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Sample records for coli clonal group

  1. Escherichia coli ST131, an Intriguing Clonal Group

    PubMed Central

    Bertrand, Xavier; Madec, Jean-Yves

    2014-01-01

    SUMMARY In 2008, a previously unknown Escherichia coli clonal group, sequence type 131 (ST131), was identified on three continents. Today, ST131 is the predominant E. coli lineage among extraintestinal pathogenic E. coli (ExPEC) isolates worldwide. Retrospective studies have suggested that it may originally have risen to prominence as early as 2003. Unlike other classical group B2 ExPEC isolates, ST131 isolates are commonly reported to produce extended-spectrum β-lactamases, such as CTX-M-15, and almost all are resistant to fluoroquinolones. Moreover, ST131 E. coli isolates are considered to be truly pathogenic, due to the spectrum of infections they cause in both community and hospital settings and the large number of virulence-associated genes they contain. ST131 isolates therefore seem to contradict the widely held view that high levels of antimicrobial resistance are necessarily associated with a fitness cost leading to a decrease in pathogenesis. Six years after the first description of E. coli ST131, this review outlines the principal traits of ST131 clonal group isolates, based on the growing body of published data, and highlights what is currently known and what we need to find out to provide public health authorities with better information to help combat ST131. PMID:24982321

  2. OCCURRENCE OF ANTIBIOTIC-RESISTANT UROPATHOGENIC ESCHERICHIA COLI CLONAL GROUP A IN WASTEWATER EFFLUENTS

    EPA Science Inventory

    Isolates of Escherichia coli belonging to clonal group A (CGA), a recently described disseminated cause of drug-resistant urinary tract infections in humans, were present in four of seven sewage effluents collected from geographically dispersed areas of the United States. ...

  3. Global distribution and epidemiologic associations of Escherichia coli clonal group A, 1998-2007.

    PubMed

    Johnson, James R; Menard, Megan E; Lauderdale, Tsai-Ling; Kosmidis, Chris; Gordon, David; Collignon, Peter; Maslow, Joel N; Andrasević, Arjana Tambić; Kuskowski, Michael A

    2011-11-01

    Escherichia coli clonal group A (CGA) was first reported in 2001 as an emerging multidrug-resistant extraintestinal pathogen. Because CGA has considerable implications for public health, we examined the trends of its global distribution, clinical associations, and temporal prevalence for the years 1998-2007. We characterized 2,210 E. coli extraintestinal clinical isolates from 32 centers on 6 continents by CGA status for comparison with trimethoprim/sulfamethoxazole (TMP/SMZ) phenotype, specimen type, inpatient/outpatient source, and adult/child host; we adjusted for clustering by center. CGA prevalence varied greatly by center and continent, was strongly associated with TMP/SMZ resistance but not with other epidemiologic variables, and exhibited no temporal prevalence trend. Our findings indicate that CGA is a prominent, primarily TMP/SMZ-resistant extraintestinal pathogen concentrated within the Western world, with considerable pathogenic versatility. The stable prevalence of CGA over time suggests full emergence by the late 1990s, followed by variable endemicity worldwide as an antimicrobial drug-resistant public health threat. PMID:22099087

  4. Global Molecular Epidemiology of the O15:K52:H1 Extraintestinal Pathogenic Escherichia coli Clonal Group: Evidence of Distribution beyond Europe

    PubMed Central

    Johnson, James R.; Stell, Adam L.; O'Bryan, Timothy T.; Kuskowski, Michael; Nowicki, Bogdan; Johnson, Candice; Maslow, Joel N.; Kaul, Anil; Kavle, Justine; Prats, Guillem

    2002-01-01

    Escherichia coli O15:K52:H1 is a significant extraintestinal pathogen in Europe (G. Prats et al., J. Clin. Microbiol. 38:201-209, 2000). To search for evidence of this clonal group outside of Europe, 75 non-European E. coli isolates of serogroup O15 were compared with five members of the O15:K52:H1 clonal group from Barcelona, Spain, according to genomic background, virulence genotypes, and antimicrobial resistance profiles. Amplification phylotyping showed that 16 (21%) of the 75 non-European O15 isolates corresponded with the O15:K52:H1 clonal group. The 16 non-European O15:K52:H1 clonal group members represented diverse geographic locales. They were isolated almost exclusively from humans with extraintestinal infections and accounted for 50% of all O15 isolates from five human clinical collections studied. Most non-European clonal group members exhibited a consensus virulence factor profile that included the F16 or F7-2 papA alleles (P fimbrial structural subunit), papG allele II (P fimbrial adhesin), iha (putative adhesin siderophore), and iutA (aerobactin receptor). This resembles the virulence profiles of (i) European representatives of the O15:K52:H1 clonal group and (ii) phylogenetically related “clonal group A,” a recently recognized significant contributor to trimethoprim-sulfamethoxazole resistance in the United States (A. R. Manges et al., N. Engl. J. Med. 345:1007-1013, 2001). Antimicrobial resistance profiles were variable, and resistance was inconsistently transferred by conjugation. These findings indicate that the O15:K52:H1 clonal group is broadly distributed beyond Europe, exhibits previously unrecognized phenotypic and genotypic diversity, and contributes significantly to extraintestinal infections in humans. PMID:12037043

  5. Prevalence and Characteristics of the Epidemic Multiresistant Escherichia coli ST131 Clonal Group among Extended-Spectrum Beta-Lactamase-Producing E. coli Isolates in Copenhagen, Denmark

    PubMed Central

    Hansen, Dennis S.; Nilsson, Frida; Frimodt-Møller, Jakob; Leihof, Rikke Fleron; Struve, Carsten; Scheutz, Flemming; Johnston, Brian; Krogfelt, Karen A.; Johnson, James R.

    2013-01-01

    We report the characteristics of 115 extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli clinical isolates, from 115 unique Danish patients, over a 1-year study interval (1 October 2008 to 30 September 2009). Forty-four (38%) of the ESBL isolates represented sequence type 131 (ST13)1, from phylogenetic group B2. The remaining 71 isolates were from phylogenetic groups D (27%), A (22%), B1 (10%), and B2 (3%). Serogroup O25 ST131 isolates (n = 42; 95% of ST131) comprised 7 different K antigens, whereas two ST131 isolates were O16:K100:H5. Compared to non-ST131 isolates, ST131 isolates were associated positively with CTX-M-15 and negatively with CTX-M-1 and CTX-M-14. They also were associated positively with 11 virulence genes, including afa and dra (Dr family adhesins), the F10 papA allele (P fimbria variant), fimH (type 1 fimbriae), fyuA (yersiniabactin receptor), iha (adhesin siderophore), iutA (aerobactin receptor), kpsM II (group 2 capsules), malX (pathogenicity island marker), ompT (outer membrane protease), sat (secreted autotransporter toxin), and usp (uropathogenicity-specific protein) and negatively with hra (heat-resistant agglutinin) and iroN (salmochelin receptor). The consensus virulence gene profile (>90% prevalence) of the ST131 isolates included fimH, fyuA, malX, and usp (100% each), ompT and the F10 papA allele (95% each), and kpsM II and iutA (93% each). ST131 isolates were also positively associated with community acquisition, extraintestinal pathogenic E. coli (ExPEC) status, and the O25, K100, and H4 antigens. Thus, among ESBL E. coli isolates in Copenhagen, ST131 was the most prevalent clonal group, was community associated, and exhibited distinctive and comparatively extensive virulence profiles, plus a greater variety of capsular antigens than reported previously. PMID:23554186

  6. Diversity and biofilm-production ability among isolates of Escherichia coli phylogroup D belonging to ST69, ST393 and ST405 clonal groups

    PubMed Central

    2013-01-01

    Background Phylogenetic group D Escherichia coli clones (ST69, ST393, ST405) are increasingly reported as multidrug resistant strains causing extra-intestinal infections. We aim to characterize inter- and intraclonal diversity of a broad sample (isolates from different geographic locations and origins with variable antibiotic resistance profiles, 1980-2010) and their ability to adhere and form biofilm by both a modified quantitative biofilm producing assay and Field Emission Scanning Electron Microscopy (FESEM). Results High virulence scores were observed among ST69 (median 14/range 9–15) and ST393 (median 14/range 8–15) clones, particularly enriched in pap alleles, iha, kpsMTII-K5 and ompT, in contrast with ST405 (median 6/range 2–14) isolates, exhibiting frequently fyuA, malX and traT. All ST69 and ST393 and only two ST405 isolates were classified as ExPEC. Biofilm production was detected in two non-clinical ST69 and three ST393 isolates from different origins showing variable virulence profiles. Within each clonal group, and despite the high diversity of PFGE-types observed, isolates from different countries and recovered over large periods of time were clustered in a few groups sharing common virulence gene profiles among ST69 (n = 10 isolates) and ST393 (n = 9 isolates) (fimH-iha-iutA-kpsMTII-K5-(traT)-sat-(ompT)-papA-papEF-papGII-papC) or ST405 (n = 6 isolates) (fimH-traT-fyuA-malX). Conclusions This study highlights the circulation of highly transmissible ST69, ST393 and ST405 variants among different settings. Biofilm production seems not to be directly correlated with their epidemiological success. PMID:23800205

  7. Insight into neonatal septicaemic Escherichia coli from India with respect to phylogroups, serotypes, virulence, extended-spectrum-β-lactamases and association of ST131 clonal group.

    PubMed

    Roy, S; Datta, S; DAS, P; Gaind, R; Pal, T; Tapader, R; Mukherjee, S; Basu, S

    2015-11-01

    The study characterizes a collection of 67 neonatal septicaemic Escherichia coli isolates on the basis of phylogroup, serotype, virulence, antibiotic resistance and also the association of CTX-M-producing E. coli and the ST131 clone in a developing country. Phylogroups B2 and D were predominant (33% and 19%, respectively). The most prevalent virulence factors (VFs) were traT (69%) and iucC (68%) and most VFs were concentrated in the B2 isolates. High levels of resistance (⩾70%) to cefotaxime, ciprofloxacin and trimethoprim/sulfamethoxazole was recorded but meropenem remained the most active antimicrobial. Six (9%) of the study isolates belonged to the ST131 clone, five of which were from the same hospital, and were either indistinguishable or closely related by pulsed-field gel electrophoresis. Although the prevalence of CTX-M-15-producing isolates was high (81%), the ST131 clone was relatively infrequent (11%) in extended spectrum β-lactamase (ESBL)-producers. The ST131 clone was characterized by the presence of bla CTX-M-15, qnrS, aac(6')-Ib-cr, IncF plasmids and virulence determinants such as iucC, papC, traT, usp, hlyA, iroN E.coli , cnf, and sat. We conclude that clonal spread of ST131 did not contribute directly to the high prevalence of CTX-M-15 in our settings. PMID:25858453

  8. Molecular Evolution of the Escherichia Coli Chromosome. III. Clonal Frames

    PubMed Central

    Milkman, R.; Bridges, M. M.

    1990-01-01

    PCR fragments, 1500-bp, from 15 previously sequenced regions in the Escherichia coli chromosome have been compared by restriction analysis in a large set of wild (ECOR) strains. Prior published observations of segmental clonality are confirmed: each of several sequence types is shared by a number of strains. The rate of recombinational replacement and the average size of the replacements are estimated in a set of closely related strains in which a clonal frame is dotted with occasional stretches of DNA belonging to other clones. A clonal hierarchy is described. Some new comparative sequencing data are presented. PMID:1979037

  9. Recent Emergence of Clonal Group O25b:K1:H4-B2-ST131 ibeA Strains among Escherichia coli Poultry Isolates, Including CTX-M-9-Producing Strains, and Comparison with Clinical Human Isolates ▿

    PubMed Central

    Mora, Azucena; Herrera, Alexandra; Mamani, Rosalia; López, Cecilia; Alonso, María Pilar; Blanco, Jesús E.; Blanco, Miguel; Dahbi, Ghizlane; García-Garrote, Fernando; Pita, Julia María; Coira, Amparo; Bernárdez, María Isabel; Blanco, Jorge

    2010-01-01

    To discern the possible spread of the Escherichia coli O25b:H4-ST131 clonal group in poultry and the zoonotic potential of avian strains, we made a retrospective search of our strain collection and compared the findings for those strains with the findings for current strains. Thus, we have characterized a collection of 19 avian O25b:H4-ST131 E. coli strains isolated from 1995 to 2010 which, interestingly, harbored the ibeA gene. Using this virulence gene as a criterion for selection, we compared those 19 avian strains with 33 human O25b:H4-ST131 ibeA-positive E. coli strains obtained from patients with extraintestinal infections (1993 to 2009). All 52 O25b:H4-ST131 ibeA-positive E. coli strains shared the fimH, kpsMII, malX, and usp genes but showed statistically significant differences in nine virulence factors, namely, papGIII, cdtB, sat, and kpsMII K5, which were associated with human strains, and iroN, kpsMII K1, cvaC, iss, and tsh, which were associated with strains of avian origin. The XbaI macrorestriction profiles of the 52 E. coli O25b:H4-ST131 ibeA-positive strains revealed 11 clusters (clusters I to XI) of >85% similarity, with four clusters including strains of human and avian origin. Cluster VII (90.9% similarity) grouped 10 strains (7 avian and 3 human strains) that mostly produced CTX-M-9 and that also shared the same virulence profile. Finally, we compared the macrorestriction profiles of the 12 CTX-M-9-producing O25b:H4-ST131 ibeA strains (7 avian and 5 human strains) identified among the 52 strains with those of 15 human O25b:H4-ST131 CTX-M-14-, CTX-M-15-, and CTX-M-32-producing strains that proved to be negative for ibeA and showed that they clearly differed in the level of similarity from the CTX-M-9-producing strains. In conclusion, E. coli clonal group O25b:H4-ST131 ibeA has recently emerged among avian isolates with the new acquisition of the K1 capsule antigen and includes CTX-M-9-producing strains. This clonal group represents a real

  10. Recent emergence of clonal group O25b:K1:H4-B2-ST131 ibeA strains among Escherichia coli poultry isolates, including CTX-M-9-producing strains, and comparison with clinical human isolates.

