used in the food industry and regulatory agencies is critical for students entering…

Evaluation of MALDI-TOF MS (Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry) for routine identification of anaerobic bacteria.

PubMed

Rodríguez-Sánchez, Belén; Alcalá, Luis; Marín, Mercedes; Ruiz, Adrián; Alonso, Elena; Bouza, Emilio

2016-12-01

Information regarding the use of MALDI-TOF MS as an alternative to conventional laboratory methods for the rapid and reliable identification of bacterial isolates is still limited. In this study, MALDI-TOF MS was evaluated on 295 anaerobic isolates previously identified by 16S rRNA gene sequencing and with biochemical tests (Rapid ID 32A system, BioMérieux). In total, 85.8% of the isolates were identified by MALDI-TOF MS at the species level vs 49.8% using the Rapid ID 32A system (p < 0.0001). None of the isolates was discordantly identified at the genus level using MALDI-TOF MS and only 9 of them could not be identified using the method. Thus, our results show that MALDI-TOF MS is a robust and reliable tool for the identification of anaerobic isolates in the microbiology laboratory. Its implementation will reduce the turnaround time for a final identification and the number of isolates that require 16S rRNA sequencing. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification and antimicrobial susceptibility testing of Staphylococcus vitulinus by the BD phoenix automated microbiology system.

PubMed

Cirković, Ivana; Hauschild, Tomasz; Jezek, Petr; Dimitrijević, Vladimir; Vuković, Dragana; Stepanović, Srdjan

2008-08-01

This study evaluated the performance of the BD Phoenix system for the identification (ID) and antimicrobial susceptibility testing (AST) of Staphylococcus vitulinus. Of the 10 S. vitulinus isolates included in the study, 2 were obtained from the Czech Collection of Microorganisms, 5 from the environment, 2 from human clinical samples, and 1 from an animal source. The results of conventional biochemical and molecular tests were used for the reference method for ID, while antimicrobial susceptibility testing performed in accordance with Clinical and Laboratory Standards Institute recommendations and PCR for the mecA gene were the reference for AST. Three isolates were incorrectly identified by the BD Phoenix system; one of these was incorrectly identified to the genus level, and two to the species level. The results of AST by the BD Phoenix system were in agreement with those by the reference method used. While the results of susceptibility testing compared favorably, the 70% accuracy of the Phoenix system for identification of this unusual staphylococcal species was not fully satisfactory.

Significance of Viable but Nonculturable Escherichia coli: Induction, Detection, and Control.

PubMed

Ding, Tian; Suo, Yuanjie; Xiang, Qisen; Zhao, Xihong; Chen, Shiguo; Ye, Xingqian; Liu, Donghong

2017-03-28

Diseases caused by foodborne or waterborne pathogens are emerging. Many pathogens can enter into the viable but nonculturable (VBNC) state, which is a survival strategy when exposed to harsh environmental stresses. Pathogens in the VBNC state have the ability to evade conventional microbiological detection methods, posing a significant and potential health risk. Therefore, controlling VBNC bacteria in food processing and the environment is of great importance. As the typical one of the gram-negatives, Escherichia coli ( E. coli ) is a widespread foodborne and waterborne pathogenic bacterium and is able to enter into a VBNC state in extreme conditions (similar to the other gram-negative bacteria), including inducing factors and resuscitation stimulus. VBNC E. coli has the ability to recover both culturability and pathogenicity, which may bring potential health risk. This review describes the concrete factors (nonthermal treatment, chemical agents, and environmental factors) that induce E. coli into the VBNC state, the condition or stimulus required for resuscitation of VBNC E. coli , and the methods for detecting VBNC E. coli . Furthermore, the mechanism of genes and proteins involved in the VBNC E. coli is also discussed in this review.

Culturomics: A New Kid on the Block of OMICS to Enable Personalized Medicine.

PubMed

Kambouris, Manousos E; Pavlidis, Cristiana; Skoufas, Efthymios; Arabatzis, Michael; Kantzanou, Maria; Velegraki, Aristea; Patrinos, George P

2018-02-01

This innovation analysis highlights the underestimated and versatile potential of the new field of culturomics and examines its relation to other OMICS system sciences such as infectiomics, metabolomics, phenomics, and pharmacomicrobiomics. The advent of molecular biology, followed by the emergence of various disciplines of the genomics, and most importantly metagenomics, brought about the sharp decline of conventional microbiology methods. Emergence of culturomics has a natural synergy with therapeutic and clinical genomic approaches so as to realize personalized medicine. Notably, the concept of culturomics expands on that of phenomics and allows a reintroduction of the culture-based phenotypic characterization into the 21st century research repertoire, bolstered by robust technology for automated and massive execution, but its potential is largely unappreciated at present; the few available references show unenthusiastic pursuit and in narrow applications. This has not to be so: depending on the specific brand of culturomics, the scope of applications may extend to medicine, agriculture, environmental sciences, pharmacomicrobiomics, and biotechnology innovation. Moreover, culturomics may produce Big Data. This calls for a new generation of data scientists and innovative ways of harnessing and valorizing Big Data beyond classical genomics. Much more detailed and objective classification and identification of microbiota may soon be at hand through culturomics, thus enabling precision diagnosis toward truly personalized medicine. Culturomics may both widen the scope of microbiology and improve its contributions to diagnostics and personalized medicine, characterizing microbes and determining their associations with health and disease dynamics.

Antimicrobial activity of wild mushroom extracts against clinical isolates resistant to different antibiotics.

PubMed

Alves, M J; Ferreira, I C F R; Martins, A; Pintado, M

2012-08-01

This work aimed to screen the antimicrobial activity of aqueous methanolic extracts of 13 mushroom species, collected in Bragança, against several clinical isolates obtained in Hospital Center of Trás-os-Montes and Alto Douro, Portugal. Microdilution method was used to determine the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC). MIC results showed that Russula delica and Fistulina hepatica extracts inhibited the growth of gram-negative (Escherichia coli, Morganella morganni and Pasteurella multocida) and gram-positive (Staphylococcus aureus, MRSA, Enterococcus faecalis, Listeria monocytogenes, Streptococcus agalactiae and Streptococcus pyogenes) bacteria. A bactericide effect of both extracts was observed in Past. multocida, Strep. agalactiae and Strep. pyogenes with MBC of 20, 10 and 5 mg ml⁻¹, respectively. Lepista nuda extract exhibited a bactericide effect upon Past. multocida at 5 mg ml⁻¹ and inhibited Proteus mirabilis at 20 mg ml⁻¹. Ramaria botrytis extract showed activity against Enterococcus faecalis and L. monocytogenes, being bactericide for Past. multocida, Strep. agalactiae (MBCs 20 mg ml⁻¹) and Strep. pyogenes (MBC 10 mg ml⁻¹). Leucopaxillus giganteus extract inhibited the growth of E. coli and Pr. mirabilis, being bactericide for Past. multocida, Strep. pyogenes and Strep. agalactiae. Fistulina hepatica, R. botrytis and R. delica are the most promising species as antimicrobial agents. Mushroom extracts could be an alternative as antimicrobials against pathogenic micro-organisms resistant to conventional treatments. © 2012The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Clinical diagnosis of ventilator associated pneumonia revisited: comparative validation using immediate post-mortem lung biopsies

PubMed Central

Fabregas, N.; Ewig, S.; Torres, A.; El-Ebiary, M.; Ramirez, J.; de la Bellacasa, J. P.; Bauer, T.; Cabello, H.

1999-01-01

BACKGROUND—A study was undertaken to assess the diagnostic value of different clinical criteria and the impact of microbiological testing on the accuracy of clinical diagnosis of suspected ventilator associated pneumonia (VAP).
METHODS—Twenty five deceased mechanically ventilated patients were studied prospectively. Immediately after death, multiple bilateral lung biopsy specimens (16 specimens/patient) were obtained for histological examination and quantitative lung cultures. The presence of both histological pneumonia and positive lung cultures was used as a reference test.
RESULTS—The presence of infiltrates on the chest radiograph and two of three clinical criteria (leucocytosis, purulent secretions, fever) had a sensitivity of 69% and a specificity of 75%; the corresponding numbers for the clinical pulmonary infection score (CPIS) were 77% and 42%. Non-invasive as well as invasive sampling techniques had comparable values. The combination of all techniques achieved a sensitivity of 85% and a specificity of 50%, and these values remained virtually unchanged despite the presence of previous treatment with antibiotics. When microbiological results were added to clinical criteria, adequate diagnoses originating from microbiological results which might have corrected false positive and false negative clinical judgements (n = 5) were countered by a similar proportion of inadequate diagnoses (n =6).
CONCLUSIONS—Clinical criteria had reasonable diagnostic values. CPIS was not superior to conventional clinical criteria. Non-invasive and invasive sampling techniques had diagnostic values comparable to clinical criteria. An algorithm guiding antibiotic treatment exclusively by microbiological results does not increase the overall diagnostic accuracy and carries the risk of undertreatment.

 PMID:10491448

Evaluation of fluorescence in situ hybridisation (FISH) for the detection of fungi directly from blood cultures and cerebrospinal fluid from patients with suspected invasive mycoses.

PubMed

Da Silva, Roberto Moreira; Da Silva Neto, João Ricardo; Santos, Carla Silvana; Frickmann, Hagen; Poppert, Sven; Cruz, Kátia Santana; Koshikene, Daniela; De Souza, João Vicente Braga

2015-01-31

The aim of this study was to evaluate the diagnostic performance of in-house FISH (fluorescence in situ hybridisation) procedures for the direct identification of invasive fungal infections in blood cultures and cerebrospinal fluid (CSF) samples and to compare these FISH results with those obtained using traditional microbiological techniques and PCR targeting of the ITS1 region of the rRNA gene. In total, 112 CSF samples and 30 positive blood cultures were investigated by microscopic examination, culture, PCR-RFLP and FISH. The sensitivity of FISH for fungal infections in CSF proved to be slightly better than that of conventional microscopy (India ink) under the experimental conditions, detecting 48 (instead of 46) infections in 112 samples. The discriminatory powers of traditional microbiology, PCR-RFLP and FISH for fungal bloodstream infections were equivalent, with the detection of 14 fungal infections in 30 samples. However, the mean times to diagnosis after the detection of microbial growth by automated blood culture systems were 5 hours, 20 hours and 6 days for FISH, PCR-RFLP and traditional microbiology, respectively. The results demonstrate that FISH is a valuable tool for the identification of invasive mycoses that can be implemented in the diagnostic routine of hospital laboratories.

[Molecular diagnostic methods of respiratory infections. Has the scheme diagnosis changed?].

PubMed

Vila Estapé, Jordi; Zboromyrska, Yuliya; Vergara Gómez, Andrea; Alejo Cancho, Izaskun; Rubio García, Elisa; Álvarez-Martínez, Miriam José; la Bellacasa Brugada, Jorge Puig de; Marcos Maeso, M Ángeles

2016-07-01

Lower respiratory tract infections remain one of the most common causes of mortality worldwide, which is why early diagnosis is crucial. Traditionally the microbiological diagnosis of these infections has been based on conventional methods including culture on artificial media for isolation of bacteria and fungi and cell cultures for virus and antibody or antigen detection using antigen-antibody reactions. The main drawback of the above mentioned methods is the time needed for an etiological diagnosis of the infection. The techniques based on molecular biology have drawn much attention in recent decades as tools for rapid diagnosis of infections. Some techniques are very expensive, especially those that can detect various microorganisms in the same reaction, therefore the question that arises is whether the cost of such testing is justified by the information obtained and by the clinical impact that its implementation will determine. In this article we make a review of the various techniques of molecular biology applied to the diagnosis of pneumonia and focus primarily on analysing the impact they may have on the management of patients with acute respiratory tract infections. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

Recent developments in the management of invasive fungal infections in patients with oncohematological diseases.

PubMed

Ruhnke, Markus; Schwartz, Stefan

2016-12-01

Patients with hematological cancer have a high risk of invasive fungal diseases (IFDs). These infections are mostly life threatening and an early diagnosis and initiation of appropriate antifungal therapy are essential for the clinical outcome. Most commonly, Aspergillus and Candida species are involved. However, other non- Aspergillus molds are increasingly be identified in cases of documented IFDs. Important risk factors are long lasting granulocytopenia with neutrophil counts below 500/μl for more than 10 days or graft- versus -host disease resulting from allogeneic stem-cell transplantation. For definite diagnosis of IFD, various diagnostic tools have to be applied, including conventional mycological culture and nonconventional microbiological tests such as antibody/antigen and molecular tests, as well as histopathology and radiology. In the last few years, various laboratory methods, like the Aspergillus GM immunoassay ( Aspergillus GM EIA), 1,3-ß-D-glucan (BG) assay or polymerase chain reaction (PCR) techniques have been developed for better diagnosis. Since no single indirect test, including radiological methods, provides the definite diagnosis of an invasive fungal infection, the combination of different diagnostic procedures, which include microbiological cultures, histological, serological and molecular methods like PCR together with the pattern of clinical presentation, may currently be the best strategy for the prompt diagnosis, initiation and monitoring of IFDs. Early start of antifungal therapy is mandatory, but clinical diagnostics often do not provide clear evidence of IFD. Integrated care pathways have been proposed for management and therapy of IFDs with either the diagnostic driven strategy using the preemptive antifungal therapy as opposed to the clinical or empirical driven strategy using the 'traditional' empirical antifungal therapy. Antifungal agents preferentially used for systemic therapy of invasive fungal infections are amphotericin B preparations, fluconazole, voriconazole, posaconazole, caspofungin, anidulafungin, micafungin, and most recently isavuconazole. Clinical decision making must consider licensing status, local experience and availability, pharmacological and economic aspects.

A review of microbiology service learning.

PubMed

Webb, Ginny

2017-02-01

Service learning is a teaching method that incorporates community engagement into the curriculum of a course. Service learning is becoming increasingly popular on college campuses and across disciplines. Studies have shown many benefits to service learning for the students and the community they serve. Service learning has been incorporated into science courses, including microbiology. This review will address the benefits to service learning and provide an overview of the various types of service-learning projects that have been completed in microbiology courses. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Pilot project for rapid Legionella testing.

PubMed

Pearson, Susan

2013-08-01

Susan Pearson BSc, a freelance journalist and communications consultant specialising in medicine and the environment (see also HEJ - April 2013), reports on discussions, at a recent educational seminar, on a pilot project undertaken by the Environmental Microbiology Unit at the Brighton and Sussex University Hospitals (BSUH) NHS Trust, which compared the effectiveness and accuracy of conventional 'culture' testing for Legionella in water systems, with a new, 'less labour-intensive', DNA-based testing system that can produce results 'in a matter of hours'.

An oral vaccine against candidiasis generated by a yeast molecular display system.

PubMed

Shibasaki, Seiji; Aoki, Wataru; Nomura, Takashi; Miyoshi, Ayuko; Tafuku, Senji; Sewaki, Tomomitsu; Ueda, Mitsuyoshi

2013-12-01

Enolase 1 (Eno1p) of Candida albicans is an immunodominant antigen. However, conventional technologies for preparing an injectable vaccine require purification of the antigenic protein and preparation of an adjuvant. To develop a novel type of oral vaccine against candidiasis, we generated Saccharomyces cerevisiae cells that display the Eno1p antigen on their surfaces. Oral delivery of the engineered S. cerevisiae cells prolonged survival rate of mice that were subsequently challenged with C. albicans. Given that a vaccine produced using molecular display technology avoids the need for protein purification, this oral vaccine offers a promising alternative to the use of conventional and injectable vaccines for preventing a range of infectious diseases. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry.

PubMed

Alcaide, F; Amlerová, J; Bou, G; Ceyssens, P J; Coll, P; Corcoran, D; Fangous, M-S; González-Álvarez, I; Gorton, R; Greub, G; Hery-Arnaud, G; Hrábak, J; Ingebretsen, A; Lucey, B; Marekoviċ, I; Mediavilla-Gradolph, C; Monté, M R; O'Connor, J; O'Mahony, J; Opota, O; O'Reilly, B; Orth-Höller, D; Oviaño, M; Palacios, J J; Palop, B; Pranada, A B; Quiroga, L; Rodríguez-Temporal, D; Ruiz-Serrano, M J; Tudó, G; Van den Bossche, A; van Ingen, J; Rodriguez-Sanchez, B

2018-06-01

The implementation of MALDI-TOF MS for microorganism identification has changed the routine of the microbiology laboratories as we knew it. Most microorganisms can now be reliably identified within minutes using this inexpensive, user-friendly methodology. However, its application in the identification of mycobacteria isolates has been hampered by the structure of their cell wall. Improvements in the sample processing method and in the available database have proved key factors for the rapid and reliable identification of non-tuberculous mycobacteria isolates using MALDI-TOF MS. The main objective is to provide information about the proceedings for the identification of non-tuberculous isolates using MALDI-TOF MS and to review different sample processing methods, available databases, and the interpretation of the results. Results from relevant studies on the use of the available MALDI-TOF MS instruments, the implementation of innovative sample processing methods, or the implementation of improved databases are discussed. Insight about the methodology required for reliable identification of non-tuberculous mycobacteria and its implementation in the microbiology laboratory routine is provided. Microbiology laboratories where MALDI-TOF MS is available can benefit from its capacity to identify most clinically interesting non-tuberculous mycobacteria in a rapid, reliable, and inexpensive manner. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Methods for collection and analysis of aquatic biological and microbiological samples

USGS Publications Warehouse

Greeson, Phillip E.; Ehlke, T.A.; Irwin, G.A.; Lium, B.W.; Slack, K.V.

1977-01-01

Chapter A4 contains methods used by the U.S. Geological Survey to collect, preserve, and analyze waters to determine their biological and microbiological properties. Part 1 discusses biological sampling and sampling statistics. The statistical procedures are accompanied by examples. Part 2 consists of detailed descriptions of more than 45 individual methods, including those for bacteria, phytoplankton, zooplankton, seston, periphyton, macrophytes, benthic invertebrates, fish and other vertebrates, cellular contents, productivity, and bioassays. Each method is summarized, and the application, interferences, apparatus, reagents, collection, analysis, calculations, reporting of results, precision and references are given. Part 3 consists of a glossary. Part 4 is a list of taxonomic references.

Competency assessment of microbiology medical laboratory technologists in Ontario, Canada.

PubMed

Desjardins, Marc; Fleming, Christine Ann

2014-08-01

Accreditation in Ontario, Canada, requires that licensed clinical laboratories participate in external quality assessment (also known as proficiency testing) and perform competency evaluation of their staff. To assess the extent of ongoing competency assessment practices, the Quality Management Program--Laboratory Services (QMP-LS) Microbiology Committee surveyed all 112 licensed Ontario microbiology laboratories. The questionnaire consisted of a total of 21 questions that included yes/no, multiple-choice, and short-answer formats. Participants were asked to provide information about existing programs, the frequency of testing, what areas are evaluated, and how results are communicated to the staff. Of the 111 responding laboratories, 6 indicated they did not have a formal evaluation program since they perform only limited bacteriology testing. Of the remaining 105 respondents, 87% perform evaluations at least annually or every 2 years, and 61% include any test or task performed, whereas 16% and 10% focus only on problem areas and high-volume complex tasks, respectively. The most common methods of evaluation were review of external quality assessment (EQA) challenges, direct observation, and worksheet review. With the exception of one participant, all communicate results to staff, and most take remedial action to correct the deficiencies. Although most accredited laboratories have a program to assess the ongoing competency of their staff, the methods used are not standardized or consistently applied, indicating that there is room for improvement. The survey successfully highlighted potential areas for improvement and allowed the QMP-LS Microbiology Committee to provide guidance to Ontario laboratories for establishing or improving existing microbiology-specific competency assessment programs. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Microbiological methods for the water recovery systems test, revision 1.1

NASA Technical Reports Server (NTRS)

Rhoads, Tim; Kilgore, M. V., Jr.; Mikell, A. T., Jr.

1990-01-01

Current microbiological parameters specified to verify microbiological quality of Space Station Freedom water quality include the enumeration of total bacteria, anaerobes, aerobes, yeasts and molds, enteric bacteria, gram positives, gram negatives, and E. coli. In addition, other parameters have been identified as necessary to support the Water Recovery Test activities to be conducted at the NASA/MSFC later this year. These other parameters include aerotolerant eutrophic mesophiles, legionellae, and an additional method for heterotrophic bacteria. If inter-laboratory data are to be compared to evaluate quality, analytical methods must be eliminated as a variable. Therefore, each participating laboratory must utilize the same analytical methods and procedures. Without this standardization, data can be neither compared nor validated between laboratories. Multiple laboratory participation represents a conservative approach to insure quality and completeness of data. Invariably, sample loss will occur in transport and analyses. Natural variance is a reality on any test of this magnitude and is further enhanced because biological entities, capable of growth and death, are specific parameters of interest. The large variation due to the participation of human test subjects has been noted with previous testing. The resultant data might be dismissed as 'out of control' unless intra-laboratory control is included as part of the method or if participating laboratories are not available for verification. The purpose of this document is to provide standardized laboratory procedures for the enumeration of certain microorganisms in water and wastewater specific to the water recovery systems test. The document consists of ten separate cultural methods and one direct count procedure. It is not intended nor is it implied to be a complete microbiological methods manual.

Estimation of the POD function and the LOD of a qualitative microbiological measurement method.

PubMed

Wilrich, Cordula; Wilrich, Peter-Theodor

2009-01-01

Qualitative microbiological measurement methods in which the measurement results are either 0 (microorganism not detected) or 1 (microorganism detected) are discussed. The performance of such a measurement method is described by its probability of detection as a function of the contamination (CFU/g or CFU/mL) of the test material, or by the LOD(p), i.e., the contamination that is detected (measurement result 1) with a specified probability p. A complementary log-log model was used to statistically estimate these performance characteristics. An intralaboratory experiment for the detection of Listeria monocytogenes in various food matrixes illustrates the method. The estimate of LOD50% is compared with the Spearman-Kaerber method.

Evaluation of the performance of the IQ-check kits and the USDA microbiology laboratory guidebook methods for detection of Shiga Toxin-Producing E. coli (STEC) and STEC and Salmonella simultaneously in ground beef

USDA-ARS?s Scientific Manuscript database

Aims: To evaluate the performance of the IQ-Check kits and the USDA Microbiology Laboratory Guidebook (MLG) methods for detection of the top 7 Shiga toxin-producing E. coli (STEC) (O157:H7, O26, O45, O103, O111, O121, and O145) in ground beef and both STEC and Salmonella in co-inoculated samples. M...

Flow cytometry and real-time quantitative PCR as tools for assessing plasmid persistence.

PubMed

Loftie-Eaton, Wesley; Tucker, Allison; Norton, Ann; Top, Eva M

2014-09-01

The maintenance of a plasmid in the absence of selection for plasmid-borne genes is not guaranteed. However, plasmid persistence can evolve under selective conditions. Studying the molecular mechanisms behind the evolution of plasmid persistence is key to understanding how plasmids are maintained under nonselective conditions. Given the current crisis of rapid antibiotic resistance spread by multidrug resistance plasmids, this insight is of high medical relevance. The conventional method for monitoring plasmid persistence (i.e., the fraction of plasmid-containing cells in a population over time) is based on cultivation and involves differentiating colonies of plasmid-containing and plasmid-free cells on agar plates. However, this technique is time-consuming and does not easily lend itself to high-throughput applications. Here, we present flow cytometry (FCM) and real-time quantitative PCR (qPCR) as alternative tools for monitoring plasmid persistence. For this, we measured the persistence of a model plasmid, pB10::gfp, in three Pseudomonas hosts and in known mixtures of plasmid-containing and -free cells. We also compared three performance criteria: dynamic range, resolution, and variance. Although not without exceptions, both techniques generated estimates of overall plasmid loss rates that were rather similar to those generated by the conventional plate count (PC) method. They also were able to resolve differences in loss rates between artificial plasmid persistence assays. Finally, we briefly discuss the advantages and disadvantages for each technique and conclude that, overall, both FCM and real-time qPCR are suitable alternatives to cultivation-based methods for routine measurement of plasmid persistence, thereby opening avenues for high-throughput analyses. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

HIV association with conventional STDS (sexual transmitted diseases) in Lagos State, Nigeria.

PubMed

Otuonye, N M; Olukoya, D K; Odunukwe, N N; Idigbe, E O; Udeaja, M N; Bamidele, M; Onyewuchie, J I; Oparaugu, C T; Ayelari, O S; Oyekunle, B

2002-01-01

The study examined a possible association between HIV infection and conventional sexually transmitted diseases (STDS) in a population of 700 patients seen in some hospitals and clinics in Lagos State between November 1997 and December 1999. The patients were drawn mainly from LUTH and Jolad hospitals in Lagos State. In these hospitals, patients who presented with symptoms of STDS were screened clinically and microbiologically for agents of STDS and HIV antibodies. Screening was carried out using conventional methods. A total of 150 (21.5%) were found positive for various STDS while 550 (78.5%) were negative Also, 109 (15.8%) were sero-positive for HIV while 591 (84.4%) were sero-negative. The frequency of STDS diagnosed were, Treponema pallidum, 38(25.3%), Neisseria gonorrhoea 3(2.0%), Chlamydia trachomatis 26(17.3), Hepatitis B virus 60(40.0%) Staphylococcus aureaus, 20 (13.3%) and Candida albicans 3(2.0%). Data showed that Syphillis was the most prevalent STDS diagnosed while Calbicans and N. gonorrhoea are the least. Amongst the 150 (21.5%) patients positive with STDS, 82(54.65%) were found to be positive for HIV antibodies. The remaining 68(45.3%) patients were negative for HIV. The difference in sero-prevalence on the true group of patients rates was significant. The higher rate in the STDS patients strongly suggest some association between HIV infections andSTDS amongst the patients studied p = 0.05. It was also recorded that HIV-1 infection is four times more prevalent than HIV-2 in these patients.

Are the defined substrate-based methods adequate to determine the microbiological quality of natural recreational waters?

PubMed

Valente, Marta Sofia; Pedro, Paulo; Alonso, M Carmen; Borrego, Juan J; Dionísio, Lídia

2010-03-01

Monitoring the microbiological quality of water used for recreational activities is very important to human public health. Although the sanitary quality of recreational marine waters could be evaluated by standard methods, they are time-consuming and need confirmation. For these reasons, faster and more sensitive methods, such as the defined substrate-based technology, have been developed. In the present work, we have compared the standard method of membrane filtration using Tergitol-TTC agar for total coliforms and Escherichia coli, and Slanetz and Bartley agar for enterococci, and the IDEXX defined substrate technology for these faecal pollution indicators to determine the microbiological quality of natural recreational waters. ISO 17994:2004 standard was used to compare these methods. The IDEXX for total coliforms and E. coli, Colilert, showed higher values than those obtained by the standard method. Enterolert test, for the enumeration of enterococci, showed lower values when compared with the standard method. It may be concluded that more studies to evaluate the precision and accuracy of the rapid tests are required in order to apply them for routine monitoring of marine and freshwater recreational bathing areas. The main advantages of these methods are that they are more specific, feasible and simpler than the standard methodology.

Colloquium and Report on Systems Microbiology: Beyond Microbial Genomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merry R. Buckley

The American Academy of Microbiology convened a colloquium June 4-6, 2004 to confer about the scientific promise of systems microbiology. Participants discussed the power of applying a systems approach to the study of biology and to microbiology in particular, specifics about current research efforts, technical bottlenecks, requirements for data acquisition and maintenance, educational needs, and communication issues surrounding the field. A number of recommendations were made for removing barriers to progress in systems microbiology and for improving opportunities in education and collaboration. Systems biology, as a concept, is not new, but the recent explosion of genomic sequences and related datamore » has revived interest in the field. Systems microbiology, a subset of systems biology, represents a different approach to investigating biological systems. It attempts to examine the emergent properties of microorganisms that arise from the interplay of genes, proteins, other macromolecules, small molecules, organelles, and the environment. It is these interactions, often nonlinear, that lead to the emergent properties of biological systems that are generally not tractable by traditional approaches. As a complement to the long-standing trend toward reductionism, systems microbiology seeks to treat the organism or community as a whole, integrating fundamental biological knowledge with genomics, metabolomics, and other data to create an integrated picture of how a microbial cell or community operates. Systems microbiology promises not only to shed light on the activities of microbes, but will also provide biology the tools and approaches necessary for achieving a better understanding of life and ecosystems. Microorganisms are ideal candidates for systems biology research because they are relatively easy to manipulate and because they play critical roles in health, environment, agriculture, and energy production. Potential applications of systems microbiology research range from improvements in the management of bacterial infections to the development of commercial-scale microbial hydrogen generation. A number of technical challenges must be met to realize the potential of systems microbiology. Development of a new, comprehensive systems microbiology database that would be available to the entire research community was identified as the single most critical need. Other challenges include difficulties in measuring single-cell parameters, limitations in identifying and measuring metabolites and other products, the inability to cultivate diverse microbes, limits on data accessibility, computational limitations associated with data integration, the lack of sufficient functional gene annotations, needs for quantitative proteomics, and the inapplicability of current high throughput methods to all areas of systems microbiology. Difficulties have also been encountered in acquiring the necessary data, assuring the quality of that data, and in making data available to the community in a useful format. Problems with data quality assurance and data availability could be partially offset by launching a dedicated systems microbiology database. To be of greatest value to the field, a database should include systems data from all levels of analysis, including sequences, microarray data, proteomics data, metabolite measurements, data on protein-protein or protein-nucleic interactions, carbohydrate and small RNA profiles, information on cell surface markers, and appropriate supporting data. Regular updates of these databases and adherence to agreed upon data format standards are critical to the success of these resources. It was recommended that educational requirements for undergraduate and graduate students in microbiology be amended to better prepare the next generation of researchers for the quantitative requirements of applying systems microbiology methods in their work. Systems microbiology research is too complex to be the sole property of any single academic discipline. The contributions of microbiologists, computer scientists, control theorists, biostatisticians, and others are all required to move the field forward. Since research in systems microbiology demands the contributions of a diverse array of professionals, collaboration across disciplines and national borders should be strongly encouraged by research bodies and funding agencies. Although the details of systems microbiology research are probably not of interest to the average individual, the potential applications and benefits of these types of investigations should be conveyed to the lay public.« less

Microbiological assay for the determination of meropenem in pharmaceutical dosage form.

PubMed

Mendez, Andreas S L; Weisheimer, Vanessa; Oppe, Tércio P; Steppe, Martin; Schapoval, Elfrides E S

2005-04-01

Meropenem is a highly active carbapenem antibiotic used in the treatment of a wide range of serious infections. The present work reports a microbiological assay, applying the cylinder-plate method, for the determination of meropenem in powder for injection. The validation method yielded good results and included linearity, precision, accuracy and specificity. The assay is based on the inhibitory effect of meropenem upon the strain of Micrococcus luteus ATCC 9341 used as the test microorganism. The results of assay were treated statistically by analysis of variance (ANOVA) and were found to be linear (r=0.9999) in the range of 1.5-6.0 microg ml(-1), precise (intra-assay: R.S.D.=0.29; inter-assay: R.S.D.=0.94) and accurate. A preliminary stability study of meropenem was performed to show that the microbiological assay is specific for the determination of meropenem in the presence of its degradation products. The degraded samples were also analysed by the HPLC method. The proposed method allows the quantitation of meropenem in pharmaceutical dosage form and can be used for the drug analysis in routine quality control.

[Special application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiological diagnostics].

PubMed

Nagy, Erzsébet; Abrók, Marianna; Bartha, Noémi; Bereczki, László; Juhász, Emese; Kardos, Gábor; Kristóf, Katalin; Miszti, Cecilia; Urbán, Edit

2014-09-21

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry as a new possibility for rapid identification of bacteria and fungi revolutionized the clinical microbiological diagnostics. It has an extreme importance in the routine microbiological laboratories, as identification of the pathogenic species rapidly will influence antibiotic selection before the final determination of antibiotic resistance of the isolate. The classical methods for identification of bacteria or fungi, based on biochemical tests, are influenced by many environmental factors. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a rapid method which is able to identify a great variety of the isolated bacteria and fungi based on the composition of conserved ribosomal proteins. Recently several other applications of the method have also been investigated such as direct identification of pathogens from the positive blood cultures. There are possibilities to identify bacteria from the urine samples in urinary tract infection or from other sterile body fluids. Using selective enrichment broth Salmonella sp from the stool samples can be identified more rapidly, too. The extended spectrum beta-lactamase or carbapenemase production of the isolated bacteria can be also detected by this method helping the antibiotic selection in some cases. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry based methods are suitable to investigate changes in deoxyribonucleic acid or ribonucleic acid, to carry out rapid antibiotic resistance determination or other proteomic analysis. The aim of this paper is to give an overview about present possibilities of using this technique in the clinical microbiological routine procedures.

Group Projects as a Method of Promoting Student Scientific Communication and Collaboration in a Public Health Microbiology Course

ERIC Educational Resources Information Center

Walton, Kristen L. W.; Baker, Jason C.

2009-01-01

Communication of scientific and medical information and collaborative work are important skills for students pursuing careers in health professions and other biomedical sciences. In addition, group work and active learning can increase student engagement and analytical skills. Students in our public health microbiology class were required to work…

Reliability and Validity of a Questionnaire to Measure Consumer Knowledge regarding Safe Practices to Prevent Microbiological Contamination in Restaurants

ERIC Educational Resources Information Center

Uggioni, Paula Lazzarin; Salay, Elisabette

2013-01-01

Objective: The objective of this study was to develop a validated and reliable questionnaire to measure consumer knowledge regarding safe practices to prevent microbiological contamination in restaurants and commercial kitchens. Methods: Non-probabilistic samples of individuals were interviewed in the city of Campinas, Brazil. Questionnaire items…

Rapid direct methods for enumeration of specific, active bacteria in water and biofilms

NASA Technical Reports Server (NTRS)

McFeters, G. A.; Pyle, B. H.; Lisle, J. T.; Broadaway, S. C.

1999-01-01

Conventional methods for detecting indicator and pathogenic bacteria in water may underestimate the actual population due to sublethal environmental injury, inability of the target bacteria to take up nutrients and other physiological factors which reduce bacterial culturability. Rapid and direct methods are needed to more accurately detect and enumerate active bacteria. Such a methodological advance would provide greater sensitivity in assessing the microbiological safety of water and food. The principle goal of this presentation is to describe novel approaches we have formulated for the rapid and simultaneous detection of bacteria plus the determination of their physiological activity in water and other environmental samples. The present version of our method involves the concentration of organisms by membrane filtration or immunomagnetic separation and combines an intracellular fluorochrome (CTC) for assessment of respiratory activity plus fluorescent-labelled antibody detection of specific bacteria. This approach has also been successfully used to demonstrate spatial and temporal heterogeneities of physiological activities in biofilms when coupled with cryosectioning. Candidate physiological stains include those capable of determining respiratory activity, membrane potential, membrane integrity, growth rate and cellular enzymatic activities. Results obtained thus far indicate that immunomagnetic separation can provide a high degree of sensitivity in the recovery of seeded target bacteria (Escherichia coli O157:H7) in water and hamburger. The captured and stained target bacteria are then enumerated by either conventional fluorescence microscopy or ChemScan(R), a new instrument that is very sensitive and rapid. The ChemScan(R) laser scanning instrument (Chemunex, Paris, France) provides the detection of individual fluorescently labelled bacterial cells using three emission channels in less than 5 min. A high degree of correlation has been demonstrated between results obtained with the ChemScan and traditional plate counts of mixed natural bacterial populations in water. The continuing evolution of these methods will be valuable in the rapid and accurate analysis of environmental samples.

Genetic diversity in commercial wineries: effects of the farming system and vinification management on wine yeasts.

PubMed

Tello, J; Cordero-Bueso, G; Aporta, I; Cabellos, J M; Arroyo, T

2012-02-01

Analysis of the diversity and distribution of wine yeasts isolated from organically and conventionally grown grapes, and during the subsequent fermentation with or without starter cultures in six different commercial wineries. PCR-RFLP screening of isolates revealed the involvement of ten different species. Saccharomyces cerevisiae, scarcely isolated from grapes, was the dominant species during the latter phases of fermentation, identifying 108 different genotypes by means of SSR analysis. Species and strains' diversity and presence were strongly influenced by the farming system used to grow the grapes and the system of vinification. Organic farming management was more beneficial in terms of diversity and abundance than the conventional one. Induced fermentation generated a great replacement of native yeasts. Although winery-resident yeasts resulted to be predominant in the process, some noncommercial strains originally in the vineyard were found in final stages of the fermentation, confirming that autochthonous strains of S. cerevisiae are capable to conduct the fermentation process up to its end. The study of natural yeast communities from commercial vineyards and wineries is an important step towards the preservation of native genetic resources. Our results have special relevance because it is the first time that the real situation of the yeast ecology of alcoholic fermentation in commercial wineries belonging to the relevant wine-producing Appellation of Origin 'Vinos de Madrid' is shown. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

groEL is a suitable genetic marker for detecting Vibrio parahaemolyticus by loop-mediated isothermal amplification assay.

PubMed

Siddique, M P; Jang, W J; Lee, J M; Ahn, S H; Suraiya, S; Kim, C H; Kong, I S

2017-08-01

A groEL gene-based loop-mediated isothermal amplification (LAMP) assay was developed to detect Vibrio parahaemolyticus in contaminated seafood and water. The assay was optimized and conducted at 63°C for 40 min using Bacillus stearothermophilus (Bst) DNA polymerase, large fragment. Amplification was analysed via multiple detection methods, including opacity, formation of white precipitate, DNA intercalating dyes (ethidium bromide and SYBR Green I), metal ion-binding indicator dye, calcein, and 2% agarose gel electrophoresis. A characteristic ladder-like band pattern on agarose gel and the desired colour changes when using different dyes were observed in positive cases, and these were species-specific for V. parahaemolyticus when compared with other closely related Vibrio spp. The limit of detection (LoD) of this assay was 100 fg per reaction, 100-fold higher than that for conventional polymerase chain reaction (PCR). When tested on artificially contaminated seafood and seawater, the LoDs of the LAMP assay were 120 and 150 fg per reaction respectively, and those of conventional PCR were 120 and 150 pg per reaction respectively. Based on our results, the groEL gene-based LAMP assay is rapid, specific, sensitive, and reliable for detecting V. parahaemolyticus, and it could be used in field diagnosis. The loop-mediated isothermal amplification (LAMP) assay using groEL gene (an abundant, highly conserved gene and member of the groESL chaperone gene family) provided rapid, species-specific and highly sensitive method for detecting Vibrio parahaemolyticus, the leading causal agent of seafood-borne diseases worldwide. Moreover, groEL LAMP revealed high efficiency than conventional PCR assay for V. parahaemolyticus using template both from pure culture and artificially contaminated seafood and water, which indicated the applicability in the field and environmental screening purpose for the organism. © 2017 The Society for Applied Microbiology.

[Clinical usefulness of urine-formed elements' information obtained from bacteria detection by flow cytometry method that uses nucleic acid staining].

PubMed

Nakagawa, Hiroko; Yuno, Tomoji; Itho, Kiichi

2009-03-01

Recently, specific detection method for Bacteria, by flow cytometry method using nucleic acid staining, was developed as a function of automated urine formed elements analyzer for routine urine testing. Here, we performed a basic study on this bacteria analysis method. In addition, we also have a comparison among urine sediment analysis, urine Gram staining and urine quantitative cultivation, the conventional methods performed up to now. As a result, the bacteria analysis with flow cytometry method that uses nucleic acid staining was excellent in reproducibility, and higher sensitivity compared with microscopic urinary sediment analysis. Based on the ROC curve analysis, which settled urine culture method as standard, cut-off level of 120/microL was defined and its sensitivity = 85.7%, specificity = 88.2%. In the analysis of scattergram, accompanied with urine culture method, among 90% of rod positive samples, 80% of dots were appeared in the area of 30 degrees from axis X. In addition, one case even indicated that analysis of bacteria by flow cytometry and scattergram of time series analysis might be helpful to trace the progress of causative bacteria therefore the information supposed to be clinically significant. Reporting bacteria information with nucleic acid staining flow cytometry method is expected to contribute to a rapid diagnostics and treatment of urinary tract infections. Besides, the contribution to screening examination of microbiology and clinical chemistry, will deliver a more efficient solution to urine analysis.

Integration of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in blood culture diagnostics: a fast and effective approach.

PubMed

Klein, Sabrina; Zimmermann, Stefan; Köhler, Christine; Mischnik, Alexander; Alle, Werner; Bode, Konrad A

2012-03-01

Sepsis is a major cause of mortality in hospitalized patients worldwide, with lethality rates ranging from 30 to 70 %. Sepsis is caused by a variety of different pathogens, and rapid diagnosis is of outstanding importance, as early and adequate antimicrobial therapy correlates with positive clinical outcome. In recent years, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) fingerprinting has become a powerful tool in microbiological diagnostics. The direct identification of micro-organisms in a positive blood culture by MALDI-TOF MS can shorten the diagnostic procedure significantly. Therefore, the aim of the present study was to evaluate whether identification rates could be improved by using the new Sepsityper kit from Bruker Daltonics for direct isolation and identification of bacteria from positive blood cultures by MALDI-TOF MS compared with the use of conventional separator gel columns, and to integrate the MALDI-TOF MS-based identification method into the routine course of blood culture diagnostics in the setting of a microbiological laboratory at a university hospital in Germany. The identification of Gram-negative bacteria by MALDI-TOF MS was significantly better using the Sepsityper kit compared with a separator gel tube-based method (99 and 68 % correct identification, respectively). For Gram-positive bacteria, only 73 % were correctly identified by MALDI-TOF with the Sepsityper kit and 59 % with the separator gel tube assay. A major problem of both methods was the poor identification of Gram-positive grape-like clustered cocci. As differentiation of Staphylococcus aureus from coagulase-negative staphylococci is of clinical importance, a PCR was additionally established that was capable of identifying S. aureus directly from positive blood cultures, thus closing this diagnostic gap. Another benefit of the PCR approach is the possibility of directly detecting the genes responsible for meticillin resistance in staphylococci and for vancomycin resistance in enterococci, which is of high importance for early adequate treatment. Both of the described methods were finally integrated into a protocol for fast and effective identification of bacteria from positive blood cultures.

Fast 2D NMR Spectroscopy for In vivo Monitoring of Bacterial Metabolism in Complex Mixtures.

PubMed

Dass, Rupashree; Grudzia Ż, Katarzyna; Ishikawa, Takao; Nowakowski, Michał; Dȩbowska, Renata; Kazimierczuk, Krzysztof

2017-01-01

The biological toolbox is full of techniques developed originally for analytical chemistry. Among them, spectroscopic experiments are very important source of atomic-level structural information. Nuclear magnetic resonance (NMR) spectroscopy, although very advanced in chemical and biophysical applications, has been used in microbiology only in a limited manner. So far, mostly one-dimensional 1 H experiments have been reported in studies of bacterial metabolism monitored in situ . However, low spectral resolution and limited information on molecular topology limits the usability of these methods. These problems are particularly evident in the case of complex mixtures, where spectral peaks originating from many compounds overlap and make the interpretation of changes in a spectrum difficult or even impossible. Often a suite of two-dimensional (2D) NMR experiments is used to improve resolution and extract structural information from internuclear correlations. However, for dynamically changing sample, like bacterial culture, the time-consuming sampling of so-called indirect time dimensions in 2D experiments is inefficient. Here, we propose the technique known from analytical chemistry and structural biology of proteins, i.e., time-resolved non-uniform sampling. The method allows application of 2D (and multi-D) experiments in the case of quickly varying samples. The indirect dimension here is sparsely sampled resulting in significant reduction of experimental time. Compared to conventional approach based on a series of 1D measurements, this method provides extraordinary resolution and is a real-time approach to process monitoring. In this study, we demonstrate the usability of the method on a sample of Escherichia coli culture affected by ampicillin and on a sample of Propionibacterium acnes , an acne causing bacterium, mixed with a dose of face tonic, which is a complicated, multi-component mixture providing complex NMR spectrum. Through our experiments we determine the exact concentration and time at which the anti-bacterial agents affect the bacterial metabolism. We show, that it is worth to extend the NMR toolbox for microbiology by including techniques of 2D z-TOCSY, for total "fingerprinting" of a sample and 2D 13 C-edited HSQC to monitor changes in concentration of metabolites in selected metabolic pathways.

Application of chemometric methods for assessment and modelling of microbiological quality data concerning coastal bathing water in Greece.

PubMed

Papaioannou, Agelos; Rigas, George; Papastergiou, Panagiotis; Hadjichristodoulou, Christos

2014-12-02

Worldwide, the aim of managing water is to safeguard human health whilst maintaining sustainable aquatic and associated terrestrial, ecosystems. Because human enteric viruses are the most likely pathogens responsible for waterborne diseases from recreational water use, but detection methods are complex and costly for routine monitoring, it is of great interest to determine the quality of coastal bathing water with a minimum cost and maximum safety. This study handles the assessment and modelling of the microbiological quality data of 2149 seawater bathing areas in Greece over 10-year period (1997-2006) by chemometric methods. Cluster analysis results indicated that the studied bathing beaches are classified in accordance with the seasonality in three groups. Factor analysis was applied to investigate possible determining factors in the groups resulted from the cluster analysis, and also two new parameters were created in each group; VF1 includes E. coli, faecal coliforms and total coliforms and VF2 includes faecal streptococci/enterococci. By applying the cluster analysis in each seasonal group, three new groups of coasts were generated, group A (ultraclean), group B (clean) and group C (contaminated). The above analysis is confirmed by the application of discriminant analysis, and proves that chemometric methods are useful tools for assessment and modeling microbiological quality data of coastal bathing water on a large scale, and thus could attribute to effective and economical monitoring of the quality of coastal bathing water in a country with a big number of bathing coasts, like Greece. Significance for public healthThe microbiological protection of coastal bathing water quality is of great interest for the public health authorities as well as for the economy. The present study proves that this protection can be achieved by monitoring only two microbiological parameters, E. coli and faecal streptococci/enterococci instead four microbiological parameters (the two mentioned above plus Total coliforms and Faecal coliforms) that are usually monitored today. As a consequence, countries, especially those with large quantities of coastal bathing sites, can perform microbiological monitoring of their bathing waters by checking only the mentioned two parameters, thus ensuring economies of scale. Thus, funds can be used in other actions to preserve the quality of coastal water and human health. This in turn, would aid in the assessment of the quality of coastal bathing waters and provide a more timely indication of bathing water quality, hence contributing to the immediate health protection of bathers.

Cost-effectiveness study of the microbiological diagnosis of tuberculosis using geneXpert MTB/RIF®.

PubMed

Herráez, Óscar; Asencio-Egea, María Ángeles; Huertas-Vaquero, María; Carranza-González, Rafael; Castellanos-Monedero, Jesús; Franco-Huerta, María; Barberá-Farré, José Ramón; Tenías-Burillo, José María

To perform a cost-effectiveness analysis of a molecular biology technique for the diagnosis of tuberculosis compared to the classical diagnostic alternative. A cost-effectiveness analysis was performed to evaluate the theoretical implementation of a molecular biology method including two alternative techniques for early detection of Mycobacterium tuberculosis Complex, and resistance to rifampicin (alternative1: one determination in selected patients; alternative2: two determinations in all the patients). Both alternatives were compared with the usual procedure for microbiological diagnosis of tuberculosis (staining and microbiological culture), and was accomplished on 1,972 patients in the period in 2008-2012. The effectiveness was measured in QALYs, and the uncertainty was assessed by univariate, multivariate and probabilistic analysis of sensitivity. A value of €8,588/QALYs was obtained by the usual method. Total expenditure with the alternative1 was €8,487/QALYs, whereas with alternative2, the cost-effectiveness ratio amounted to €2,960/QALYs. Greater diagnostic efficiency was observed by applying the alternative2, reaching a 75% reduction in the number of days that a patient with tuberculosis remains without an adequate treatment, and a 70% reduction in the number of days that a patient without tuberculosis remains in hospital. The implementation of a molecular microbiological technique in the diagnosis of tuberculosis is extremely cost-effective compared to the usual method. Its introduction into the routine diagnostic procedure could lead to an improvement in quality care for patients, given that it would avoid both unnecessary hospitalisations and treatments, and reflected in economic savings to the hospital. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Sampling and Data Analysis for Environmental Microbiology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murray, Christopher J.

2001-06-01

A brief review of the literature indicates the importance of statistical analysis in applied and environmental microbiology. Sampling designs are particularly important for successful studies, and it is highly recommended that researchers review their sampling design before heading to the laboratory or the field. Most statisticians have numerous stories of scientists who approached them after their study was complete only to have to tell them that the data they gathered could not be used to test the hypothesis they wanted to address. Once the data are gathered, a large and complex body of statistical techniques are available for analysis ofmore » the data. Those methods include both numerical and graphical techniques for exploratory characterization of the data. Hypothesis testing and analysis of variance (ANOVA) are techniques that can be used to compare the mean and variance of two or more groups of samples. Regression can be used to examine the relationships between sets of variables and is often used to examine the dependence of microbiological populations on microbiological parameters. Multivariate statistics provides several methods that can be used for interpretation of datasets with a large number of variables and to partition samples into similar groups, a task that is very common in taxonomy, but also has applications in other fields of microbiology. Geostatistics and other techniques have been used to examine the spatial distribution of microorganisms. The objectives of this chapter are to provide a brief survey of some of the statistical techniques that can be used for sample design and data analysis of microbiological data in environmental studies, and to provide some examples of their use from the literature.« less

Whole genome sequencing in clinical and public health microbiology

PubMed Central

Kwong, J. C.; McCallum, N.; Sintchenko, V.; Howden, B. P.

2015-01-01

SummaryGenomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology. The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology. Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories. As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future. Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure. PMID:25730631

Whole genome sequencing in clinical and public health microbiology.

PubMed

Kwong, J C; McCallum, N; Sintchenko, V; Howden, B P

2015-04-01

Genomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology.The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology.Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories.As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future.Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure.

[Epidemiology, clinical and microbiological characteristics of invasive streptococcal infections in Turkey, 2010-2011].

PubMed

Topkaya, Aynur Eren; Balıkcı, Ahmet; Aydın, Faruk; Hasçelik, Gülşen; Kayman, Tuba; Kesli, Recep; Aydemir, Söhret; Akyar, Işın; Gökalp, Aslı; Dündar, Günnur; Gürler, Nezahat; Perçin, Duygu; Fındık, Duygu; Avunduk, Haluk; Bayraktar, Banu

2014-01-01

A one-year active surveillance study was conducted to investigate the epidemiological and microbiological characteristics of invasive group A streptococci (GAS) infections in Turkey and to provide data for the establishment of national preventive strategies related to invasive GAS infections. A total of 46 clinical microbiology laboratories from 12 different regions of Turkey (Istanbul; Eastern and Western Marmara; Eastern and Western Blacksea; Aegean; Mediterranean; Western, Central, Northeastern, Middle-eastern and Southeastern Anatolia) participated in the study. Accordingly, GAS strains isolated from sterile body sites (blood, cerebrospinal, synovial, pleural, peritoneal, pericardial fluids) in the study centers between June 2010-June 2011, were sent to Maltepe University Hospital Clinical Microbiology Laboratory for microbiological confirmation and further analysis. The isolates were identified by conventional methods, and for serotyping, opacity factor (OF) and T protein types were investigated. For genotyping GAS lysate preparation, emm gene amplification and sequencing were performed by using the protocols recommended by Centers for Disease Control and Prevention. A total of 65 invasive GAS strains were isolated in 15 of the participant centers, during the study period. The rate of invasive GAS isolation exhibited regional variation, with the highest rates in the Eastern Blacksea (Trabzon, n= 19), followed by Istanbul (n= 17) and Western Anatolia (Ankara, Konya, n= 14). Of the patients with invasive GAS infection 33 were female, 32 were male, with the age range of 0-89 years. GAS strains were most commonly isolated from soft tissue specimens (n= 18), followed by abscess material (n= 10), sterile body fluids (n= 8) and blood (n= 7) samples. Serotyping revealed that 55% (36/65) of the strains were OF positive, and the majority of T protein was polygroup T (n= 20), followed by U (n= 14), B (n= 5), X (n= 3) and Y (n= 2). T protein was not detected in 22 isolates. The strains were found to have 17 different emm types;emm1 (n= 13), emm4 (n= 6), emm6 (n= 6), emm12 (n= 6), emm24 (n= 4), emm14 (n= 3) and emm28 (n= 3). Nine of the strains could not be typed by sequencing. The correlation between emm typing and serotyping was detected as 58%. It was observed that 26-valent vaccines included 70.5% of the invasive GAS strains included in this study. Our study provided initial data concerning the epidemiological properties of invasive GAS infections and characterization of GAS strains in Turkey. The incidence of invasive GAS infections is low in our country. Although immunization programme by 26-valent GAS vaccine is not currently an urgent public health issue for our country, the results of this study indicated that emm types 4 and 24 should better be included in such a vaccine to be used in Turkey. Additionally, since epidemiological features of GAS infections and the microbiological characteristics of the strains can vary by time, for the diagnosis of invasive streptococcal infections and to take the necessary preventive measures, epidemiological studies should be conducted repeatedly.

ViDiT-CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications.

PubMed

Verhoeven, Joost Theo Petra; Canuti, Marta; Munro, Hannah J; Dufour, Suzanne C; Lang, Andrew S

2018-04-19

High-throughput sequencing (HTS) technologies are becoming increasingly important within microbiology research, but aspects of library preparation, such as high cost per sample or strict input requirements, make HTS difficult to implement in some niche applications and for research groups on a budget. To answer these necessities, we developed ViDiT, a customizable, PCR-based, extremely low-cost (<5 US dollars per sample) and versatile library preparation method, and CACTUS, an analysis pipeline designed to rely on cloud computing power to generate high-quality data from ViDiT-based experiments without the need of expensive servers. We demonstrate here the versatility and utility of these methods within three fields of microbiology: virus discovery, amplicon-based viral genome sequencing and microbiome profiling. ViDiT-CACTUS allowed the identification of viral fragments from 25 different viral families from 36 oropharyngeal-cloacal swabs collected from wild birds, the sequencing of three almost complete genomes of avian influenza A viruses (>90% coverage), and the characterization and functional profiling of the complete microbial diversity (bacteria, archaea, viruses) within a deep-sea carnivorous sponge. ViDiT-CACTUS demonstrated its validity in a wide range of microbiology applications and its simplicity and modularity make it easily implementable in any molecular biology laboratory, towards various research goals.

Multiplex ligation-dependant probe amplification study of children with idiopathic mental retardation in South India

PubMed Central

John, Neetha; Rajasekhar, Moka; Girisha, Katta Mohan; Sharma, Podila Satya Venkata Narasimha; Gopinath, Puthiya Mundyat

2013-01-01

BACKGROUND: Mental retardation (MR) is a heterogeneous dysfunction of the central nervous system exhibiting complex phenotypes and has an estimated prevalence of 1-3% in the general population. However, in about 50% of the children diagnosed with any form of intellectual disability or developmental delay the cause goes undetected contributing to idiopathic intellectual disability. MATERIALS AND METHODS: A total of 122 children with developmental delay/MR were studied to identify the microscopic and submicroscopic chromosome rearrangements by using the conventional cytogenetics and multiplex ligation dependent probe amplification (MLPA) analysis using SALSA MLPA kits from Microbiology Research Centre Holland [MRC] Holland. RESULTS: All the recruited children were selected for this study, after thorough clinical assessment and metaphases prepared were analyzed by using automated karyotyping system. None was found to have chromosomal abnormality; MLPA analysis was carried out in all subjects and identified in 11 (9%) patients. CONCLUSION: Karyotype analysis in combination with MLPA assays for submicroscopic micro-deletions may be recommended for children with idiopathic MR. PMID:24019617

Detection of spatial fluctuations of non-point source fecal pollution in coral reef surrounding waters in southwestern Puerto Rico using PCR-based assays.

PubMed

Bonkosky, M; Hernández-Delgado, E A; Sandoz, B; Robledo, I E; Norat-Ramírez, J; Mattei, H

2009-01-01

Human fecal contamination of coral reefs is a major cause of concern. Conventional methods used to monitor microbial water quality cannot be used to discriminate between different fecal pollution sources. Fecal coliforms, enterococci, and human-specific Bacteroides (HF183, HF134), general Bacteroides-Prevotella (GB32), and Clostridium coccoides group (CP) 16S rDNA PCR assays were used to test for the presence of non-point source fecal contamination across the southwestern Puerto Rico shelf. Inshore waters were highly turbid, consistently receiving fecal pollution from variable sources, and showing the highest frequency of positive molecular marker signals. Signals were also detected at offshore waters in compliance with existing microbiological quality regulations. Phylogenetic analysis showed that most isolates were of human fecal origin. The geographic extent of non-point source fecal pollution was large and impacted extensive coral reef systems. This could have deleterious long-term impacts on public health, local fisheries and in tourism potential if not adequately addressed.

Development and validation of micellar liquid chromatographic methods for the determination of antibiotics in different matrixes.

PubMed

Rambla-Alegre, Maria; Esteve-Romero, Josep; Carda-Broch, Samuel

2011-01-01

Antibiotics are the most important bioactive and chemotherapeutic compounds to be produced by microbiological synthesis, and they have proved their worth in a variety of fields, such as medicinal chemistry, agriculture, and the food industry. Interest in antibiotics has grown in parallel with an increasingly high degree of productivity in the field of analytical applications. Therefore, it is necessary to develop chromatographic procedures capable of determining various drugs simultaneously in the shortest possible time. Micellar liquid chromatography (MLC) is an RP-HPLC technique that offers advantages over conventional HPLC as far as sample preparation, selectivity, and versatility are concerned. Its main advantage is that samples can be injected directly into the chromatographic system with no previous preparation step. This paper mainly focuses on the results of the authors' own recent research and reports the chromatographic conditions for determination of various antibiotics (penicillins, quinolones, and sulfonamides) in different matrixes (pharmaceuticals, biological fluids, and food). The work of other authors on MLC-based antibiotic determination has been included.

Level of impact on the public health of universal human immunodeficiency virus screening in an Emergency Department.

PubMed

Reyes-Urueña, Juliana; Fernàndez-López, Laura; Force, Luis; Daza, Manel; Agustí, Cristina; Casabona, Jordi

The aim of this study was to determine the prevalence of HIV and the acceptability of rapid testing in an emergency department (ED), Barcelona (6/07/2011 to 8/03/2013). A convenience sample was used, depending on nurse availability in the ED. Participants signed an informed consent. Results were confirmed by conventional methods. A total of 2,140 individuals were offered testing, and 5% rejected taking part (107/2,140). Three subjects (3/2,033 [0.15%]) had confirmed reactive test. Individuals with a higher education were more likely to perform a rapid HIV test in ED (P<.005). A low prevalence of new HIV diagnoses was found among participants, although there was a high acceptability rate to perform rapid testing in the ED. Copyright © 2015 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Efficiency tests of samplers for microbiological aerosols, a review

NASA Technical Reports Server (NTRS)

Henningson, E.; Faengmark, I.

1984-01-01

To obtain comparable results from studies using a variety of samplers of microbiological aerosols with different collection performances for various particle sizes, methods reported in the literature were surveyed, evaluated, and tabulated for testing the efficiency of the samplers. It is concluded that these samplers were not thoroughly tested, using reliable methods. Tests were conducted in static air chambers and in various outdoor and work environments. Results are not reliable as it is difficult to achieve stable and reproducible conditions in these test systems. Testing in a wind tunnel is recommended.