    PubMed

    Mora, Azucena; Herrera, Alexandra; Mamani, Rosalia; López, Cecilia; Alonso, María Pilar; Blanco, Jesús E; Blanco, Miguel; Dahbi, Ghizlane; García-Garrote, Fernando; Pita, Julia María; Coira, Amparo; Bernárdez, María Isabel; Blanco, Jorge

    2010-11-01

    To discern the possible spread of the Escherichia coli O25b:H4-ST131 clonal group in poultry and the zoonotic potential of avian strains, we made a retrospective search of our strain collection and compared the findings for those strains with the findings for current strains. Thus, we have characterized a collection of 19 avian O25b:H4-ST131 E. coli strains isolated from 1995 to 2010 which, interestingly, harbored the ibeA gene. Using this virulence gene as a criterion for selection, we compared those 19 avian strains with 33 human O25b:H4-ST131 ibeA-positive E. coli strains obtained from patients with extraintestinal infections (1993 to 2009). All 52 O25b:H4-ST131 ibeA-positive E. coli strains shared the fimH, kpsMII, malX, and usp genes but showed statistically significant differences in nine virulence factors, namely, papGIII, cdtB, sat, and kpsMII K5, which were associated with human strains, and iroN, kpsMII K1, cvaC, iss, and tsh, which were associated with strains of avian origin. The XbaI macrorestriction profiles of the 52 E. coli O25b:H4-ST131 ibeA-positive strains revealed 11 clusters (clusters I to XI) of >85% similarity, with four clusters including strains of human and avian origin. Cluster VII (90.9% similarity) grouped 10 strains (7 avian and 3 human strains) that mostly produced CTX-M-9 and that also shared the same virulence profile. Finally, we compared the macrorestriction profiles of the 12 CTX-M-9-producing O25b:H4-ST131 ibeA strains (7 avian and 5 human strains) identified among the 52 strains with those of 15 human O25b:H4-ST131 CTX-M-14-, CTX-M-15-, and CTX-M-32-producing strains that proved to be negative for ibeA and showed that they clearly differed in the level of similarity from the CTX-M-9-producing strains. In conclusion, E. coli clonal group O25b:H4-ST131 ibeA has recently emerged among avian isolates with the new acquisition of the K1 capsule antigen and includes CTX-M-9-producing strains. This clonal group represents a real

  11. Clonal relationships among bloodstream isolates of Escherichia coli.

    PubMed Central

    Maslow, J N; Whittam, T S; Gilks, C F; Wilson, R A; Mulligan, M E; Adams, K S; Arbeit, R D

    1995-01-01

    The clonal relationships among 187 bloodstream isolates of Escherichia coli from 179 patients at Boston, Mass., Long Beach, Calif., and Nairobi, Kenya, were determined by multilocus enzyme electrophoresis (MLEE), analysis of polymorphisms associated with the ribosomal operon (ribotyping), and serotyping. MLEE based on 20 enzymes resolved 101 electrophoretic types (ETs), forming five clusters; ribotyping resolved 56 distinct patterns concordant with the analysis by MLEE. The isolates at each study site formed a genetically diverse group and demonstrated similar clonal structures, with the same small subset of lineages accounting for the majority of isolates at each site. Moreover, two ribotypes accounted for approximately 30% of the isolates at each study site. One cluster contained the majority (65%) of isolates and, by direct comparison of the ETs and ribotypes of individual isolates, was genetically indistinguishable from the largest cluster for each of two other collections of E. coli causing pyelonephritis and neonatal meningitis (R. K. Selander, T. K. Korhonen, V. Väisänen-Rhen, P. H. Williams, P. E. Pattison, and D. A. Caugent, Infect. Immun. 52:213-222, 1986; M. Arthur, C. E. Johnson, R. H. Rubin, R. D. Arbeit, C. Campanelli, C. Kim, S. Steinbach, M. Agarwal, R. Wilkinson, and R. Goldstein, Infect. Immun. 57:303-313, 1989), thus defining a virulent set of lineages. The isolates within these virulent lineages typically carried DNA homologous to the adhesin operon pap or sfa and the hemolysin operon hly and expressed O1, O2, O4, O6, O18, O25, or O75 antigens. DNA homologous to pap was distributed among isolates of each major cluster, whereas hly was restricted to isolates of two clusters, typically detected in pap-positive strains, and sfa was restricted to isolates of one cluster, typically detected in pap- and hly-positive strains. The occurrence of pap-positive isolates in the same geographically and genetically divergent lineages suggests that this

  12. Temporal trends in antimicrobial resistance and virulence-associated traits within the Escherichia coli sequence type 131 clonal group and its H30 and H30-Rx subclones, 1968 to 2012.

    PubMed

    Olesen, Bente; Frimodt-Møller, Jakob; Leihof, Rikke Fleron; Struve, Carsten; Johnston, Brian; Hansen, Dennis S; Scheutz, Flemming; Krogfelt, Karen A; Kuskowski, Michael A; Clabots, Connie; Johnson, James R

    2014-11-01

    To identify possible explanations for the recent global emergence of Escherichia coli sequence type (ST) 131 (ST131), we analyzed temporal trends within ST131 O25 for antimicrobial resistance, virulence genes, biofilm formation, and the H30 and H30-Rx subclones. For this, we surveyed the WHO E. coli and Klebsiella Centre's E. coli collection (1957 to 2011) for ST131 isolates, characterized them extensively, and assessed them for temporal trends. Overall, antimicrobial resistance increased temporally in prevalence and extent, due mainly to the recent appearance of the H30 (1997) and H30-Rx (2005) ST131 subclones. In contrast, neither the total virulence gene content nor the prevalence of biofilm production increased temporally, although non-H30 isolates increasingly qualified as extraintestinal pathogenic E. coli (ExPEC). Whereas virotype D occurred from 1968 forward, virotypes A and C occurred only after 2000 and 2002, respectively, in association with the H30 and H30-Rx subclones, which were characterized by multidrug resistance (including extended-spectrum-beta-lactamase [ESBL] production: H30-Rx) and absence of biofilm production. Capsular antigen K100 occurred exclusively among H30-Rx isolates (55% prevalence). Pulsotypes corresponded broadly with subclones and virotypes. Thus, ST131 should be regarded not as a unitary entity but as a group of distinctive subclones, with its increasing antimicrobial resistance having a strong clonal basis, i.e., the emergence of the H30 and H30-Rx ST131 subclones, rather than representing acquisition of resistance by diverse ST131 strains. Distinctive characteristics of the H30-Rx subclone-including specific virulence genes (iutA, afa and dra, kpsII), the K100 capsule, multidrug resistance, and ESBL production-possibly contributed to epidemiologic success, and some (e.g., K100) might serve as vaccine targets. PMID:25199783

  13. Temporal Trends in Antimicrobial Resistance and Virulence-Associated Traits within the Escherichia coli Sequence Type 131 Clonal Group and Its H30 and H30-Rx Subclones, 1968 to 2012

    PubMed Central

    Frimodt-Møller, Jakob; Leihof, Rikke Fleron; Struve, Carsten; Johnston, Brian; Hansen, Dennis S.; Scheutz, Flemming; Krogfelt, Karen A.; Kuskowski, Michael A.; Clabots, Connie; Johnson, James R.

    2014-01-01

    To identify possible explanations for the recent global emergence of Escherichia coli sequence type (ST) 131 (ST131), we analyzed temporal trends within ST131 O25 for antimicrobial resistance, virulence genes, biofilm formation, and the H30 and H30-Rx subclones. For this, we surveyed the WHO E. coli and Klebsiella Centre's E. coli collection (1957 to 2011) for ST131 isolates, characterized them extensively, and assessed them for temporal trends. Overall, antimicrobial resistance increased temporally in prevalence and extent, due mainly to the recent appearance of the H30 (1997) and H30-Rx (2005) ST131 subclones. In contrast, neither the total virulence gene content nor the prevalence of biofilm production increased temporally, although non-H30 isolates increasingly qualified as extraintestinal pathogenic E. coli (ExPEC). Whereas virotype D occurred from 1968 forward, virotypes A and C occurred only after 2000 and 2002, respectively, in association with the H30 and H30-Rx subclones, which were characterized by multidrug resistance (including extended-spectrum-beta-lactamase [ESBL] production: H30-Rx) and absence of biofilm production. Capsular antigen K100 occurred exclusively among H30-Rx isolates (55% prevalence). Pulsotypes corresponded broadly with subclones and virotypes. Thus, ST131 should be regarded not as a unitary entity but as a group of distinctive subclones, with its increasing antimicrobial resistance having a strong clonal basis, i.e., the emergence of the H30 and H30-Rx ST131 subclones, rather than representing acquisition of resistance by diverse ST131 strains. Distinctive characteristics of the H30-Rx subclone—including specific virulence genes (iutA, afa and dra, kpsII), the K100 capsule, multidrug resistance, and ESBL production—possibly contributed to epidemiologic success, and some (e.g., K100) might serve as vaccine targets. PMID:25199783

  14. Characteristics and prevalence within serogroup O4 of a J96-like clonal group of uropathogenic Escherichia coli O4:H5 containing the class I and class III alleles of papG.

    PubMed Central

    Johnson, J R; Stapleton, A E; Russo, T A; Scheutz, F; Brown, J J; Maslow, J N

    1997-01-01

    The recent discovery of a geographically dispersed clonal group of Escherichia coli O4:H5 that includes prototypic uropathogenic strain J96 prompted us to determine the prevalence of J96-like strains within serogroup O4 and to further assess the characteristics of such strains. We used O:K:H;F serotyping, PCR-based genomic fingerprinting, pulsed-field gel electrophoresis (PFGE), multilocus enzyme electrophoresis (MLEE), and PCR detection of the three papG alleles and of the cytotoxic necrotizing factor 1 (cnf1) and aerobactin (aer) gene sequences to characterize the 15 O4 strains among 336 E. coli isolates from three clinical collections (187 from mixed-source bacteremia, 75 from urosepsis, and 74 from acute cystitis). J96-like strains constituted approximately half of the O4 strains, or 2% of the total population. In contrast to other O4 strains, the J96-like strains characteristically exhibited specific group III capsular antigens, the H5 flagellar and F13 fimbrial antigens, a distinctive PCR genomic fingerprint, the class III papG allele (plus, in 50% of strains, the enigmatic class I papG allele), and cnf1 but lacked aer. A subset of these strains was remarkably homogeneous with respect to all these characteristics and exhibited a distinctive PFGE fingerprint and MLEE pattern. These findings clarify the epidemiological relevance of J96 as a model extraintestinal pathogen, provide further evidence of the class I papG allele outside of strain J96, and offer insights into the evolution of E. coli serogroup O4. PMID:9169745

  15. Clonal analysis and virulent traits of pathogenic extraintestinal Escherichia coli isolates from swine in China

    PubMed Central

    2012-01-01

    Background Extraintestinal pathogenic Escherichia coli (ExPEC) can cause a variety of infections outside the gastrointestinal tract in humans and animals. Infections due to swine ExPECs have been occurring with increasing frequency in China. These ExPECs may now be considered a new food-borne pathogen that causes cross-infections between humans and pigs. Knowledge of the clonal structure and virulence genes is needed as a framework to improve the understanding of phylogenetic traits of porcine ExPECs. Results Multilocus sequence typing (MLST) data showed that the isolates investigated in this study could be placed into four main clonal complexes, designated as CC10, CC1687, CC88 and CC58. Strains within CC10 were classified as phylogroup A, and these accounted for most of our porcine ExPEC isolates. Isolates in the CC1687 clonal complex, formed by new sequence types (STs), was classified as phylogroup D, with CC88 isolates considered as B2 and CC58 isolates as B1. Porcine ExPECs in these four clonal complexes demonstrated significantly different virulence gene patterns. A few porcine ExPECs were indentified in phylogroup B2, the phylogroup in which human ExPECs mainly exist. However some STs in the four clonal groups of porcine ExPECs were reported to cause extraintestinal infections in human, based on data in the MLST database. Conclusion Porcine ExPECs have different virulence gene patterns for different clonal complexes. However, these strains are mostly fell in phylogenentic phylogroup A, B1 and D, which is different from human ExPECs that concentrate in phylogroup B2. Our findings provide a better understanding relating to the clonal structure of ExPECs in diseased pigs and indicate a need to re-evaluate their contribution to human ExPEC diseases. PMID:22909380

  16. High-Resolution Two-Locus Clonal Typing of Extraintestinal Pathogenic Escherichia coli

    PubMed Central

    Johnson, James R.; Tchesnokova, Veronika; Billig, Mariya; Dykhuizen, Daniel; Riddell, Kim; Rogers, Peggy; Qin, Xuan; Butler-Wu, Susan; Cookson, Brad T.; Fang, Ferric C.; Scholes, Delia; Chattopadhyay, Sujay

    2012-01-01

    Multilocus sequence typing (MLST) is usually based on the sequencing of 5 to 8 housekeeping loci in the bacterial chromosome and has provided detailed descriptions of the population structure of bacterial species important to human health. However, even strains with identical MLST profiles (known as sequence types or STs) may possess distinct genotypes, which enable different eco- or pathotypic lifestyles. Here we describe a two-locus, sequence-based typing scheme for Escherichia coli that utilizes a 489-nucleotide (nt) internal fragment of fimH (encoding the type 1 fimbrial adhesin) and the 469-nt internal fumC fragment used in standard MLST. Based on sequence typing of 191 model commensal and pathogenic isolates plus 853 freshly isolated clinical E. coli strains, this 2-locus approach—which we call CH (fumC/fimH) typing—consistently yielded more haplotypes than standard 7-locus MLST, splitting large STs into multiple clonal subgroups and often distinguishing different within-ST eco- and pathotypes. Furthermore, specific CH profiles corresponded to specific STs, or ST complexes, with 95% accuracy, allowing excellent prediction of MLST-based profiles. Thus, 2-locus CH typing provides a genotyping tool for molecular epidemiology analysis that is more economical than standard 7-locus MLST but has superior clonal discrimination power and, at the same time, corresponds closely to MLST-based clonal groupings. PMID:22226951

  17. High levels of multiresistance in quinolone resistant urinary tract isolates of Escherichia coli from Norway; a non clonal phenomen?

    PubMed Central

    2014-01-01

    Background The problem of emerging ciprofloxacin resistance is compounded by its frequent association with multiresistance, the reason for which is not fully understood. In this study we compare multiresistance, clonal similarities and phylogenetic group in urinary tract isolates of Escherichia coli sensitive and resistant to the quinolone antimicrobials nalidixic acid and ciprofloxacin. Results Quinolone resistant isolates were more resistant to non-quinolone antibiotics than sensitive isolates, with resistance to ampicillin, mecillinam, sulphonamide, trimethoprim, tetracycline, kanamycin and chloramphenicol significantly increased. Fifty-one percent of quinolone-resistant isolates were multiresistant. Although multiresistance was most prevalent (63%) in isolates showing high-level ciprofloxacin resistance, it was still highly prevalent (41%) in nalidixic acid resistant isolates with low-level ciprofloxacin resistance. Multiresistance was more frequent among singleton isolates (61%) than clonal isolates (40%) of quinolone resistant Escherichia coli. Ciprofloxacin resistance was associated with certain specific clones, among them the globally distributed clonal Group A. However, there was no significant difference in the overall degree of clonality between quinolone sensitive and resistant isolates. Ciprofloxacin resistance was positively associated with phylogroup D and negatively associated with phylogroup B2. This correlation was not associated with clonal isolates. Conclusion This study supports earlier findings of association between ciprofloxacin resistance and resistance to other antibiotics. The prevalence of multiresistance in quinolone-resistant isolates that have not yet developed high-level ciprofloxacin resistance suggest that multiresistance arises early in the development of quinolone resistance. This is consistent with exposure to quinolones causing quinolone resistance by mutations and mobilization of multiresistance elements by induction of the

  18. Fluoroquinolone Resistance among Clonal Complex 1 Group B Streptococcus Strains

    PubMed Central

    Teatero, Sarah; Patel, Samir N.

    2016-01-01

    Fluoroquinolone resistance in group B Streptococcus is increasingly being reported worldwide. Here, we correlated fluoroquinolone resistance with mutations in gyrA, gyrB, parC, and parE genes, identified by mining whole-genome sequencing (WGS) data of 190 clonal complex 1 group B Streptococcus strains recovered from patients with invasive diseases in North America. We report a high prevalence of fluoroquinolone resistance (12%) among GBS strains in our collection. Our approach is the first step towards accurate prediction of fluoroquinolone resistance from WGS data in this opportunistic pathogen. PMID:27559344

  19. Fluoroquinolone Resistance among Clonal Complex 1 Group B Streptococcus Strains.

    PubMed

    Neemuchwala, Alefiya; Teatero, Sarah; Patel, Samir N; Fittipaldi, Nahuel

    2016-01-01

    Fluoroquinolone resistance in group B Streptococcus is increasingly being reported worldwide. Here, we correlated fluoroquinolone resistance with mutations in gyrA, gyrB, parC, and parE genes, identified by mining whole-genome sequencing (WGS) data of 190 clonal complex 1 group B Streptococcus strains recovered from patients with invasive diseases in North America. We report a high prevalence of fluoroquinolone resistance (12%) among GBS strains in our collection. Our approach is the first step towards accurate prediction of fluoroquinolone resistance from WGS data in this opportunistic pathogen. PMID:27559344

  20. Clonal spread and interspecies transmission of clinically relevant ESBL-producing Escherichia coli of ST410--another successful pandemic clone?