Microbiological assay of the Marshall Space Flight Center neutral buoyancy simulator

NASA Technical Reports Server (NTRS)

Beyerle, F. J.

1973-01-01

A neutral buoyancy simulator tank system is described in terms of microbiological and medical safety for astronauts. The system was designed to simulate a gravity-free state for evaluation of orbital operations in a microorganism-free environment. Methods for the identification and elimination of specific microorganisms are dealt with as measures for a pure system of space environment simulation.

Use of Long-Term E. Coli Cultures: To Study Generation of Genetic Diversity & Teach General Microbiology Laboratory Skills

ERIC Educational Resources Information Center

Petrie, Angela; Finkel, Steven E.; Erbe, Jarrod

2005-01-01

A novel method of studying the generation of genetic diversity in an undergraduate microbiology laboratory is described. The basis of this approach is the accumulation of mutations that confer a competitive advantage, or growth advantage in stationary phase (GASP) phenotype, to E. coli grown in stationary phase for extended periods of time.

Microbiological effectiveness of household water treatment technologies under field use conditions in rural Tanzania.

PubMed

Mohamed, Hussein; Clasen, Thomas; Njee, Robert Mussa; Malebo, Hamisi M; Mbuligwe, Stephen; Brown, Joe

2016-01-01

To assess the microbiological effectiveness of several household water treatment and safe storage (HWTS) options in situ in Tanzania, before consideration for national scale-up of HWTS. Participating households received supplies and instructions for practicing six HWTS methods on a rotating 5-week basis. We analysed 1202 paired samples (source and treated) of drinking water from 390 households, across all technologies. Samples were analysed for thermotolerant (TTC) coliforms, an indicator of faecal contamination, to measure effectiveness of treatment in situ. All HWTS methods improved microbial water quality, with reductions in TTC of 99.3% for boiling, 99.4% for Waterguard ™ brand sodium hypochlorite solution, 99.5% for a ceramic pot filter, 99.5% for Aquatab ® sodium dichloroisocyanurate (NaDCC) tablets, 99.6% for P&G Purifier of Water ™ flocculent/disinfectant sachets, and 99.7% for a ceramic siphon filter. Microbiological performance was relatively high compared with other field studies and differences in microbial reductions between technologies were not statistically significant. Given that microbiological performance across technologies was comparable, decisions regarding scale-up should be based on other factors, including uptake in the target population and correct, consistent, and sustained use over time. © 2015 John Wiley & Sons Ltd.

Infection control in healthcare settings: perspectives for mfDNA analysis in monitoring sanitation procedures.

PubMed

Valeriani, Federica; Protano, Carmela; Gianfranceschi, Gianluca; Cozza, Paola; Campanella, Vincenzo; Liguori, Giorgio; Vitali, Matteo; Divizia, Maurizio; Romano Spica, Vincenzo

2016-08-09

Appropriate sanitation procedures and monitoring of their actual efficacy represent critical points for improving hygiene and reducing the risk of healthcare-associated infections. Presently, surveillance is based on traditional protocols and classical microbiology. Innovation in monitoring is required not only to enhance safety or speed up controls but also to prevent cross infections due to novel or uncultivable pathogens. In order to improve surveillance monitoring, we propose that biological fluid microflora (mf) on reprocessed devices is a potential indicator of sanitation failure, when tested by an mfDNA-based approach. The survey focused on oral microflora traces in dental care settings. Experimental tests (n = 48) and an "in field" trial (n = 83) were performed on dental instruments. Conventional microbiology and amplification of bacterial genes by multiple real-time PCR were applied to detect traces of salivary microflora. Six different sanitation protocols were considered. A monitoring protocol was developed and performance of the mfDNA assay was evaluated by sensitivity and specificity. Contaminated samples resulted positive for saliva traces by the proposed approach (CT < 35). In accordance with guidelines, only fully sanitized samples were considered negative (100 %). Culture-based tests confirmed disinfectant efficacy, but failed in detecting incomplete sanitation. The method provided sensitivity and specificity over 95 %. The principle of detecting biological fluids by mfDNA analysis seems promising for monitoring the effectiveness of instrument reprocessing. The molecular approach is simple, fast and can provide a valid support for surveillance in dental care or other hospital settings.

Rapid and cost-effective identification and antimicrobial susceptibility testing in patients with Gram-negative bacteremia directly from blood-culture fluid.

PubMed

Sakarikou, Christina; Altieri, Anna; Bossa, Maria Cristina; Minelli, Silvia; Dolfa, Camilla; Piperno, Micol; Favalli, Cartesio

2018-03-01

Rapid pathogen identification (ID) and antimicrobial susceptibility testing (AST) in bacteremia cases or sepsis could improve patient prognosis. Thus, it is important to provide timely reports, which make it possible for clinicians to set up appropriate antibiotic therapy during the early stages of bloodstream infection (BSI). This study evaluates an in-house microbiological protocol for early ID as well as AST on Gram negative bacteria directly from positive monomicrobial and polymicrobial blood cultures (BCs). A total of 102 non-duplicated positive BCs from patients with Gram-negative bacteremia were tested. Both IDs and ASTs were performed from bacterial pellets extracted directly from BCs using our protocol, which was applied through the combined use of a MALDI-TOF MS and Vitek2 automated system. The results of our study showed a 100% agreement in bacterial ID and 98.25% categorical agreement in AST when compared to those obtained by routine conventional methods. We recorded only a 0.76% minor error (mE), 0.76% major error (ME) and a 0.20% very major error (VME). Moreover, the turnaround time (TAT) regarding the final AST report was significantly shortened (ΔTAT = 8-20 h, p < 0.00001). This in-house protocol is rapid, easy to perform and cost effective and could be successfully introduced into any clinical microbiology laboratory. A final same-day report of ID and AST improves patient management, by early and appropriate antimicrobial treatment and could potentially optimize antimicrobial stewardship programs. Copyright © 2018 Elsevier B.V. All rights reserved.

The Phantom Menace for Patients with Hepatobiliary Diseases: Shewanella haliotis, Often Misidentified as Shewanella algae in Biochemical Tests and MALDI-TOF Analysis.

PubMed

Byun, Jung-Hyun; Park, Hyunwoong; Kim, Sunjoo

2017-03-24

Although Shewanella algae has been known to have weak pathogenicity, case reports on infections with this species have been steadily increasing. S. algae and S. haliotis are difficult to distinguish from each other with conventional phenotypic methods. We reviewed the microbiological and clinical features of S. algae and S. haliotis infections at our institute. Bacterial culture and identification reports from patient samples from 2010 to 2014 were reviewed to screen the cases of Shewanella infections. In addition to conventional biochemical tests, 16S rRNA gene sequence analysis and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry were performed for 19 stored bacterial isolates. Medical records were reviewed for clinical characteristics and laboratory findings. All isolates were identified as S. algae by using VITEK 2. MALDI-TOF also identified all isolates as S. algae with a 99.9 confidence value. In contrast, 16S rRNA analysis identified 10 isolates as S. algae and 9 isolates as S. haliotis. Both S. algae (60%) and S. haliotis (77%) infections were strongly associated with diseases of the hepatobiliary tract and pancreas. To distinguish between S. algae and S. haliotis, 16S rRNA gene sequence analysis seems more accurate than biochemical tests or MALDI-TOF. Patients with underlying diseases in the hepatobiliary tract and pancreas seem to be susceptible to these marine pathogens.

Utility of Gram stain for the microbiological analysis of burn wound surfaces.

PubMed

Elsayed, Sameer; Gregson, Daniel B; Lloyd, Tracie; Crichton, Marilyn; Church, Deirdre L

2003-11-01

Surface swab cultures have attracted attention as a potential alternative to biopsy histology or quantitative culture methods for microbiological burn wound monitoring. To our knowledge, the utility of adding a Gram-stained slide in this context has not been evaluated previously. To determine the degree of correlation of Gram stain with culture for the microbiological analysis of burn wound surfaces. Prospective laboratory analysis. Urban health region/centralized diagnostic microbiology laboratory. Burn patients hospitalized in any Calgary Health Region burn center from November 2000 to September 2001. Gram stain plus culture of burn wound surface swab specimens obtained during routine dressing changes or based on clinical signs of infection. Degree of correlation (complete, high, partial, none), including weighted kappa statistic (kappa(w)), of Gram stain with culture based on quantitative microscopy and degree of culture growth. A total of 375 specimens from 50 burn patients were evaluated. Of these, 239 were negative by culture and Gram stain, 7 were positive by Gram stain only, 89 were positive by culture only, and 40 were positive by both methods. The degree of complete, high, partial, and no correlation of Gram stain with culture was 70.9% (266/375), 1.1% (4/375), 2.4% (9/375), and 25.6% (96/375), respectively. The degree of correlation for all 375 specimens, as expressed by the weighted kappa statistic, was found to be fair (kappa(w) = 0.32).Conclusion.-The Gram stain is not suitable for the microbiological analysis of burn wound surfaces.

Development, fabrication and testing of a magnetically connected plastic vacuum probe surface sampler

NASA Technical Reports Server (NTRS)

Phillips, G. B.; Pace, V. A., Jr.

1972-01-01

The sampler utilizes permanent magnets and soft metal pole pieces to connect the cone/filter assembly to the sampling head and vacuum supply. The cone/filter assembly is packaged in a plastic container and presterilized so that the need for any human contact during the sampling procedure is completely eliminated. Microbiological tests have demonstrated that the sampling efficiency is not affected by the magnetic coupling apparatus and that the probe appears to function as efficiently as the conventional plastic and Sandia vacuum probes.

Mycoplasma hominis periaortic abscess following heart-lung transplantation.

PubMed

Hagiya, Hideharu; Yoshida, Hisao; Yamamoto, Norihisa; Kimura, Keigo; Ueda, Akiko; Nishi, Isao; Akeda, Yukihiro; Tomono, Kazunori

2017-06-01

We report the first case of Mycoplasma hominis periaortic abscess after heart-lung transplantation. The absence of sternal wound infection delayed the diagnosis, but the patient successfully recovered with debridement surgeries and long-term antibiotic therapy. Owing to the difficulty in detection and the intrinsic resistance to beta-lactams, M. hominis infections are prone to being misdiagnosed and undertreated. M. hominis should be suspected in cases where conventional microbiological identification and treatment approaches fail. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Space Tourism and Safety from Infection

NASA Astrophysics Data System (ADS)

Ilyin, V. K.; Tiurina, D. A.; Usanova, N. A.; Starkova, L. V.; Soloviova, Z. O.; Morozova, Ju. A.; Kirjukhina, N. V.; Webb, A.

This paper highlights the major scenarios of the microbiological changes which occur in the human organism in space missions, i.e. the increasing of the conventional pathogen population share in human microflora and changes in antibiotic susceptibility, and substantiates compatible countermeasures based on probiotics consumption. Special attention is given to the prospects of the consumption of probiotics made of strains which are representative of human commensurate microflora for the support of resistance during a space journey. It is a most important technique and one which will be acceptable for space tourists.

Antimicrobial Testing Methods & Procedures Developed by EPA's Microbiology Laboratory

EPA Pesticide Factsheets

We develop antimicrobial testing methods and standard operating procedures to measure the effectiveness of hard surface disinfectants against a variety of microorganisms. Find methods and procedures for antimicrobial testing.

Production Methods in Industrial Microbiology.

ERIC Educational Resources Information Center

Gaden, Elmer L., Jr.

1981-01-01

Compares two methods (batch and continuous) in which microorganisms are used to produce industrial chemicals. Describes batch and continuous stirred-tank reactors and offers reasons why the batch method may be preferred. (JN)

Corridor consultations and the medical microbiological record: is patient safety at risk?

PubMed Central

Heard, S R; Roberts, C; Furrows, S J; Kelsey, M; Southgate, L

2003-01-01

The performance procedures of the General Medical Council are aimed at identifying seriously deficient performance in a doctor. The performance procedures require the medical record to be of a standard that enables the next doctor seeing the patient to give adequate care based on the available information. Setting standards for microbiological record keeping has proved difficult. Over one fifth of practising medical microbiologists (including virologists) in the UK (139 of 676) responded to a survey undertaken by the working group developing the performance procedures for microbiology, to identify current practice and to develop recommendations for agreement within the profession about the standards of the microbiological record. The cumulative frequency for the surveyed recording methods used indicated that at various times 65% (90 of 139) of respondents used a daybook, 62% (86 of 139) used the back of the clinical request card, 57% (79 of 139) used a computer record, and 22% (30 of 139) used an index card system to record microbiological advice, suggesting wide variability in relation to how medical microbiologists maintain clinical records. PMID:12499432

Basic research for the future: Opportunities in microbiology for the coming decade

DOE Office of Scientific and Technical Information (OSTI.GOV)

Payne, W.J.

1996-12-31

Not since Leeuwenhoek reported finding {open_quotes}animalcules{close_quotes} in a variety of natural materials have research opportunities in microbiology looked so promising. Researchers have developed methods to analyze the historic and evolutionary progression of bacteria, fungi, and viruses. The significance of the remarkable diversity found in the microbial realm is just beginning to emerge. Biotechnology companies are exploiting microorganisms in remarkable ways. Seemingly new, devastating pathogens have appeared and {open_quotes}old{close_quotes} pathogens have become resistant to antiobiotics. All these factors serve to invigorate interest in microbiology. Seldom have the challenges seemed more intense or more exciting. Recognizing the significance of these issues, themore » American Academy of Microbiology convened a colloquium of experts in the microbiological sciences May 4-7, 1996, in Washington, D.C. The colloquim sought primarily to identify those research areas most clearly deserving future attention, those most likely to provide optimal return on scientific and monetary investment, and those offering the greatest promise for solving critical problems over the coming decade.« less

Evaluation of the performance of quantitative detection of the Listeria monocytogenes prfA locus with droplet digital PCR.

PubMed

Witte, Anna Kristina; Fister, Susanne; Mester, Patrick; Schoder, Dagmar; Rossmanith, Peter

2016-11-01

Fast and reliable pathogen detection is an important issue for human health. Since conventional microbiological methods are rather slow, there is growing interest in detection and quantification using molecular methods. The droplet digital polymerase chain reaction (ddPCR) is a relatively new PCR method for absolute and accurate quantification without external standards. Using the Listeria monocytogenes specific prfA assay, we focused on the questions of whether the assay was directly transferable to ddPCR and whether ddPCR was suitable for samples derived from heterogeneous matrices, such as foodstuffs that often included inhibitors and a non-target bacterial background flora. Although the prfA assay showed suboptimal cluster formation, use of ddPCR for quantification of L. monocytogenes from pure bacterial cultures, artificially contaminated cheese, and naturally contaminated foodstuff was satisfactory over a relatively broad dynamic range. Moreover, results demonstrated the outstanding detection limit of one copy. However, while poorer DNA quality, such as resulting from longer storage, can impair ddPCR, internal amplification control (IAC) of prfA by ddPCR, that is integrated in the genome of L. monocytogenes ΔprfA, showed even slightly better quantification over a broader dynamic range. Graphical Abstract Evaluating the absolute quantification potential of ddPCR targeting Listeria monocytogenes prfA.

Rapid detection of carbapenemase-producing Klebsiella pneumoniae strains derived from blood cultures by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS).

PubMed

Sakarikou, Christina; Ciotti, Marco; Dolfa, Camilla; Angeletti, Silvia; Favalli, Cartesio

2017-03-08

Carbapenemase-producing Enterobacteriaceae (CPE), particularly carbapenemase-producing Klebsiella pneumoniae isolates, are important causative agents of nosocomial infections associated with significant mortality rates mostly in critical wards. The rapid detection and typing of these strains is critical either for surveillance purposes and to prevent outbreaks and optimize antibiotic therapy. In this study, the MALDI-TOF MS method was used to detect rapidly these isolates from blood cultures (BCs) and to obtain proteomic profiles enable to discriminate between carbapenemase-producing and non-carbapenemase-producing strains. Fifty-five K. pneumoniae strains were tested. Identification and carbapenemase-production detection assay using Ertapenem were performed both from bacterial pellets extracted directly from BCs flasks and from subcultures of these strains. For all isolates, a complete antimicrobial susceptibility testing and a genotypic characterization were performed. We found 100% agreement between the carbapenemase-producing profile generated by MALDI TOF MS and that obtained using conventional methods. The assay detected and discriminated different carbapenemase-producing K. pneumoniae isolates within 30 min to 3 h after incubation with Ertapenem. MALDI-TOF MS is a promising, rapid and economical method for the detection of carbapenemase-producing K. pneumoniae strains that could be successfully introduced into the routine diagnostic workflow of clinical microbiology laboratories.

Semi-Quantitative Method for Streptococci Magnetic Detection in Raw Milk.

PubMed

Duarte, Carla; Costa, Tiago; Carneiro, Carla; Soares, Rita; Jitariu, Andrei; Cardoso, Susana; Piedade, Moisés; Bexiga, Ricardo; Freitas, Paulo

2016-04-27

Bovine mastitis is the most costly disease for dairy farmers and the most frequent reason for the use of antibiotics in dairy cattle; thus, control measures to detect and prevent mastitis are crucial for dairy farm sustainability. The aim of this study was to develop and validate a sensitive method to magnetically detect Streptococcus agalactiae (a Group B streptococci) and Streptococcus uberis in raw milk samples. Mastitic milk samples were collected aseptically from 44 cows with subclinical mastitis, from 11 Portuguese dairy farms. Forty-six quarter milk samples were selected based on bacterial identification by conventional microbiology. All samples were submitted to PCR analysis. In parallel, these milk samples were mixed with a solution combining specific antibodies and magnetic nanoparticles, to be analyzed using a lab-on-a-chip magnetoresistive cytometer, with microfluidic sample handling. This paper describes a point of care methodology used for detection of bacteria, including analysis of false positive/negative results. This immunological recognition was able to detect bacterial presence in samples spiked above 100 cfu/mL, independently of antibody and targeted bacteria used in this work. Using PCR as a reference, this method correctly identified 73% of positive samples for streptococci species with an anti-S. agalactiae antibody, and 41% of positive samples for an anti-GB streptococci antibody.

Semi-Quantitative Method for Streptococci Magnetic Detection in Raw Milk

PubMed Central

Duarte, Carla; Costa, Tiago; Carneiro, Carla; Soares, Rita; Jitariu, Andrei; Cardoso, Susana; Piedade, Moisés; Bexiga, Ricardo; Freitas, Paulo

2016-01-01

Bovine mastitis is the most costly disease for dairy farmers and the most frequent reason for the use of antibiotics in dairy cattle; thus, control measures to detect and prevent mastitis are crucial for dairy farm sustainability. The aim of this study was to develop and validate a sensitive method to magnetically detect Streptococcus agalactiae (a Group B streptococci) and Streptococcus uberis in raw milk samples. Mastitic milk samples were collected aseptically from 44 cows with subclinical mastitis, from 11 Portuguese dairy farms. Forty-six quarter milk samples were selected based on bacterial identification by conventional microbiology. All samples were submitted to PCR analysis. In parallel, these milk samples were mixed with a solution combining specific antibodies and magnetic nanoparticles, to be analyzed using a lab-on-a-chip magnetoresistive cytometer, with microfluidic sample handling. This paper describes a point of care methodology used for detection of bacteria, including analysis of false positive/negative results. This immunological recognition was able to detect bacterial presence in samples spiked above 100 cfu/mL, independently of antibody and targeted bacteria used in this work. Using PCR as a reference, this method correctly identified 73% of positive samples for streptococci species with an anti-S. agalactiae antibody, and 41% of positive samples for an anti-GB streptococci antibody. PMID:27128950

Microbiological monitoring for the US Geological Survey National Water-Quality Assessment Program

USGS Publications Warehouse

Francy, Donna S.; Myers, Donna N.; Helsel, Dennis R.

2000-01-01

Data to characterize the microbiological quality of the Nation?s fresh, marine, and estuarine waters are usually collected for local purposes, most often to judge compliance with standards for protection of public health in swimmable or drinkable waters. Methods and procedures vary with the objectives and practices of the parties collecting data and are continuously being developed or modified. Therefore, it is difficult to provide a nationally consistent picture of the microbial quality of the Nation?s waters. Study objectives and guidelines for a national microbiological monitoring program are outlined in this report, using the framework of the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) program. A national program is designed to provide long-term data on the presence of microbiological pathogens and indicators in ground water and surface water to support effective water policy and management. Three major groups of waterborne pathogens affect the public health acceptability of waters in the United States?bacteria, protozoa, and viruses. Microbiological monitoring in NAWQA would be designed to assess the occurrence, distribution, and trends of pathogenic organisms and indicators in surface waters and ground waters; relate the patterns discerned to factors that help explain them; and improve our understanding of the processes that control microbiological water quality.

Assimilable organic carbon (AOC) determination using GFP-tagged Pseudomonas fluorescens P-17 in water by flow cytometry.

PubMed

Tang, Peng; Wu, Jie; Liu, Hou; Liu, Youcai; Zhou, Xingding

2018-01-01

One of the newly developed methods for Assimilable organic carbon (AOC) determination is leveraged on the cell enumeration by flow cytometry (FC) which could provide a rapid and automated solution for AOC measurement. However, cell samples staining with fluorescence dye is indispensable to reduce background and machine noise. This step would bring additional cost and time consuming for this method. In this study, a green fluorescence protein (GFP) tagged strain derived of AOC testing strain Pseudomonas fluorescens P-17 (GFP-P17) was generated using Tn5 transposon mutagenesis. Continuous culture of this mutant GFP-P17 showed stable expression of eGFP signal detected by flow cytometry without staining step. In addition, this GFP-P17 strain displayed faster growth rate and had a wider range of carbon substrate utilization patterns as compared with P17 wild-type. With this strain, the capability of a new FC method with no dye staining was explored in standard acetate solution, which suggests linear correlation of counts with acetate carbon concentration. Furthermore, this FC method with GFP-P17 strain is applicable in monitoring GAC/BAC efficiency and condition as similar trends of AOC level in water treatment process were measured by both FC method and conventional spread plating count method. Therefore, this fast and easily applicable GFP-P17 based FC method could serve as a tool for routine microbiological drinking water monitoring.

Diagnostic trends in Clostridium difficile detection in Finnish microbiology laboratories.

PubMed

Könönen, Eija; Rasinperä, Marja; Virolainen, Anni; Mentula, Silja; Lyytikäinen, Outi

2009-12-01

Due to increased interest directed to Clostridium difficile-associated infections, a questionnaire survey of laboratory diagnostics of toxin-producing C. difficile was conducted in Finland in June 2006. Different aspects pertaining to C. difficile diagnosis, such as requests and criteria used for testing, methods used for its detection, yearly changes in diagnostics since 1996, and the total number of investigations positive for C. difficile in 2005, were asked in the questionnaire, which was sent to 32 clinical microbiology laboratories, including all hospital-affiliated and the relevant private clinical microbiology laboratories in Finland. The situation was updated by phone and email correspondence in September 2008. In June 2006, 28 (88%) laboratories responded to the questionnaire survey; 24 of them reported routinely testing requested stool specimens for C. difficile. Main laboratory methods included toxin detection (21/24; 88%) and/or anaerobic culture (19/24; 79%). In June 2006, 18 (86%) of the 21 laboratories detecting toxins directly from feces, from the isolate, or both used methods for both toxin A (TcdA) and B (TcdB), whereas only one laboratory did so in 1996. By September 2008, all of the 23 laboratories performing diagnostics for C. difficile used methods for both TcdA and TcdB. In 2006, the number of specimens processed per 100,000 population varied remarkably between different hospital districts. In conclusion, culturing C. difficile is common and there has been a favorable shift in toxin detection practice in Finnish clinical microbiology laboratories. However, the variability in diagnostic activity reported in 2006 creates a challenge for national monitoring of the epidemiology of C. difficile and related diseases.

Black Stains: a microbiological analysis and a view on familiarity and susceptibility to tooth decay of patients in childhood.

PubMed

Tripodi, D; Martinelli, D; Pasini, M; Giuca, M R; D'Ercole, S

2016-12-01

Assess prevalence, familial predisposition and susceptibility to caries of Black Stains (BS). Evaluate the microbiological composition of BS, saliva and subgingival plaque. Sixty nine subjects with BS (test group) and 120 subjects without BS (control group) were analysed for oral status. For each BS-patient, a BS-deposit, 1 ml of saliva and subgingival plaque were collected and microbiologically analysed. Five deciduous teeth with BS were observed under SEM. This study showed a BS prevalence similar to that of the Mediterranean area and a familiality. The microbiological origin of BS was confirmed by SEM and culture method and the BS flora differ from that of supragingival plaque. Predominance in BS and saliva of Actinomycetes and the low salivary prevalence of S. mutans and L. acidophilus may be related with low caries incidence in BS patients. The high presence of Actinomyces spp can be a causative factor for BS.

Microbiological and biochemical spoilage of smoke-dried fishes sold in West African open markets.

PubMed

Ikutegbe, Victoria; Sikoki, Francis

2014-10-15

Proximate composition and microbiological characteristics of pre-dried Chrysichthys nigrodigitatus and Pseudotolithus typus were studied over a period of 4weeks to determine the health risks associated with delayed consumption. All analyses were conducted using standard microbiological and chemical methods. Results showed a general decline in microbiological safety and nutritive characteristics of both fish species over time, with an observed increase in microbial loads over time. Aspergillus flavus was also present on both species which makes consumption of the fishes hazardous to the health of consumers due to its ability to produce carcinogenic aflatoxins. In order to minimise the health risks to consumers, it is recommended that smoke-dried fishes be consumed with minimal delay and cooked properly before consumption. The findings of this study will prove important in the development of more stringent regulations regarding food safety in Nigeria. Copyright © 2014 Elsevier Ltd. All rights reserved.

Candida spp. in oral cancer and oral precancerous lesions.

PubMed

Gall, Francesca; Colella, Giuseppe; Di Onofrio, Valeria; Rossiello, Raffaele; Angelillo, Italo Francesco; Liguori, Giorgio

2013-07-01

To assess the presence of Candida spp. in lesions of the oral cavity in a sample of patients with precancer or cancer of the mouth and evaluate the limitations and advantages of microbiological and histological methods, 103 subjects with precancerous or cancerous lesions and not treated were observed between 2007 and 2009. The presence of Candida in the lesions was analyzed by microbiological and histological methods. Cohen's k statistic was used to assess the agreement between culture method and staining techniques. Forty-eight (47%) patients had cancer and 55 (53%) patients had precancerous lesions. Candida spp. were isolated from 31 (30%) patients with cancerous lesions and 33 (32%) with precancerous lesions. C. albicans was the most frequent species isolated in the lesions. The k value showed a fair overall agreement for comparisons between culture method and PAS (0.2825) or GMS (0.3112). This study supports the frequent presence of Candida spp. in cancer and precancerous lesions of the oral cavity. Both microbiological investigations and histological techniques were reliable for detection of Candida spp. It would be desirable for the two techniques to be considered complementary in the detection of yeast infections in these types of lesions.

Laboratory Workflow Analysis of Culture of Periprosthetic Tissues in Blood Culture Bottles.

PubMed

Peel, Trisha N; Sedarski, John A; Dylla, Brenda L; Shannon, Samantha K; Amirahmadi, Fazlollaah; Hughes, John G; Cheng, Allen C; Patel, Robin

2017-09-01

Culture of periprosthetic tissue specimens in blood culture bottles is more sensitive than conventional techniques, but the impact on laboratory workflow has yet to be addressed. Herein, we examined the impact of culture of periprosthetic tissues in blood culture bottles on laboratory workflow and cost. The workflow was process mapped, decision tree models were constructed using probabilities of positive and negative cultures drawn from our published study (T. N. Peel, B. L. Dylla, J. G. Hughes, D. T. Lynch, K. E. Greenwood-Quaintance, A. C. Cheng, J. N. Mandrekar, and R. Patel, mBio 7:e01776-15, 2016, https://doi.org/10.1128/mBio.01776-15), and the processing times and resource costs from the laboratory staff time viewpoint were used to compare periprosthetic tissues culture processes using conventional techniques with culture in blood culture bottles. Sensitivity analysis was performed using various rates of positive cultures. Annualized labor savings were estimated based on salary costs from the U.S. Labor Bureau for Laboratory staff. The model demonstrated a 60.1% reduction in mean total staff time with the adoption of tissue inoculation into blood culture bottles compared to conventional techniques (mean ± standard deviation, 30.7 ± 27.6 versus 77.0 ± 35.3 h per month, respectively; P < 0.001). The estimated annualized labor cost savings of culture using blood culture bottles was $10,876.83 (±$337.16). Sensitivity analysis was performed using various rates of culture positivity (5 to 50%). Culture in blood culture bottles was cost-effective, based on the estimated labor cost savings of $2,132.71 for each percent increase in test accuracy. In conclusion, culture of periprosthetic tissue in blood culture bottles is not only more accurate than but is also cost-saving compared to conventional culture methods. Copyright © 2017 American Society for Microbiology.

Detection of five potentially periodontal pathogenic bacteria in peri-implant disease: A comparison of PCR and real-time PCR.