    PubMed

    Schaufler, Katharina; Semmler, Torsten; Wieler, Lothar H; Wöhrmann, Michael; Baddam, Ramani; Ahmed, Niyaz; Müller, Kerstin; Kola, Axel; Fruth, Angelika; Ewers, Christa; Guenther, Sebastian

    2016-01-01

    Clinically relevant extended-spectrum beta-lactamase (ESBL)-producing multi-resistant Escherichia coli have been on the rise for years. Initially restricted to mostly a clinical context, recent findings prove their prevalence in extraclinical settings independent of the original occurrence of antimicrobial resistance in the environment. To get further insights into the complex ecology of potentially clinically relevant ESBL-producing E. coli, 24 isolates from wild birds in Berlin, Germany, and 40 ESBL-producing human clinical E. coli isolates were comparatively analyzed. Isolates of ST410 occurred in both sample groups (six). In addition, three ESBL-producing E. coli isolates of ST410 from environmental dog feces and one clinical dog isolate were included. All 10 isolates were clonally analyzed showing almost identical macrorestriction patterns. They were chosen for whole-genome sequencing revealing that the whole-genome content of these 10 E. coli isolates showed a very high genetic similarity, differing by low numbers of single nucleotide polymorphisms only. This study gives initial evidence for a recent interspecies transmission of a new successful clone of ST410 E. coli between wildlife, humans, companion animals and the environment. The results underline the zoonotic potential of clinically relevant multi-resistant bacteria found in the environment as well as the mandatory nature of the 'One Health' approach. PMID:26656065

  1. Clonal diversity of Shiga toxin-producing Escherichia coli O103:H2/H(-) in Germany.

    PubMed

    Prager, Rita; Liesegang, Almut; Voigt, W; Rabsch, W; Fruth, Angelika; Tschäpe, H

    2002-07-01

    Shiga toxin producing Escherichia coli O103:H2/H(-) belong to the third most frequently isolated EHEC serotypes in Germany following isolates of O157:H7/H(-) and O26:H11/H(-). A total of 145 respective E. coli 103 isolates from single cases of diarrhoea and haemolytic uremic syndrome (HUS) in 1997-2000 were characterised by a range of molecular subtyping methods (PFGE, P-gene profiling, ribotyping, electrotyping) and phage typing in order to analyse their genetic relatedness and the practicability for new epidemiological tracing back. All isolates cluster into a distinct EHEC subgroup and reveal a high clonal diversity together with a considerable stability. Since strains of this serotype rank up to the third most frequently isolated EHEC in Germany a large population of this serotype, and therefore, a great supply of such strains may exist in this country. PMID:12798005

  2. Clonal groups of Salmonella typhimurium in New York State.

    PubMed Central

    McDonough, P L; Timoney, J F; Jacobson, R H; Khakhria, R

    1989-01-01

    The epidemiology of 278 strains of Salmonella typhimurium isolated from 1973 to 1981 from animals in New York State was studied by using four "fingerprinting" techniques, bacteriophage type (B.R. Callow, J. Hyg. 57:346-359, 1959), biotype (J. P. Duguid, E. S. Anderson, G. A. Alfredsson, R. Barker, and D. C. Old, J. Med. Microbiol. 8:149-166, 1975), plasmid profile, and antibiogram. Phage type with biotype was the most useful marker for distinguishing clonal groups of S. typhimurium. Four clones of S. typhimurium predominated, i.e., phage type/biotypes U275/26, 49/26, 10/3, and 2/3. U275/26 and 49/26 were commonly found until 1976, but clones 10/3 and 2/3 were predominant after 1976. Comparison of results with data from Canada suggested a dissemination of strains of S. typhimurium between Canada and New York. Cattle were a common source of phage type 49, as has been observed in other countries. PMID:2656740

  3. Predictive Diagnostics for Escherichia coli Infections Based on the Clonal Association of Antimicrobial Resistance and Clinical Outcome

    PubMed Central

    Tchesnokova, Veronika; Billig, Mariya; Chattopadhyay, Sujay; Linardopoulou, Elena; Aprikian, Pavel; Roberts, Pacita L.; Skrivankova, Veronika; Johnston, Brian; Gileva, Alena; Igusheva, Irina; Toland, Angus; Riddell, Kim; Rogers, Peggy; Qin, Xuan; Butler-Wu, Susan; Cookson, Brad T.; Fang, Ferric C.; Kahl, Barbara; Price, Lance B.; Weissman, Scott J.; Limaye, Ajit; Scholes, Delia; Johnson, James R.

    2013-01-01

    The ability to identify bacterial pathogens at the subspecies level in clinical diagnostics is currently limited. We investigated whether splitting Escherichia coli species into clonal groups (clonotypes) predicts antimicrobial susceptibility or clinical outcome. A total of 1,679 extraintestinal E. coli isolates (collected from 2010 to 2012) were collected from one German and 5 U.S. clinical microbiology laboratories. Clonotype identity was determined by fumC and fimH (CH) sequencing. The associations of clonotype with antimicrobial susceptibility and clinical variables were evaluated. CH typing divided the isolates into >200 CH clonotypes, with 93% of the isolates belonging to clonotypes with ≥2 isolates. Antimicrobial susceptibility varied substantially among clonotypes but was consistent across different locations. Clonotype-guided antimicrobial selection significantly reduced “drug-bug” mismatch compared to that which occurs with the use of conventional empirical therapy. With trimethoprim-sulfamethoxazole and fluoroquinolones, the drug-bug mismatch was predicted to decrease 62% and 78%, respectively. Recurrent or persistent urinary tract infection and clinical sepsis were significantly correlated with specific clonotypes, especially with CH40-30 (also known as H30), a recently described clonotype within sequence type 131 (ST131). We were able to clonotype directly from patient urine samples within 1 to 3 h of obtaining the specimen. In E. coli, subspecies-level identification by clonotyping can be used to significantly improve empirical predictions of antimicrobial susceptibility and clinical outcomes in a timely manner. PMID:23843485

  4. Restriction Profiling of 23S Microheterogenic Ribosomal Repeats for Detection and Characterizing of E. coli and Their Clonal, Pathogenic, and Phylogroups

    PubMed Central

    Jayasree Rajagopalan Nair, Parvathi

    2015-01-01

    Correlating ribosomal microheterogenicity with unique restriction profiles can prove to be an efficacious and cost-effective approach compared with sequencing for microbial identification. An attempt to peruse restriction profiling of 23S ribosomal assemblage was ventured; digestion patterns with Bfa I discriminated E. coli from its colony morphovars, while Hae III profiles assisted in establishing distinct clonal groups. Among the gene pool of 399 ribosomal sequences extrapolated from 57 E. coli genomes, varying degree of predominance (I > III > IV > II) of Hae III pattern was observed. This was also corroborated in samples collected from clinical, commensal, and environmental origin. K-12 and its descendants showed type I pattern whereas E. coli-B and its descendants exhibited type IV, both of these patterns being exclusively present in E. coli. A near-possible association between phylogroups and Hae III profiles with presumable correlation between the clonal groups and different pathovars was established. The generic nature, conservation, and barcode gap of 23S rRNA gene make it an ideal choice and substitute to 16S rRNA gene, the most preferred region for molecular diagnostics in bacteria. PMID:26885397

  5. Molecular characterization and clonal relationships among Escherichia coli strains isolated from broiler chickens with colisepticemia.

    PubMed

    Barbieri, Nicolle Lima; de Oliveira, Aline Luísa; Tejkowski, Thiago Moreira; Pavanelo, Daniel Brisotto; Matter, Letícia Beatriz; Pinheiro, Sandra Regina Schincariol; Vaz, Tânia Mara Ibelli; Nolan, Lisa K; Logue, Catherine M; de Brito, Benito Guimarães; Horn, Fabiana

    2015-01-01

    This study characterized 52 Escherichia coli isolates from distinct diseased organs of 29 broiler chickens with clinical symptoms of colibacillosis in the Southern Brazilian state of Rio Grande do Sul. Thirty-eight isolates were highly virulent and 14 were virtually avirulent in 1-day-old chicks, yet all isolates harbored virulence factors characteristic of avian pathogenic E. coli (APEC), including those related to adhesion, iron acquisition, and serum resistance. E. coli reference collection phylogenetic typing showed that isolates belonged mostly to group D (39%), followed by group A (29%), group B1 (17%), and group B2 (15%). Phylogenetic analyses using the Amplified Ribosomal DNA Restriction Analysis and pulse-field gel electrophoresis methods were used to discriminate among isolates displaying the same serotype, revealing that five birds were infected with two distinct APEC strains. Among the 52 avian isolates, 2 were members of the pandemic E. coli O25:H4-B2-ST131 clone. PMID:25514382

  6. A Comparative Genomic Analysis of Diverse Clonal Types of Enterotoxigenic Escherichia coli Reveals Pathovar-Specific Conservation▿ †

    PubMed Central

    Sahl, Jason W.; Steinsland, Hans; Redman, Julia C.; Angiuoli, Samuel V.; Nataro, James P.; Sommerfelt, Halvor; Rasko, David A.

    2011-01-01

    Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrheal illness in children less than 5 years of age in low- and middle-income nations, whereas it is an emerging enteric pathogen in industrialized nations. Despite being an important cause of diarrhea, little is known about the genomic composition of ETEC. To address this, we sequenced the genomes of five ETEC isolates obtained from children in Guinea-Bissau with diarrhea. These five isolates represent distinct and globally dominant ETEC clonal groups. Comparative genomic analyses utilizing a gene-independent whole-genome alignment method demonstrated that sequenced ETEC strains share approximately 2.7 million bases of genomic sequence. Phylogenetic analysis of this “core genome” confirmed the diverse history of the ETEC pathovar and provides a finer resolution of the E. coli relationships than multilocus sequence typing. No identified genomic regions were conserved exclusively in all ETEC genomes; however, we identified more genomic content conserved among ETEC genomes than among non-ETEC E. coli genomes, suggesting that ETEC isolates share a genomic core. Comparisons of known virulence and of surface-exposed and colonization factor genes across all sequenced ETEC genomes not only identified variability but also indicated that some antigens are restricted to the ETEC pathovar. Overall, the generation of these five genome sequences, in addition to the two previously generated ETEC genomes, highlights the genomic diversity of ETEC. These studies increase our understanding of ETEC evolution, as well as provide insight into virulence factors and conserved proteins, which may be targets for vaccine development. PMID:21078854

  7. Analysis of non-clonal chromosome abnormalities observed in hematologic malignancies among Southwest Oncology Group patients

    SciTech Connect

    McConnell, T.S.; Dobin, S.M.

    1994-09-01

    From 1987-1994, the Southwest Oncology Group Cytogenetics Committee reviewed 1571 studies in 590 adult patient cases with ALL, AML, CML or CLL. These were analyzed for the presence of clinically important non-clonal abnormalities (NCA). Abnormalities were defined as non-clonal if one metaphase had a structural abnormality or an extra chromosome. Chromosome loss was not analyzed due to the possibility of random loss. In 72 cases (12%) comprising 136 studies, at least one NCA was observed. In 21 of these cases (29%), NCAs consisted of obvious clonal evolution or instability, and thus were not included in the analysis. At least one structural NCA was observed in which the abnormality differed from the mainline in 36 (50%) patients. Seventeen of the 36 cases had a normal mode. Nineteen of the 36 patients had an abnormal or normal/abnormal mode. At least one numerical NCA was found in 15 cases (21%). Fifteen cases (21%) contained at least one marker chromosome. Several cases involved NCA in more than one of the above divisions. NCAs could be classified into several categories: (1){open_quotes}the clone to come{close_quotes}, (2) evolving clones which then disappeared, (3) NCAs with putative clinical importance that never became clonal, (4) NCAs during remission identical to the preceding clonal abnormality, (5) NCAs which indicated clonal evolution or instability. Examples include one metaphase with t(9;22) or del(20q) or inv(16) or +8 which either preceded or followed clonal findings of the same aberration. Such findings should be communicated to the clinician.

  8. Molecular Evolution of Typical Enteropathogenic Escherichia coli: Clonal Analysis by Multilocus Sequence Typing and Virulence Gene Allelic Profiling▿ †

    PubMed Central

    Lacher, David W.; Steinsland, Hans; Blank, T. Eric; Donnenberg, Michael S.; Whittam, Thomas S.

    2007-01-01

    Enteropathogenic Escherichia coli (EPEC) infections are a leading cause of infantile diarrhea in developing nations. Typical EPEC isolates are differentiated from other types of pathogenic E. coli by two distinctive phenotypes, attaching effacement and localized adherence. The genes specifying these phenotypes are found on the locus of enterocyte effacement (LEE) and the EPEC adherence factor (EAF) plasmid. To describe how typical EPEC has evolved, we characterized a diverse collection of strains by multilocus sequence typing (MLST) and performed restriction fragment length polymorphism (RFLP) analysis of three virulence genes (eae, bfpA, and perA) to assess allelic variation. Among 129 strains representing 20 O-serogroups, 21 clonal genotypes were identified using MLST. RFLP analysis resolved nine eae, nine bfpA, and four perA alleles. Each bfpA allele was associated with only one perA allele class, suggesting that recombination has not played a large role in shuffling the bfpA and perA loci between separate EAF plasmids. The distribution of eae alleles among typical EPEC strains is more concordant with the clonal relationships than the distribution of the EAF plasmid types. These results provide further support for the hypothesis that the EPEC pathotype has evolved multiple times within E. coli through separate acquisitions of the LEE island and EAF plasmid. PMID:17098897

  9. [Investigation of beta-lactamase genes and clonal relationship among the extended-spectrum beta-lactamase producing nosocomial Escherichia coli isolates].

    PubMed

    Görgeç, Sündüz; Kuzucu, Çiğdem; Otlu, Barış; Yetkin, Funda; Ersoy, Yasemin

    2015-01-01

    Extended-spectrum beta-lactamase (ESBL) producing microorganisms currently cause a major problem. Among theseCTX-M beta-lactamase producing Escherichia coli has also disseminated worldwide as an important cause of both nosocomial and community-acquired infections. The aims of this study were to determine the prevalence of the beta-lactamase genes, antibiotic susceptibilities and clonal relationships of ESBL-producing nosocomial E.coli isolates. A total of 76 ESBL-producing E.coli strains isolated from urine (n= 26), blood (n= 25) and wound (n= 25) specimens of hospitalized patients identified as nosocomial infection agents according to the CDC criteria between June 2010-June 2011 were included in the study. Antibiotic susceptibilities of the isolates were detected by Kirby-Bauer disc diffusion method according to CLSI recommendations. ESBL production was tested by double disc diffusion method, and cefotaxime/cefotaxime-clavulanic acid E-test strips (AB Biodisk, Sweden) were used for indeterminate results. Presence of TEM, SHV, CTX-M, OXA-2 group, 0XA-10 group, PER, VEB and GES beta-lactamase genes were investigated by polymerase chain reaction (PCR) using specific primers. Pulsed-field gel electrophoresis (PFGE) method was used for the detection of clonal relationships among the strains. Most of the ESBL-producing E.coli strains were isolated from samples of inpatients in intensive care (35%), internal medicine (16%) and general surgery (13%) units. All of the 76 strains were found susceptible to imipenem, meropenem and amikacin; however all were resistant to cefotaxime and ceftriaxone. The susceptibility rates of the isolates to cefoxitin, ertapenem, cefoperazone/sulbactam, piperacillin-tazobactam, gentamicin, ciprofloxacin, cefepime, amoxicillin-clavulanic acid, aztreonam and ceftazidime were 96%, 83%, 63%, 61%, 50%, 41%, 25%, 21%, 20% and 18%, respectively. Among E.coli isolates, the frequency of CTX-M, TEM, OXA-2 group, PER, SHV and OXA-10 group beta

  10. Clonal relationship between human and avian ciprofloxacin-resistant Escherichia coli isolates in North-Eastern Algeria.