PubMed

Schmalz, Gerhard; Tsigaras, Sandra; Rinke, Sven; Kottmann, Tanja; Haak, Rainer; Ziebolz, Dirk

2016-07-01

The aim of this study was to compare the microbial analysis methods of polymerase chain reaction (PCR) and real-time PCR (RT-PCR) in terms of detection of five selected potentially periodontal pathogenic bacteria in peri-implant disease. Therefore 45 samples of healthy, mucositis and peri-implantitis (n = 15 each) were assessed according to presence of the following bacteria using PCR (DNA-strip technology) and RT-PCR (fluorescent dye SYBR green-system): Aggregatibacter actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), Treponema denticola (Td), Tanerella forsythia (Tf), and Fusobacterium nucleatum (Fn). There were no significant correlations between the bacterial and disease patterns, so the benefit of using microbiological tests for the diagnosis of peri-implant diseases is questionable. Correlations between the methods were highest for Tf (Kendall's Tau: 0.65, Spearman: 0.78), Fn (0.49, 0.61) and Td (0.49, 0.59). For Aa (0.38, 0.42) and Pg (0.04, 0.04), lower correlation values were detected. Accordingly, conventional semi-quantitative PCR seems to be sufficient for analyzing potentially periodontal pathogenic bacterial species. Copyright © 2016 Elsevier Inc. All rights reserved.

The microbiology of Bandji, palm wine of Borassus akeassii from Burkina Faso: identification and genotypic diversity of yeasts, lactic acid and acetic acid bacteria.

PubMed

Ouoba, L I I; Kando, C; Parkouda, C; Sawadogo-Lingani, H; Diawara, B; Sutherland, J P

2012-12-01

To investigate physicochemical characteristics and especially genotypic diversity of the main culturable micro-organisms involved in fermentation of sap from Borassus akeassii, a newly identified palm tree from West Africa. Physicochemical characterization was performed using conventional methods. Identification of micro-organisms included phenotyping and sequencing of: 26S rRNA gene for yeasts, 16S rRNA and gyrB genes for lactic acid bacteria (LAB) and acetic acid bacteria (AAB). Interspecies and intraspecies genotypic diversities of the micro-organisms were screened respectively by amplification of the ITS1-5.8S rDNA-ITS2/16S-23S rDNA ITS regions and repetitive sequence-based PCR (rep-PCR). The physicochemical characteristics of samples were: pH: 3.48-4.12, titratable acidity: 1.67-3.50 mg KOH g(-1), acetic acid: 0.16-0.37%, alcohol content: 0.30-2.73%, sugars (degrees Brix): 2.70-8.50. Yeast included mainly Saccharomyces cerevisiae and species of the genera Arthroascus, Issatchenkia, Candida, Trichosporon, Hanseniaspora, Kodamaea, Schizosaccharomyces, Trigonopsis and Galactomyces. Lactobacillus plantarum was the predominant LAB species. Three other species of Lactobacillus were also identified as well as isolates of Leuconostoc mesenteroides, Fructobacillus durionis and Streptococcus mitis. Acetic acid bacteria included nine species of the genus Acetobacter with Acetobacter indonesiensis as predominant species. In addition, isolates of Gluconobacter oxydans and Gluconacetobacter saccharivorans were also identified. Intraspecies diversity was observed for some species of micro-organisms including four genotypes for Acet. indonesiensis, three for Candida tropicalis and Lactobacillus fermentum and two each for S. cerevisiae, Trichosporon asahii, Candida pararugosa and Acetobacter tropicalis. fermentation of palm sap from B. akeassii involved multi-yeast-LAB-AAB cultures at genus, species and intraspecies level. First study describing microbiological and physicochemical characteristics of palm wine from B. akeassii. Genotypic diversity of palm wine LAB and AAB not reported before is demonstrated and this constitutes valuable information for better understanding of the fermentation which can be used to improve the product quality and develop added value by-products. © 2012 The Society for Applied Microbiology.

Radiolabelled leucocyte scintigraphy versus conventional radiological imaging for the management of late, low-grade vascular prosthesis infections.

PubMed

Erba, P A; Leo, G; Sollini, M; Tascini, C; Boni, R; Berchiolli, R N; Menichetti, F; Ferrari, M; Lazzeri, E; Mariani, G

2014-02-01

In this study we evaluated the diagnostic performance of (99m)Tc-HMPAO-leucocyte ((99m)Tc-HMPAO-WBC) scintigraphy in a consecutive series of 55 patients (46 men and 9 women, mean age 71 ± 9 years, range 50 - 88 years) with a suspected late or a low-grade late vascular prosthesis infection (VPI), also comparing the diagnostic accuracy of WBC with that of other radiological imaging methods. All patients suspected of having VPI underwent clinical examination, blood tests, microbiology, US and CT, and were classified according to the Fitzgerald criteria. A final diagnosis of VPI was established in 47 of the 55 patients, with microbiological confirmation after surgical removal of the prosthesis in 36 of the 47. In the 11 patients with major contraindications to surgery, the final diagnosis was based on microbiology and clinical follow-up of at least 18 months. (99m)Tc-HMPAO-WBC planar, SPECT and SPECT/CT imaging identified VPI in 43 of 47 patients (20 of these also showed infection at extra-prosthetic sites). In the remaining eight patients without VPI, different sites of infections were found. The use of SPECT/CT images led to a significant reduction in the number of false-positive findings in 37% of patients (sensitivity and specificity 100 %, versus 85.1% and 62.5% for stand-alone SPECT). Sensitivity and specificity were 34% and 75% for US, 48.9% and 83.3% for CT, and 68.1% and 62.5% for the FitzGerald classification. Perioperative mortality was 5.5%, mid-term mortality 12%, and long-term mortality 27%. Survival rates were similar in patients treated with surgery and antimicrobial therapy compared to patients treated with antimicrobial therapy alone (61% versus 63%, respectively), while infection eradication at 12 months was significantly higher following surgery (83.3% versus 45.5%). (99m)Tc-HMPAO-WBC SPECT/CT is useful for detecting, localizing and defining the extent of graft infection in patients with late and low-grade late VPI with inconclusive radiological findings. (99m)Tc-HMPAO-WBC SPECT/CT might be used to optimize patient management.

The comparative evaluation of xanthan gel with chlorhexidine (Chlosite) in smokers and non-smokers: A clinical and microbiological assessment

PubMed Central

Chandra, Chetan; Valavalkar, Narayan; Vandana, K. L.

2011-01-01

Background and Objectives: Prevention of the periodontal disease progression is the primary goal of periodontal therapy. When conventional therapy is found inadequate to attain periodontal health in chronic periodontitis, local antimicrobial agents have been used as an adjunct with scaling and root planning (SRP) which has reproduced encouraging results. Hence, this study was undertaken to evaluate the new sustained released local drug Chlosite clinically and microbiologically in smokers and non-smokers. Materials and Methods: The patients were grouped into experimental group A treated with SRP plus Chlosite (SRP + CHL), experimental group B treated with Chlosite alone (CHL), and control group C treated only with SRP alone. A total number of 141 sites from six patients (67 sites from three non-smoker patients and 74 sites from three smoker patients) participated in this study. The clinical parameters, Plaque index (PI), Gingival index (GI), Bleeding index (BI), and Relative attachment level (RAL), were recorded and subgingival plaque samples were collected and subjected to microbiological analysis. Results: On comparison of smokers and non-smokers, in SRP group, non-smokers showed a higher reduction in BI and GI and smokers showed a higher reduction in PI. There was no significant gain in RAL of both smokers and non-smokers. In SRP + CHL group, non-smokers showed a higher reduction in relation to BI and GI and smokers showed a higher reduction in relation to PI. There was no significant gain in RAL of both smokers and non-smokers. In CHL group, both smokers and non-smokers showed a nonsignificant reduction in BI, GI, and RAL, but smokers showed a significant reduction in PI as compared with non-smokers. All the groups showed reduction in the microbial count of Fusobacterium nucleatum, Porphyromonas gingivalis, and Tannerella forsythia which were found to be statistically not significant when it was compared between non-smokers and smokers. Interpretation and Conclusion: In this study, all treatment groups were found to be efficacious in the treatment of periodontal disease as demonstrated by improvement in PI, GI, BI, and RAL. Combination of SRP and Chlosite resulted in added benefits compared with the two treatment groups. PMID:22028508

Assessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis.

PubMed

Korsak, N; Taminiau, B; Hupperts, C; Delhalle, L; Nezer, C; Delcenserie, V; Daube, G

2017-04-17

The aim of this study was to investigate the influence of the slaughter technique (Halal vs Classical slaughter) on the superficial contamination of cattle carcasses, by using traditional microbiological procedures and 16S rDNA metagenetics. The purpose was also to investigate the neck area to identify bacteria originating from the digestive or the respiratory tract. Twenty bovine carcasses (10 from each group) were swabbed at the slaughterhouse, where both slaughtering methods are practiced. Two swabbing areas were chosen: one "legal" zone of 1600cm 2 (composed of zones from rump, flank, brisket and forelimb) and locally on the neck area (200cm 2 ). Samples were submitted to classical microbiology for aerobic Total Viable Counts (TVC) at 30°C and Enterobacteriaceae counts, while metagenetic analysis was performed on the same samples. The classical microbiological results revealed no significant differences between both slaughtering practices; with values between 3.95 and 4.87log CFU/100cm 2 and 0.49 and 1.94log CFU/100cm 2 , for TVC and Enterobacteriaceae respectively. Analysis of pyrosequencing data showed that differences in the bacterial population abundance between slaughtering methods were mainly observed in the "legal" swabbing zone compared to the neck area. Bacterial genera belonging to the Actinobacteria phylum were more abundant in the "legal" swabbing zone in "Halal" samples, while Brevibacterium and Corynebacterium were encountered more in "Halal" samples, in all swabbing areas. This was also the case for Firmicutes bacterial populations (families of Aerococcaceae, Planococcaceae). Except for Planococcoceae, the analysis of Operational Taxonomic Unit (OTU) abundances of bacteria from the digestive or respiratory tract revealed no differences between groups. In conclusion, the slaughtering method does not influence the superficial microbiological pattern in terms of specific microbiological markers of the digestive or respiratory tract. However, precise analysis of taxonomy at the genus level taxonomy highlights differences between swabbing areas. Although not clearly proven in this study, differences in hygiene practices used during both slaughtering protocols could explain the differences in contamination between carcasses from both slaughtering groups. Copyright © 2016 Elsevier B.V. All rights reserved.

Diagnostic methods to determine microbiology of postpartum endometritis in South Asia: laboratory methods protocol used in the Postpartum Sepsis Study: a prospective cohort study.

PubMed

Shakoor, Sadia; Reller, Megan E; LeFevre, Amnesty; Hotwani, Aneeta; Qureshi, Shahida M; Yousuf, Farheen; Islam, Mohammad Shahidul; Connor, Nicholas; Rafiqullah, Iftekhar; Mir, Fatima; Arif, Shabina; Soofi, Sajid; Bartlett, Linda A; Saha, Samir

2016-02-25

The South Asian region has the second highest risk of maternal death in the world. To prevent maternal deaths due to sepsis and to decrease the maternal mortality ratio as per the World Health Organization Millenium Development Goals, a better understanding of the etiology of endometritis and related sepsis is required. We describe microbiological laboratory methods used in the maternal Postpartum Sepsis Study, which was conducted in Bangladesh and Pakistan, two populous countries in South Asia. Postpartum maternal fever in the community was evaluated by a physician and blood and urine were collected for routine analysis and culture. If endometritis was suspected, an endometrial brush sample was collected in the hospital for aerobic and anaerobic culture and molecular detection of bacterial etiologic agents (previously identified and/or plausible). The results emanating from this study will provide microbiologic evidence of the etiology and susceptibility pattern of agents recovered from patients with postpartum fever in South Asia, data critical for the development of evidence-based algorithms for management of postpartum fever in the region.

Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry in Clinical Microbiology: What Are the Current Issues?

PubMed Central

Welker, Martin; Pincus, David; Charrier, Jean-Philippe; Girard, Victoria

2017-01-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microbial species in clinical microbiology laboratories. MALDI-TOF-MS has swiftly become the new gold-standard method owing to its key advantages of simplicity and robustness. However, as with all new methods, adoption of the MALDI-TOF MS approach is still not widespread. Optimal sample preparation has not yet been achieved for several applications, and there are continuing discussions on the need for improved database quality and the inclusion of additional microbial species. New applications such as in the field of antimicrobial susceptibility testing have been proposed but not yet translated to the level of ease and reproducibility that one should expect in routine diagnostic systems. Finally, during routine identification testing, unexpected results are regularly obtained, and the best methods for transmitting these results into clinical care are still evolving. We here discuss the success of MALDI-TOF MS in clinical microbiology and highlight fields of application that are still amenable to improvement. PMID:28840984

Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry in Clinical Microbiology: What Are the Current Issues?

PubMed

van Belkum, Alex; Welker, Martin; Pincus, David; Charrier, Jean Philippe; Girard, Victoria

2017-11-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microbial species in clinical microbiology laboratories. MALDI-TOF-MS has swiftly become the new gold-standard method owing to its key advantages of simplicity and robustness. However, as with all new methods, adoption of the MALDI-TOF MS approach is still not widespread. Optimal sample preparation has not yet been achieved for several applications, and there are continuing discussions on the need for improved database quality and the inclusion of additional microbial species. New applications such as in the field of antimicrobial susceptibility testing have been proposed but not yet translated to the level of ease and reproducibility that one should expect in routine diagnostic systems. Finally, during routine identification testing, unexpected results are regularly obtained, and the best methods for transmitting these results into clinical care are still evolving. We here discuss the success of MALDI-TOF MS in clinical microbiology and highlight fields of application that are still amenable to improvement. © The Korean Society for Laboratory Medicine.

Conventional versus laser-assisted therapy of periimplantitis: a five-year comparative study.

PubMed

Bach, G; Neckel, C; Mall, C; Krekeler, G

2000-01-01

Between 1994 and 1999, 50 patients were treated with either profound parodontopathy (30) or periimplantitis (20). Half of each of the two groups of patients was treated conventionally, and the other half was treated with laser support. Before the operation, microbiological examinations were carried out, in addition to registering the clinical findings and taking x-rays. These procedures were repeated after the operation, and again after 6, 12, 24, 36, 48, and 60 months. The surgical part of therapy for each half of the patient groups included surface decontamination with diode laser light (1-watt output, maximum of 20 seconds) in addition to conventional procedures. The values of the laser-supported therapy were lower than those specified in the relevant literature. The relapse rate of the two diseases (13% for the periimplantitis and 23% for the parodontopathy group) after 5 years was lower than the comparative values of researched literature where decontamination was not included in the therapy. We think that integrating diode laser light decontamination in the approved treatment schemes for periimplantitis and parodontitis contributes considerably to the success of this therapy.

Gingival response in orthodontic patients: Comparative study between self-ligating and conventional brackets.

PubMed

Folco, Alejandra A; Benítez-Rogé, Sandra C; Iglesias, Marina; Calabrese, Diana; Pelizardi, Cristina; Rosa, Alcira; Brusca, Marisa I; Hecht, Pedro; Mateu, María E

2014-01-01

Orthodontic brackets contribute to the accumulation of bacterial plaque on tooth surfaces because they hinder oral hygiene. In contrast to conventional brackets, self-ligating brackets do not require additional parts to support the arches, thus improving dental hygiene. The aim of this study was to compare the gingival response in orthodontic patients wearing self-ligating or conventional brackets. A sample of 22 patients aged 16 to 30 years was divided into two groups: Group A, treated with selfligating brackets (Damon system) and Group B, treated with conventional brackets (Roth technique). The following were assessed during the treatment: Plaque Index (PI), Gingival Index (GI) and Probing Depth (PD), and sub-gingival samples were taken from teeth 14/24 for microbiological observation. No statistically significant difference was found between Groups A and B; p>0.05 (sign-ranked) or between PI, GI and PD at the different times (Friedman's Analysis of Variance), even though the indices were found to increase at 14 days, particularly for self-ligating brackets. The quantity and quality of microorganisms present were compatible with health on days 0, 28 and 56. As from day 14 there is a predominance of microbiota compatible with gingivitis in both groups. In the samples studied, orthodontic treatment increases bacterial plaque and inflammatory gingival response, but gingival-periodontal health can be maintained with adequate basic therapy. Self-ligating and conventional brackets produced similar gingival response.

Frequency and correlation of some enteric indicator bacteria and Salmonella in ready-to-eat raw vegetable salads from Mexican restaurants.

PubMed

Gómez-Aldapa, Carlos A; Rangel-Vargas, Esmeralda; Castro-Rosas, Javier

2013-08-01

Data about Salmonella presence in ready-to-eat raw vegetable salads (REVS) consumed in restaurants or sold as REVS in México is not available. The objective of the study was to measure the frequency of coliform bacteria (CB), fecal coliform (FC), Escherichia coli, and Salmonella in REVS from different types of restaurants and determine the correlations of CB, FC, and E. coli versus Salmonella from frequencies and concentration data. The REVS were purchased from 3 types of restaurants: national chain restaurants (A1 , A2 ); local restaurants (B1 , B2 ); and small restaurants in local markets (C1 , C2 , C3 ). Two restaurants for each A and B, and 3 for C, were included. Forty REVS were purchased at each A and B restaurant, and 20 at each C restaurant. CB were tested by plate count using violet red bile agar, FC and E. coli were detected by the most probable number method and E. coli confirmed using IMViC test; conventional method of culture was used for Salmonella. Of 220 analyzed samples, 100% had CB, 95.5% had FC, 83.2% had E. coli, and 6.8% had Salmonella. E. coli frequency was equal to or exceeded 75% in all the cases: 75% (A1 , C1 , C2 ), 80% (B2 ), 85% (B1 , C3 ), and 100% (A2 ). Salmonella frequency was equal to or exceeded 2.5% in all cases: 2.5% (A1 ), 5% (B2 , C2 ), 7.5% (B1 ), and 10% (A2 , C1 , C3 ). No correlation was observed between FC or E. coli versus Salmonella in the analyzed salads. All the tested salads were of poor quality microbiologically, and microbiological quality did not differ between the restaurants types. © 2013 Institute of Food Technologists®

Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology.

PubMed

Rossen, J W A; Friedrich, A W; Moran-Gilad, J

2018-04-01

Next generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology adopted in microbiology, the integration of NGS into clinical and routine workflows must be carefully managed. To review the practical aspects of implementing bacterial whole genome sequencing (WGS) in routine diagnostic laboratories. Review of the literature and expert opinion. In this review, we discuss when and how to integrate whole genome sequencing (WGS) in the routine workflow of the clinical laboratory. In addition, as the microbiology laboratories have to adhere to various national and international regulations and criteria for their accreditation, we deliberate on quality control issues for using WGS in microbiology, including the importance of proficiency testing. Furthermore, the current and future place of this technology in the diagnostic hierarchy of microbiology is described as well as the necessity of maintaining backwards compatibility with already established methods. Finally, we speculate on the question of whether WGS can entirely replace routine microbiology in the future and the tension between the fact that most sequencers are designed to process multiple samples in parallel whereas for optimal diagnosis a one-by-one processing of the samples is preferred. Special reference is made to the cost and turnaround time of WGS in diagnostic laboratories. Further development is required to improve the workflow for WGS, in particular to shorten the turnaround time, reduce costs, and streamline downstream data analyses. Only when these processes reach maturity will reliance on WGS for routine patient management and infection control management become feasible, enabling the transformation of clinical microbiology into a genome-based and personalized diagnostic field. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Is This the Carbapenemase Test We've Been Waiting for? A Multicenter Evaluation of the Modified Carbapenem Inactivation Method.

PubMed

Butler-Wu, Susan M; Abbott, April N

2017-08-01

A plethora of phenotypic methods exist for the detection of carbapenemases; however, clinical laboratories have struggled for years with accurate, objective phenotypic detection of carbapenemase activity in Enterobacteriaceae In this issue of the Journal of Clinical Microbiology , V. M. Pierce et al. (J Clin Microbiol 55:2321-2333, 2017, https://doi.org/10.1128/JCM.00193-17) report on a multicenter evaluation of the modified carbapenem inactivation method (mCIM). The high sensitivity, specificity, reproducibility, and ease of interpretation associated with the mCIM for Enterobacteriaceae will likely lead to its adoption by clinical laboratories. Copyright © 2017 American Society for Microbiology.

Quantitative analysis of periodontal pathogens by ELISA and real-time polymerase chain reaction.

PubMed

Hamlet, Stephen M

2010-01-01

The development of analytical methods enabling the accurate identification and enumeration of bacterial species colonizing the oral cavity has led to the identification of a small number of bacterial pathogens that are major factors in the etiology of periodontal disease. Further, these methods also underpin more recent epidemiological analyses of the impact of periodontal disease on general health. Given the complex milieu of over 700 species of microorganisms known to exist within the complex biofilms found in the oral cavity, the identification and enumeration of oral periodontopathogens has not been an easy task. In recent years however, some of the intrinsic limitations of the more traditional microbiological analyses previously used have been overcome with the advent of immunological and molecular analytical methods. Of the plethora of methodologies reported in the literature, the enzyme-linked immunosorbent assay (ELISA), which combines the specificity of antibody with the sensitivity of simple enzyme assays and the polymerase chain reaction (PCR), has been widely utilized in both laboratory and clinical applications. Although conventional PCR does not allow quantitation of the target organism, real-time PCR (rtPCR) has the ability to detect amplicons as they accumulate in "real time" allowing subsequent quantitation. These methods enable the accurate quantitation of as few as 10(2) (using rtPCR) to 10(4) (using ELISA) periodontopathogens in dental plaque samples.

Application of an oligonucleotide microarray-based nano-amplification technique for the detection of fungal pathogens.

PubMed

Lu, Weiping; Gu, Dayong; Chen, Xingyun; Xiong, Renping; Liu, Ping; Yang, Nan; Zhou, Yuanguo

2010-10-01

The traditional techniques for diagnosis of invasive fungal infections in the clinical microbiology laboratory need improvement. These techniques are prone to delay results due to their time-consuming process, or result in misidentification of the fungus due to low sensitivity or low specificity. The aim of this study was to develop a method for the rapid detection and identification of fungal pathogens. The internal transcribed spacer two fragments of fungal ribosomal DNA were amplified using a polymerase chain reaction for all samples. Next, the products were hybridized with the probes immobilized on the surface of a microarray. These species-specific probes were designed to detect nine different clinical pathogenic fungi including Candida albicans, Candida tropocalis, Candida glabrata, Candida parapsilosis, Candida krusei, Candida lusitaniae, Candida guilliermondii, Candida keyfr, and Cryptococcus neoformans. The hybridizing signals were enhanced with gold nanoparticles and silver deposition, and detected using a flatbed scanner or visually. Fifty-nine strains of fungal pathogens, including standard and clinically isolated strains, were correctly identified by this method. The sensitivity of the assay for Candida albicans was 10 cells/mL. Ten cultures from clinical specimens and 12 clinical samples spiked with fungi were also identified correctly. This technique offers a reliable alternative to conventional methods for the detection and identification of fungal pathogens. It has higher efficiency, specificity and sensitivity compared with other methods commonly used in the clinical laboratory.

Residual antibiotics in decontaminated human cardiovascular tissues intended for transplantation and risk of falsely negative microbiological analyses.

PubMed

Buzzi, Marina; Guarino, Anna; Gatto, Claudio; Manara, Sabrina; Dainese, Luca; Polvani, Gianluca; Tóthová, Jana D'Amato

2014-01-01

We investigated the presence of antibiotics in cryopreserved cardiovascular tissues and cryopreservation media, after tissue decontamination with antibiotic cocktails, and the impact of antibiotic residues on standard tissue bank microbiological analyses. Sixteen cardiovascular tissues were decontaminated with bank-prepared cocktails and cryopreserved by two different tissue banks according to their standard operating procedures. Before and after decontamination, samples underwent microbiological analysis by standard tissue bank methods. Cryopreserved samples were tested again with and without the removal of antibiotic residues using a RESEP tube, after thawing. Presence of antibiotics in tissue homogenates and processing liquids was determined by a modified agar diffusion test. All cryopreserved tissue homogenates and cryopreservation media induced important inhibition zones on both Staphylococcus aureus- and Pseudomonas aeruginosa-seeded plates, immediately after thawing and at the end of the sterility test. The RESEP tube treatment markedly reduced or totally eliminated the antimicrobial activity of tested tissues and media. Based on standard tissue bank analysis, 50% of tissues were found positive for bacteria and/or fungi, before decontamination and 2 out of 16 tested samples (13%) still contained microorganisms after decontamination. After thawing, none of the 16 cryopreserved samples resulted positive with direct inoculum method. When the same samples were tested after removal of antibiotic residues, 8 out of 16 (50%) were contaminated. Antibiotic residues present in tissue allografts and processing liquids after decontamination may mask microbial contamination during microbiological analysis performed with standard tissue bank methods, thus resulting in false negatives.

Residual Antibiotics in Decontaminated Human Cardiovascular Tissues Intended for Transplantation and Risk of Falsely Negative Microbiological Analyses

PubMed Central

Gatto, Claudio; Manara, Sabrina; Dainese, Luca; Polvani, Gianluca; Tóthová, Jana D'Amato

2014-01-01

We investigated the presence of antibiotics in cryopreserved cardiovascular tissues and cryopreservation media, after tissue decontamination with antibiotic cocktails, and the impact of antibiotic residues on standard tissue bank microbiological analyses. Sixteen cardiovascular tissues were decontaminated with bank-prepared cocktails and cryopreserved by two different tissue banks according to their standard operating procedures. Before and after decontamination, samples underwent microbiological analysis by standard tissue bank methods. Cryopreserved samples were tested again with and without the removal of antibiotic residues using a RESEP tube, after thawing. Presence of antibiotics in tissue homogenates and processing liquids was determined by a modified agar diffusion test. All cryopreserved tissue homogenates and cryopreservation media induced important inhibition zones on both Staphylococcus aureus- and Pseudomonas aeruginosa-seeded plates, immediately after thawing and at the end of the sterility test. The RESEP tube treatment markedly reduced or totally eliminated the antimicrobial activity of tested tissues and media. Based on standard tissue bank analysis, 50% of tissues were found positive for bacteria and/or fungi, before decontamination and 2 out of 16 tested samples (13%) still contained microorganisms after decontamination. After thawing, none of the 16 cryopreserved samples resulted positive with direct inoculum method. When the same samples were tested after removal of antibiotic residues, 8 out of 16 (50%) were contaminated. Antibiotic residues present in tissue allografts and processing liquids after decontamination may mask microbial contamination during microbiological analysis performed with standard tissue bank methods, thus resulting in false negatives. PMID:25397402

ADSA Foundation Scholar Award: Trends in culture-independent methods for assessing dairy food quality and safety: emerging metagenomic tools.

PubMed

Yeung, Marie

2012-12-01

Enhancing the quality and safety of dairy food is critical to maintaining the competitiveness of dairy products in the food and beverage market and in reinforcing consumer confidence in the dairy industry. Raw milk quality has a significant effect on finished product quality. Several microbial groups found in raw milk have been shown to adversely affect the shelf life of pasteurized milk. Current microbiological criteria used to define milk quality are based primarily on culture-dependent methods, some of which are perceived to lack the desired sensitivity and specificity. To supplement traditional methods, culture-independent methods are increasingly being used to identify specific species or microbial groups, and to detect indicator genes or proteins in raw milk or dairy products. Some molecular subtyping techniques have been developed to track the transmission of microbes in dairy environments. The burgeoning "-omics" technologies offer new and exciting opportunities to enhance our understanding of food quality and safety in relation to microbes. Metagenomics has the potential to characterize microbial diversity, detect nonculturable microbes, and identify unique sequences or other factors associated with dairy product quality and safety. In this review, fluid milk will be used as the primary example to examine the adequacy and validity of conventional methods, the current trend of culture-independent methods, and the potential applications of metagenomics in dairy food research. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Internal audit in a microbiology laboratory.

PubMed Central

Mifsud, A J; Shafi, M S

1995-01-01

AIM--To set up a programme of internal laboratory audit in a medical microbiology laboratory. METHODS--A model of laboratory based process audit is described. Laboratory activities were examined in turn by specimen type. Standards were set using laboratory standard operating procedures; practice was observed using a purpose designed questionnaire and the data were analysed by computer; performance was assessed at laboratory audit meetings; and the audit circle was closed by re-auditing topics after an interval. RESULTS--Improvements in performance scores (objective measures) and in staff morale (subjective impression) were observed. CONCLUSIONS--This model of process audit could be applied, with amendments to take local practice into account, in any microbiology laboratory. PMID:7665701

Nonlinear dynamic phase contrast microscopy for microfluidic and microbiological applications

NASA Astrophysics Data System (ADS)

Denz, C.; Holtmann, F.; Woerdemann, M.; Oevermann, M.

2008-08-01

In live sciences, the observation and analysis of moving living cells, molecular motors or motion of micro- and nano-objects is a current field of research. At the same time, microfluidic innovations are needed for biological and medical applications on a micro- and nano-scale. Conventional microscopy techniques are reaching considerable limits with respect to these issues. A promising approach for this challenge is nonlinear dynamic phase contrast microscopy. It is an alternative full field approach that allows to detect motion as well as phase changes of living unstained micro-objects in real-time, thereby being marker free, without contact and non destructive, i.e. fully biocompatible. The generality of this system allows it to be combined with several other microscope techniques such as conventional bright field or fluorescence microscopy. In this article we will present the dynamic phase contrast technique and its applications in analysis of micro organismic dynamics, micro flow velocimetry and micro-mixing analysis.

Ultra-High Pressure Homogenization improves oxidative stability and interfacial properties of soy protein isolate-stabilized emulsions.

PubMed

Fernandez-Avila, C; Trujillo, A J

2016-10-15

Ultra-High Pressure Homogenization (100-300MPa) has great potential for technological, microbiological and nutritional aspects of fluid processing. Its effect on the oxidative stability and interfacial properties of oil-in-water emulsions prepared with 4% (w/v) of soy protein isolate and soybean oil (10 and 20%, v/v) were studied and compared to emulsions treated by conventional homogenization (15MPa). Emulsions were characterized by particle size, emulsifying activity index, surface protein concentration at the interface and by transmission electron microscopy. Primary and secondary lipid oxidation products were evaluated in emulsions upon storage. Emulsions with 20% oil treated at 100 and 200MPa exhibited the most oxidative stability due to higher amount of oil and protein surface load at the interface. This manuscript addresses the improvement in oxidative stability in emulsions treated by UHPH when compared to conventional emulsions. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Microbiological validation of the composition of "decaceol", an antiseptic prolonged-release drug].

PubMed

Dykyĭ, I L; Zaĭtsev, O I; Filimonova, N I

2002-01-01

With the aid of different microbiological methods, antimicrobal properties of decametoxine, a home-produced antiseptic, were studied together with those of the synthetic zoelite NaA-base drug preparation. The antimicrobial activity of the above drug has been shown to be of a synergistic character that makes it a very promising medical agent which will, we believe, come to be widely used in medical practice.

Competency Assessment of Microbiology Medical Laboratory Technologists in Ontario, Canada

PubMed Central

Fleming, Christine Ann

2014-01-01

Accreditation in Ontario, Canada, requires that licensed clinical laboratories participate in external quality assessment (also known as proficiency testing) and perform competency evaluation of their staff. To assess the extent of ongoing competency assessment practices, the Quality Management Program—Laboratory Services (QMP-LS) Microbiology Committee surveyed all 112 licensed Ontario microbiology laboratories. The questionnaire consisted of a total of 21 questions that included yes/no, multiple-choice, and short-answer formats. Participants were asked to provide information about existing programs, the frequency of testing, what areas are evaluated, and how results are communicated to the staff. Of the 111 responding laboratories, 6 indicated they did not have a formal evaluation program since they perform only limited bacteriology testing. Of the remaining 105 respondents, 87% perform evaluations at least annually or every 2 years, and 61% include any test or task performed, whereas 16% and 10% focus only on problem areas and high-volume complex tasks, respectively. The most common methods of evaluation were review of external quality assessment (EQA) challenges, direct observation, and worksheet review. With the exception of one participant, all communicate results to staff, and most take remedial action to correct the deficiencies. Although most accredited laboratories have a program to assess the ongoing competency of their staff, the methods used are not standardized or consistently applied, indicating that there is room for improvement. The survey successfully highlighted potential areas for improvement and allowed the QMP-LS Microbiology Committee to provide guidance to Ontario laboratories for establishing or improving existing microbiology-specific competency assessment programs. PMID:24899030

Microbiological purity assessment of cosmetics used by one and several persons and cosmetics after their expiry date

PubMed

Skowron, Krzysztof; Jakubicz, Agnieszka; Budzyńska, Anna; Kaczmarek, Agnieszka; Grudlewska, Katarzyna; Reśliński, Adrian; Gospodarek-Komkowska, Eugenia

Microbiological purity of cosmetics provides safety of users during their use, prevents physicochemical changes of a preparation, infections and diseases of the skin. The aim of this study was to assess the level of microbiological contamination of cosmetics used by one person and by several people and cosmetics after their expiry date in relations to standards for marketed cosmetics, ensuring safety of their use. This study was conducted using 55 samples representing 19 types of cosmetics, divided into three groups: used by one person, used by several people and after the expiry date. In cosmetic samples the general numbers of aerobic mesophilic bacteria were determined with the spread plate method on tryptic-soy agar. The presence of Staphylococcus aureus, Pseudomonas aeruginosa and Candida albicans were also checked. The number of aerobic mesophylic bacteria in the tested cosmetics ranged from the level below the method detectability to 1.3×107 cfu/g or ml. The presence of Staphylococcus spp. was found in 11 (20.0%) tested cosmetic samples and of P. aeruginosa in one tested preparation. Yeasts C. albicans were not detected, whereas contamination with fungi Aspergillus spp. and Penicillium spp. ranging from 0.5×101 to 1.5×101 cfu/g or ml was recorded in four cosmetics. The level of microbiological contamination of cosmetics used by several people was higher than that of cosmetics used by one person. Cosmetics after the expiry date showed the highest microbiological contamination. The number of users of cosmetic and it expiry date exceeding influenced the level of microbial contamination of preparations.

Swab Protocol for Rapid Laboratory Diagnosis of Cutaneous Anthrax

PubMed Central

Marston, Chung K.; Bhullar, Vinod; Baker, Daniel; Rahman, Mahmudur; Hossain, M. Jahangir; Chakraborty, Apurba; Khan, Salah Uddin; Hoffmaster, Alex R.

2012-01-01

The clinical laboratory diagnosis of cutaneous anthrax is generally established by conventional microbiological methods, such as culture and directly straining smears of clinical specimens. However, these methods rely on recovery of viable Bacillus anthracis cells from swabs of cutaneous lesions and often yield negative results. This study developed a rapid protocol for detection of B. anthracis on clinical swabs. Three types of swabs, flocked-nylon, rayon, and polyester, were evaluated by 3 extraction methods, the swab extraction tube system (SETS), sonication, and vortex. Swabs were spiked with virulent B. anthracis cells, and the methods were compared for their efficiency over time by culture and real-time PCR. Viability testing indicated that the SETS yielded greater recovery of B. anthracis from 1-day-old swabs; however, reduced viability was consistent for the 3 extraction methods after 7 days and nonviability was consistent by 28 days. Real-time PCR analysis showed that the PCR amplification was not impacted by time for any swab extraction method and that the SETS method provided the lowest limit of detection. When evaluated using lesion swabs from cutaneous anthrax outbreaks, the SETS yielded culture-negative, PCR-positive results. This study demonstrated that swab extraction methods differ in their efficiency of recovery of viable B. anthracis cells. Furthermore, the results indicated that culture is not reliable for isolation of B. anthracis from swabs at ≥7 days. Thus, we recommend the use of the SETS method with subsequent testing by culture and real-time PCR for diagnosis of cutaneous anthrax from clinical swabs of cutaneous lesions. PMID:23035192

Exposure assessment for dioxin-like PCBs intake from organic and conventional meat integrating cooking and digestion effects.

PubMed

Tressou, Jessica; Ben Abdallah, Nadia; Planche, Christelle; Dervilly-Pinel, Gaud; Sans, Pierre; Engel, Erwan; Albert, Isabelle

2017-12-01

In this paper, exposure to Polychlorinated biphenyls (PCBs) related to bovine meat consumption is assessed based on multiples sources of data, namely data collected within the national research project "SoMeat" that objectively assesses the potential risks and benefits of organic and conventional food production systems in terms of contaminants respective contents. The work focuses on dioxin like PCBs in bovine meat in France. A modular Bayesian approach is proposed including measures after production, effect of cooking, levels and frequency of consumption and effect of digestion. In each module, a model is built and prior information can be integrated through previously acquired data commonly used in food risk assessment or vague priors. The output of the global model is the exposure including both production modes (organic and conventional) for three different cooking intensities (rare, medium, and well-done), before digestion and after digestion. The main results show that organic meat is more contaminated than conventional meat in mean after production stage and after cooking although cooking reduces the contamination level. This work is a first step of refined risk assessment integrating different steps such as cooking and digestion in the context of chemical risk assessment similarly to current microbiological risk assessments. Copyright © 2017 Elsevier Ltd. All rights reserved.

A new approach in the first-line treatment of bacterial and mycotic vulvovaginitis with topical lipohydroperoxides and glycyrrhetic acid: a comparative study.

PubMed

Mainini, G; Rotondi, M; Scaffa, C

2011-01-01

PURPOSE OF INVESTIGATIONS: The aim of this randomized controlled trial was to evaluate efficacy and tolerability of a new association of lipohydroperoxides and glycyrrhetic acid on topical treatment of bacterial and mycotic vulvovaginitis. One hundred consecutive patients with bacterial or mycotic vulvovaginitis were randomly assigned to a study group treated with vaginal lipohydroperoxides and a derivative of glycyrrhetic acid for three days (n = 50), and a control group using vaginal antibacterial metronidazole (500 mg) or antimycotic econazole (150 mg) for six days (n = 50). A clinical and microbiological response was achieved in 80.4% and 88.9% in investigational and control group, respectively (p > 0.05). Compared to traditional antimicrobial drugs, the effect appears to be faster and safer, even if not significantly. The 6-month recurrence rate was 7.7% and 5.6% in the investigational and control group, respectively. Topical medication based on lipohydroperoxides and glycyrrhetic acid showed a clinical and microbiological efficacy in the first-line treatment of bacterial and mycotic vulvovaginitis, comparable to conventional drugs.

Effects of high hydrostatic pressure and thermal processing on bioactive compounds, antioxidant activity, and volatile profile of mulberry juice.

PubMed

Wang, Fan; Du, Bao-Lei; Cui, Zheng-Wei; Xu, Li-Ping; Li, Chun-Yang

2017-03-01

The aim of this study was to investigate the effects of high hydrostatic pressure and thermal processing on microbiological quality, bioactive compounds, antioxidant activity, and volatile profile of mulberry juice. High hydrostatic pressure processing at 500 MPa for 10 min reduced the total viable count from 4.38 log cfu/ml to nondetectable level and completely inactivated yeasts and molds in raw mulberry juice, ensuring the microbiological safety as thermal processing at 85 ℃ for 15 min. High hydrostatic pressure processing maintained significantly (p < 0.05) higher contents of total phenolic, total flavonoid and resveratrol, and antioxidant activity of mulberry juice than thermal processing. The main volatile compounds of mulberry juice were aldehydes, alcohols, and ketones. High hydrostatic pressure processing enhanced the volatile compound concentrations of mulberry juice while thermal processing reduced them in comparison with the control. These results suggested that high hydrostatic pressure processing could be an alternative to conventional thermal processing for production of high-quality mulberry juice.

Brewing for Students: An Inquiry-Based Microbiology Lab †

PubMed Central

Sato, Brian K.; Alam, Usman; Dacanay, Samantha J.; Lee, Amanda K.; Shaffer, Justin F.

2015-01-01

In an effort to improve and assess student learning, there has been a push to increase the incorporation of discovery-driven modules and those that contain real-world relevance into laboratory curricula. To further this effort, we have developed, implemented, and assessed an undergraduate microbiology laboratory experiment that requires students to use the scientific method while brewing beer. The experiment allows students to brew their own beer and characterize it based on taste, alcohol content, calorie content, pH, and standard reference method. In addition, we assessed whether students were capable of achieving the module learning objectives through a pre-/posttest, student self-evaluation, exam-embedded questions, and an associated worksheet. These objectives included describing the role of the brewing ingredients and predicting how altering the ingredients would affect the characteristics of the beer, amongst others. By completing this experimental module, students accomplished the module objectives, had greater interest in brewing, and were more likely to view beer in scientific terms. Journal of Microbiology & Biology Education PMID:26753030

Effect of different packaging methods and storage temperature on microbiological and physicochemical quality characteristics of meatball.

PubMed

Yilmaz, I; Demirci, M

2010-06-01

The objective of this research was to determine physicochemical changes and microbiological quality of the different packaged meatball samples. Meatball samples in polystyrene tray were closed with polyethylene film (PS packs), vacuumed and modified atmosphere packaged, (MAP) (65% N(2), 35% CO(2)), and held under refrigerated display (4 °C) for 8, 16 and 16 days for PS packs, vacuum and MAP, respectively. Microbial load, free fatty acids and thiobarbituric acid values of the samples tended to increase with storage time. Bacteria counts of the raw meatball samples increased 2 log cycles at the end of storage compared with initial values. Meatball samples can be stored without any microbiological problem for 7 days at 4 °C. Results from this study suggested that shelf-life assigned to modified-MAP and vacuum-packed meatballs may be appropriate. Meatball samples underwent physical deformation when they were packed before vacuum process. With these negative factors considered, MAP is superior to other two packs methods.

Brewing for Students: An Inquiry-Based Microbiology Lab.

PubMed

Sato, Brian K; Alam, Usman; Dacanay, Samantha J; Lee, Amanda K; Shaffer, Justin F

2015-12-01

In an effort to improve and assess student learning, there has been a push to increase the incorporation of discovery-driven modules and those that contain real-world relevance into laboratory curricula. To further this effort, we have developed, implemented, and assessed an undergraduate microbiology laboratory experiment that requires students to use the scientific method while brewing beer. The experiment allows students to brew their own beer and characterize it based on taste, alcohol content, calorie content, pH, and standard reference method. In addition, we assessed whether students were capable of achieving the module learning objectives through a pre-/posttest, student self-evaluation, exam-embedded questions, and an associated worksheet. These objectives included describing the role of the brewing ingredients and predicting how altering the ingredients would affect the characteristics of the beer, amongst others. By completing this experimental module, students accomplished the module objectives, had greater interest in brewing, and were more likely to view beer in scientific terms. Journal of Microbiology & Biology Education.

A study of the impact of collaborative learning on student learning of major concepts in a microbiology laboratory exercise

NASA Astrophysics Data System (ADS)

Baumgarten, Kristyne A.

This study investigated the possible relationship between collaborative learning strategies and the learning of core concepts. This study examined the differences between two groups of nursing students enrolled in an introductory microbiology laboratory course. The control group consisted of students enrolled in sections taught in the traditional method. The experimental group consisted of those students enrolled in the sections using collaborative learning strategies. The groups were assessed on their degrees of learning core concepts using a pre-test/post-test method. Scores from the groups' laboratory reports were also analyzed. There was no difference in the two group's pre-test scores. The post-test scores of the experimental group averaged 11 points higher than the scores of the control group. The lab report scores of the experimental group averaged 15 points higher than those scores of the control group. The data generated from this study demonstrated that collaborative learning strategies can be used to increase students learning of core concepts in microbiology labs.

[Microbiological analysis of red octopus in fishing ports of Campeche, Mexico].

PubMed

Estrella-Gómez, Neyi; Escalante-Réndiz, Diana; González-Burgos, Araceli; Sosa-Cordero, Delta; Rojas-Herrera, Rafael

2016-08-01

In this work we studied the microbiological quality of the red octopus given its important economic and social impact on the region South-Southeast of Mexico. Samples were taken in different areas of capture of the species and analyzed with biochemical tests described in the Mexican official standards, identifying strains belonging to the genus Vibrio, Salmonella and faecal coliforms, and E. coli O157: H7. We used the BAx System for the identification of microorganisms through their bacterial DNA. The results obtained in biochemical and molecular methods were confirmed. Bland-Altman statistical method pointed out that both techniques can be used interchangeably. McNemar test showed that both methods have the same efficacy for the identification of pathogens (value X2=0.5 ρ=0.4795). The microbiological quality of the octopus in the South-Southeast region of Mexico is deficient due to the presence of pathogenic intestinal flora that might represent an epidemiological risk. The indexes established by the regulations suggest the need to apply effective and rapid identification technologies, such as the BAx System.This alternative method of analysis can contribute to the implementation of effective strategies that allow compliance with the minimal sanitary specifications during the processing of fishing products, thus strengthening the control systems to decrease the risks of epidemiological outbreaks in the region.

[Microbiological point of care tests].

PubMed

Book, Malte; Lehmann, Lutz Eric; Zhang, Xianghong; Stüber, Frank

2010-11-01

It is well known that the early initiation of a specific antiinfective therapy is crucial to reduce the mortality in severe infection. Procedures culturing pathogens are the diagnostic gold standard in such diseases. However, these methods yield results earliest between 24 to 48 hours. Therefore, severe infections such as sepsis need to be treated with an empirical antimicrobial therapy, which is ineffective in an unknown fraction of these patients. Today's microbiological point of care tests are pathogen specific and therefore not appropriate for an infection with a variety of possible pathogens. Molecular nucleic acid diagnostics such as polymerase chain reaction (PCR) allow the identification of pathogens and resistances. These methods are used routinely to speed up the analysis of positive blood cultures. The newest PCR based system allows the identification of the 25 most frequent sepsis pathogens by PCR in parallel without previous culture in less than 6 hours. Thereby, these systems might shorten the time of possibly insufficient antiinfective therapy. However, these extensive tools are not suitable as point of care diagnostics. Miniaturization and automating of the nucleic acid based method is pending, as well as an increase of detectable pathogens and resistance genes by these methods. It is assumed that molecular PCR techniques will have an increasing impact on microbiological diagnostics in the future. © Georg Thieme Verlag Stuttgart · New York.

Microbiological sampling of returned Surveyor 3 electrical cabling

NASA Technical Reports Server (NTRS)

Knittel, M. D.; Favero, M. S.; Green, R. H.

1972-01-01

A piece of electrical wiring bundle running from the television camera to another part of the spacecraft was selected for microbiological examination. Sampling methods are discussed. The results presented show that no viable microorganisms were recovered from the part of the Surveyor 3 cable which was tested. Factors that could have contributed to the sterility of the cable are thermal vacuum testing, natural dieoff, change in pressure during launch, and lunar vacuum and temperature.

A Review of Green Strategies to Prevent or Mitigate Microbiologically Influenced Corrosion

DTIC Science & Technology

2007-01-01

microbiologically influenced corrosion (MIC) has may provide nutrients for regrowth. been to use oxidising (e.g. chlorine, bromine, ozone ) Videla et al...MPN method: 6cells/cm2 Total bacteria Figure 6. Number of bacteria in biofilm using two detection techniques : fluorescent antibody (FA) and most...nitrite, lation of nitrate- utilising bacteria in the system. nitrous oxide or nitrogen and oxidising sulfide to Hubert et al. (2006) suggested that

A cylinder-plate method for microbiological assay of clavulanic acid.

PubMed

Hamedi, J; Shahverdi, A R; Samadi, N; Mohammadi, A; Shiran, M; Akhondi, S

2006-12-01

Clavulanic acid is a natural occurring beta-lactam product of Streptomyces clavuligerus and is a potent inhibitor of bacterial beta-lactamases. The present work reports a microbiological assay based on the cylinder-plate method for determination of clavulanic acid. The assay is based on the inhibitory effect of clavulanic acid in combination with penicillin G upon Escherichia coli ATCC 35218, which is used as the test organism. The correlation between clavulanic acid concentration and the inhibitory effect on E. coli was linear (r > 0.99) and in the range of 8-20 microg/ml. These results indicate that the proposed method is appropriate for the determination of clavulanic acid in commercial samples and can be used in routine quality control.

Kinetics and efficiency of ozone for treatment of landfill leachate including the effect of previous microbiological treatment.

PubMed

Lovato, María; Buffelli, José Real; Abrile, Mariana; Martín, Carlos

2018-03-19

The application of conventional physicochemical and microbiological techniques for the removal of organic pollutants has limitations for its utilization on wastewaters as landfill leachates because of their high concentration of not easily biodegradable organic compounds. The use of ozone-based technologies is an alternative and complementary treatment for this type of wastewaters. This paper reports the study of the degradation of landfill leachates from different stages of a treatment plant using ozone and ozone + UV. The experimental work included the determination of the temporal evolution of COD, TOC, UV254, and color. Along the experimental runs, the instantaneous off-gas ozone concentration was measured. The reaction kinetics follows a global second order expression with respect to COD and ozone concentrations. A kinetic model which takes into account the gas liquid mass transfer coupled with the chemical reaction was developed, and the corresponding parameters of the reacting system were determined. The mathematical model is able to appropriately simulate COD and ozone concentrations but exhibiting limitations when varying the leachate type. The potential application of ozone was verified, although the estimated efficiencies for COD removal and ozone consumption as well as the effect of UV radiation show variations on their trends. In this sense, it is interesting to note that the relative ozone yield has significant oscillations as the reaction proceeds. Finally, the set of experimental results demonstrates the crucial importance of the selection of process conditions to improve ozone efficiencies. This approach should consider variations in the ozone supply in order to minimize losses as well as the design of exhaustion methods as multiple stage reactors using chemical engineering design tools.

Use of matrix-assisted laser desorption/ionisation-time of flight mass spectrometry analyser in a diagnostic microbiology laboratory in a developing country.

PubMed

Bulane, Atang; Hoosen, Anwar

2017-01-01

Rapid and accurate identification of pathogens is of utmost importance for management of patients. Current identification relies on conventional phenotypic methods which are time consuming. Matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF MS) is based on proteomic profiling and allows for rapid identification of pathogens. We compared MALDI-TOF MS against two commercial systems, MicroScan Walkaway and VITEK 2 MS. Over a three-month period from July 2013 to September 2013, a total of 227 bacteria and yeasts were collected from an academic microbiology laboratory ( N = 121; 87 Gram-negatives, seven Gram-positives, 27 yeasts) and other laboratories ( N = 106; 35 Gram-negatives, 34 Gram-positives, 37 yeasts). Sixty-five positive blood cultures were initially processed with Bruker Sepsityper kit for direct identification. From the 65 blood culture bottles, four grew more than one bacterial pathogen and MALDI-TOF MS identified only one isolate. The blood cultures yielded 21 Gram-negatives, 43 Gram-positives and one Candida . There were 21 Escherirchia coli isolates which were reported by the MALDI-TOF MS as E. coli / Shigella . Of the total 292 isolates, discrepant results were found for one bacterial and three yeast isolates. Discrepant results were resolved by testing with the API system with MALDI-TOF MS showing 100% correlation. The MALDI-TOF MS proved to be very useful for rapid and reliable identification of bacteria and yeasts directly from blood cultures and after culture of other specimens. The difference in time to identification was significant for all isolates. However, for positive blood cultures with minimal sample preparation time there was a massive difference in turn-around time with great appreciation by clinicians.

Evaluation of the Efficacy and Safety of High Dose Short Duration Enrofloxacin Treatment Regimen for Uncomplicated Urinary Tract Infections in Dogs

PubMed Central

Westropp, JL; Sykes, JE; Irom, S; Daniels, JB; Smith, A; Keil, D; Settje, T; Wang, Y; Chew, DJ

2012-01-01

Background Uncomplicated urinary tract infections (UTI) in dogs usually are treated with antimicrobial drugs for 10–14 days. Shorter duration antimicrobial regimens have been evaluated in human patients. Hypothesis A high dose short duration (HDSD) enrofloxacin protocol administered to dogs with uncomplicated UTI will not be inferior to a 14-day treatment regimen with amoxicillin-clavulanic acid. Animals Client-owned adult, otherwise healthy dogs with aerobic bacterial urine culture yielding ≥103 CFU/mL of bacteria after cystocentesis. Methods Prospective, multicenter, controlled, randomized blinded clinical trial. Enrolled dogs were randomized to group 1 (enrofloxacin 18–20 mg/kg PO q24h for 3 days) or group 2 (amoxicillin-clavulanic acid 13.75–25 mg/kg PO q12h for 14 days). Urine cultures were obtained at days 0, 10, and 21. Microbiologic and clinical cure rates were evaluated 7 days after antimicrobial treatment was discontinued. Lower urinary tract signs and adverse events also were recorded. Results There were 35 dogs in group 1 and 33 in group 2. The microbiologic cure rate was 77.1 and 81.2% for groups 1 and 2, respectively. The clinical cure rate was 88.6 and 87.9% for groups 1 and 2, respectively. Cure rates between groups did not differ according to the selected margin of noninferiority. Conclusions and Clinical Importance HDSD enrofloxacin treatment was not inferior to a conventional amoxicillin-clavulanic acid protocol for the treatment of uncomplicated bacterial UTI in dogs. Further research is warranted to determine if this protocol will positively impact owner compliance and decrease the emergence of antimicrobial resistance. PMID:22486931

Microbiological concerns and methodological approaches related to bacterial water quality in spaceflight

NASA Technical Reports Server (NTRS)

Pyle, Barry H.; Mcfeters, Gordon A.

1992-01-01

A number of microbiological issues are of critical importance to crew health and system performance in spacecraft water systems. This presentation reviews an army of these concerns which include factors that influence water treatment and disinfection in spaceflight such as biofilm formation and the physiological responses of bacteria in clean water systems. Factors associated with spaceflight like aerosol formation under conditions of microgravity are also discussed within the context of airborne infections such as Legionellosis. Finally, a spectrum of analytical approaches is reviewed to provide an evaluation of methodological alternatives that have been suggested or used to detect microorganisms of interest in water systems. These range from classical approaches employing colony formation on specific microbiological growth media to direct (i.e. microscopic) and indirect (e.g. electrochemical) methods as well as the use of molecular approaches and gene probes. These techniques are critically evaluated for their potential utility in determining microbiological water quality through the detection of microorganisms under the influence of ambient environmental stress inherent in spaceflight water systems.

[Dr Guillermo Contreras Da Silva, a relevant figure in the development of Chilean microbiology].

PubMed

Cabello, Felipe C

2008-02-01

The influence of the work of Dr. Guillermo Contreras Da Silva and his colaborators on the evolution of microbiology in Chile is briefly analyzed. Dr. Contreras was trained in modern virology at Yale University with Dr. J. Melnick under the sponsorhip of the Rockefeller Foundation. During this training, he used serological methods to classify Cocksakie viruses. After his return to Chile, he studied the epidemiology of enteroviruses, including poliovirus. His laboratory, the country's first in modern virology, took an active role in Chile's first Sabin polio vaccination in 1961. Dr. Contreras and his group transformed the teaching and the character of microbiology in Chile from a descriptive medically oriented discipline into an autonomous, quantitative and experimental science. They modernized microbiology with the introduction of molecular biology and microbial genetics and fostered collaborations with allied biological sciences. Dr. Contreras was a Guggenheim Fellow, and until his retirement, was the Chief of the Viral Products Division, Bureau of Biologies, Ottawa, Canada.

Trichomycosis (Trichobacteriosis): Clinical and Microbiological Experience with 56 Cases

PubMed Central

Bonifaz, Alexandro; Váquez-González, Denisse; Fierro, Leonel; Araiza, Javier; Ponce, Rosa María

2013-01-01

Background: Trichomycosis is asymptomatic bacterial infection of the axillary hairs caused by Corynebacterium sp. Objective: to bring a series of cases of trichomycosis, its clinical and microbiological experience. Materials and Methods: This report consists in a linear and observational retrospective study of 15 years of cases of trichomycosis confirmed clinically and microbiologically. Results: Fifty six confirmed cases of trichomycosis were included in this report. The majority were men 53/56 (94.6%), mean age was 32.5 years. The most commonly affected area was the axilla (92%), trichomycosis flava was the principal variant 55/56 (98.2%) and signs and symptoms associated were hyperhidrosis (87.5%), hairs’ texture change (57.1%) and odor (35.7%). Bacterial concretions were observed in all cases, and the predominant causative agent in 89.3% of all cases was Corynebacterium sp. Thirty patients were included in therapeutic portion of the study, and 28 (93.3%) of them experienced a clinical and microbiological cure. Conclusion: Trichomycosis is asymptomatic, superficial infection, which primarily affects axillary hairs. PMID:23960390

Microbial Safety Improvement of Sea Buckthorn by Electron Beam Irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nemtanu, Monica R.; Minea, R.; Mazilu, Elena

2007-04-23

The commercialization of medicinal plants and/or their products is highly increased in Romania lately. One of the most used herbs is sea buckthorn being well known for its quality with a large potential for curing some diseases. Sea buckthorn can be contaminated with undesirable microorganisms which may affect negatively its quality. The paper presents the results regarding the action of a non-conventional technology meaning electron beam technique on sea buckthorn in order to improve its microbiological quality. Our study revealed that the sea buckthorn microbial load has been improved after 3 kGy irradiation keeping its active principles.

Microbial Safety Improvement of Sea Buckthorn by Electron Beam Irradiation

NASA Astrophysics Data System (ADS)

Nemţanu, Monica R.; Minea, R.; Mazilu, Elena; Rǎdulescu, Nora

2007-04-01

The commercialization of medicinal plants and/or their products is highly increased in Romania lately. One of the most used herbs is sea buckthorn being well known for its quality with a large potential for curing some diseases. Sea buckthorn can be contaminated with undesirable microorganisms which may affect negatively its quality. The paper presents the results regarding the action of a non-conventional technology meaning electron beam technique on sea buckthorn in order to improve its microbiological quality. Our study revealed that the sea buckthorn microbial load has been improved after 3 kGy irradiation keeping its active principles.

Automated food microbiology: potential for the hydrophobic grid-membrane filter.

PubMed Central

Sharpe, A N; Diotte, M P; Dudas, I; Michaud, G L

1978-01-01

Bacterial counts obtained on hydrophobic grid-membrane filters were comparable to conventional plate counts for Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus in homogenates from a range of foods. The wide numerical operating range of the hydrophobic grid-membrane filters allowed sequential diluting to be reduced or even eliminated, making them attractive as components in automated systems of analysis. Food debris could be rinsed completely from the unincubated hydrophobic grid-membrane filter surface without affecting the subsequent count, thus eliminating the possibility of counting food particles, a common source of error in electronic counting systems. PMID:100054

Amphotericin B formulations: a comparative review of efficacy and toxicity.