    PubMed

    Agabou, A; Lezzar, N; Ouchenane, Z; Khemissi, S; Satta, D; Sotto, A; Lavigne, J-P; Pantel, A

    2016-02-01

    The objectives of this study were to determine rates, patterns, and mechanisms of antibiotic resistance, and to assess connections between chicken commensal, human commensal, and pathogenic ciprofloxacin-resistant Escherichia coli isolates. All E. coli isolates collected from chickens, their farmers, and patients in the Constantine region (North-east Algeria) were analyzed for bla and plasmid-mediated quinolone resistance (PMQR) gene contents, phylogroups, Rep-PCR profiles, and multilocus sequence types. A high prevalence of resistance to fluoroquinolones (51.4 % to ciprofloxacin) was recorded in avian isolates. Of these, 22.2 % carried the aac(6')-Ib-cr gene, whereas lower resistance levels to these antibiotics were recorded in chicken farmers' isolates. None of the commensal isolates harbored the qnr, qepA, or oqxAB genes. One human pathogenic isolate was ertapenem-resistant and harbored the bla OXA-48 gene, 84 showed an extended-spectrum β-lactamase phenotype, with bla CTX-M-15 gene prevalent in 87.2 % of them. Seventy isolates were resistant to fluoroquinolones, with aac(6')-Ib-cr present in 72.8 %, qnrB in 5.7 %, and qnrS in 10 %. Three Rep-PCR profiles were common to chicken commensal and human pathogenic isolates (phylogroups D and B1; ST21, ST48, and ST471 respectively); one was found in both chicken and chicken-farmer commensal strains (D; ST108), while another profile was identified in a chicken-farmer commensal strain and a human pathogenic one (B1; ST19). These findings suggest clonal and epidemiologic links between chicken and human ciprofloxacin-resistant E. coli isolates and the important role that poultry may play in the epidemiology of human E. coli infections in the Constantine region. PMID:26634353

  11. Clonal Population Structure and Specific Genotypes of Multi-drug Resistant Campylobacter coli from Turkeys.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Commercial turkey flocks in eastern North Carolina have been found to be colonized frequently with Campylobacter coli strains that are resistant to several antimicrobials (tetracycline, streptomycin, erythromycin, kanamycin, and ciprofloxacin/nalidixic acid); such strains have been designated multid...

  12. Clonal Structure, Extended-Spectrum β-Lactamases, and Acquired AmpC-Type Cephalosporinases of Escherichia coli Populations Colonizing Patients in Rehabilitation Centers in Four Countries

    PubMed Central

    Izdebski, R.; Baraniak, A.; Fiett, J.; Adler, A.; Kazma, M.; Salomon, J.; Lawrence, C.; Rossini, A.; Salvia, A.; Vidal Samso, J.; Fierro, J.; Paul, M.; Lerman, Y.; Malhotra-Kumar, S.; Lammens, C.; Goossens, H.; Hryniewicz, W.; Brun-Buisson, C.; Carmeli, Y.

    2013-01-01

    The prospective project MOSAR was conducted in five rehabilitation units: the Berck Maritime Hôpital (Berck, France), Fondazione Santa Lucia (Rome, Italy), Guttmann Institute (GI; Barcelona, Spain), and Loewenstein Hospital and Tel-Aviv Souraski Medical Center (TA) (Tel-Aviv, Israel). Patients were screened for carriage of Enterobacteriaceae resistant to expanded-spectrum cephalosporins (ESCs) from admission until discharge. The aim of this study was to characterize the clonal structure, extended-spectrum β-lactamases (ESBLs), and acquired AmpC-like cephalosporinases in the Escherichia coli populations collected. A total of 376 isolates were randomly selected. The overall number of sequence types (STs) was 76, including 7 STs that grouped at least 10 isolates from at least three centers each, namely, STs 10, 38, 69, 131, 405, 410, and 648. These clones comprised 65.2% of all isolates, and ST131 alone comprised 41.2%. Of 54 STs observed only in one center, some STs played a locally significant role, like ST156 and ST393 in GI or ST372 and ST398 in TA. Among 16 new STs, five arose from evolution within the ST10 and ST131 clonal complexes. ESBLs and AmpCs accounted for 94.7% and 5.6% of the ESC-hydrolyzing β-lactamases, respectively, being dominated by the CTX-M-like enzymes (79.9%), followed by the SHV (13.5%) and CMY-2 (5.3%) types. CTX-M-15 was the most prevalent β-lactamase overall (40.6%); other ubiquitous enzymes were CTX-M-14 and CMY-2. Almost none of the common clones correlated strictly with one β-lactamase; although 58.7% of ST131 isolates produced CTX-M-15, the clone also expressed nine other enzymes. A number of clone variants with specific pulsed-field gel electrophoresis and ESBL types were spread in some locales, potentially representing newly emerging E. coli epidemic strains. PMID:23114774

  13. ENTEROTOXIGENIC ESCHERICHIA COLI O169:HUT FROM A DIARRHEAL PATIENT: PHYLOGENETIC GROUP AND ANTIMICROBIAL SUSCEPTIBILITY.

    PubMed

    Sirikaew, Siriwan; Patungkaro, Wichien; Rattanachuay, Pattamarat; Sukkua, Kannika; Sukhumungoon, Pharanai

    2014-11-01

    Enterotoxigenic Escherichia coli (ETEC) is one of the most common pathogenic E. coli pathotypes causing diarrhea in children worldwide. Its enterotoxins, LT and ST, including colonization factors mainly are responsible for human pathogenesis. From 239 rectal swabs of diarrheal patients at Hat Yai and Pattani Hospitals during August 2013 and May 2014, five isolates from only a single E. coli sample demonstrated the possession of estA1, encoding porcine heat-stable enterotoxin (STp). These isolates all belonged to serotype 0169:H Untypeable (HUT) and carried astA, encoding enteroaggregative heat-stable enterotoxin 1. A PCR-based phylogenetic group investigation classified them as members of the virulent E. coli phylogenetic group D. The isolates were resistant to cephalothin, penicillin G, streptomycin, tetracycline and vancomycin. Confirmation of their clonality was conducted by enterobacterial repetitive intergenic consensus sequence PCR typing, which revealed that these ETEC were derived from the same clone. This is the first report of ETEC O169:HUT in southern Thailand. PMID:26466423

  14. Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic

    PubMed Central

    Driebe, Elizabeth M.; MacCannell, Duncan R.; Roe, Chandler; Lemmer, Darrin; de Man, Tom; Rasheed, J. Kamile; Engelthaler, David M.; Keim, Paul; Limbago, Brandi M.

    2015-01-01

    Multidrug-resistant Klebsiella pneumoniae producing the KPC carbapenemase have rapidly spread throughout the world, causing severe healthcare-associated infections with limited antimicrobial treatment options. Dissemination of KPC-producing K. pneumoniae is largely attributed to expansion of a single dominant strain, ST258. In this study, we explore phylogenetic relationships and evolution within ST258 and its clonal group, CG258, using whole genome sequence analysis of 167 isolates from 20 countries collected over 17 years. Our results show a common ST258 ancestor emerged from its diverse parental clonal group around 1995 and likely acquired blaKPC prior to dissemination. Over the past two decades, ST258 has remained highly clonal despite diversity in accessory elements and divergence in the capsule polysaccharide synthesis locus. Apart from the large recombination event that gave rise to ST258, few mutations set it apart from its clonal group. However, one mutation occurs in a global transcription regulator. Characterization of outer membrane protein sequences revealed a profile in ST258 that includes a truncated OmpK35 and modified OmpK37. Our work illuminates potential genomic contributors to the pathogenic success of ST258, helps us better understand the global dissemination of this strain, and identifies genetic markers unique to ST258. PMID:26196384

  15. The Escherichia coli phylogenetic group B2 with integrons prevails in childhood recurrent urinary tract infections.

    PubMed

    Kõljalg, Siiri; Truusalu, Kai; Stsepetova, Jelena; Pai, Kristiine; Vainumäe, Inga; Sepp, Epp; Mikelsaar, Marika

    2014-05-01

    The aim of our study was to characterize the phylogenetic groups of Escherichia coli, antibiotic resistance, and containment of class 1 integrons in the first attack of pyelonephritis and in subsequent recurrences in young children. Altogether, 89 urine E. coli isolates from 41 children with urinary tract infection (UTI) were studied for prevalence and persistence of phylogenetic groups by pulsed-field gel electrophoresis (PFGE), antibacterial resistance by minimal inhibitory concentrations (MIC) and class 1 integrons by PCR. Phylogenetic group B2 was most common (57%), followed by D (20%), A (18%) and B1 (5%). Overall resistance to betalactams was 61%, trimethoprim-sulfamethoxazole 28%, and was not associated with phylogenetic groups. According to PFGE, the same clonal strain persisted in 77% of patients. The persistence was detected most often in phylogenetic group B2 (70%). Phylogenetic group B2 more often contained class 1 integrons than group A. Integron positive strains had higher MIC values of cefuroxime, cefotaxime, and gentamicin. In conclusion, phylogenetic group B2 was the most common cause of the first episode of pyelonephritis, as well as in case of the persistence of the same strain and contained frequently class 1 integrons in childhood recurrent UTI. An overall frequent betalactam resistance was equally distributed among phylogenetic groups. PMID:24033434

  16. Prolonged clonal spreading and dynamic changes in antimicrobial resistance of Escherichia coli ST68 among patients who stayed in a respiratory care ward.

    PubMed

    Chen, Chih-Ming; Ke, Se-Chin; Li, Chia-Ru; Chiou, Chien-Shun; Chang, Chao-Chin

    2014-11-01

    From 2007 to 2009, we collected a total of 83 bacteraemic isolates of Escherichia coli with reduced susceptibility or resistance to third-generation cephalosporins (TGCs). Isolates were genotyped by PFGE and multilocus sequence typing (MLST). The PFGE patterns revealed two highly correlated clusters (cluster E: nine isolates; cluster G: 22 isolates) associated with this prolonged clonal spreading. Compared with cluster E isolates, cluster G isolates were significantly more likely to harbour aac(6')-Ib-cr (P<0.05), and most of these isolates were isolated during a later year than cluster E isolates (P<0.05). By MLST analysis, 94% of cluster E and G isolates (29/31) were ST68. Although no time or space clustering could be identified by the conventional hospital-acquired infection monitoring system, E. coli cases caused by cluster E and G isolates were significantly associated with having stayed in our hospital's respiratory care ward (P<0.05). Isolates obtained from patients who had stayed in the respiratory care ward had a significantly higher rate of aac(6')-Ib-cr and blaCTX-M-14 positivity, and were more likely to belong to ST68/S68-like (all P<0.05). To our knowledge, this is the first report of prolonged clonal spreading caused by E. coli ST68 associated with a stay in a long-term care facility. Using epidemiological investigations and PFGE and MLST analyses, we have identified long-term clonal spreading caused by E. coli ST68, with extra antimicrobial-resistance genes possibly acquired during the prolonged spreading period. PMID:25168964

  17. Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups.

    PubMed

    Bialek-Davenet, Suzanne; Criscuolo, Alexis; Ailloud, Florent; Passet, Virginie; Jones, Louis; Delannoy-Vieillard, Anne-Sophie; Garin, Benoit; Le Hello, Simon; Arlet, Guillaume; Nicolas-Chanoine, Marie-Hélène; Decré, Dominique; Brisse, Sylvain

    2014-11-01

    Multidrug-resistant and highly virulent Klebsiella pneumoniae isolates are emerging, but the clonal groups (CGs) corresponding to these high-risk strains have remained imprecisely defined. We aimed to identify K. pneumoniae CGs on the basis of genome-wide sequence variation and to provide a simple bioinformatics tool to extract virulence and resistance gene data from genomic data. We sequenced 48 K. pneumoniae isolates, mostly of serotypes K1 and K2, and compared the genomes with 119 publicly available genomes. A total of 694 highly conserved genes were included in a core-genome multilocus sequence typing scheme, and cluster analysis of the data enabled precise definition of globally distributed hypervirulent and multidrug-resistant CGs. In addition, we created a freely accessible database, BIGSdb-Kp, to enable rapid extraction of medically and epidemiologically relevant information from genomic sequences of K. pneumoniae. Although drug-resistant and virulent K. pneumoniae populations were largely nonoverlapping, isolates with combined virulence and resistance features were detected. PMID:25341126

  18. Evaluation of emm gene types, toxin gene profiles and clonal relatedness of group A streptococci

    PubMed Central

    Mengeloglu, Firat Zafer; Aktas, Elif; Otlu, Baris; Cömert, Füsun; Külah, Canan; Tas, Ebru; Sümbüloglu, Vildan

    2013-01-01

    The aim of this study is to evaluate antibiotic susceptibilities, emm gene types, toxin gene profiles and clonal relatedness of group A streptococci (GAS) isolates obtained from patients and carriers. A total of 79 clinical isolates from patients and 60 isolates from carriers were included in the study. Emm typing, toxin gene detection for speA, speB, speC, speG and smeZ genes and pulsed-field gel electrophoresis (PFGE) was performed. Twenty-one distinct emm types were detected; the most common types were emm12, emm89, emm 1, emm77, emm4 and emm3. The detection rates of both emm types and the toxin genes didn’t differ significantly between patients and carriers. The presence of speA and smeZ was significantly higher in emm1 and speG was significantly lower in emm4 when compared to the other emm types. The rate of clustering obtained with PFGE wasn’t significantly different in patients and carriers. As a result, twelve of the 21 emm types detected in this study were covered by the 26-valent vaccine, constituting 77.7% of the emm typeable isolates; however the emm4 type which is one of the most common types in the present study is not among this coverage. PMID:23988167

  19. Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany.

    PubMed

    Falgenhauer, Linda; Imirzalioglu, Can; Ghosh, Hiren; Gwozdzinski, Konrad; Schmiedel, Judith; Gentil, Katrin; Bauerfeind, Rolf; Kämpfer, Peter; Seifert, Harald; Michael, Geovana Brenner; Schwarz, Stefan; Pfeifer, Yvonne; Werner, Guido; Pietsch, Michael; Roesler, Uwe; Guerra, Beatriz; Fischer, Jennie; Sharp, Hannah; Käsbohrer, Annemarie; Goesmann, Alexander; Hille, Katja; Kreienbrock, Lothar; Chakraborty, Trinad

    2016-06-01

    Multidrug-resistant Escherichia coli encoding CTX-M-type extended-spectrum β-lactamases (ESBLs) are isolated in increasing numbers from humans, companion animals and livestock, raising concern regarding the exchange and spread of isolates in these populations. In this study, whole-genome sequencing of CTX-M-15-producing E. coli isolates recently sampled from humans, companion animals, livestock and farm environments was performed. In total, 26 different sequence types (STs) were detected, of which ST410 was the most frequent and was the only ST present in all populations studied. Five clades (designated A-E) were detected within the ST410 isolates. In particular, isolates of clade B were present in all four populations and had core genomes that differed by less than 70 single nucleotide polymorphisms (SNPs). Isolates of clades B and C were also clonally marked, exhibiting identical chromosomal insertions of blaCTX-M-15 at distinct loci. These data provide strong evidence for the clonal dissemination of specific clades of CTX-M-15-producing E. coli ST410 in human and animal populations. PMID:27208899

  20. Group B Streptococci Causing Neonatal Infections in Barcelona Are a Stable Clonal Population: 18-Year Surveillance▿

    PubMed Central

    Martins, E. R.; Andreu, A.; Correia, P.; Juncosa, T.; Bosch, J.; Ramirez, M.; Melo-Cristino, J.