PubMed

Hamill, Richard J

2013-06-01

Because of the increasing prevalence and changing microbiological spectrum of invasive fungal infections, some form of amphotericin B still provides the most reliable and broad spectrum therapeutic alternative. However, the use of amphotericin B deoxycholate is accompanied by dose-limited toxicities, most importantly, infusion-related reactions and nephrotoxicity. In an attempt to improve the therapeutic index of amphotericin B, three lipid-associated formulations were developed, including amphotericin B lipid complex (ABLC), liposomal amphotericin B (L-AmB), and amphotericin B colloidal dispersion (ABCD). The lipid composition of all three of these preparations differs considerably and contributes to substantially different pharmacokinetic parameters. ABLC is the largest of the lipid preparations. Because of its size, it is taken up rapidly by macrophages and becomes sequestered in tissues of the mononuclear phagocyte system such as the liver and spleen. Consequently, compared with the conventional formulation, it has lower circulating amphotericin B serum concentrations, reflected in a marked increase in volume of distribution and clearance. Lung levels are considerably higher than those achieved with other lipid-associated preparations. The recommended therapeutic dose of ABLC is 5 mg/kg/day. Because of its small size and negative charge, L-AmB avoids substantial recognition and uptake by the mononuclear phagocyte system. Therefore, a single dose of L-AmB results in a much higher peak plasma level (Cmax) than conventional amphotericin B deoxycholate and a much larger area under the concentration-time curve. Tissue concentrations in patients receiving L-AmB tend to be highest in the liver and spleen and much lower in kidneys and lung. Recommended therapeutic dosages are 3-6 mg/kg/day. After intravenous infusion, ABCD complexes remain largely intact and are rapidly removed from the circulation by cells of the macrophage phagocyte system. On a milligram-to-milligram basis, the Cmax achieved is lower than that attained by conventional amphotericin B, although the larger doses of ABCD that are administered produce an absolute level that is similar to amphotericin B. ABCD exhibits dose-limiting, infusion-related toxicities; consequently, the administered dosages should not exceed 3-4 mg/kg/day. The few comparative clinical trials that have been completed with the lipid-associated formulations have not demonstrated important clinical differences among these agents and amphotericin B for efficacy, although there are significant safety benefits of the lipid products. Furthermore, only one published trial has ever compared one lipid product against another for any indication. The results of these trials are particularly difficult to interpret because of major heterogeneities in study design, disease definitions, drug dosages, differences in clinical and microbiological endpoints as well as specific outcomes examined. Nevertheless, it is possible to derive some general conclusions given the available data. The most commonly studied syndrome has been empiric therapy for febrile neutropenic patients, where the lipid-associated preparations did not appear to provide a survival benefit over conventional amphotericin B deoxycholate, but did offer a significant advantage for the prevention of various breakthrough invasive fungal infections. For treatment of documented invasive fungal infections that usually involved hematological malignancy patients, no individual randomized trial has demonstrated a mortality benefit due to therapy with one of the lipid formulations. Results from meta-analyses have been contradictory, with one demonstrating a mortality benefit from all-cause mortality and one that did not demonstrate a mortality benefit. In the only published study to examine HIV-infected patients with disseminated histoplasmosis, clinical success and mortality were significantly better with L-AmB compared with amphotericin B deoxycholate; there were no differences in microbiological outcomes between treatment groups. The lipid-associated preparations were not significantly better than amphotericin B deoxycholate for treatment of AIDS-associated acute cryptococcal meningitis for either clinical or microbiological outcomes that were studied. In all of the trials that specifically examined renal toxicity, the lipid-associated formulations were significantly less nephrotoxic than amphotericin B deoxycholate. Infusion-related reactions occurred less frequently with L-AmB when compared with amphotericin B deoxycholate; however, ABCD had equivalent or more frequent infusion-related reactions than conventional amphotericin B, and this resulted in the cessation of at least one clinical trial. At the present time, this particular lipid formulation is no longer commercially available. For the treatment of most invasive fungal infections, an amphotericin B lipid formulation provides a safer alternative than conventional amphotericin B, with at least equivalent efficacy. As the cost of therapy with these agents continues to decline, these drugs will likely maintain their important role in the antifungal drug armamentarium because of their efficacy and improved safety profile.

[Microbiological surveillance in patients treated by bone marrow transplantation (author's transl)].

PubMed

Haralambie, E; Linzenmeier, G; Nowrousian, M; Schäfer, R; Schmidt, C G

1980-01-01

Patients suffering from acute leukemia were treated by bone marrow transplantation under strict gnotobiotic conditions. The microbiological surveillance was performed during three phases: the admission phase, the phase of decontamination and reverse isolation and the reconventionalisation phase. During the second phase no infections of exogenous origine occurred. All clinically manifest infections in this phase were induced by unsuppressed endogenous bacteria. In our study the bacteria of oropharynx was the main source of infections therefore this biotop deserves special attention during the microbiological surveillance of the immune compromised host. In leukemia patients selective decontamination will be the method of choice, but considering the possibility of GvHR in patients with bone marrow transplantation a complete decontamination should be achieved.

Microbiological survey of imported produce available at retail across Canada.

PubMed

Allen, Kevin J; Kovacevic, Jovana; Cancarevic, Ana; Wood, Jayde; Xu, Jieqing; Gill, Bradford; Allen, Jennifer K; Mesak, Lili R

2013-03-15

Increasing consumption and year-round consumer demand for fresh, minimally processed green vegetables have been observed in Canada and other developed countries. However, in the past two decades, produce has been increasingly implicated in outbreaks and correspondingly recognized as a vector for the transmission of pathogenic microorganisms. To this end, we examined the microbiological quality of imported produce available at retail across Canada during a period of limited domestic availability. In total, 106 samples obtained from five Canadian cities were purchased from retail outlets and subjected to microbiological analyses, including aerobic plate (APC) and coliform counts, and enrichments for enterococci, indicator Escherichia coli, E. coli O157:H7 and Salmonella spp. Also, recovered Enterococcus faecalis and Enterococcus faecium were screened for antimicrobial resistance (AMR). Overall, samples included herbs (n=61), leafy greens (n=25), and spinach (n=20) deriving from five countries (Columbia, Dominican Republic, Guatemala, Mexico, and the United States [US]). APCs were consistent across commodities regardless of country, ranging from mean log10 CFU/g of 6.1 to 7.4, with no significant differences observed. Excluding a single leafy green sample from Guatemala, the lowest prevalence of coliforms was for Mexican herbs (22.2%), with a high of 66.7% on US leafy greens. With the exception of spinach, concentrations of coliforms varied widely, ranging from undetectable to too numerous to count (>8.5 log10 CFU/g). Of the commodities assessed, Mexican and US spinach had the lowest coliform concentrations (undetectable to 4.0 log10 CFU/g). Organic herbs and conventional leafy greens possessed significantly lower (p<0.05) prevalence of coliforms compared to conventional herbs and organic leafy greens, respectively. The most frequent recovery of indicator E. coli was observed for herbs, with 11.1, 8.3, and 3.7% prevalence observed in samples from Columbia, US, and Mexico, respectively. For spinach, 0 and 6.7% of Mexican and US samples tested positive, while no leafy green samples from either country were positive. No E. coli O157:H7 or Salmonella spp. were detected. E. faecium and E. faecalis were recovered from 15.1 and 5.7% of samples, respectively. Although no glycopeptide resistance was observed, resistance to other clinically relevant antibiotics was noteworthy in both species. Overall, though microbiological quality indicators were frequently high, E. coli O157:H7 and Salmonella were not detected. However, the presence of resistance and reduced susceptibility to clinically relevant antimicrobials in recovered enterococci demonstrate imported fresh produce may serve as a vehicle for the transmission of antimicrobial resistance across national borders. Copyright © 2013 Elsevier B.V. All rights reserved.

Internal quality assurance in diagnostic microbiology: A simple approach for insightful data

PubMed Central

Scherz, Valentin; Durussel, Christian

2017-01-01

Given the importance of microbiology results on patient care, high quality standards are expected. Internal quality assurance (IQA) could mitigate the limitations of internal quality control, competency assessment and external quality assurance, adding a longitudinal insight, including pre- and post-analytical steps. Here, we implemented an IQA program in our clinical microbiology facilities with blind resubmission of routine samples during 22 months. One-hundred-and-twenty-one out of 123 (98.4%) serological analyses and 112 out of 122 (91.8%) molecular analyses were concordant. Among the discordances in molecular biology analyses, 6 results were low positive samples that turned out negative, likely due to stochastic repartition of nucleic acids. Moreover, one identified retranscription error led us to implement automated results transmission from the Applied Biosystems instruments to the laboratory information system (LIS). Regarding Gram stain microscopy, 560 out of 745 (75.2%) of compared parameters were concordant. As many as 67 out of 84 (79.8%) pairs of culture results were similar, including 16 sterile pairs, 27 having identical identification or description and semi-quantification and 24 only showing variations in semi-quantification with identical description or identification of colonies. Seventeen pairs had diverging identification or description of colonies. Culture was twice only done for one member of the pairs. Regarding antibiotic susceptibility testing, a major discrepancy was observed in 5 out of 48 results (10.4%). In conclusion, serological tests were highly reproducible. Molecular diagnosis also revealed to be robust except when the amounts of nucleic acids present in the sample were close to the limits of detection. Conventional microbiology was less robust with major discrepancies reaching 39.5% of the samples for microscopy. Similarly, culture and antibiotic susceptibility testing were prone to discrepancies. This work was ground for reconsidering multiples aspects of our practices and demonstrates the importance of IQA to complete the other quality management procedures. PMID:29135992

Internal quality assurance in diagnostic microbiology: A simple approach for insightful data.

PubMed

Scherz, Valentin; Durussel, Christian; Greub, Gilbert

2017-01-01

Given the importance of microbiology results on patient care, high quality standards are expected. Internal quality assurance (IQA) could mitigate the limitations of internal quality control, competency assessment and external quality assurance, adding a longitudinal insight, including pre- and post-analytical steps. Here, we implemented an IQA program in our clinical microbiology facilities with blind resubmission of routine samples during 22 months. One-hundred-and-twenty-one out of 123 (98.4%) serological analyses and 112 out of 122 (91.8%) molecular analyses were concordant. Among the discordances in molecular biology analyses, 6 results were low positive samples that turned out negative, likely due to stochastic repartition of nucleic acids. Moreover, one identified retranscription error led us to implement automated results transmission from the Applied Biosystems instruments to the laboratory information system (LIS). Regarding Gram stain microscopy, 560 out of 745 (75.2%) of compared parameters were concordant. As many as 67 out of 84 (79.8%) pairs of culture results were similar, including 16 sterile pairs, 27 having identical identification or description and semi-quantification and 24 only showing variations in semi-quantification with identical description or identification of colonies. Seventeen pairs had diverging identification or description of colonies. Culture was twice only done for one member of the pairs. Regarding antibiotic susceptibility testing, a major discrepancy was observed in 5 out of 48 results (10.4%). In conclusion, serological tests were highly reproducible. Molecular diagnosis also revealed to be robust except when the amounts of nucleic acids present in the sample were close to the limits of detection. Conventional microbiology was less robust with major discrepancies reaching 39.5% of the samples for microscopy. Similarly, culture and antibiotic susceptibility testing were prone to discrepancies. This work was ground for reconsidering multiples aspects of our practices and demonstrates the importance of IQA to complete the other quality management procedures.

Stability of extemporaneously prepared preservative-free prochlorperazine nasal spray.

PubMed

Yellepeddi, Venkata K

2018-01-01

The stability of an extemporaneously prepared preservative-free prochlorperazine 5-mg/mL nasal spray was evaluated. The preservative-free prochlorperazine nasal spray was prepared by adding 250 mg of prochlorperazine edisylate to 50 mL of citrate buffer in a low-density polyethylene nasal spray bottle. A stability-indicating high-performance liquid chromatography (HPLC) method was developed and validated using the major degradant prochlorperazine sulfoxide and by performing forced-degradation studies. For chemical stability studies, 3 100-μL samples of the preservative-free prochlorperazine from 5 nasal spray bottles stored at room temperature were collected at days 0, 20, 30, 45, and 60 and were assayed in triplicate using the stability-indicating HPLC method. Microbiological testing involved antimicrobial effectiveness testing based on United States Pharmacopeia ( USP ) chapter 51 and quantitative microbiological enumeration of aerobic bacteria, yeasts, and mold based on USP chapter 61. Samples for microbiological testing were collected at days 0, 30, and 60. The stability-indicating HPLC method clearly identified the degradation product prochlorperazine sulfoxide without interference from prochlorperazine. All tested solutions retained over 90% of the initial prochlorperazine concentration for the 60-day study period. There were no detectable changes in color, pH, and viscosity in any sample. There was no growth of bacteria, yeast, and mold for 60 days in all samples tested. An extemporaneously prepared preservative-free nasal spray solution of prochlorperazine edisylate 5 mg/mL was physically, chemically, and microbiologically stable for 60 days when stored at room temperature in low-density polyethylene bottles. Copyright © 2018 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

Application of Microbiological Method Direct Epifluorescence Filter Techique/Aerobic Plate Count Agar in the Identification of Irradiated Herbs and Spices

PubMed Central

Di Schiavi, Maria Teresa; Foti, Marina; Mosconi, Maria Cristina; Mattiolo, Giuseppina; Cavallina, Roberta

2014-01-01

Irradiation is a preservation technology used to improve the safety and hygienic quality of food. Aim of this study was to assess the applicability and validity of the microbiological screening method direct epifluorescence filter technique (DEFT)/aerobic plate count (APC) (EN 13783:2001) for the identification of irradiated herbs and spices. Tests on non-irradiated and irradiated samples of dried herbs and spices were performed. The method was based on the comparison of APC and count obtained using DEFT. In accordance with the standard reference, this method is not applicable to samples with APC<103 colony forming units (CFU)/g and this is its main limit. The results obtained in our laboratories showed that in 50% of cases of non-irradiated samples and in 96% of the samples treated with ionising radiation, the method was not applicable due to a value of CFU/g <103. PMID:27800348

Evolution of microbiological analytical methods for dairy industry needs

PubMed Central

Sohier, Danièle; Pavan, Sonia; Riou, Armelle; Combrisson, Jérôme; Postollec, Florence

2014-01-01

Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry’s needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards. PMID:24570675

Evolution of microbiological analytical methods for dairy industry needs.

PubMed

Sohier, Danièle; Pavan, Sonia; Riou, Armelle; Combrisson, Jérôme; Postollec, Florence

2014-01-01

Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry's needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards.

A two-hour antibiotic susceptibility test by ATP-bioluminescence.

PubMed

March Rosselló, Gabriel Alberto; García-Loygorri Jordán de Urries, María Cristina; Gutiérrez Rodríguez, María Purificación; Simarro Grande, María; Orduña Domingo, Antonio; Bratos Pérez, Miguel Ángel

2016-01-01

The antibiotic susceptibility test (AST) in Clinical Microbiology laboratories is still time-consuming, and most procedures take 24h to yield results. In this study, a rapid antimicrobial susceptibility test using ATP-bioluminescence has been developed. The design of method was performed using five ATCC collection strains of known susceptibility. This procedure was then validated against standard commercial methods on 10 strains of enterococci, 10 staphylococci, 10 non-fermenting gram negative bacilli, and 13 Enterobacteriaceae from patients. The agreement obtained in the sensitivity between the ATP-bioluminescence method and commercial methods (E-test, MicroScan and VITEK2) was 100%. In summary, the preliminary results obtained in this work show that the ATP-bioluminescence method could provide a fast and reliable AST in two hours. Copyright © 2015 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Bacteriophage Amplification-Coupled Detection and Identification of Bacterial Pathogens

NASA Astrophysics Data System (ADS)

Cox, Christopher R.; Voorhees, Kent J.

Current methods of species-specific bacterial detection and identification are complex, time-consuming, and often require expensive specialized equipment and highly trained personnel. Numerous biochemical and genotypic identification methods have been applied to bacterial characterization, but all rely on tedious microbiological culturing practices and/or costly sequencing protocols which render them impractical for deployment as rapid, cost-effective point-of-care or field detection and identification methods. With a view towards addressing these shortcomings, we have exploited the evolutionarily conserved interactions between a bacteriophage (phage) and its bacterial host to develop species-specific detection methods. Phage amplification-coupled matrix assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) was utilized to rapidly detect phage propagation resulting from species-specific in vitro bacterial infection. This novel signal amplification method allowed for bacterial detection and identification in as little as 2 h, and when combined with disulfide bond reduction methods developed in our laboratory to enhance MALDI-TOF-MS resolution, was observed to lower the limit of detection by several orders of magnitude over conventional spectroscopy and phage typing methods. Phage amplification has been combined with lateral flow immunochromatography (LFI) to develop rapid, easy-to-operate, portable, species-specific point-of-care (POC) detection devices. Prototype LFI detectors have been developed and characterized for Yersinia pestis and Bacillus anthracis, the etiologic agents of plague and anthrax, respectively. Comparable sensitivity and rapidity was observed when phage amplification was adapted to a species-specific handheld LFI detector, thus allowing for rapid, simple, POC bacterial detection and identification while eliminating the need for bacterial culturing or DNA isolation and amplification techniques.

Conventional Microscopy vs. Computer Imagery in Chiropractic Education.

PubMed

Cunningham, Christine M; Larzelere, Elizabeth D; Arar, Ilija

2008-01-01

As human tissue pathology slides become increasingly difficult to obtain, other methods of teaching microscopy in educational laboratories must be considered. The purpose of this study was to evaluate our students' satisfaction with newly implemented computer imagery based laboratory instruction and to obtain input from their perspective on the advantages and disadvantages of computerized vs. traditional microscope laboratories. This undertaking involved the creation of a new computer laboratory. Robbins and Cotran Pathologic Basis of Disease, 7(th)ed, was chosen as the required text which gave students access to the Robbins Pathology website, including complete content of text, Interactive Case Study Companion, and Virtual Microscope. Students had experience with traditional microscopes in their histology and microbiology laboratory courses. Student satisfaction with computer based learning was assessed using a 28 question survey which was administered to three successive trimesters of pathology students (n=193) using the computer survey website Zoomerang. Answers were given on a scale of 1-5 and statistically analyzed using weighted averages. The survey data indicated that students were satisfied with computer based learning activities during pathology laboratory instruction. The most favorable aspect to computer imagery was 24-7 availability (weighted avg. 4.16), followed by clarification offered by accompanying text and captions (weighted avg. 4.08). Although advantages and disadvantages exist in using conventional microscopy and computer imagery, current pathology teaching environments warrant investigation of replacing traditional microscope exercises with computer applications. Chiropractic students supported the adoption of computer-assisted instruction in pathology laboratories.

Analytical procedures for water-soluble vitamins in foods and dietary supplements: a review.

PubMed

Blake, Christopher J

2007-09-01

Water-soluble vitamins include the B-group vitamins and vitamin C. In order to correctly monitor water-soluble vitamin content in fortified foods for compliance monitoring as well as to establish accurate data banks, an accurate and precise analytical method is a prerequisite. For many years microbiological assays have been used for analysis of B vitamins. However they are no longer considered to be the gold standard in vitamins analysis as many studies have shown up their deficiencies. This review describes the current status of analytical methods, including microbiological assays and spectrophotometric, biosensor and chromatographic techniques. In particular it describes the current status of the official methods and highlights some new developments in chromatographic procedures and detection methods. An overview is made of multivitamin extractions and analyses for foods and supplements.

Flow cytometry as a method for the evaluation of raw material, product and process in the dairy industry.

PubMed

Ruszczyńska, A; Szteyn, J; Wiszniewska-Laszczych, A

2007-01-01

Producing dairy products which are safe for consumers requires the constant monitoring of the microbiological quality of raw material, the production process itself and the end product. Traditional methods, still a "gold standard", require a specialized laboratory working on recognized and validated methods. Obtaining results is time- and labor-consuming and do not allow rapid evaluation. Hence, there is a need for a rapid, precise method enabling the real-time monitoring of microbiological quality, and flow cytometry serves this function well. It is based on labeling cells suspended in a solution with fluorescent dyes and pumping them into a measurement zone where they are exposed to a precisely focused laser beam. This paper is aimed at presenting the possibilities of applying flow cytometry in the dairy industry.

Quality in the molecular microbiology laboratory.

PubMed

Wallace, Paul S; MacKay, William G

2013-01-01

In the clinical microbiology laboratory advances in nucleic acid detection, quantification, and sequence analysis have led to considerable improvements in the diagnosis, management, and monitoring of infectious diseases. Molecular diagnostic methods are routinely used to make clinical decisions based on when and how to treat a patient as well as monitor the effectiveness of a therapeutic regime and identify any potential drug resistant strains that may impact on the long term patient treatment program. Therefore, confidence in the reliability of the result provided by the laboratory service to the clinician is essential for patient treatment. Hence, suitable quality assurance and quality control measures are important to ensure that the laboratory methods and service meet the necessary regulatory requirements both at the national and international level. In essence, the modern clinical microbiology laboratory ensures the appropriateness of its services through a quality management system that monitors all aspects of the laboratory service pre- and post-analytical-from patient sample receipt to reporting of results, from checking and upholding staff competency within the laboratory to identifying areas for quality improvements within the service offered. For most European based clinical microbiology laboratories this means following the common International Standard Organization (ISO9001) framework and ISO15189 which sets out the quality management requirements for the medical laboratory (BS EN ISO 15189 (2003) Medical laboratories-particular requirements for quality and competence. British Standards Institute, Bristol, UK). In the United States clinical laboratories performing human diagnostic tests are regulated by the Centers for Medicare and Medicaid Services (CMS) following the requirements within the Clinical Laboratory Improvement Amendments document 1988 (CLIA-88). This chapter focuses on the key quality assurance and quality control requirements within the modern microbiology laboratory providing molecular diagnostics.

Intersecting Virtual Patients and Microbiology: Fostering a culture of learning.

PubMed

McCarthy, David; O'Gorman, Ciaran; Gormley, Gerard

2015-10-01

The use and integration of Technology Enhanced Learning (TEL) resources in medical education has attracted considerable commentary and support. "Virtual Patients" are one such resource. Whilst evidence exists supporting the benefits of these resources, there has not been specific consideration of their implications for teaching microbiology; nor attention paid to both the internal and external factors that influence learner engagement with virtual patients. The principle aims of this study are to identify factors that explicitly and implicitly influence the student's interaction with a microbiology virtual patient resource and how these interactions reflect upon the use of the resource. A mixed method quantitative (online questionnaire; n=161) and qualitative (student focus groups; N=11) study was undertaken amongst third year medical students enrolled at Queen's University Belfast in the academic year 2012-2013. The results supported prior evidence that virtual patients are a useful learning tool (mean score of 5.09 out of 7) that helped them to integrate microbiology principles with clinical experiences. How students used the virtual patients and the depth of the subsequent benefits was dependent upon their perception of the importance of the resource. This was influenced by a number of factors including how the resources were presented and positioned within the curriculum, whether they were formally examined or timetabled and the importance attributed by peers who had already completed the examinations. Integration of virtual patients into the microbiology curriculum is widely endorsed and may even be considered superior to other methods of teaching. How students use these resources is dependent upon a positive perception of their importance. Educators should be aware of the factors that shape this perception when integrating TEL resources into curricula.

Microbiological quality of take-away cooked rice and chicken sandwiches: effectiveness of food hygiene training of the management.

PubMed

Little, C L; Barnes, J; Mitchell, R T

2002-12-01

During August 2001 a microbiological study of ready-to-eat cooked rice from take-aways and of chicken sandwiches made on the premises from sandwich bars was undertaken. The intention was to identify risk factors in the production, storage and handling of cooked rice and sandwiches, and to establish their effect on microbiological quality. Examination of cooked rice revealed that the majority of samples (87%; 442 of 508) were of satisfactory/acceptable microbiological quality; 50 (10%) were unsatisfactory, and 16 (3%) were of unacceptable quality due to Bacillus cereus and/or other Bacillus spp in excess of 10(5) cfu/g. The microbiological quality of cooked rice was associated with cuisine type (p < 0.00001), rice type (p < 0.01), cooking (p < 0.01), serving methods (p < 0.00001), and management food hygiene training (p < 0.01). Examination of chicken sandwiches found that most (75%; 335 of 449) were of satisfactory/acceptable microbiological quality and 114 (25%) were unsatisfactory. Acceptable microbiological quality of sandwiches was associated with sandwich bars that had hazard analysis in place (p < 0.05). Smaller businesses, as indicated by Local Authority Inspectors' Consumer at Risk scores, were more likely to have samples classified as unsatisfactory or unacceptable compared to larger businesses (p < 0.001). The majority (90%) of premises had hand-washing facilities accessible and available for use, although only over half (55%) were correctly used as judged by the sampling officer. Where the manager of the premises had received some form of food hygiene training, food safety procedures such as the hazard analysis system were more likely to be in place (p < 0.0001).

Super-long Anabiosis of Ancient Microorganisms in Ice and Terrestrial Models for Development of Methods to Search for Life on Mars, Europa and other Planetary Bodies

NASA Technical Reports Server (NTRS)

Abyzov, S. S.; Duxbury, N. S.; Bobin, N. E.; Fukuchi, M.; Hoover, R. B.; Kanda, H.; Mitskevich, I. N.; Mulyukin, A. L.; Naganuma, T.; Poglazova, M. N.;

Role of microbiological culture and polymerase chain reaction (PCR) of actinomyces in medication-related osteonecrosis of the jaw (MRONJ).

PubMed

Panya, Sappasith; Fliefel, Riham; Probst, Florian; Tröltzsch, Matthias; Ehrenfeld, Michael; Schubert, Sören; Otto, Sven

2017-03-01

We hypothesized that local infection plays a critical role in the pathogenesis of medication-related osteonecrosis of the jaw (MRONJ). Recent developments in molecular methods have revolutionized new approaches for the rapid detection of microorganisms including those difficult to culture. The aim of our study is to identify the bacterial profiles in MRONJ by microbiological culture and polymerase chain reactions (PCR). A retrospective analysis was performed on MRONJ patients from 2008 to 2014. The bacterial profile from MRONJ bone samples was determined using microbiological culture and PCR. Ninety five patients fulfilled the inclusion criteria with mean age of 69.85 ± 8.71 years. A female predilection was detected. The mandible was more commonly affected than maxilla. Tooth extraction was the frequent triggering factor. Breast cancer was the primary cause for administration and intravenous bisphosphonates were the most commonly administrated antiresorptive drugs. The majority of patients were classified as stage 2. Posterior teeth were most commonly affected. Based on bone culture results, the most common microorganism were both actinomyces and mixed flora. PCR confirmed the presence of actinomyces in 55 patients. Our data suggest that PCR might be an innovative method for detection of microorganisms difficult to culture using traditional microbiological techniques. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Comparison of the quantitative dry culture methods with both conventional media and most probable number method for the enumeration of coliforms and Escherichia coli/coliforms in food.

PubMed

Teramura, H; Sota, K; Iwasaki, M; Ogihara, H

2017-07-01

Sanita-kun™ CC (coliform count) and EC (Escherichia coli/coliform count), sheet quantitative culture systems which can avoid chromogenic interference by lactase in food, were evaluated in comparison with conventional methods for these bacteria. Based on the results of inclusivity and exclusivity studies using 77 micro-organisms, sensitivity and specificity of both Sanita-kun™ met the criteria for ISO 16140. Both media were compared with deoxycholate agar, violet red bile agar, Merck Chromocult™ coliform agar (CCA), 3M Petrifilm™ CC and EC (PEC) and 3-tube MPN, as reference methods, in 100 naturally contaminated food samples. The correlation coefficients of both Sanita-kun™ for coliform detection were more than 0·95 for all comparisons. For E. coli detection, Sanita-kun™ EC was compared with CCA, PEC and MPN in 100 artificially contaminated food samples. The correlation coefficients for E. coli detection of Sanita-kun™ EC were more than 0·95 for all comparisons. There were no significant differences in all comparisons when conducting a one-way analysis of variance (anova). Both Sanita-kun™ significantly inhibited colour interference by lactase when inhibition of enzymatic staining was assessed using 40 natural cheese samples spiked with coliform. Our results demonstrated Sanita-kun™ CC and EC are suitable alternatives for the enumeration of coliforms and E. coli/coliforms, respectively, in a variety of foods, and specifically in fermented foods. Current chromogenic media for coliforms and Escherichia coli/coliforms have enzymatic coloration due to breaking down of chromogenic substrates by food lactase. The novel sheet culture media which have film layer to avoid coloration by food lactase have been developed for enumeration of coliforms and E. coli/coliforms respectively. In this study, we demonstrated these media had comparable performance with reference methods and less interference by food lactase. These media have a possibility not only to be useful alternatives but also to contribute for accurate enumeration of these bacteria in a variety of foods, and specifically in fermented foods. © 2017 The Society for Applied Microbiology.

Cost analysis in a clinical microbiology laboratory.

PubMed

Brezmes, M F; Ochoa, C; Eiros, J M

2002-08-01

The use of models for business management and cost control in public hospitals has led to a need for microbiology laboratories to know the real cost of the different products they offer. For this reason, a catalogue of microbiological products was prepared, and the costs (direct and indirect) for each product were analysed, along with estimated profitability. All tests performed in the microbiology laboratory of the "Virgen de la Concha" Hospital in Zamora over a 2-year period (73192 tests) were studied. The microbiological product catalogue was designed using homogeneity criteria with respect to procedures used, workloads and costs. For each product, the direct personnel costs (estimated from workloads following the method of the College of American Pathologists, 1992 version), the indirect personnel costs, the direct and indirect material costs and the portion of costs corresponding to the remaining laboratory costs (capital and structural costs) were calculated. The average product cost was 16.05 euros. The average cost of a urine culture (considered, for purposes of this study, as a relative value unit) reached 13.59 euros, with a significant difference observed between positive and negative cultures (negative urine culture, 10.72 euros; positive culture, 29.65 euros). Significant heterogeneity exists, both in the costs of different products and especially in the cost per positive test. The application of a detailed methodology of cost analysis facilitates the calculation of the real cost of microbiological products. This information provides a basic tool for establishing clinical management strategies.

Microbiological Challenge Testing for Listeria Monocytogenes in Ready-to-Eat Food: A Practical Approach.

PubMed

Spanu, Carlo; Scarano, Christian; Ibba, Michela; Pala, Carlo; Spanu, Vincenzo; De Santis, Enrico Pietro Luigi

2014-12-09

Food business operators (FBOs) are the primary responsible for the safety of food they place on the market. The definition and validation of the product's shelf-life is an essential part for ensuring microbiological safety of food and health of consumers. In the frame of the Regulation (EC) No 2073/2005 on microbiological criteria for foodstuffs, FBOs shall conduct shelf-life studies in order to assure that their food does not exceed the food safety criteria throughout the defined shelf-life. In particular this is required for ready-to-eat (RTE) food that supports the growth of Listeria monocytogenes . Among other studies, FBOs can rely on the conclusion drawn by microbiological challenge tests. A microbiological challenge test consists in the artificial contamination of a food with a pathogen microorganism and aims at simulating its behaviour during processing and distribution under the foreseen storage and handling conditions. A number of documents published by international health authorities and research institutions describes how to conduct challenge studies. The authors reviewed the existing literature and described the methodology for implementing such laboratory studies. All the main aspects for the conduction of L. monocytogenes microbiological challenge tests were considered, from the selection of the strains, preparation and choice of the inoculum level and method of contamination, to the experimental design and data interpretation. The objective of the present document is to provide an exhaustive and practical guideline for laboratories that want to implement L. monocytogenes challenge testing on RTE food.

Microbiological Challenge Testing for Listeria Monocytogenes in Ready-to-Eat Food: A Practical Approach

PubMed Central

Scarano, Christian; Ibba, Michela; Pala, Carlo; Spanu, Vincenzo; De Santis, Enrico Pietro Luigi

2014-01-01

Food business operators (FBOs) are the primary responsible for the safety of food they place on the market. The definition and validation of the product’s shelf-life is an essential part for ensuring microbiological safety of food and health of consumers. In the frame of the Regulation (EC) No 2073/2005 on microbiological criteria for foodstuffs, FBOs shall conduct shelf-life studies in order to assure that their food does not exceed the food safety criteria throughout the defined shelf-life. In particular this is required for ready-to-eat (RTE) food that supports the growth of Listeria monocytogenes. Among other studies, FBOs can rely on the conclusion drawn by microbiological challenge tests. A microbiological challenge test consists in the artificial contamination of a food with a pathogen microorganism and aims at simulating its behaviour during processing and distribution under the foreseen storage and handling conditions. A number of documents published by international health authorities and research institutions describes how to conduct challenge studies. The authors reviewed the existing literature and described the methodology for implementing such laboratory studies. All the main aspects for the conduction of L. monocytogenes microbiological challenge tests were considered, from the selection of the strains, preparation and choice of the inoculum level and method of contamination, to the experimental design and data interpretation. The objective of the present document is to provide an exhaustive and practical guideline for laboratories that want to implement L. monocytogenes challenge testing on RTE food. PMID:27800369

Rapid detection of Listeria monocytogenes in foods, by a combination of PCR and DNA probe.

PubMed

Ingianni, A; Floris, M; Palomba, P; Madeddu, M A; Quartuccio, M; Pompei, R

2001-10-01

Listeria monocytogenes is a frequent contaminant of water and foods. Its rapid detection is needed before some foods can be prepared for marketing. In this work L. monocytogenes has been searched for in foods, by a combination of polymerase chain reaction (PCR) and a DNA probe. Both PCR and the probe were prepared for recognizing a specific region of the internalin gene, which is responsible for the production of one of the most important pathogenic factors of Listeria. The combined use of PCR and the DNA probe was used for the detection of L. monocytogenes in over 180 environmental and food samples. Several detection methods were compared in this study, namely conventional culture methods; direct PCR; PCR after an enrichment step; a DNA probe alone; a DNA probe after enrichment and another commercially available gene-probe. Finally PCR and the DNA probe were used in series on all the samples collected. When the DNA probe was associated with the PCR, specific and accurate detection of listeria in the samples could be obtained in about a working-day. The present molecular method showed some advantages in terms of rapidity and specificity in comparison to the other aforementioned tests. In addition, it resulted as being easy to handle, even for non-specialized personnel in small diagnostic microbiology laboratories. Copyright 2001 Academic Press.

Accurate differentiation of Mycobacterium chimaera from Mycobacterium intracellulare by MALDI-TOF MS analysis.

PubMed

Pranada, Arthur B; Witt, Ellen; Bienia, Michael; Kostrzewa, Markus; Timke, Markus

2017-05-01

The increasing number of infections caused by nontuberculous mycobacteria (NTM) has prompted the need for rapid and precise identification methods of these pathogens. Several studies report the applicability of MALDI-TOF mass spectrometry (MS) for identification of NTM. However, some closely related species have very similar spectral mass fingerprints, and until recently, Mycobacterium chimaera and M. intracellulare could not be separated from each other by MALDI-TOF MS. The conventional identification methods used in routine diagnostics have similar limitations. Recently, the differentiation of these two species within the Mycobacterium avium complex has become increasingly important due to reports of M. chimaera infections related to open heart surgery in Europe and in the USA. In this report, a method for the distinct differentiation of M. chimaera and M. intracellulare using a more detailed analysis of MALDI-TOF mass spectra is presented. Species-specific peaks could be identified and it was possible to assign all isolates (100 %) from reference strain collections as well as clinical isolates to the correct species. We have developed a model for the accurate identification of M. chimaera and M. intracellulare by MALDI-TOF MS. This approach has the potential for routine use in microbiology laboratories, as the model itself can be easily implemented into the software of the currently available systems by MALDI-TOF MS manufacturers.

Development of a rapid DNA extraction method and one-step nested PCR for the detection of Naegleria fowleri from the environment.

PubMed

Ahmad, Arine Fadzlun; Lonnen, James; Andrew, Peter W; Kilvington, Simon

2011-10-15

Naegleria fowleri is a small free-living amoebo-flagellate found in natural and manmade thermal aquatic habitats worldwide. The organism is pathogenic to man causing fatal primary amoebic meningoencephalitis (PAM). Infection typically results from bathing in contaminated water and is usually fatal. It is, therefore, important to identify sites containing N. fowleri in the interests of preventive public health microbiology. Culture of environmental material is the conventional method for the isolation of N. fowleri but requires several days incubation and subsequent biochemical or molecular tests to confirm identification. Here, a nested one-step PCR test, in conjunction with a direct DNA extraction from water or sediment material, was developed for the rapid and reliable detection of N. fowleri from the environment. Here, the assay detected N, fowleri in 18/109 river water samples associated with a nuclear power plant in South West France and 0/10 from a similar site in the UK. Although culture of samples yielded numerous thermophilic free-living amoebae, none were N. fowleri or other thermophilic Naegleria spp. The availability of a rapid, reliable and sensitive one-step nested PCR method for the direct detection of N. fowleri from the environment may aid ecological studies and enable intervention to prevent PAM cases. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Comparison of high-pressure liquid chromatography and microbiological assay for determination of ciprofloxacin tablets in human plasma employed in bioequivalence and pharmacokinetics study.

PubMed

Khan, Muhammad Khalid; Khan, Muhammad Farid; Mustafa, Ghulam; Sualah, Mohammed

2012-01-01

Ciprofloxacin was given orally to 28 healthy male volunteers for single oral dose of 500mg; Plasma samples were collected at different time's interval between 0 and 12h and analyzed both by high pressure liquid chromatography and by a microbiological assay. The detection limits (LOD) were 0.02μg/ml and 0.1μg/ml, for both methods respectively. For each method, coefficients of variation (R(2)) were 0.9995 and 0.9918 in plasma and limit of quantitation (LOQ).02 and 0.5μg/ml. The Comparison of means maximum concentration 2.68 μg/ml at 1.5 hr for test and 2.43 μg/ml are attain in HPLC method of Reference at 2hrs respectively. The plasma concentrations measured by microbiological assay of reference tablet are 3.95μg/ml (mean ± SE) at 1 hour and 3.80μg/ml (mean ± SE) at 1 hour. The concentrations in plasma measured by microbiological method were markedly higher than the high-pressure liquid chromatography values which indicates the presence of antimicrobially active metabolites. The mean ± SE values of pharmacokinetic parameters calculated by HPLC method, for total area under the curve (AUC 0-oo) were 13.11, and 11.91 h.mg/l for both test and reference tablets respectively. The mean ± SE values of clearance measured in l/h were 44.91 and 48.42 respectively. The elimination rate constant Kel [l/h] showed 0.17 l/h for test and 0.15 l/h reference tablets and likewise, absorption half-life expressed in hours shown 0.67 h for test and 1.04 h for reference respectively. The Mean Residence Time for test is 5.48 h and 5.49 h for reference. The mean ± SE values of pharmacokinetic parameters (Microbiological assay) for total area under the curve (AUC 0-oo) were 22.11 and 19.33 h.mg/l for both test and reference tablets respectively. The mean ± SE values of clearance measured in l/h were 29.02 and 31.63 respectively. The elimination rate constant Kel [l/h] showed 0.21 l/h for test and 0.20 l/h reference tablets and likewise, absorption half-life expressed in hours shown 0.86h for test and 0.56 h for reference respectively. The Mean Residence Time for test is 5.27 h and 4.67 h for reference. Significant difference observed between two methods.

Development of a Colloidal Gold-Based Immunochromatographic Strip for Rapid Detection of Klebsiella pneumoniae Serotypes K1 and K2.

PubMed

Siu, L Kristopher; Tsai, Yu-Kuo; Lin, Jung-Chung; Chen, Te-Li; Fung, Chang-Phone; Chang, Feng-Yee

2016-12-01

In this study, a novel colloidal gold-based immunochromatographic strip (ICS) containing anti-Klebsiella pneumoniae capsular polysaccharide polyclonal antibodies was developed to specifically detect K. pneumoniae serotypes K1 and K2. Capsular polysaccharide K1 and K2 antigens were first used to produce polyclonal anti-K1 and anti-K2 antibodies. Reference strains with different serotypes, nontypeable K. pneumoniae strains, and other bacterial species were then used to assess the sensitivity and specificity of these test strips. The detection limit was found to be 10 5 CFU, and the ICSs were stable for 6 months when stored at room temperature. No false-positive or false-negative results were observed, and equivalent results were obtained compared to those of more conventional test methods, such as PCR or serum agglutination. In conclusion, the ICS developed here requires no technical expertise and allows for the specific, rapid, and simultaneous detection of K. pneumoniae serotypes K1 and K2. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

AN INVESTIGATION OF THE POSSIBILITIES OF APPLYING IONIZING RADIATION FOR THE CONSERVATION OF SOFT FRUITS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langerak, D.I.

After harvest. the quality oi- soft fruits, such as strawberries, raspberries, blackberries, red and black currants, eherries, and plums deteriorates rapidly, primarily because of mold damage. Conventional measures to prevent microbiological deterioration were not sulficient to prevent a loss from 6 to 18 million guilders each year from a total harvest value of approximately 60 million guilders. Therefore, the possibilities were explored for reducing the enornmous economic loss by exposing the harvested fruits to ionizing radiation, giving preference to the fruits to be exported. Several methods of conservation by ionizing radiation are mentioned. For the surface sterilization or soft fruits,more » the Dynamitron cascade accelerator can be used. The installation cost of the accelerator was estimated to be 360000 guilders. From this estimate the total cost per hour of operation was calculated to be 60 guilders. At a dosage rate of 5 x 10/sup 5/ rad, 6 tons of fruits can be processed at a cost of 1 cent/ kg. This compares favorably with the costs of refrigeration which lie between 2 and 4 cents/kg. (OID)« less

A study of bacterial pathogens and antibiotic susceptibility patterns in chronic suppurative otitis media.

PubMed

Mofatteh, M R; Shahabian Moghaddam, F; Yousefi, M; Namaei, M H

2018-01-01

To assess the frequency of bacterial agents in chronic suppurative otitis media and the antibiotic susceptibility patterns of isolates among patients. A total of 185 patients clinically diagnosed with chronic suppurative otitis media were interviewed and middle-ear effusion samples were collected using sterile swabs. All bacterial isolates were identified by conventional microbiological methods. Antibiotic susceptibility patterns of the isolates were determined by Kirby-Bauer disc diffusion. Staphylococci spp. (64.9 per cent) were the most prevalent bacteria isolated, followed by Klebsiella spp. (12.9 per cent) and Pseudomonas aeruginosa (10.3 per cent). The most effective antibiotic for treatment of bacterial chronic suppurative otitis media was ciprofloxacin. Statistical analysis showed no significant difference in bacterial infestations among chronic suppurative otitis media patients and the antimicrobial susceptibility patterns of the bacterial isolates based on gender and age (p > 0.05). Our findings highlight the importance of a continuous and periodic evaluation of the bacteriological profile and antibiotic susceptibility patterns in chronic suppurative otitis media patients for efficacious treatment of the infection.

[Molecular aspects of the antiviral response against hepatitis C virus implicated in vaccines development].

PubMed

Llanes, María Soledad; Palacios, Natalia Soledad; Piccione, Magalí; Ruiz, María Guillermina; Layana, Carla

2015-04-01

Hepatitis C is a contagious liver disease caused by hepacivirus of the Flaviviridae family. It has a RNA genome, a unique highly variable molecule. It encodes ten proteins which are necessary to infect cells and multiply. Replication occurs only in hepatocytes. Because of its wide genomic variability and the absence of symptoms, it is difficult to make an early diagnosis and successful treatment. In this review we analyze the molecular mechanism by which the virus infects the hepatocytes and causes the disease. We focused the analysis on different therapies, with the possibility of improving treatment with the use of new specific vaccines. We highlight the use of new therapies based on nucleic acids, mainly DNA vectors. In the near future, once this treatment is adequately evaluated in clinical trials, and the costs are calculated, it could be a very beneficial alternative to conventional methods. Copyright © 2013 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Update on: Shigella new serogroups/serotypes and their antimicrobial resistance.

PubMed

Muthuirulandi Sethuvel, D P; Devanga Ragupathi, N K; Anandan, S; Veeraraghavan, B

2017-01-01

Shigellosis represents a major burden of disease in developing countries. A low infectious dose allows the disease to be spread effectively. Although shigellosis is mostly a self-limiting disease, antibiotics are recommended to reduce deaths, disease symptoms and organism-shedding time. However, in India, antimicrobial resistance among the genus Shigella is more common than among any other enteric bacteria. Notably, new serotypes or subserotypes in Shigella are reported from various parts of the world. Identification of new subserotypes of Shigella spp. is becoming a major issue as these strains are nontypeable by conventional serotyping. The commercially available antisera may not cover all possible epitopes of the O lipopolysaccharide antigen of Shigella serotypes. Therefore, molecular methods which most closely approach the resolution of full serotyping are necessary to identify such strains. In addition, the knowledge of a prevalent serotype in various geographic regions may assist in formulating strategies such as the development of a vaccine to prevent infection especially when the immunity to disease is serotype specific, and to understand the disease burden caused by new Shigella serotypes. © 2016 The Society for Applied Microbiology.

New clustered regularly interspaced short palindromic repeat locus spacer pair typing method based on the newly incorporated spacer for Salmonella enterica.

PubMed

Li, Hao; Li, Peng; Xie, Jing; Yi, Shengjie; Yang, Chaojie; Wang, Jian; Sun, Jichao; Liu, Nan; Wang, Xu; Wu, Zhihao; Wang, Ligui; Hao, Rongzhang; Wang, Yong; Jia, Leili; Li, Kaiqin; Qiu, Shaofu; Song, Hongbin

2014-08-01

A clustered regularly interspaced short palindromic repeat (CRISPR) typing method has recently been developed and used for typing and subtyping of Salmonella spp., but it is complicated and labor intensive because it has to analyze all spacers in two CRISPR loci. Here, we developed a more convenient and efficient method, namely, CRISPR locus spacer pair typing (CLSPT), which only needs to analyze the two newly incorporated spacers adjoining the leader array in the two CRISPR loci. We analyzed a CRISPR array of 82 strains belonging to 21 Salmonella serovars isolated from humans in different areas of China by using this new method. We also retrieved the newly incorporated spacers in each CRISPR locus of 537 Salmonella isolates which have definite serotypes in the Pasteur Institute's CRISPR Database to evaluate this method. Our findings showed that this new CLSPT method presents a high level of consistency (kappa = 0.9872, Matthew's correlation coefficient = 0.9712) with the results of traditional serotyping, and thus, it can also be used to predict serotypes of Salmonella spp. Moreover, this new method has a considerable discriminatory power (discriminatory index [DI] = 0.8145), comparable to those of multilocus sequence typing (DI = 0.8088) and conventional CRISPR typing (DI = 0.8684). Because CLSPT only costs about $5 to $10 per isolate, it is a much cheaper and more attractive method for subtyping of Salmonella isolates. In conclusion, this new method will provide considerable advantages over other molecular subtyping methods, and it may become a valuable epidemiologic tool for the surveillance of Salmonella infections. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Prevention and Control of Antimicrobial Resistant Healthcare-Associated Infections: The Microbiology Laboratory Rocks!

PubMed

Simões, Alexandra S; Couto, Isabel; Toscano, Cristina; Gonçalves, Elsa; Póvoa, Pedro; Viveiros, Miguel; Lapão, Luís V

2016-01-01

In Europe, each year, more than four milion patients acquire a healthcare-associated infection (HAI) and almost 40 thousand die as a direct consequence of it. Regardless of many stategies to prevent and control HAIs, they remain an important cause of morbidity and mortality worldwide with a significant economic impact: a recent estimate places it at the ten billion dollars/year. The control of HAIs requires a prompt and efficient identification of the etiological agent and a rapid communication with the clinician. The Microbiology Laboratory has a significant role in the prevention and control of these infections and is a key element of any Infection Control Program. The work of the Microbiology Laboratory covers microbial isolation and identification, determination of antimicrobial susceptibility patterns, epidemiological surveillance and outbreak detection, education, and report of quality assured results. In this paper we address the role and importance of the Microbiology Laboratory in the prevention and control of HAI and in Antibiotic Stewardship Programs and how it can be leveraged when combined with the use of information systems. Additionally, we critically review some challenges that the Microbiology Laboratory has to deal with, including the selection of analytic methods and the proper use of communication channels with other healthcare services.

Comparison of high-pressure liquid chromatography and microbiological assay for the determination of biliary elimination of ciprofloxacin in humans.

PubMed Central

Brogard, J M; Jehl, F; Monteil, H; Adloff, M; Blickle, J F; Levy, P

1985-01-01

Serum kinetics and biliary, urinary, and fecal elimination of ciprofloxacin, a new quinolone derivative, were studied in 12 recently cholecystectomized patients provided with T-tube drainage during 24 h after oral administration of a single 500-mg dose of this substance. Drug concentrations were measured by both high-pressure liquid chromatography (HPLC) and microbiological assay. The results were comparable for the concentrations in serum (average of peaks, 2.0 +/- 0.2 micrograms/ml by HPLC and 2.3 +/- 0.3 micrograms/ml by the microbiological method) and urine (0 to 6 h, 267 +/- 74 and 241 +/- 58 micrograms/ml, respectively). This was not the case for biliary values, for which the microbiological assay yielded significantly higher concentrations than did HPLC (average of peak concentrations, 21.2 +/- 2.6 and 16.0 +/- 2.5 micrograms/ml, respectively [P less than 0.02]), nor for total 24-h biliary output (2,167 +/- 288 and 1,587 +/- 222 micrograms, respectively [P less than 0.01]). This suggests hepatic biotransformation of ciprofloxacin into microbiologically active metabolites. The apparent broad antibacterial spectrum of ciprofloxacin and its higher biliary levels than simultaneously determined serum concentrations suggest that this derivative is suitable for the treatment of biliary tract infections. PMID:2939796

Learning to Write Like a Scientist: A Writing-Intensive Course for Microbiology/Health Science Students †

PubMed Central

Grzyb, Kimi; Snyder, Wesley; Field, Katharine G.

2018-01-01

Learning the tools and conventions of expert communication in the sciences provides multiple benefits to bioscience students, yet often these skills are not formally taught. To address this need, we designed a writing-intensive microbiology course on emerging infectious diseases to provide upper-division students with science-specific writing skills along with disciplinary course content. The course followed the guidelines of our university’s Writing Intensive Curriculum (WIC) program. Students wrote a press release, a case study, a controversy/position paper, and a grant prospectus, and revised drafts after feedback. To assess the course, in 2015 and 2016 we administered pre-post surveys and collected writing samples for analysis. Students reported on their experience, training, skills, and knowledge before taking the course. They then rated the extent to which the assignments, lectures, in-class activities, and writing activities contributed to their attainment of the learning outcomes of the course. Students entering the class were inexperienced in tools of science writing and the specific genres covered by the class. Their confidence levels rose in both skills and knowledge. Feedback from instructors was cited as most helpful in the majority of the areas where students reported the most gains. The survey provided evidence that discipline-specific knowledge had been acquired through writing activities. Teaching science writing by allowing the students to write “fiction” (e.g., a case report about a fictional patient) was effective in maintaining a high level of interest, both in learning the conventions of the genre and in seeking out detailed information about emerging infectious diseases. Both the course structure and the specific assignments would be useful at other institutions to teach science writing. PMID:29904515

The antimicrobial effectiveness of photodynamic therapy used as an addition to the conventional endodontic re-treatment: a clinical study.

PubMed

Jurič, Ivona Bago; Plečko, Vanda; Pandurić, Dragana Gabrić; Anić, Ivica

2014-12-01

The purpose of the study was to evaluate the efficacy of antimicrobial photodynamic therapy (aPDT) used as an adjunct to the endodontic re-treatment in the eradication of microorganisms from previously filled root canals. The study sample consisted of 21 randomly selected patients with root filled and infected root canal system with chronic apical periodontitis on incisors or canines, who have had previously endodontic treatment. Microbiological samples from the root canals were collected after accessing the canal, following the endodontic re-treatment and after the aPDT procedure. During instrumentation, the root canals were irrigated with 2.5% sodium hypochlorite (NaOCl), and the final irrigation protocol included 17% ethylenediaminetetraacetic acid followed by NaOCl. Root canals were filled with a phenothiazinium chloride and irradiated with a diode laser (λ=660 nm, 100 mW) for 1 min. Microbiological samples from the root canals were cultivated on selective plates, and the identification was done by micromorphology, macromorphology and different API strips as well as bacterial counts (colony forming units). Fourteen bacteria species were isolated from the root canals initially, with a mean value of 4.57 species per canal. Although endodontic re-treatment alone produced a significant reduction in the number of bacteria species (p<0.001), the combination of endodontic treatment and aPDT was statistically more effective (p<0.001). No bacteria were cultivated from the main root canals of 11 teeth. The results indicated that the aPDT used as an adjunct to the conventional endodontic therapy achieved a significant further reduction of intracanal microbial load. Copyright © 2014 Elsevier B.V. All rights reserved.

Effect of continuous ohmic heating to inactivate Escherichia coli O157:H7, Salmonella Typhimurium and Listeria monocytogenes in orange juice and tomato juice.

PubMed

Lee, S-Y; Sagong, H-G; Ryu, S; Kang, D-H

2012-04-01

The purpose of this study was to investigate the efficacy of continuous ohmic heating for reducing Escherichia coli O157:H7, Salmonella Typhimurium and Listeria monocytogenes in orange juice and tomato juice. Orange juice and tomato juice were treated with electric field strengths in the range of 25-40 V cm(-1) for different treatment times. The temperature of the samples increased with increasing treatment time and electric field strength. The rate of temperature change for tomato juice was higher than for orange juice at all voltage gradients applied. Higher electric field strength or longer treatment time resulted in a greater reduction of pathogens. Escherichia coli O157:H7 was reduced by more than 5 log after 60-, 90- and 180-s treatments in orange juice with 40, 35 and 30 V cm(-1) electric field strength, respectively. In tomato juice, treatment with 25 V cm(-1) for 30 s was sufficient to achieve a 5-log reduction in E. coli O157:H7. Similar results were observed in Salm. Typhimurium and L. monocytogenes. The concentration of vitamin C in continuous ohmic heated juice was significantly higher than in conventionally heated juice (P < 0·05). Continuous ohmic heating can be effective in killing foodborne pathogens on orange juice and tomato juice with lower degradation of quality than conventional heating. These results suggest that continuous ohmic heating might be effectively used to pasteurize fruit and vegetable juices in a short operating time and that the effect of inactivation depends on applied electric field strengths, treatment time and electric conductivity. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Use of the MicroSeq 500 16S rRNA Gene-Based Sequencing for Identification of Bacterial Isolates That Commercial Automated Systems Failed To Identify Correctly

PubMed Central

Fontana, Carla; Favaro, Marco; Pelliccioni, Marco; Pistoia, Enrico Salvatore; Favalli, Cartesio

2005-01-01

Reliable automated identification and susceptibility testing of clinically relevant bacteria is an essential routine for microbiology laboratories, thus improving patient care. Examples of automated identification systems include the Phoenix (Becton Dickinson) and the VITEK 2 (bioMérieux). However, more and more frequently, microbiologists must isolate “difficult” strains that automated systems often fail to identify. An alternative approach could be the genetic identification of isolates; this is based on 16S rRNA gene sequencing and analysis. The aim of the present study was to evaluate the possible use of MicroSeq 500 (Applera) for sequencing the 16S rRNA gene to identify isolates whose identification is unobtainable by conventional systems. We analyzed 83 “difficult” clinical isolates: 25 gram-positive and 58 gram-negative strains that were contemporaneously identified by both systems—VITEK 2 and Phoenix—while genetic identification was performed by using the MicroSeq 500 system. The results showed that phenotypic identifications by VITEK 2 and Phoenix were remarkably similar: 74% for gram-negative strains (43 of 58) and 80% for gram-positive strains were concordant by both systems and also concordant with genetic characterization. The exceptions were the 15 gram-negative and 9 gram-positive isolates whose phenotypic identifications were contrasting or inconclusive. For these, the use of MicroSeq 500 was fundamental to achieving species identification. In clinical microbiology the use of MicroSeq 500, particularly for strains with ambiguous biochemical profiles (including slow-growing strains), identifies strains more easily than do conventional systems. Moreover, MicroSeq 500 is easy to use and cost-effective, making it applicable also in the clinical laboratory. PMID:15695654

Towards objective hand hygiene technique assessment: validation of the ultraviolet-dye-based hand-rubbing quality assessment procedure.

PubMed

Lehotsky, Á; Szilágyi, L; Bánsághi, S; Szerémy, P; Wéber, G; Haidegger, T

2017-09-01

Ultraviolet spectrum markers are widely used for hand hygiene quality assessment, although their microbiological validation has not been established. A microbiology-based assessment of the procedure was conducted. Twenty-five artificial hand models underwent initial full contamination, then disinfection with UV-dyed hand-rub solution, digital imaging under UV-light, microbiological sampling and cultivation, and digital imaging of the cultivated flora were performed. Paired images of each hand model were registered by a software tool, then the UV-marked regions were compared with the pathogen-free sites pixel by pixel. Statistical evaluation revealed that the method indicates correctly disinfected areas with 95.05% sensitivity and 98.01% specificity. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

MALDI-TOF MS in the Microbiology Laboratory: Current Trends.

PubMed

Schubert, Sören; Kostrzewa, Markus

2017-01-01

Within less than a decade matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become a gold standard for microbial identification in clinical microbiology laboratories. Besides identification of microorganisms the typing of single strains as well as the antibiotic and antimycotic resistance testing has come into focus in order to speed up the microbiological diagnostic. However, the full potential of MALDI-TOF MS has not been tapped yet and future technological advancements will certainly expedite this method towards novel applications and enhancement of current practice. So, the following chapter shall be rather a brainstorming and forecast of how MALDI-TOF MS will develop to influence clinical diagnostics and microbial research in the future. It shall open up the stage for further discussions and does not claim for overall validity.

Genomics and metagenomics in medical microbiology.

PubMed

Padmanabhan, Roshan; Mishra, Ajay Kumar; Raoult, Didier; Fournier, Pierre-Edouard

2013-12-01

Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology. Copyright © 2013 Elsevier B.V. All rights reserved.

New immuno-PCR assay for detection of low concentrations of shiga toxin 2 and its variants.

PubMed

Zhang, Wenlan; Bielaszewska, Martina; Pulz, Matthias; Becker, Karsten; Friedrich, Alexander W; Karch, Helge; Kuczius, Thorsten

2008-04-01

Shiga toxin (Stx)-producing Escherichia coli (STEC) strains secrete toxins that are major virulence factors and diagnostic targets, but some STEC strains secrete Stx in amounts that cannot be detected using conventional cell cytotoxicity or immunological assays. Therefore, there is an urgent need for more-sensitive Stx detection methods. We describe the development of an assay that can detect low concentrations of Stx2 and its variants. An immuno-PCR Stx2 assay was developed based on an enzyme immunoassay (EIA) combining antibody capture and DNA amplification to increase the signal. The immuno-PCR assay detected 10 pg/ml of purified Stx2, compared to 1 ng/ml Stx2 detected by commercial EIA. Consequently, immuno-PCR detected Stx2 and its variants in STEC strains that produce the toxins at levels that are nondetectable by using the EIA, as well as the Stx2 in EIA-negative enriched stool cultures from patients. Our data demonstrate that the immuno-PCR developed here is a highly sensitive and specific method for the detection of trace amounts of Stx2 and Stx2 variants. It is therefore suitable for use by clinical microbiological laboratories to improve the toxin detection in clinical samples.

New Immuno-PCR Assay for Detection of Low Concentrations of Shiga Toxin 2 and Its Variants▿

PubMed Central

Zhang, Wenlan; Bielaszewska, Martina; Pulz, Matthias; Becker, Karsten; Friedrich, Alexander W.; Karch, Helge; Kuczius, Thorsten

2008-01-01

Shiga toxin (Stx)-producing Escherichia coli (STEC) strains secrete toxins that are major virulence factors and diagnostic targets, but some STEC strains secrete Stx in amounts that cannot be detected using conventional cell cytotoxicity or immunological assays. Therefore, there is an urgent need for more-sensitive Stx detection methods. We describe the development of an assay that can detect low concentrations of Stx2 and its variants. An immuno-PCR Stx2 assay was developed based on an enzyme immunoassay (EIA) combining antibody capture and DNA amplification to increase the signal. The immuno-PCR assay detected 10 pg/ml of purified Stx2, compared to 1 ng/ml Stx2 detected by commercial EIA. Consequently, immuno-PCR detected Stx2 and its variants in STEC strains that produce the toxins at levels that are nondetectable by using the EIA, as well as the Stx2 in EIA-negative enriched stool cultures from patients. Our data demonstrate that the immuno-PCR developed here is a highly sensitive and specific method for the detection of trace amounts of Stx2 and Stx2 variants. It is therefore suitable for use by clinical microbiological laboratories to improve the toxin detection in clinical samples. PMID:18272709

Genetic characteristics and molecular epidemiology of vancomycin-resistant Enterococci isolates from Caribbean countries

PubMed Central

Jayaratne, Padman; Wilson, Clyde; Golding, George R.; Nicholson, Alison M.; Lewis, Delores B.; Hermelijn, Sandra M.