    2011-01-01

    We analyzed 212 group B streptococci (GBS) from newborns with invasive infections in the area of Barcelona, Spain, between 1992 and 2009, with the aim of documenting changes in the prevalences of serotypes, antimicrobial resistance, and genetic lineages and evaluating their associations with either early-onset disease (EOD) or late-onset disease (LOD). Serotypes III (n = 118) and Ia (n = 47) together accounted for nearly 78% of the isolates. All isolates carried an alpha or alpha-like protein gene, and specific associations between genes and serotypes, such as serotype Ib and bca, serotype II and bca, serotype III and rib, and serotype V and alp3, reflected the presence of particular genetic lineages. Macrolide resistance (14.2%) was significantly associated with serotype V. Pulsed-field gel electrophoresis (PFGE) clustering was an excellent predictor of serotype and antibiotic resistance. The combination of PFGE and multilocus sequence typing revealed a large number of genetically distinct lineages. Still, specific lineages were dominant in our collection, particularly the serotype III/ST17/rib lineage, which had enhanced potential to cause LOD. Serotype Ia was concentrated in a single PFGE cluster composed of two genetic lineages: ST23/eps and ST24/bca. The ST24/bca sublineage of serotype Ia, which is found infrequently elsewhere, may be emerging as an important cause of neonatal invasive infections in the Mediterranean region. In spite of the introduction of prophylaxis, resulting in a pronounced decline in the frequency of EOD, the study revealed a remarkably stable clonal structure of GBS causing neonatal infections in Barcelona over a period of 18 years. PMID:21697333

  1. Phylogenetic Group Determination of Escherichia coli Isolated from Animals Samples.

    PubMed

    Coura, Fernanda Morcatti; Diniz, Soraia de Araújo; Silva, Marcos Xavier; Mussi, Jamili Maria Suhet; Barbosa, Silvia Minharro; Lage, Andrey Pereira; Heinemann, Marcos Bryan

    2015-01-01

    This study analyzes the occurrence and distribution of phylogenetic groups of 391 strains of Escherichia coli isolated from poultry, cattle, and water buffalo. The frequency of the phylogroups was A = 19%, B1 = 57%, B2 = 2.3%, C = 4.6%, D = 2.8%, E = 11%, and F = 3.3%. Phylogroups A (P < 0.001) and F (P = 0.018) were associated with E. coli strains isolated from poultry, phylogroups B1 (P < 0.001) and E (P = 0.002) were associated with E. coli isolated from cattle, and phylogroups B2 (P = 0.003) and D (P = 0.017) were associated with E. coli isolated from water buffalo. This report demonstrated that some phylogroups are associated with the host analyzed and the results provide knowledge of the phylogenetic composition of E. coli from domestic animals. PMID:26421310

  2. Phylogenetic Group Determination of Escherichia coli Isolated from Animals Samples

    PubMed Central

    Morcatti Coura, Fernanda; Diniz, Soraia de Araújo; Silva, Marcos Xavier; Mussi, Jamili Maria Suhet; Barbosa, Silvia Minharro; Lage, Andrey Pereira; Heinemann, Marcos Bryan

    2015-01-01

    This study analyzes the occurrence and distribution of phylogenetic groups of 391 strains of Escherichia coli isolated from poultry, cattle, and water buffalo. The frequency of the phylogroups was A = 19%, B1 = 57%, B2 = 2.3%, C = 4.6%, D = 2.8%, E = 11%, and F = 3.3%. Phylogroups A (P < 0.001) and F (P = 0.018) were associated with E. coli strains isolated from poultry, phylogroups B1 (P < 0.001) and E (P = 0.002) were associated with E. coli isolated from cattle, and phylogroups B2 (P = 0.003) and D (P = 0.017) were associated with E. coli isolated from water buffalo. This report demonstrated that some phylogroups are associated with the host analyzed and the results provide knowledge of the phylogenetic composition of E. coli from domestic animals. PMID:26421310

  3. Population Structure of a Hybrid Clonal Group of Methicillin-Resistant Staphylococcus aureus, ST239-MRSA-III

    PubMed Central

    Smyth, Davida S.; McDougal, Linda K.; Gran, Frode W.; Manoharan, Anand; Enright, Mark C.; Song, Jae-Hoon; de Lencastre, Herminia; Robinson, D. Ashley

    2010-01-01

    The methicillin-resistant Staphylococcus aureus (MRSA) clonal group known as ST239-MRSA-III is notable for its hybrid origin and for causing sustained hospital epidemics worldwide since the late 1970s. We studied the population structure of this MRSA clonal group using a sample of 111 isolates that were collected over 34 years from 29 countries. Genetic variation was assessed using typing methods and novel ascertainment methods, resulting in approximately 15 kb of sequence from 32 loci for all isolates. A single most parsimonious tree, free of homoplasy, partitioned 28 haplotypes into geographically-associated clades, including prominent European, Asian, and South American clades. The rate of evolution was estimated to be approximately 100× faster than standard estimates for bacteria, and dated the most recent common ancestor of these isolates to the mid-20th century. Associations were discovered between the ST239 phylogeny and the ccrB and dru loci of the methicillin resistance genetic element, SCCmec type III, but not with the accessory components of the element that are targeted by multiplex PCR subtyping tools. In summary, the evolutionary history of ST239 can be characterized by rapid clonal diversification that has left strong evidence of geographic and temporal population structure. SCCmec type III has remained linked to the ST239 chromosome during clonal diversification, but it has undergone homoplasious losses of accessory components. These results provide a population genetics framework for the precise identification of emerging ST239 variants, and invite a re-evaluation of the markers used for subtyping SCCmec. PMID:20062529

  4. Oropharyngeal Carriage of Meningococcus in Portugal by Group and Clonal Complex 6 Years After Adolescent Vaccine Campaign.

    PubMed

    Rodrigues, Fernanda; Morales-Aza, Begonia; Christensen, Hannah; Giles, Jessica; Ferreira, Muriel; Sikora, Paulina; Madanelo, Ines; Lucidarme, Jay; Januário, Luis; Finn, Adam

    2015-11-01

    Portugal introduced (2+1) conjugate Meningococcal group C vaccine in 2006 with high coverage catch up to 18 years and has given only 1 dose at 1 year since 2012. Among 601 student oropharyngeal swabs, meningococcal carriage rate was 13.3% (A-0%, B-5.3%, C-0.3%, W-0.2%, X-0.2% and Y-1.7%). C and W strains were of potentially disease-causing clonal complexes (cc) but not the hyperinvasive cc11. PMID:26222062

  5. Clonal Complex 17 Group B Streptococcus strains causing invasive disease in neonates and adults originate from the same genetic pool

    PubMed Central

    Teatero, Sarah; Ramoutar, Erin; McGeer, Allison; Li, Aimin; Melano, Roberto G.; Wasserscheid, Jessica; Dewar, Ken; Fittipaldi, Nahuel

    2016-01-01

    A significant proportion of group B Streptococcus (GBS) neonatal disease, particularly late-onset disease, is associated with strains of serotype III, clonal complex (CC) 17. CC17 strains also cause invasive infections in adults. Little is known about the phylogenetic relationships of isolates recovered from neonatal and adult CC17 invasive infections. We performed whole-genome-based phylogenetic analysis of 93 temporally and geographically matched CC17 strains isolated from both neonatal and adult invasive infections in the metropolitan region of Toronto/Peel, Canada. We also mined the whole-genome data to reveal mobile genetic elements carrying antimicrobial resistance genes. We discovered that CC17 GBS strains causing neonatal and adult invasive disease are interspersed and cluster tightly in a phylogenetic tree, signifying that they are derived from the same genetic pool. We identified limited variation due to recombination in the core CC17 genome. We describe that loss of Pilus Island 1 and acquisition of different mobile genetic elements carrying determinants of antimicrobial resistance contribute to CC17 genetic diversity. Acquisition of some of these mobile genetic elements appears to correlate with clonal expansion of the strains that possess them. Our results provide a genome-wide portrait of the population structure and evolution of a major disease-causing clone of an opportunistic pathogen. PMID:26843175

  6. [Toxic shock syndrome by group A beta-hemolytic streptococcus. Study of clonal relationship between a case and its contacts].

    PubMed

    Fernández, J; Fica, A; Caorsi, B; Contreras, J; Luppi, M; Heitmann, I

    1998-08-01

    Group A Streptococcal infections have increased in severity and frequency worldwide. We report a female patient that was admitted by Group A Streptococcal lethal toxic shock syndrome due to pharyngitis as the primary focus and without cutaneous involvement. Streptococcus pyogenes was isolated from blood cultures and case definition fulfilled standard recommendations. Epidemiological studies among family members showed, that two children (aged 5 and 12 years) harbored the same strain in their pharynxes as confirmed by arbitrarily primed PCR (AP-PCR) using primers ERIC and Pn-1. Control strains were included in the analysis. None of three health care workers involved in intubation and laryngoscopic procedures with the patient carried S pyogenes. AP-PCR appears to be a useful and rapid procedure to demonstrate clonal relatedness among S pyogenes strains. PMID:9830749

  7. Natural rpoS mutations contribute to the phenotypic heterogeneity of clonal populations in Escherichia coli O157:H7

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We previously reported the distinct acid resistance between the curli-producing (C+) and curli-deficient (C-) variants of E. coli O157:H7, although the curli fimbriae were not associated with this intra-strain phenotypic divergence. Here we investigated the underlying molecular mechanism by examinin...

  8. An Environmental Shiga Toxin-Producing Escherichia coli O145 Clonal Population Exhibits High-Level Phenotypic Variation That Includes Virulence Traits

    PubMed Central

    Quinones, Beatriz; He, Xiaohua; Zhong, Wayne; Louie, Jacqueline W.; Lee, Bertram G.; Yambao, Jaszemyn C.; Mandrell, Robert E.; Cooley, Michael B.

    2015-01-01

    Shiga toxin-producing Escherichia coli (STEC) serotype O145 is one of the major non-O157 serotypes associated with severe human disease. Here we examined the genetic diversity, population structure, virulence potential, and antimicrobial resistance profiles of environmental O145 strains recovered from a major produce production region in California. Multilocus sequence typing analyses revealed that sequence type 78 (ST-78), a common ST in clinical strains, was the predominant genotype among the environmental strains. Similarly, all California environmental strains belonged to H28, a common H serotype in clinical strains. Although most environmental strains carried an intact fliC gene, only one strain retained swimming motility. Diverse stx subtypes were identified, including stx1a, stx2a, stx2c, and stx2e. Although no correlation was detected between the stx genotype and Stx1 production, high Stx2 production was detected mainly in strains carrying stx2a only and was correlated positively with the cytotoxicity of Shiga toxin. All environmental strains were capable of producing enterohemolysin, whereas only 10 strains were positive for anaerobic hemolytic activity. Multidrug resistance appeared to be common, as nearly half of the tested O145 strains displayed resistance to at least two different classes of antibiotics. The core virulence determinants of enterohemorrhagic E. coli were conserved in the environmental STEC O145 strains; however, there was large variation in the expression of virulence traits among the strains that were highly related genotypically, implying a trend of clonal divergence. Several cattle isolates exhibited key virulence traits comparable to those of the STEC O145 outbreak strains, emphasizing the emergence of hypervirulent strains in agricultural environments. PMID:26637597

  9. Emergence of extended-spectrum β-lactam resistance among Escherichia coli at a US academic children’s hospital is clonal at the sequence type level for CTX-M-15, but not for CMY-2

    PubMed Central

    Weissman, Scott J.; Adler, Amanda; Qin, Xuan; Zerr, Danielle M.

    2013-01-01

    Resistance to extended-spectrum β-lactams is increasing worldwide among Escherichia coli and has been linked to a small number of emergent clones (e.g. ST38, ST131 and ST405) recovered from extraintestinal infections in community and hospital settings. There are, however, limited data about the relative contributions of bacterial strains, plasmids and β-lactamase genes to extended-spectrum β-lactam resistance in paediatric infections. We performed an extensive molecular analysis of phylogenetic, virulence and antibiotic resistance-related properties of 49 previously reported serial E. coli isolates recovered during 1999–2007 at Seattle Children’s Hospital (Seattle, WA). Class C enzyme CMY-2 and class A enzyme CTX-M-15 were the most prominent extended-spectrum β-lactam resistance enzymes in the collection, first appearing in this patient population in 2001 and 2003, respectively, and then steadily increasing in frequency over the remainder of the study period. Among 19 CMY-2-positive isolates, 16 distinct STs were detected (D = 98.25%, 95% CI 96–100.25%), indicating that CMY spread is non-clonal at the host strain level. In contrast, among ten CTX-M-15-positive isolates, three STs were detected (D = 37.78%, 95% CI 2.36–73.20%), of which eight represented the worldwide-disseminated ST131 lineage, consistent with clonal spread of CTX-M-15-associated resistance. fimHTR subtyping of ten ST131 isolates (including two CTX-M-negative isolates) revealed that, within ST131, carriage of allele fimHTR30 correlated with CTX-M-15 positivity, whilst carriage of non-fimHTR30 alleles correlated with carriage of non-CTX-M enzymes. Thus, spread of CMY-2 is non-clonal at the ST level, but clonal spread of CTX-M-15 may be associated with a specific fimHTR-defined sublineage of ST131. PMID:23434250

  10. Clonal dissemination of highly virulent extended-spectrum beta-lactamase-producing Escherichia coli strains isolated from the urine of non-hospitalised patients in Zagreb region.

    PubMed

    Vranes, Jasmina; Marijan, Tatjana; Bedenic, Branka; Mlinaric-Dzepina, Ana; Katic, Stjepan; Kalenic, Smilja

    2008-02-01

    Recent data suggest that extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is an emergent cause of urinary tract infections in non-hospitalised patients in different countries. The aim of this study was to characterise ESBL-producing E. coli strains isolated from the urine of outpatients in the Zagreb region of Croatia. During the 5-month study period, a total of 2451 E. coli strains were isolated from the urine of non-hospitalised patients with significant bacteriuria. A total of 39 ESBL-producing E. coli strains (1.59%) were collected and characterised. PMID:17936594

  11. Influences of clonality on plant sexual reproduction

    PubMed Central

    Barrett, Spencer C. H.

    2015-01-01

    Flowering plants possess an unrivaled diversity of mechanisms for achieving sexual and asexual reproduction, often simultaneously. The commonest type of asexual reproduction is clonal growth (vegetative propagation) in which parental genotypes (genets) produce vegetative modules (ramets) that are capable of independent growth, reproduction, and often dispersal. Clonal growth leads to an expansion in the size of genets and increased fitness because large floral displays increase fertility and opportunities for outcrossing. Moreover, the clonal dispersal of vegetative propagules can assist “mate finding,” particularly in aquatic plants. However, there are ecological circumstances in which functional antagonism between sexual and asexual reproductive modes can negatively affect the fitness of clonal plants. Populations of heterostylous and dioecious species have a small number of mating groups (two or three), which should occur at equal frequency in equilibrium populations. Extensive clonal growth and vegetative dispersal can disrupt the functioning of these sexual polymorphisms, resulting in biased morph ratios and populations with a single mating group, with consequences for fertility and mating. In populations in which clonal propagation predominates, mutations reducing fertility may lead to sexual dysfunction and even the loss of sex. Recent evidence suggests that somatic mutations can play a significant role in influencing fitness in clonal plants and may also help explain the occurrence of genetic diversity in sterile clonal populations. Highly polymorphic genetic markers offer outstanding opportunities for gaining novel insights into functional interactions between sexual and clonal reproduction in flowering plants. PMID:26195747

  12. An environmental shiga toxin-producing escherichia coli O145 clonal population exhibits high-level phenotypic variation that includes virulence traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Shiga toxin-producing Escherichia coli (STEC) serotype O145 is one of the major non-O157 serotypes associated with severe human disease. Here we examined the genetic diversity, population structure, virulence potential, and antibiotic resistance profile of environmental O145 strains isolated from a ...

  13. An environmental shiga toxin-producing Escherichia coli O145 clonal population exhibits high-level phenotypic variation that includes virulence traits

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Shiga toxin-producing Escherichia coli (STEC) serotype O145 is one of the major non-O157 serotypes associated with severe human disease. Here we examined the genetic diversity, population structure, virulence potential, and antibiotic resistance profile of environmental O145 strains isolated from a ...

  14. Fitness of outbreak and environmental strains of Escherichia coli O157:H7 in aerosolizable soil and association of clonal variation in stress gene regulation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Airborne dust from feedlots is a potential mechanism of contamination of nearby vegetable crops with Escherichia coli O157:H7 (EcO157). We compared the fitness of clinical and environmental strains of EcO157 in <45 µm soil from a spinach farm. Differences in survival were observed among the 35 strai...

  15. Molecular epidemiology of Legionella pneumophila serogroup 1 isolates identify a prevalent sequence type, ST505, and a distinct clonal group of clinical isolates in Toyama Prefecture, Japan.

    PubMed

    Kanatani, Jun-Ichi; Isobe, Junko; Kimata, Keiko; Shima, Tomoko; Shimizu, Miwako; Kura, Fumiaki; Sata, Tetsutaro; Watahiki, Masanori

    2013-08-01

    We performed comparative analyses of Legionella pneumophila serogroup (SG) 1 isolates obtained during 2005-2012 in Toyama Prefecture, Japan, by sequence-based typing (SBT) and pulsed-field gel electrophoresis (PFGE). Seventy-three isolates of L. pneumophila SG 1, including 17 isolates from patients, 51 from public baths, 4 from cooling towers, and 1 from a shower, were analyzed. The isolates were classified into 43 sequence types (STs) by SBT and 52 types by PFGE. Fourteen STs were unique to Toyama Prefecture, as determined from the SBT database of European Working Group for Legionella Infections (EWGLI), as of October 31, 2012. ST505 strain was identified in 4 isolates from patients and 5 isolates from public baths, and these isolates belonged to 2 PFGE types. These, however, were similar because of the difference with only two restriction fragments, indicating that ST505 strain was prevalent among L. pneumophila SG 1 isolates in this area. ST505 strains isolated from patients and public baths were distributed along the river in a western part of Toyama Prefecture. SBT and PFGE profiles of 3 clinical isolates were identical with those of 3 environmental isolates from the suspected origins of the infection in each case, respectively. This finding suggested that SBT and PFGE were useful for epidemiological study. Furthermore, by SBT analysis, we identified a clonal group formed only by 7 clinical isolates that are not associated with bathwater, suggesting that they were derived from unrecognized sources. PMID:23269379

  16. Group A Escherichia coli-Related Purpura Fulminans: an Unusual Manifestation Due to an Unusual Strain?

    PubMed Central

    Amara, Marlène; Bonacorsi, Stéphane; Bedel, Jérôme; Mira, Jean-Paul; Laurent, Virginie; Socha, Koryna; Bruneel, Fabrice; Pangon, Béatrice; Bédos, Jean-Pierre

    2014-01-01

    We describe an exceptional case of life-threatening group A Escherichia coli-induced purpura fulminans. Genotyping of common polymorphisms in genes involved in innate immunity or coagulation did not reveal known susceptibility to such a manifestation. Genetic analysis of the strain revealed an unusual conserved virulence plasmidic region, pointing out its potential virulence. PMID:25232165

  17. Expanded MLST genotyping and comparative genomic hybridization evidence for host preferred groups in Campylobacter coli

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The majority of previous work on campylobacteriosis has centered on the species Campylobacter jejuni, however, Campylobacter coli, the sister group to C. jejuni, is also a significant problem, but remains a much less studied organism. The purpose of this work was to develop and apply an expanded 16 ...

  18. Escherichia coli Strains Isolated from the Uteri Horn, Mouth, and Rectum of Bitches Suffering from Pyometra: Virulence Factors, Antimicrobial Susceptibilities, and Clonal Relationships among Strains.

    PubMed

    Agostinho, Juliana M A; de Souza, Andressa; Schocken-Iturrino, Ruben P; Beraldo, Lívia G; Borges, Clarissa A; Avila, Fernando A; Marin, José M

    2014-01-01

    Pyometra is recognized as one of the main causes of disease and death in the bitch, and Escherichia coli is the major pathogen associated with this disease. In this study, 70 E. coli isolates from the uteri horn, mouth, and rectum of bitches suffering from the disease and 43 E. coli isolates from the rectum of clinically healthy bitches were examined for the presence of uropathogenic virulence genes and susceptibility to antimicrobial drugs. DNA profiles of isolates from uteri horn and mouth in bitches with pyometra were compared by REP, ERIC, and BOX-PCR. Virulence gene frequencies detected in isolates from canine pyometra were as follows: 95.7% fim, 27.1% iss, 25.7% hly, 18.5% iuc, and 17.1% usp. Predominant resistance was determined for cephalothin, ampicillin, and nalidixic acid among the isolates from all sites examined. Multidrug resistance was found on ∼ 50% pyometra isolates. Using the genotypic methods some isolates from uteri, pus, and saliva of the same bitch proved to have identical DNA profiles which is a reason for concern due to the close relationship between household pets and humans. PMID:24734047

  19. Phylogenetic grouping and pathotypic comparison of urine and fecal Escherichia coli isolates from children with urinary tract infection

    PubMed Central

    Navidinia, Masoumeh; Peerayeh, Shahin Najar; Fallah, Fatemeh; Bakhshi, Bita; Sajadinia, Raheleh Sadat

    2014-01-01

    The aim of this study was to investigate the phylogenetic background and to assess hlyD (involved in the secretion of haemolysin A) and intI1 (encoding a class 1 integrase) in Escherichia coli isolates derived from urinary and fecal specimens. A total of 200 E. coli isolates was collected from patients presenting with urinary tract infection (UTI) during September 2009 to September 2010 and screened for hlyD and intI1 genes by polymerase chain reaction (PCR). Phylogenetic analysis showed that E. coli is composed of four main phylogenetic groups (A, B1, B2 and D) and that uropathogenic E. coli (UPEC) isolates mainly belong to groups B2 (54%) and D (34%) whereas group A (44%) and D (26%) are predominant among commensal E. coli isolates. In this study, hlyD was present in 26% of UPEC and 2% of commensal E. coli isolates. However, hemolytic activity was detected for 42% of UPEC and 6% of commensal E. coli isolates (p < 0.05). intI1 gene was more frequently expressed in UPEC (24%) in comparison with commensal E. coli isolates (12%). Resistance to aztreonam, co-trimoxazole and cefpodoxime were frequently found among UPEC isolates whereas commensal E. coli isolates were commonly resistant to co-trimoxazole, nalidixic acid and cefotaxime. Concluding, a considerable difference between UPEC and commensal E. coli isolates was observed regarding their phylogenetic groups, presence of class 1 integron and hlyD gene, hemolysin activity and resistance pattern. The detection of class 1 integrons and hlyD gene was higher among UPEC compared with commensal E. coli isolates. These findings may contribute for a better understanding of the factors involved in the pathogenesis of UPEC. PMID:25242935

  20. Enteroaggregative Escherichia coli O78:H10, the Cause of an Outbreak of Urinary Tract Infection

    PubMed Central

    Scheutz, Flemming; Andersen, Rebecca L.; Menard, Megan; Boisen, Nadia; Johnston, Brian; Hansen, Dennis S.; Krogfelt, Karen A.; Nataro, James P.; Johnson, James R.

    2012-01-01

    In 1991, multiresistant Escherichia coli O78:H10 strains caused an outbreak of urinary tract infections in Copenhagen, Denmark. The phylogenetic origin, clonal background, and virulence characteristics of the outbreak isolates, and their relationship to nonoutbreak O78:H10 strains according to these traits and resistance profiles, are unknown. Accordingly, we extensively characterized 51 archived E. coli O78:H10 isolates (48 human isolates from seven countries, including 19 Copenhagen outbreak isolates, and 1 each of calf, avian, and unknown-source isolates), collected from 1956 through 2000. E. coli O78:H10 was clonally heterogeneous, comprising one dominant clonal group (61% of isolates, including all 19 outbreak isolates) from ST10 (phylogenetic group A) plus several minor clonal groups (phylogenetic groups A and D). All ST10 isolates, versus 25% of non-ST10 isolates, were identified by molecular methods as enteroaggregative E. coli (EAEC) (P < 0.001). Genes present in >90% of outbreak isolates included fimH (type 1 fimbriae; ubiquitous in E. coli); fyuA, traT, and iutA (associated with extraintestinal pathogenic E. coli [ExPEC]); and sat, pic, aatA, aggR, aggA, ORF61, aaiC, aap, and ORF3 (associated with EAEC). An outbreak isolate was lethal in a murine subcutaneous sepsis model and exhibited characteristic EAEC “stacked brick” adherence to cultured epithelial cells. Thus, the 1991 Copenhagen outbreak was caused by a tight, non-animal-associated subset within a broadly disseminated O78:H10 clonal group (ST10; phylogenetic group A), members of which exhibit both ExPEC and EAEC characteristics, whereas O78:H10 isolates overall are phylogenetically diverse. Whether ST10 O78:H10 EAEC strains are both uropathogenic and diarrheagenic warrants further investigation. PMID:22972830

  1. Characterization of Escherichia coli Phylogenetic Groups Associated with Extraintestinal Infections in South Indian Population

    PubMed Central

    Chakraborty, A; Saralaya, V; Adhikari, P; Shenoy, S; Baliga, S; Hegde, A

    2015-01-01

    Background: Escherichia coli strains mainly fall into four phylogenetic groups (A, B1, B2, and D) and that virulent extra-intestinal strains mainly belong to groups B2 and D. Aim: The aim was to determine the association between phylogenetic groups of E. coli causing extraintestinal infections (ExPEC) regarding the site of infection, expression of virulence factors, antimicrobial resistance patterns, and clinical outcome. This descriptive study was carried out in a multi-specialty Tertiary Care Hospital. Materials and Methods: A total of 300 E. coli causing ExPEC were studied. Triplex polymerase chain reaction was used to classify the phylogenetic groups; hemolysin production was assessed on sheep blood agar and biofilm production in a microtiter plate assay. Production of extended spectrum of beta-lactamase (ESBLs) was detected by combination disk method; AmpC was detected by AmpC disk test, Carbapenemase production was detected by modified Hodge test and metallo-β-lactamase by metallo-beta-lactamases (MBL) E-test. Results: Of 300 isolates, 61/300 (20%) belonged to phylogroup A, 27/300 (9%) to phylogroup B1, 104/300 (35%) were B2 and 108/300 (36%) belonged to group D, respectively. Phylogroups B2 and D were the most predominant groups in urinary tract infection and sepsis. Prognoses were better in infections with group A and B1 isolates, and relapses and death were common in infections with B2 and D. Expression of biofilm was greatest in B1 and hemolysin in group B2. Group A and B1 showed higher resistance to ciprofloxacin and were most frequent β-lactamase (ESBL, AmpC, Carbapenemase and MBL) producers. Conclusions: Phylogenetic group B2 and D were predominant in ExPEC and exhibited least antimicrobial resistance among the groups. Resistance to multiple antibiotics was most prevalent in group A and B1. Regular monitoring of antimicrobial susceptibility in commensal strains is essential as they might transfer the property of antimicrobial resistance to pathogenic

  2. Inhibitor-resistant TEM- and OXA-1-producing Escherichia coli isolates resistant to amoxicillin-clavulanate are more clonal and possess lower virulence gene content than susceptible clinical isolates.

    PubMed

    Oteo, Jesús; González-López, Juan José; Ortega, Adriana; Quintero-Zárate, J Natalia; Bou, Germán; Cercenado, Emilia; Conejo, María Carmen; Martínez-Martínez, Luis; Navarro, Ferran; Oliver, Antonio; Bartolomé, Rosa M; Campos, José

    2014-07-01

    In a previous prospective multicenter study in Spain, we found that OXA-1 and inhibitor-resistant TEM (IRT) β-lactamases constitute the most common plasmid-borne mechanisms of genuine amoxicillin-clavulanate (AMC) resistance in Escherichia coli. In the present study, we investigated the population structure and virulence traits of clinical AMC-resistant E. coli strains expressing OXA-1 or IRT and compared these traits to those in a control group of clinical AMC-susceptible E. coli isolates. All OXA-1-producing (n = 67) and IRT-producing (n = 45) isolates were matched by geographical and temporal origin to the AMC-susceptible control set (n = 56). We performed multilocus sequence typing and phylogenetic group characterization for each isolate and then studied the isolates for the presence of 49 virulence factors (VFs) by PCR and sequencing. The most prevalent clone detected was distinct for each group: group C isolates of sequence type (ST) 88 (C/ST88) were the most common in OXA-1 producers, B2/ST131 isolates were the most common in IRT producers, and B2/ST73 isolates were the most common in AMC-susceptible isolates. The median numbers of isolates per ST were 3.72 in OXA-1 producers, 2.04 in IRT producers, and 1.69 in AMC-susceptible isolates; the proportions of STs represented by one unique isolate in each group were 19.4%, 31.1%, and 48.2%, respectively. The sum of all VFs detected, calculated as a virulence score, was significantly higher in AMC-susceptible isolates than OXA-1 and IRT producers (means, 12.5 versus 8.3 and 8.2, respectively). Our findings suggest that IRT- and OXA-1-producing E. coli isolates resistant to AMC have a different and less diverse population structure than AMC-susceptible clinical E. coli isolates. The AMC-susceptible population also contains more VFs than AMC-resistant isolates. PMID:24777096

  3. Inhibitor-Resistant TEM- and OXA-1-Producing Escherichia coli Isolates Resistant to Amoxicillin-Clavulanate Are More Clonal and Possess Lower Virulence Gene Content than Susceptible Clinical Isolates

    PubMed Central

    González-López, Juan José; Ortega, Adriana; Quintero-Zárate, J. Natalia; Bou, Germán; Cercenado, Emilia; Conejo, María Carmen; Martínez-Martínez, Luis; Navarro, Ferran; Oliver, Antonio; Bartolomé, Rosa M.; Campos, José

    2014-01-01

    In a previous prospective multicenter study in Spain, we found that OXA-1 and inhibitor-resistant TEM (IRT) β-lactamases constitute the most common plasmid-borne mechanisms of genuine amoxicillin-clavulanate (AMC) resistance in Escherichia coli. In the present study, we investigated the population structure and virulence traits of clinical AMC-resistant E. coli strains expressing OXA-1 or IRT and compared these traits to those in a control group of clinical AMC-susceptible E. coli isolates. All OXA-1-producing (n = 67) and IRT-producing (n = 45) isolates were matched by geographical and temporal origin to the AMC-susceptible control set (n = 56). We performed multilocus sequence typing and phylogenetic group characterization for each isolate and then studied the isolates for the presence of 49 virulence factors (VFs) by PCR and sequencing. The most prevalent clone detected was distinct for each group: group C isolates of sequence type (ST) 88 (C/ST88) were the most common in OXA-1 producers, B2/ST131 isolates were the most common in IRT producers, and B2/ST73 isolates were the most common in AMC-susceptible isolates. The median numbers of isolates per ST were 3.72 in OXA-1 producers, 2.04 in IRT producers, and 1.69 in AMC-susceptible isolates; the proportions of STs represented by one unique isolate in each group were 19.4%, 31.1%, and 48.2%, respectively. The sum of all VFs detected, calculated as a virulence score, was significantly higher in AMC-susceptible isolates than OXA-1 and IRT producers (means, 12.5 versus 8.3 and 8.2, respectively). Our findings suggest that IRT- and OXA-1-producing E. coli isolates resistant to AMC have a different and less diverse population structure than AMC-susceptible clinical E. coli isolates. The AMC-susceptible population also contains more VFs than AMC-resistant isolates. PMID:24777096

  4. Biosynthesis of polyhydroxyalkanoates containing hydroxyl group from glycolate in Escherichia coli.

    PubMed

    Insomphun, Chayatip; Kobayashi, Shingo; Fujiki, Tetsuya; Numata, Keiji

    2016-12-01

    Polyhydroxyalkanoates (PHAs) containing hydroxyl groups in a side chain were produced in recombinant Escherichia coli JM109 using glycolate as the sole carbon source. The propionate-CoA transferase (pct) gene from Megasphaera elsdenii and the β-ketothiolase (bktB) gene and phaCAB operon from Ralstonia eutropha H16 were introduced into E. coli JM109. A novel monomer containing a hydroxyl group, dihydroxybutyrate (DHBA), was the expected product of the condensation of glycolyl-CoA and acetyl-CoA by BktB. The recombinant strain produced a PHA containing 1 mol% DHBA. The incorporation of DHBA may have been restricted because the expression of phaAB1 competes for acetyl-CoA. The PHA containing DHBA units were evaluated regarding thermal properties, such as melting temperature, glass transition temperature and thermal degradation temperature. The current study demonstrates a potential use of PHA containing hydroxyl groups as renewable resources in biological materials. PMID:27075993

  5. Phylogenetic group-associated differences in regulation of the common colonization factor Mat fimbria in Escherichia coli.