2017-01-01

Emergence of vancomycin-resistant Enterococci (VRE) that first appeared on the stage about three decades ago is now a major concern worldwide as it has globally reached every continent. Our aim was to simply undertake a multinational study to delineate the resistance and virulence genes of clinical isolates of VRE isolates from the Caribbean. We employed both conventional (standard microbiological methods including use of E-test strips, chromogenic agar) and molecular methods (polymerase chain reactions–PCR, pulsed-field gel electrophoresis–PFGE and multilocus sequence typing–MLST) to analyze and characterize 245 Enterococci species and 77 VRE isolates from twelve hospitals from eight countries in the Caribbean. The PCR confirmed and demonstrated the resistance and virulence genes (vanA and esp) among all confirmed VRE isolates. The PFGE delineated clonally related isolates from patients from the same country and other countries in the region. The main sequence types of the VRE isolates from the region included STs 412, 750, 203, 736 and 18, all from the common ancestor for clonal complex 17 (CC17). Despite this common ancestor and association of outbreaks of this lineage clones, there has been no reports of outbreaks of infection by VRE in several hospitals in the Caribbean. PMID:29020115

Advances in biosensor development for the screening of antibiotic residues in food products of animal origin - A comprehensive review.

PubMed

Gaudin, Valérie

2017-04-15

Antibiotic residues may be found in food of animal origin, since veterinary drugs are used for preventive and curative purposes to treat animals. The control of veterinary drug residues in food is necessary to ensure consumer safety. Screening methods are the first step in the control of antibiotic residues in food of animal origin. Conventional screening methods are based on different technologies, microbiological methods, immunological methods or physico-chemical methods (e.g. thin-layer chromatography, HPLC, LC-MS/MS). Screening methods should be simple, quick, inexpensive and specific, with low detection limits and high sample throughput. Biosensors can meet some of these requirements. Therefore, the development of biosensors for the screening of antibiotic residues has been increasing since the 1980s. The present review provides extensive and up-to-date findings on biosensors for the screening of antibiotic residues in food products of animal origin. Biosensors are constituted of a bioreceptor and a transducer. In the detection of antibiotic residues, even though antibodies were the first bioreceptors to be used, new kinds of bioreceptors are being developed more and more (enzymes, aptamers, MIPs); their advantages and drawbacks are discussed in this review. The different categories of transducers (electrochemical, mass-based biosensors, optical and thermal) and their potential applications for the screening of antibiotic residues in food are presented. Moreover, the advantages and drawbacks of the different types of transducers are discussed. Lastly, outlook and the future development of biosensors for the control of antibiotic residues in food are highlighted. Copyright © 2016. Published by Elsevier B.V.

Compilation of Annual Reports of the Navy ELF (Extremely Low Frequency) Communications System Ecological Monitoring Program. Volume 1. Tabs A-E.

DTIC Science & Technology

1984-07-01

mhhhhmhhmmm EEmhohEEmhmhEE EohhEohEEEEohI 1111 11111_L25 1.18 6 MICROCOPY RESOLUTION TESI CHART 95. Pedon Classification: Typic Dystrochrept, sandy, mixed...prepared by team researchers in the MTU Forestry Department and delivered to the Environmental Microbiology lab in the Department of Biological Sciences...unsuccessful. Using methods given in a presentation at the 1982 American Society for Microbiology Annual Meetings, virtually no bacteria of any type were

Comparative Analysis of Subtyping Methods against a Whole- Genome-Sequencing Standard for Salmonella enterica Serotype Enteritidis

DTIC Science & Technology

2015-01-01

enterica serovar En- teritidis. Food Microbiology 34:164 –173. http://dx.doi.org/10.1016/j.fm .2012.11.012. 11. Dewaele I, Rasschaert G, Bertrand S...MVLST showed the potential to trace major lineages and ecological origins of S. enterica serotype Enteritidis. Our results suggested that whole-genome...in Journal of Clinical Microbiology , Vol. 53 (1) (2015), (3 (1). DoD Components reserve a royalty-free, nonexclusive and irrevocable right to

Researching Seeds: Films, Sanitation Methods, Microbiological Growth, Viability, and Selection for New Crops

NASA Technical Reports Server (NTRS)

Padgett, Niki; Smith, Trent

2018-01-01

A major factor in long-term human exploration of the solar system is crop growth in microgravity. Space crops can provide fresh, nutritious food to supplement diets for astronauts. Important factors impacting space plant growth and consumption are water delivery to root zone in microgravity, sanitation methods for microbiological safety, plant responses to light quality/spectrum, and identifying optimal edible plants suitable for growth on the International Space Station (ISS). Astronauts growing their own food on the ISS provides necessary data for crop production for long duration deep space missions. The seed film project can be used in Advanced Plant Habitat and Veggies that are currently being utilized on the ISS.

A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?

PubMed

Garrity, George M

2016-08-01

Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins contemporary microbiology and serves as a principal means of shaping and referencing knowledge. Using methods drawn from the field of exploratory data analysis, this minireview examines the current state of the field as it transitions from a taxonomy based on 16S rRNA gene sequences to one based on whole-genome sequences and tests the validity of some commonly held beliefs. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Surface microbial contamination in hospitals: A pilot study on methods of sampling and the use of proposed microbiologic standards.

PubMed

Claro, Tânia; O'Reilly, Marese; Daniels, Stephen; Humphreys, Hilary

2015-09-01

Contamination of hospital surfaces by bacteria is increasingly recognized. We assessed commonly touched surfaces using contact plates and Petrifilms (3M, St. Paul, MN) and compared the results against proposed microbiology standards. Toilet door handles were the most heavily contaminated (7.97 ± 0.68 colony forming units [CFU]/cm(2)) and exceeded proposed standards on 74% of occasions. Petrifilms detected statistically higher CFU from bedside lockers. Further research is required on the use of standards and methods of sampling. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Viable Mycobacterium avium ssp. paratuberculosis isolated from calf milk replacer.

PubMed

Grant, Irene R; Foddai, Antonio C G; Tarrant, James C; Kunkel, Brenna; Hartmann, Faye A; McGuirk, Sheila; Hansen, Chungyi; Talaat, Adel M; Collins, Michael T

2017-12-01

When advising farmers on how to control Johne's disease in an infected herd, one of the main recommendations is to avoid feeding waste milk to calves and instead feed calf milk replacer (CMR). This advice is based on the assumption that CMR is free of viable Mycobacterium avium ssp. paratuberculosis (MAP) cells, an assumption that has not previously been challenged. We tested commercial CMR products (n = 83) obtained from dairy farms around the United States by the peptide-mediated magnetic separation (PMS)-phage assay, PMS followed by liquid culture (PMS-culture), and direct IS900 quantitative PCR (qPCR). Conventional microbiological analyses for total mesophilic bacterial counts, coliforms, Salmonella, coagulase-negative staphylococci, streptococci, nonhemolytic Corynebacterium spp., and Bacillus spp. were also performed to assess the overall microbiological quality of the CMR. Twenty-six (31.3%) of the 83 CMR samples showed evidence of the presence of MAP. Seventeen (20.5%) tested positive for viable MAP by the PMS-phage assay, with plaque counts ranging from 6 to 1,212 pfu/50 mL of reconstituted CMR (average 248.5 pfu/50 mL). Twelve (14.5%) CMR samples tested positive for viable MAP by PMS-culture; isolates from all 12 of these samples were subsequently confirmed by whole-genome sequencing to be different cattle strains of MAP. Seven (8.4%) CMR samples tested positive for MAP DNA by IS900 qPCR. Four CMR samples tested positive by both PMS-based tests and 5 CMR samples tested positive by IS900 qPCR plus one or other of the PMS-based tests, but only one CMR sample tested positive by all 3 MAP detection tests applied. All conventional microbiology results were within current standards for whole milk powders. A significant association existed between higher total bacterial counts and presence of viable MAP indicated by either of the PMS-based assays. This represents the first published report of the isolation of viable MAP from CMR. Our findings raise concerns about the potential ability of MAP to survive manufacture of dried milk-based products. The Authors. Published by the Federation of Animal Science Societies and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Rapid test for the detection of hazardous microbiological material

NASA Astrophysics Data System (ADS)

Mordmueller, Mario; Bohling, Christian; John, Andreas; Schade, Wolfgang

2009-09-01

After attacks with anthrax pathogens have been committed since 2001 all over the world the fast detection and determination of biological samples has attracted interest. A very promising method for a rapid test is Laser Induced Breakdown Spectroscopy (LIBS). LIBS is an optical method which uses time-resolved or time-integrated spectral analysis of optical plasma emission after pulsed laser excitation. Even though LIBS is well established for the determination of metals and other inorganic materials the analysis of microbiological organisms is difficult due to their very similar stoichiometric composition. To analyze similar LIBS-spectra computer assisted chemometrics is a very useful approach. In this paper we report on first results of developing a compact and fully automated rapid test for the detection of hazardous microbiological material. Experiments have been carried out with two setups: A bulky one which is composed of standard laboratory components and a compact one consisting of miniaturized industrial components. Both setups work at an excitation wavelength of λ=1064nm (Nd:YAG). Data analysis is done by Principal Component Analysis (PCA) with an adjacent neural network for fully automated sample identification.

EPA METHOD STUDY 8, TOTAL MERCURY IN WATER

EPA Science Inventory

The Environmental Monitoring and Support Laboratory-Cincinnati of EPA conducts EPA's quality assurance program for the water laboratories and assists EPA laboratories in the choice of methods for physical, chemical, biological and microbiological analyses. The responsibility for ...

Biotechnology Laboratory Methods.

ERIC Educational Resources Information Center

Davis, Robert H.; Kompala, Dhinakar S.

1989-01-01

Describes a course entitled "Biotechnology Laboratory" which introduces a variety of laboratory methods associated with biotechnology. Describes the history, content, and seven experiments of the course. The seven experiments are selected from microbiology and molecular biology, kinetics and fermentation, and downstream…

Current and Future Technologies for Microbiological Decontamination of Cereal Grains.

PubMed

Los, Agata; Ziuzina, Dana; Bourke, Paula

2018-06-01

Cereal grains are the most important staple foods for mankind worldwide. The constantly increasing annual production and yield is matched by demand for cereals, which is expected to increase drastically along with the global population growth. A critical food safety and quality issue is to minimize the microbiological contamination of grains as it affects cereals both quantitatively and qualitatively. Microorganisms present in cereals can affect the safety, quality, and functional properties of grains. Some molds have the potential to produce harmful mycotoxins and pose a serious health risk for consumers. Therefore, it is essential to reduce cereal grain contamination to the minimum to ensure safety both for human and animal consumption. Current production of cereals relies heavily on pesticides input, however, numerous harmful effects on human health and on the environment highlight the need for more sustainable pest management and agricultural methods. This review evaluates microbiological risks, as well as currently used and potential technologies for microbiological decontamination of cereal grains. © 2018 Institute of Food Technologists®.

Microbial populations in contaminant plumes

USGS Publications Warehouse

Haack, S.K.; Bekins, B.A.

2000-01-01

Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation.

Microbiological assay for the analysis of certain macrolides in pharmaceutical dosage forms.

PubMed

Mahmoudi, A; Fourar, R E-A; Boukhechem, M S; Zarkout, S

2015-08-01

Clarithromycin (CLA) and roxithromycin (ROX) are macrolide antibiotics with an expanded spectrum of activity that are commercially available as tablets. A microbiological assay, applying the cylinder-plate method and using a strain of Micrococcus luteus ATCC 9341 as test organism, has been used and validated for the quantification of two macrolide drugs; CLA and ROX in pure and pharmaceutical formulations. The validation of the proposed method was carried out for linearity, precision, accuracy and specificity. The linear dynamic ranges were from 0.1 to 0.5μg/mL for both compounds. Logarithmic calibration curve was obtained for each macrolide (r>0.989) with statistically equal slopes varying from 3.275 to 4.038, and a percentage relative standard deviation in the range of 0.24-0.92%. Moreover, the method was applied successfully for the assay of the studied drugs in pharmaceutical tablet dosage forms. Recovery from standard addition experiments in commercial products was 94.71-96.91% regarding clarithromycin and 93.94-98.12% regarding roxithromycin, with a precision (%RSD) 1.32-2.11%. Accordingly, this microbiological assay can be used for routine quality control analysis of titled drugs in tablet formulations. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparison of environmental and egg microbiology associated with conventional and free-range laying hen management.

PubMed

Jones, D R; Anderson, K E; Musgrove, M T

2011-09-01

Eggs from alternative production practices are a growing niche in the market. Meeting consumer requests for greater diversity in retail egg options has resulted in some unique challenges such as understanding the food safety implications of eggs from alternative production practices. A study was conducted to determine what, if any, differences exist between nest run conventional cage-produced eggs and free range-produced eggs. A sister flock of brown egg layers was maintained in conventional cage and free-range production with egg and environmental sampling every 6 wk from 20 to 79 wk of age. Aerobic, coliform, and yeast and mold populations were monitored. Environmental microbial levels were not always indicative of egg contamination levels. When significant differences (P < 0.05 and P < 0.0001, dependent on season) were observed among treatments for coliforms, shell contamination levels of free-range nest box eggs and free-range floor eggs were always greater than those of conventional cage eggs, which remained low throughout the study (0.42-0.02 log cfu/mL). Shell yeast and mold levels were significantly greater in free-range floor eggs than in free-range nest box eggs and conventional cage eggs throughout the entire study. Egg contents contamination levels were extremely low for all monitored populations and treatments. Season of the year played a role in both environmental and egg microbial levels. Winter had the lowest levels of all populations monitored for all treatments, except for aerobic free-range floor egg shell emulsions, which were increased (3.6 log cfu/mL). Understanding the differences in microbial populations present on conventional cage-produced and free range-produced eggs can lead to the development of effective cleaning procedures, enhancing food safety.

Development, Validation, and Application of the Microbiology Concept Inventory †

PubMed Central

Paustian, Timothy D.; Briggs, Amy G.; Brennan, Robert E.; Boury, Nancy; Buchner, John; Harris, Shannon; Horak, Rachel E. A.; Hughes, Lee E.; Katz-Amburn, D. Sue; Massimelli, Maria J.; McDonald, Ann H.; Primm, Todd P.; Smith, Ann C.; Stevens, Ann M.; Yung, Sunny B.

2017-01-01

If we are to teach effectively, tools are needed to measure student learning. A widely used method for quickly measuring student understanding of core concepts in a discipline is the concept inventory (CI). Using the American Society for Microbiology Curriculum Guidelines (ASMCG) for microbiology, faculty from 11 academic institutions created and validated a new microbiology concept inventory (MCI). The MCI was developed in three phases. In phase one, learning outcomes and fundamental statements from the ASMCG were used to create T/F questions coupled with open responses. In phase two, the 743 responses to MCI 1.0 were examined to find the most common misconceptions, which were used to create distractors for multiple-choice questions. MCI 2.0 was then administered to 1,043 students. The responses of these students were used to create MCI 3.0, a 23-question CI that measures students’ understanding of all 27 fundamental statements. MCI 3.0 was found to be reliable, with a Cronbach’s alpha score of 0.705 and Ferguson’s delta of 0.97. Test item analysis demonstrated good validity and discriminatory power as judged by item difficulty, item discrimination, and point-biserial correlation coefficient. Comparison of pre- and posttest scores showed that microbiology students at 10 institutions showed an increase in understanding of concepts after instruction, except for questions probing metabolism (average normalized learning gain was 0.15). The MCI will enable quantitative analysis of student learning gains in understanding microbiology, help to identify misconceptions, and point toward areas where efforts should be made to develop teaching approaches to overcome them. PMID:29854042

Tillage system affects microbiological properties of soil

NASA Astrophysics Data System (ADS)

Delgado, A.; de Santiago, A.; Avilés, M.; Perea, F.

2012-04-01

Soil tillage significantly affects organic carbon accumulation, microbial biomass, and subsequently enzymatic activity in surface soil. Microbial activity in soil is a crucial parameter contributing to soil functioning, and thus a basic quality factor for soil. Since enzymes remain soil after excretion by living or disintegrating cells, shifts in their activities reflect long-term fluctuations in microbial biomass. In order to study the effects of no-till on biochemical and microbiological properties in comparison to conventional tillage in a representative soil from South Spain, an experiment was conducted since 1982 on the experimental farm of the Institute of Agriculture and Fisheries Research of Andalusia (IFAPA) in Carmona, SW Spain (37o24'07''N, 5o35'10''W). The soil at the experimental site was a very fine, montomorillonitic, thermic Chromic Haploxerert (Soil Survey Staff, 2010). A randomized complete block design involving three replications and the following two tillage treatments was performed: (i) Conventional tillage, which involved mouldboard plowing to a depth of 50 cm in the summer (once every three years), followed by field cultivation to a depth of 15 cm before sowing; crop residues being burnt, (ii) No tillage, which involved controlling weeds before sowing by spraying glyphosate and sowing directly into the crop residue from the previous year by using a planter with double-disk openers. For all tillage treatments, the crop rotation (annual crops) consisted of winter wheat, sunflower, and legumes (pea, chickpea, or faba bean, depending on the year), which were grown under rainfed conditions. Enzymatic activities (ß-glucosidase, dehydrogenase, aryl-sulphatase, acid phosphatase, and urease), soil microbial biomass by total viable cells number by acridine orange direct count, the density of cultivable groups of bacteria and fungi by dilution plating on semi-selective media, the physiological profiles of the microbial communities by BiologR, and the Shannon (H') and Gini (1-G) diversity index of microbial communities were determined in soil samples (0-10 cm depth) taken in autumn 2009. All the enzymatic activities and the biomass estimated by viable cell counting were significantly higher under no-till than under conventional tillage. However, only fluorescents pseudomonas population was increased under no-till, meanwhile oligotrophic bacteria and actinomycetes populations were higher with conventional tillage than with no-till. Overall, there was a higher use all the group of carbon sources used in the BiologR test with conventional tillage than with no-till, by except amines and phenols which showed non-significant differences. This reveals different physiological profiles in the microbial communities under both tillage systems. The Gini diversity was significantly lower with no-till than with conventional tillage. It can be concluded that no-till increases microbial biomass in soil and subsequently enzymatic activities likely ascribed to an increased organic matter content. Under low availability of hydrocarbon sources in soil due to conventional tillage, which promotes a decrease in the organic matter content of the soil, populations of oligotrophods and the diversity of microbial communities are increased. Under these conditions, there must not be dominant carbon sources promoting the selection of microorganisms with a given physiological profile. The reduced hydrocarbon availability and the higher diversity contribute to explain the increased use of carbon sources used in Biolog with conventional tillage than with no-till.

Thiazolidinedione derivatives as novel agents against Propionibacterium acnes biofilms.

PubMed

Brackman, G; Forier, K; Al Quntar, A A A; De Canck, E; Enk, C D; Srebnik, M; Braeckmans, K; Coenye, T

2014-03-01

The aim of the present study was to determine the effect of two thiazolidinedione derivatives on Propionibacterium acnes biofilm formation in vitro and to assess their effect on the susceptibility of P. acnes biofilms towards antimicrobials. The compounds were shown to have a moderate to strong antibiofilm activity when used in subinhibitory concentrations. These compounds do not affect P. acnes attachment but lead to increased dispersal of biofilm cells. This dispersal results in an increased killing of the P. acnes biofilm cells by conventional antimicrobials. The antibiofilm effect and the effect on biofilm susceptibility of the thiazolidinedione-derived quorum sensing inhibitors were clearly demonstrated. Propionibacterium acnes infections are difficult to treat due to the presence of biofilms at the infection site and the associated resistance towards conventional antimicrobials. Our results indicate that these thiazolidinedione derivatives can be promising leads used for the treatment of P. acnes infections and as anti-acne drugs. © 2013 The Society for Applied Microbiology.

[Medical honey in the treatment of wound-healing disorders in the head and neck area].

PubMed

Knipping, S; Grünewald, B; Hirt, R

2012-09-01

Already in ancient times honey was used as a drug and for the treatment of wounds. In recent years the different effects of honey on wound-healing processes have been reexamined. Based on this, the antibacterial and fungicidal qualities of honey could be confirmed. Between January 2009 and July 2011 medical honey was used on 36 patients suffering from different wound-healing disorders in the head and neck area after unsuccessful conventional treatment. The healing process was registered by microbiological investigations, measurements of the wound edges and adequate photo documentation. Medical honey can be used without problems or detectable side effects on problematic wounds of the head and neck area. Constant treatment leads to fast wound lavation, granulation, reduction of putrid smells and a decrease in inflammation. In the treatment of poorly healing and infected wounds within the head and neck area, medical honey can be used successfully without problems as an effective alternative to conventional treatment options.

[Identification of mycobacteria to the species level by molecular methods in the Public Health Laboratory of Bogotá, Colombia].

PubMed

Hernández-Toloza, Johana Esther; Rincón-Serrano, María de Pilar; Celis-Bustos, Yamile Adriana; Aguillón, Claudia Inés

2016-01-01

Global epidemiology of non-tuberculous mycobacteria (NTM) is unknown due to the fact that notification is not required in many countries, however the number of infection reports and outbreaks caused by NTM suggest a significant increase in the last years. Traditionally, mycobacteria identification is made through biochemical profiles which allow to differentiate M. tuberculosis from NTM, and in some cases the mycobacteria species. Nevertheless, these methods are technically cumbersome and time consuming. On the other hand, the introduction of methods based on molecular biology has improved the laboratory diagnosis of NTM. To establish the NTM frequency in positive cultures for acid-fast bacilli (AAFB) which were sent to Laboratorio de Salud Pública de Bogotá over a 12 month period. A total of 100 positive cultures for acid-fast bacilli from public and private hospitals from Bogotá were identified by both biochemical methods and the molecular methods PRA (PCR-restriction enzyme analysis) and multiplex-PCR. Furthermore, low prevalence mycobacteria species and non-interpretable results were confirmed by 16SrDNA sequentiation analysis. Identification using the PRA method showed NMT occurrence in 11% of cultures. In addition, this molecular methodology allowed to detect the occurrence of more than one mycobacteria in 4% of the cultures. Interestingly, a new M. kubicae pattern of PCR-restriction analysis is reported in our study. Using a mycobacteria identification algorithm, which includes the molecular method PRA, improves the diagnostic power of conventional methods and could help to advance both NTM epidemiology knowledge and mycobacteriosis control. Copyright © 2015 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Gemi: PCR Primers Prediction from Multiple Alignments

PubMed Central

Sobhy, Haitham; Colson, Philippe

2012-01-01

Designing primers and probes for polymerase chain reaction (PCR) is a preliminary and critical step that requires the identification of highly conserved regions in a given set of sequences. This task can be challenging if the targeted sequences display a high level of diversity, as frequently encountered in microbiologic studies. We developed Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes based on multiple aligned sequences. This tool can be used for the purpose of real-time and conventional PCR and can deal efficiently with large sets of sequences of a large size. PMID:23316117

An evaluation of the efficacy of Aqualox for microbiological control of industrial cooling tower systems.

PubMed

Prince, E L; Muir, A V G; Thomas, W M; Stollard, R J; Sampson, M; Lewis, J A

2002-12-01

A comprehensive sampling protocol was employed to evaluate the efficacy of Aqualox, a biocide based on electrochemically activated water, against legionellae and heterotrophic bacteria in two industrial cooling tower systems. Both of the towers in the study remained free from evidence of Legionella spp. contamination throughout a five-month evaluation period, despite the previously demonstrated presence of legionellae in one of the test towers, and in two other towers on the same site, at levels well in excess of UK Health and Safety Commission (HSC) Approved Code of Practice and Guidance (ACOP) upper action limits. Levels of heterotrophic bacteria were controlled below 10(4) cfu/mL in both towers throughout most of the trial. Results also provided indirect evidence of significant activity against biofilm bacteria, with biofilm removal beginning almost immediately after commissioning of the Aqualox treatment systems. The results were particularly encouraging as the two towers studied had a long history of poor microbiological control using conventional bromine-based biocide products. Significant differences were observed between laboratory measurements of total viable counts on frequent liquid samples and those obtained from dip slides following HSC recommendations. Copyright 2002 The Hospital Infection Society

[Search for life in deep biospheres].

PubMed

Naganuma, Takeshi

2003-12-01

The life in deep biospheres bridges conventional biology and future exobiology. This review focuses the microbiological studies from the selected deep biospheres, i.e., deep-sea hydrothermal vents, sub-hydrothermal vents, terrestrial subsurface and a sub-glacier lake. The dark biospheres facilitate the emergence of organisms and communities dependent on chemolithoautotrophy, which are overwhelmed by photoautotrophy (photosynthesis) in the surface biospheres. The life at deep-sea hydrothermal vents owes much to chemolithoautotrophy based on the oxidation of sulfide emitted from the vents. It is likely that similarly active bodies such as the Jovian satellite Europa may have hydrothermal vents and associated biological communities. Anoxic or anaerobic condition is characteristic of deep subsurface biospheres. Subsurface microorganisms exploit available oxidants, or terminal electron acceptors (TEA), for anaerobic respiration. Sulfate, nitrate, iron (III) and CO2 are the representative TEAs in the deep subsurface. Below the 3000-4000 m-thick glacier on Antarctica, there have been >70 lakes with liquid water located. One of such sub-glacial lakes, Lake Vostok, is about to be drill-penetrated for microbiological studies. These deep biosphere "platforms" provide new knowledge about the diversity and potential of the Earth's life. The expertise obtained from the deep biosphere expeditions will facilitate the capability of exobiologial exploration.

76 FR 63615 - Environmental Science Center Microbiology Laboratory; Notice of Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-13

...-dilution method (UDM) and the status and implementation of a new test method, the Organization for Economic... using the method for registration purposes, the method is currently in use as part of the post market... associated with the S. aureus and P. aeruginosa methodologies, which are designed to further optimize and...

CRENAME, A Molecular Microbiology Method Enabling Multiparametric Assessment of Potable/Drinking Water.

PubMed

Bissonnette, Luc; Maheux, Andrée F; Bergeron, Michel G

2017-01-01

The microbial assessment of potable/drinking water is done to ensure that the resource is free of fecal contamination indicators or waterborne pathogens. Culture-based methods for verifying the microbial safety are limited in the sense that a standard volume of water is generally tested for only one indicator (family) or pathogen.In this work, we describe a membrane filtration-based molecular microbiology method, CRENAME (Concentration Recovery Extraction of Nucleic Acids and Molecular Enrichment), exploiting molecular enrichment by whole genome amplification (WGA) to yield, in less than 4 h, a nucleic acid preparation which can be repetitively tested by real-time PCR for example, to provide multiparametric presence/absence tests (1 colony forming unit or microbial particle per standard volume of 100-1000 mL) for bacterial or protozoan parasite cells or particles susceptible to contaminate potable/drinking water.

Actinomyces and related organisms in human infections.

PubMed

Könönen, Eija; Wade, William G

2015-04-01

Actinomyces israelii has long been recognized as a causative agent of actinomycosis. During the past 3 decades, a large number of novel Actinomyces species have been described. Their detection and identification in clinical microbiology laboratories and recognition as pathogens in clinical settings can be challenging. With the introduction of advanced molecular methods, knowledge about their clinical relevance is gradually increasing, and the spectrum of diseases associated with Actinomyces and Actinomyces-like organisms is widening accordingly; for example, Actinomyces meyeri, Actinomyces neuii, and Actinomyces turicensis as well as Actinotignum (formerly Actinobaculum) schaalii are emerging as important causes of specific infections at various body sites. In the present review, we have gathered this information to provide a comprehensive and microbiologically consistent overview of the significance of Actinomyces and some closely related taxa in human infections. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Proteome-based bacterial identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS): A revolutionary shift in clinical diagnostic microbiology.

PubMed

Nomura, Fumio

2015-06-01

Rapid and accurate identification of microorganisms, a prerequisite for appropriate patient care and infection control, is a critical function of any clinical microbiology laboratory. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a quick and reliable method for identification of microorganisms, including bacteria, yeast, molds, and mycobacteria. Indeed, there has been a revolutionary shift in clinical diagnostic microbiology. In the present review, the state of the art and advantages of MALDI-TOF MS-based bacterial identification are described. The potential of this innovative technology for use in strain typing and detection of antibiotic resistance is also discussed. This article is part of a Special Issue entitled: Medical Proteomics. Copyright © 2014 Elsevier B.V. All rights reserved.

[External quality control system in medical microbiology and parasitology in the Czech Republic].

PubMed

Slosárek, M; Petrás, P; Kríz, B

2004-11-01

The External Quality Control System (EQAS) of laboratory activities in medical microbiology and parasitology was implemented in the Czech Republic in 1993 with coded sera samples for diagnosis of viral hepatitis and bacterial strains for identification distributed to first participating laboratories. The number of sample types reached 31 in 2003 and the number of participating laboratories rised from 79 in 1993 to 421 in 2003. As many as 15.130 samples were distributed to the participating laboratories in 2003. Currently, almost all microbiology and parasitology laboratories in the Czech Republic involved in examination of clinical material participate in the EQAS. Based on the 11-year experience gained with the EQAS in the Czech Republic, the following benefits were observed: higher accuracy of results in different tests, standardisation of methods and the use of most suitable test kits.