    PubMed

    Lehti, Timo A; Bauchart, Philippe; Kukkonen, Maini; Dobrindt, Ulrich; Korhonen, Timo K; Westerlund-Wikström, Benita

    2013-03-01

    Heterogeneity of cell population is a key component behind the evolutionary success of Escherichia coli. The heterogeneity supports species adaptation and mainly results from lateral gene transfer. Adaptation may also involve genomic alterations that affect regulation of conserved genes. Here we analysed regulation of the mat (or ecp) genes that encode a conserved fimbrial adhesin of E. coli. We found that the differential and temperature-sensitive expression control of the mat operon is dependent on mat promoter polymorphism and closely linked to phylogenetic grouping of E. coli. In the mat promoter lineage favouring fimbriae expression, the mat operon-encoded regulator MatA forms a positive feedback loop that overcomes the repression by H-NS and stabilizes the fimbrillin mRNA under low growth temperature, acidic pH or elevated levels of acetate. The study exemplifies phylogenetic group-associated expression of a highly common surface organelle in E. coli. PMID:23347101

  6. Defining Clonal Color in Fluorescent Multi-Clonal Tracking

    PubMed Central

    Wu, Juwell W.; Turcotte, Raphaël; Alt, Clemens; Runnels, Judith M.; Tsao, Hensin; Lin, Charles P.

    2016-01-01

    Clonal heterogeneity and selection underpin many biological processes including development and tumor progression. Combinatorial fluorescent protein expression in germline cells has proven its utility for tracking the formation and regeneration of different organ systems. Such cell populations encoded by combinatorial fluorescent proteins are also attractive tools for understanding clonal expansion and clonal competition in cancer. However, the assignment of clonal identity requires an analytical framework in which clonal markings can be parameterized and validated. Here we present a systematic and quantitative method for RGB analysis of fluorescent melanoma cancer clones. We then demonstrate refined clonal trackability of melanoma cells using this scheme. PMID:27073117

  7. Clonal reproduction in fungi

    PubMed Central

    Taylor, John W.; Hann-Soden, Christopher; Branco, Sara; Sylvain, Iman; Ellison, Christopher E.

    2015-01-01

    Research over the past two decades shows that both recombination and clonality are likely to contribute to the reproduction of all fungi. This view of fungi is different from the historical and still commonly held view that a large fraction of fungi are exclusively clonal and that some fungi have been exclusively clonal for hundreds of millions of years. Here, we first will consider how these two historical views have changed. Then we will examine the impact on fungal research of the concept of restrained recombination [Tibayrenc M, Ayala FJ (2012) Proc Natl Acad Sci USA 109 (48):E3305–E3313]. Using animal and human pathogenic fungi, we examine extrinsic restraints on recombination associated with bottlenecks in genetic variation caused by geographic dispersal and extrinsic restraints caused by shifts in reproductive mode associated with either disease transmission or hybridization. Using species of the model yeast Saccharomyces and the model filamentous fungus Neurospora, we examine intrinsic restraints on recombination associated with mating systems that range from strictly clonal at one extreme to fully outbreeding at the other and those that lie between, including selfing and inbreeding. We also consider the effect of nomenclature on perception of reproductive mode and a means of comparing the relative impact of clonality and recombination on fungal populations. Last, we consider a recent hypothesis suggesting that fungi thought to have the most severe intrinsic constraints on recombination actually may have the fewest. PMID:26195774

  8. Complete Genome Sequence of the Wild-Type Commensal Escherichia coli Strain SE15, Belonging to Phylogenetic Group B2▿

    PubMed Central

    Toh, Hidehiro; Oshima, Kenshiro; Toyoda, Atsushi; Ogura, Yoshitoshi; Ooka, Tadasuke; Sasamoto, Hiroyuki; Park, Sang-Hee; Iyoda, Sunao; Kurokawa, Ken; Morita, Hidetoshi; Itoh, Kikuji; Taylor, Todd D.; Hayashi, Tetsuya; Hattori, Masahira

    2010-01-01

    Escherichia coli SE15 (O150:H5) is a human commensal bacterium recently isolated from feces of a healthy adult and classified into E. coli phylogenetic group B2, which includes the majority of extraintestinal pathogenic E. coli. Here, we report the finished and annotated genome sequence of this organism. PMID:20008064

  9. CTX-M-producing Escherichia coli in Lithuania: associations between sites of infection, coresistance, and phylogenetic groups.

    PubMed

    Giedraitienė, Agnė; Vitkauskienė, Astra; Ašmonienė, Virginija; Plančiūnienė, Rita; Simonytė, Sandrita; Pavilonis, Alvydas; Arlet, Guillaume

    2013-01-01

    Increasing resistance of Escherichia coli (E. coli) to antibiotics, especially to the third-generation cephalosporins, has prompted studies on widespread resistance genes such as blaCTX-M and differentiation of E. coli to phylogenetic groups. The aim of this study was to determine the associations between the CTX-M type and the phylogenetic group, the site of infection, and coresistance in Lithuanian E. coli isolates producing β-lactamases. MATERIAL AND METHODS. A total of 90 E. coli ESBL strains were recovered from the lower respiratory tract, the urinary tract, sterile body sites, wounds, and other body sites between 2008 and 2012. The E. coli isolates resistant to at least 2 antibiotics with different modes of action along with resistance to cefotaxime were considered as multiresistant. The blaCTX-M, blaTEM, blaOXA-1, and blaSHV genes, the phylogenetic groups, and the resistance profiles were analyzed. RESULTS. Of the 90 isolates, 84 (93.3%) were classified as multiresistant and 6 (6.6%) as resistant. The blaCTX-M-15 gene was the most prevalent gene followed by the blaCTX-M-14 and blaCTX-M-92 genes. The logistic regression analysis revealed the associations between CTX-M-15 and resistance to ceftriaxone, between CTX-M-14 and resistance to cefoxitin, aztreonam, ampicillin/sulbactam, ticarcillin/clavulanic acid, and tobramycin, and between CTX-M-92 and resistance to cefepime, piperacillin/tazobactam, gentamicin, and tobramycin. CONCLUSIONS. The results of this study showed a significant association between CTX-M-15, CTX-M-14, and CTX-M-92 β-lactamases and resistance to some antibiotics as well as CTX‑M-14 β-lactamase and phylogenetic group A in the Lithuanian population. The associations between the CTX-M type and the site of infection were not determined. PMID:24589574

  10. Distribution of lipopolysaccharide core types among avian pathogenic Escherichia coli in relation to the major phylogenetic groups.

    PubMed

    Dissanayake, D R A; Wijewardana, T G; Gunawardena, G A; Poxton, I R

    2008-12-10

    Five distinct lipopolysaccharide (LPS) core types, namely R1-R4 and K12 have been identified in Escherichia coli. The aims of this study were to determine, primarily by means of PCR, the distribution of those oligosaccharide core types among avian pathogenic E. coli and their relationship to phylogenetic groups. To identify putative avian pathogenic E. coli, serum resistance and the presence of three virulence genes encoding temperature sensitive haemagglutinin (tsh), increased serum survival (iss) and colicin V (cvaC) were determined. Of the 143 clinical isolates examined 62% possessed the R1 core, 22% were R3, 13% were R4 and 3% were R2. Fifty commensal isolates consisted of 58% with R1 core, 38% with R3 core, 4% with R4 core, and none with R2. None of the isolates were of K12 core type. The distribution of core oligosaccharide types in clinical and commensal isolates were not statistically significant (P=0.51). Three genes, tsh, iss and cvaC were found in E. coli of all four core types. The genes tsh (P<0.001) and iss (P=0.03412) were significantly associated with the R4 core oligosaccharide type. The isolates containing R4 core type LPS were mainly confined to phylogenetic group D. The widespread R1 core type showed less ability to possess virulence genes and 83% were in the phylogenetic group A. Results of this study indicated that E. coli with R1, R2, R3 and R4 were important in causing infections in chickens and further, the E. coli with R4 core type were less common among commensals, possessed more virulence genes and were related to phylogenetic groups pathogenic for poultry. PMID:18597955

  11. Characteristics of Escherichia coli causing persistence or relapse of urinary tract infections: phylogenetic groups, virulence factors and biofilm formation.

    PubMed

    Ejrnæs, Karen; Stegger, Marc; Reisner, Andreas; Ferry, Sven; Monsen, Tor; Holm, Stig E; Lundgren, Bettina; Frimodt-Møller, Niels

    2011-01-01

    Recurrent urinary tract infections (RUTIs) pose a major problem but little is known about characteristics of Escherichia coli associated with RUTI. This study includes E. coli from 155 women with community-acquired lower urinary tract infections (UTIs) randomized to one of three dosing regiments of pivmecillinam and aimed to identify associations between the presence of 29 virulence factor genes (VFGs), phylogenetic groups and biofilm formation and the course of infection during follow-up visits at 8-10 and 35-49 days post-inclusion, respectively. E. coli causing persistence or relapse were more often of phylogenetic group B2 and had a significantly higher aggregate VFG score than E. coli that were not detectable at follow-up. Specifically, these E. coli causing persistence or relapse were characterized by a higher prevalence of hemolysis and 12 VFGs (sfa/focDE, papAH, agn43, chuA, fyuA, iroN, kpsM II, kpsM II K2, cnf1, hlyD, malX and usp). KpsM II K2 and agn43a(CFT073) were independently associated with persistence or relapse. No specific combination of presence/absence of VFGs could serve as a marker to predict RUTI. Stratifying for VFGs, seven days of pivmecillinam treatment reduced the prevalence of persistence or relapse of UTI compared with three days. In vitro biofilm formation was not higher among E. coli causing persistence or relapse. The presence of agn43a(CFT073) or agn43b(CFT073) was associated with biofilm forming capacity. In conclusion, our results show potential targets for prevention and treatment of persistence/relapse of UTI and potential markers for selecting treatment lengths and warrant studies of these and new VFGs. PMID:22030858

  12. Phylogenetic grouping, epidemiological typing, analysis of virulence genes, and antimicrobial susceptibility of Escherichia coli isolated from healthy broilers in Japan

    PubMed Central

    2014-01-01

    Background The aim of our study was to investigate the possible etiology of avian colibacillosis by examining Escherichia coli isolates from fecal samples of healthy broilers. Findings Seventy-eight E. coli isolates from fecal samples of healthy broilers in Japan were subjected to analysis of phylogenetic background, virulence-associated gene profiling, multi-locus sequence typing (MLST), and antimicrobial resistance profiling. Phylogenetic analysis demonstrated that 35 of the 78 isolates belonged to group A, 28 to group B1, one to group B2, and 14 to group D. Virulence-associated genes iutA, iss, cvaC, tsh, iroN, ompT, and hlyF were found in 23 isolates (29.5%), 16 isolates (20.5%), nine isolates (11.5%), five isolates (6.4%), 19 isolates (24.4%), 23 isolates (29.5%), and 22 isolates (28.2%) respectively. Although the genetic diversity of group D isolates was revealed by MLST, the group D isolates harbored iutA (10 isolates, 71.4%), iss (6 isolates, 42.9%), cvaC (5 isolates, 35.7%), tsh (3 isolates, 21.4%), hlyF (9 isolates, 64.3%), iroN (7 isolates, 50.0%), and ompT (9 isolates, 64.3%). Conclusions Our results indicated that E. coli isolates inhabiting the intestines of healthy broilers pose a potential risk of causing avian colibacillosis. PMID:25061511

  13. Novel genetic markers define a subgroup of pathogenic Escherichia coli strains belonging to the B2 phylogenetic group.

    PubMed

    Deshpande, Nandan P; Wilkins, Marc R; Mitchell, Hazel M; Kaakoush, Nadeem O

    2015-11-01

    The B2 phylogenetic group of Escherichia coli contains important pathogens such as extraintestinal pathogenic, adherent-invasive, and uropathogenic strains. In this study, we used comparative genomics and statistical methods to identify genetic variations that define a subset of pathogenic strains belonging to the B2 phylogenetic group. An initial proof of concept analysis indicated that five of the 62 E. coli strains available in the Kyoto Encyclopedia of Genes and Genomes database showed close association with B2 adherent-invasive E. coli, forming a subgroup within the B2 phylogenetic group. The tool, kSNP which uses a k-mer approach, and the statistical phenotype prediction tool PPFS2 were then employed to identify 29 high-resolution SNPs, which reaffirmed this grouping. PPFS2 analysis also provided indications that the clustering of this subgroup was highly consistent, and thus, could have a strong phenotypic basis rather than being only evolutionary. Protein homology analyses identified three proteins to be conserved across this subgrouping, two CRISPR-Cas proteins and a hypothetical protein. Functional analyses of these genetic and protein variations may provide insights into the phenotype of these strains. PMID:26459886

  14. The population genetics of clonal and partially clonal diploids.

    PubMed Central

    Balloux, François; Lehmann, Laurent; de Meeûs, Thierry

    2003-01-01

    The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci). PMID:12930767

  15. [Study on virulence factors associated with biofilm formation and phylogenetic groupings in Escherichia coli strains isolated from patients with cystitis].

    PubMed

    Tiba, Monique Ribeiro; Nogueira, Gustavo Prado; Leite, Domingos da Silva

    2009-01-01

    Escherichia coli samples isolated from female patients with cystitis were characterized with regard to the presence of virulence factors associated with biofilm formation and phylogenetic groupings. Polymerase chain reaction results demonstrated that all the samples were positive for the gene fimH (type 1 fimbriae), 91 for fliC (flagellins), 50 for papC (P fimbriae), 44 for kpsMTII (capsules) and 36 for flu (antigen 43). The results from assays to quantify the biofilm formation demonstrated that 44 samples produced biofilm on polystyrene microplates and 56 samples produced weak or no biofilm. We also confirmed that Escherichia coli samples were present in phylogenetic groups B2 and D. PMID:19287937

  16. Identification of integrons and phylogenetic groups of drug-resistant Escherichia coli from broiler carcasses in China.

    PubMed

    Wu, Hao; Xia, Shibo; Bu, Fanyun; Qi, Jing; Liu, Yuqing; Xu, Hai

    2015-10-15

    The dissemination of drug-resistant Escherichia coli in poultry products is becoming a public concern, as it endangers food security and human health. It is very common for E. coli to exhibit drug resistance in the poultry industry in China due to the excessive use of antibiotics. However, few studies have examined the drug resistance endowed by integrons and integron-associated gene cassettes in different phylogenetic groups of E. coli isolated from broiler carcasses. In this study, 373 antibiotic-resistant E. coli strains were isolated from the surfaces or insides of broiler carcasses from a slaughterhouse in Shandong Province, China. According to phylogenetic assays of chuA, yjaA, and an anonymous DNA fragment, TSPE4-C2, these isolates belong to four phylogenetic groups (A, B1, B2, and D) and seven subgroups (A0, A1, B1, B21, B22, D1, and D2). Of the tested isolates, 95.71% (n=357) are multi-drug resistant, among which group B1 was predominant, accounting for 33.51% (n=125) of the tested isolates. A high percentage of the E. coli isolates were resistant to amoxicillin-clavulanic acid (99.20%, n=370), doxycycline (92.23%, n=344), sulfamethoxazole-trimethoprim (90.88%, n=339), ciprofloxacin, (64.61%, n=241), sulbactam-cefoperazone (51.21%, n=191), and amikacin (33.78%, n=126). Furthermore, among the 373 isolates, class 1 and 2 integrons were identified in 292 (78.28%) and 49 (13.14%) of the isolates, respectively, while no class 3 integrons were detected. The most prevalent gene cassette arrays were dfrA17-aadA5 and dfrA12-orfF-aadA2 in the variable region of class 1 integrons, while only one gene cassette array (dfrA1-sat2-aadA1) was detected in the variable region of class 2 integrons. Class 1 integrons were distributed in various physiological subtypes, whereas no predominant phylogenetic groups could be identified. The presence of class 2 integrons in the B21 subtype was significantly higher than in the other subtypes, and it coexisted with the class 1

  17. Genetic relationships among pathogenic Escherichia coli of serogroup O157.

    PubMed Central

    Whittam, T S; Wilson, R A

    1988-01-01

    Escherichia coli strains of serotype O157:H7 are a newly described clonal pathogenic form associated with recent outbreaks of hemorrhagic colitis in humans. Although O157 strains of various H types have long been recognized as enterotoxigenic in animals, little is known about how these pathogenic animal strains are related to those of serotype O157:H7. To determine the genetic relatedness of O157:H7 isolates to animal O157 strains, we examined 194 O157 isolates, representing 12 distinct flagellar antigens (H serotypes), obtained from a variety of animal and human infections. To characterize isolates, we assayed allelic variation at 19 enzyme loci by multilocus enzyme electrophoresis. Genotypic comparisons of isolates revealed extensive variation among 33 distinct clonal genotypes that differed, on average, at 44% of the enzyme loci. K88 fimbriae were expressed in 72% of the isolates and occurred in a diversity of chromosomal genotypic backgrounds. Five major clonal groups were recognized; one group was clearly associated with porcine colibacillosis, and another was associated with human urinary tract infections. The O157:H7 genotype was not closely allied with any of the major groups of clones. The results indicate that O157 E. coli are genetically diverse and strongly suggest that the O157:H7 lineage was not recently derived from other pathogenic strains of the O157 serogroup. PMID:2457555

  18. Is Bordetella pertussis clonal?

    PubMed Central

    Khattak, M. N.; Matthews, R. C.; Burnie, J. P.

    1992-01-01

    OBJECTIVE--To establish whether Bordetella pertussis is essentially clonal. DESIGN--Analysis of restriction fragments of XbaI digests of DNA from clinical and control isolates of B pertussis by pulse field gel electrophoresis. MATERIALS--105 isolates of B pertussis: 67 clinical isolates from throughout the United Kingdom and 23 from Germany (collected during the previous 18 months); vaccine strains 2991 and 3700; and 13 control isolates from Manchester University's culture collection. MAIN OUTCOME MEASURES--Frequency of DNA types according to country of origin and classical serotyping. RESULTS--17 DNA types were identified on the basis of the variation in 11 fragments, banding at 200-412 kilobases; 15 types were found in the clinical and control isolates from the United Kingdom and seven in those from Germany. There was no correlation with serotype. DNA type 1 was the commonest overall (22/105 strains, 22%), predominating in serotypes 1,2 and 1,2,3 and including the vaccine strains but not the isolates from Germany. CONCLUSIONS--Current infections due to B pertussis are not caused by a clonal pathogen as multiple strains are circulating in a given population at one time. There is also considerable epidemiological variation in the pathogen population between countries. These findings may have implications for the design of acellular vaccines. Images FIG 1 FIG 2 FIG 3 PMID:1392709

  19. The clonal origin and clonal evolution of epithelial tumours

    PubMed Central

    Garcia, Sergio Britto; Novelli, Marco; Wright, Nicholas A

    2000-01-01

    While the origin of tumours, whether from one cell or many, has been a source of fascination for experimental oncologists for some time, in recent years there has been a veritable explosion of information about the clonal architecture of tumours and their antecedents, stimulated, in the main, by the ready accessibility of new molecular techniques. While most of these new results have apparently confirmed the monoclonal origin of human epithelial (and other) tumours, there are a significant number of studies in which this conclusion just cannot be made. Moreover, analysis of many articles show that the potential impact of such considerations as patch size and clonal evolution on determinations of clonality have largely been ignored, with the result that a number of these studies are confounded. However, the clonal architecture of preneoplastic lesions provide some interesting insights — many lesions which might have been hitherto regarded as hyperplasias are apparently clonal in derivation. If this is indeed true, it calls into some question our hopeful corollary that a monoclonal origin presages a neoplastic habitus. Finally, it is clear, for many reasons, that methods of analysis which involve the disaggregation of tissues, albeit microdissected, are far from ideal and we should be putting more effort into techniques where the clonal architecture of normal tissues, preneoplastic and preinvasive lesions and their derivative tumours can be directly visualized in situ. PMID:10762440

  20. PCR techniques for clonality assays.

    PubMed

    Diaz-Cano, S J; Blanes, A; Wolfe, H J

    2001-03-01

    Clonal overgrowths represent the hallmark of neoplastic proliferations, and their demonstration has been proved useful clinically for the diagnosis of malignant lymphomas based on the detection of specific and dominant immunoglobulin and/or T-cell receptor gene rearrangements. Nonrandom genetic alterations can also be used to test clonal expansions and the clonal evolution of neoplasms, especially analyzing hypervariable deoxyribonucleic acid (DNA) regions from patients heterozygous for a given marker. These tests rely basically on the demonstration of loss of heterozygosity (LOH) resulting from either hemizygosity (nonrandom interstitial DNA deletions) or homozygosity of mutant alleles observed in neoplasms. LOH analyses identify clonal expansions of a tumor cell population, and point to monoclonal proliferation when multiple and consistent LOH are demonstrated. Based on the methylation-related inactivation of one X chromosome in female subjects, X-linked markers (e.g., androgen receptor gene) will provide clonality information using LOH analyses after DNA digestion with methylation-sensitive restriction endonucleases. Therefore, both non-X-linked and X-linked analyses give complementary information, related and not related to the malignant transformation pathway respectively. Applied appropriately, these tools can establish the clonal evolution of tumor cell populations (tumor heterogeneity), identify early relapses, distinguish recurrent tumors from other metachronic neoplasms, and differentiate field transformation from metastatic tumor growths in synchronic and histologically identical neoplasms. PMID:11277392

  1. Characterization of fHbp, nhba (gna2132), nadA, porA, Sequence Type (ST), and Genomic Presence of IS1301 in Group B Meningococcal ST269 Clonal Complex Isolates from England and Wales▿

    PubMed Central

    Lucidarme, Jay; Comanducci, Maurizio; Findlow, Jamie; Gray, Stephen J.; Kaczmarski, Edward B.; Guiver, Malcolm; Kugelberg, Elisabeth; Vallely, Pamela J.; Oster, Philipp; Pizza, Mariagrazia; Bambini, Stefania; Muzzi, Alessandro; Tang, Christoph M.; Borrow, Ray

    2009-01-01

    Highly effective glycoconjugate vaccines exist against four of the five major pathogenic groups of meningococci: A, C, W-135, and Y. An equivalent vaccine against group B meningococci (menB) has remained elusive due to the poorly immunogenic capsular polysaccharide. A promising alternative, the investigational recombinant menB (rMenB)- outer membrane vesicle (OMV) vaccine, contains fHBP, NHBA (previously GNA2132), NadA, and outer membrane vesicles (OMVs) from the New Zealand MeNZB vaccine. MenB currently accounts for 90% of meningococcal disease in England and Wales, where the multilocus sequence type (ST) 269 (ST269) clonal complex (cc269) has recently expanded to account for a third of menB cases. To assess the potential cc269 coverage of the rMenB-OMV vaccine, English and Welsh cc269 isolates from the past decade were genetically characterized with respect to fHBP, NHBA, and NadA. All of the isolates harbored fHbp and nhba alleles, while 98% of the cc269 isolates were devoid of nadA. Subvariant profiling of fHbp, nhba, and porA against STs revealed the presence of two broadly distinct and well-defined clusters of isolates, centered around ST269 and ST275, respectively. An additional molecular marker, insertion sequence IS1301, was found to be present in 100% and <2% of isolates of the respective clusters. On the basis of the genetic data, the potential rMenB-OMV coverage of cc269 in England and Wales is high (up to 100%) within both clusters. Expression studies and serum bactericidal antibody assays will serve to enhance predictions of coverage and will augment ongoing studies regarding the significance of IS1301 within the ST269 cluster. PMID:19759227

  2. Antimicrobial resistance in fecal Escherichia coli isolates from healthy urban children of two age groups in relation to their antibiotic therapy.

    PubMed

    Literak, Ivan; Petro, Radim; Dolejska, Monika; Gruberova, Erika; Dobiasova, Hana; Petr, Jan; Cizek, Alois

    2011-06-01

    The study was performed in the Czech Republic during 2007 to 2009. Of Escherichia coli isolates from 275 children aged 6 weeks, 36% (n = 177) were resistant to 1 to 7 antibiotics. Of isolates from 253 children aged 6 to 17 years, 24% (n = 205) were resistant to 1 to 5 antibiotics. There was no significant difference in the prevalences of antibiotic-resistant E. coli isolates between these groups of children, even though the consumptions of antibiotics were quite different. PMID:21464246

  3. Antimicrobial Resistance in Fecal Escherichia coli Isolates from Healthy Urban Children of Two Age Groups in Relation to Their Antibiotic Therapy▿

    PubMed Central

    Literak, Ivan; Petro, Radim; Dolejska, Monika; Gruberova, Erika; Dobiasova, Hana; Petr, Jan; Cizek, Alois

    2011-01-01

    The study was performed in the Czech Republic during 2007 to 2009. Of Escherichia coli isolates from 275 children aged 6 weeks, 36% (n = 177) were resistant to 1 to 7 antibiotics. Of isolates from 253 children aged 6 to 17 years, 24% (n = 205) were resistant to 1 to 5 antibiotics. There was no significant difference in the prevalences of antibiotic-resistant E. coli isolates between these groups of children, even though the consumptions of antibiotics were quite different. PMID:21464246

  4. Functional groups in the activity and regulation of Escherichia coli citrate synthase

    PubMed Central

    Danson, Michael J.; Weitzman, P. David J.

    1973-01-01

    1. Citrate synthase has been purified from Escherichia coli and shown to exist at an equilibrium between three forms: monomer (mol.wt. 57000), tetramer (mol.wt. 230000) and, possibly, octamer. Modification of the enzyme by photo-oxidation and by treatment with specific chemical reagents has been carried out to gain information on the amino acid residues involved in enzymic activity and in the inhibition of activity by NADH and α-oxoglutarate. 2. Several photo-oxidizable amino acids appear to be involved in activity. The nature of the pH-dependence of their rates of photo-oxidation with Methylene Blue suggests that these are histidines, a conclusion supported by the greater rate of photo-inactivation with Rose Bengal and the destruction of activity by diethyl pyrocarbonate. 3. The participation of histidine at the α-oxoglutarate effector site is indicated by photo-oxidation and the participation of cysteine at the NADH effector site suggested by photo-oxidation is confirmed by the desensitization to NADH produced by treatment with 5,5′-dithiobis-(2-nitrobenzoate). Inactivation of the enzyme after modification with this reagent suggests the additional involvement of cysteine in catalytic activity. 4. Amino acid analyses of native and photo-oxidized enzyme are consistent with these conclusions. 5. Modification with 2-hydroxy-5-nitrobenzyl bromide indicates the participation of tryptophan in the activity of the enzyme. PMID:4359019

  5. Synthetic clonal reproduction through seeds.

    PubMed

    Marimuthu, Mohan P A; Jolivet, Sylvie; Ravi, Maruthachalam; Pereira, Lucie; Davda, Jayeshkumar N; Cromer, Laurence; Wang, Lili; Nogué, Fabien; Chan, Simon W L; Siddiqi, Imran; Mercier, Raphaël

    2011-02-18

    Cloning through seeds has potential revolutionary applications in agriculture, because it would allow vigorous hybrids to be propagated indefinitely. However, asexual seed formation or apomixis, avoiding meiosis and fertilization, is not found in the major food crops. To develop de novo synthesis of apomixis, we crossed Arabidopsis MiMe and dyad mutants that produce diploid clonal gametes to a strain whose chromosomes are engineered to be eliminated after fertilization. Up to 34% of the progeny were clones of their parent, demonstrating the conversion of clonal female or male gametes into seeds. We also show that first-generation cloned plants can be cloned again. Clonal reproduction through seeds can therefore be achieved in a sexual plant by manipulating two to four conserved genes. PMID:21330535

  6. Influence of the age and sex of human hosts on the distribution of Escherichia coli ECOR groups and virulence traits.

    PubMed

    Gordon, David M; Stern, Steven E; Collignon, Peter J

    2005-01-01

    Escherichia coli were isolated from the faeces of 266 individuals living in the Canberra region of Australia. The isolates were characterized for their ECOR group membership (A, B1, B2 or D) and for the presence of 29 virulence-associated traits. Overall, 19.5 % of the strains were members of group A, 12.4 % B1, 45.1 % B2 and 22.9 % D. The frequency with which strains belonging to the four ECOR groups were observed varied with the age and sex of the hosts from which they were isolated. In males, the probability of isolating A or D strains increased with host age, whilst the probability of detecting a group B2 strain declined. In females, the probability of recovering A or B2 strains increased with increasing host age and there was a concomitant decline in the likelihood of isolating B1 or D strains. Of the 29 virulence-associated traits examined, 24 were detected in more than one strain. The likelihood of detecting most traits varied with a strain's ECOR membership, with the exception of afa/draBC, astA, cvaC, eaeA, iss and iutA, for which there was no statistically significant evidence of an association with ECOR group. The frequency with which fimH, iha, eaeA, iroN, hlyD, iss, ompT and K1 were detected in a strain depended on the age or sex of the host from which the strain was isolated. In group B2 strains many of the virulence traits were non-randomly associated, with some co-occurring in a strain less often than expected by chance, whilst others were co-associated. In 17 cases, the extent to which two virulence traits were co-associated was found to depend on host sex and age. The results of this study suggest that the morphological, physiological and dietary differences that occur among human individuals of different sex or age may influence the distribution of E. coli genotypes. PMID:15632421

  7. Phylogenetic groups, extended-spectrum β-lactamases and metallo-β-lactamase in Escherichia coli isolated from fecal samples of patients with diarrhea in Iran

    PubMed Central

    Alizade, Hesam; Fallah, Fatemeh; Ghanbarpour, Reza; Aflatoonian, Mohammad Reza; Goudarzi, Hossein; Sharifi, Hamid

    2015-01-01

    Aim: The aims of this study were to investigate the phenotypic and genotypic of extended-spectrum β-lactamase (ESBL) and metallo-β-lactamases (MBLs) and determine phylogenetic background E. coli isolates from fecal samples of patients with diarrhea in Kerman, southeast of Iran Background: The emergence of ESBLs and MBLs-producing E. coli caused problems in antibiotic treatments. E. coli strains can be assigned to four main phylog-groups, including: A, B1, B2 and D. Patients and methods: E. coli isolates (n=216) were obtained from fecal samples of patients with diarrhea between June and December 2013. ESBLs and MBLs were confirmed by disk-diffusion and broth micro-dilution methods. Using PCR, the ESBL-positive isolates were screened to determine the phylo-groups and the presence of blaCTX-M-15, blaOXA-1, blaPER-1, blaVIM and blaIMP genes. Results: ESBL-positive isolates (n= 56) were detected. Among ESBL-positive isolates, 51 isolates were positive for blaCTX-M15 and one isolate was positive for both blaCTX-M-15 and blaOXA-1 genes. None of the isolates were positive for blaPER-1, blaVIM and blaIMP genes. PCR assay for phylotyping of isolates indicated that the isolates were belonged to groups A (54.16%), B1 (11.11%), B2 (12.96%) and D (21.75%). The isolates possessed blaCTX-M-15 gene were belonged to A (35 isolates), B1 (5), B2 (3) and D (8) phylo-groups. Conclusion: Our results indicate that blaCTX-M-15 gene is widespread among diarrheagenic E. coli isolates. ESBL-producing E. coli isolates were disseminated among a diversity of phylo-groups. Further studies are necessary to identify the ESBL genes in relation to phylogenetic groups. PMID:26328043

  8. Prevalence and Persistence of Escherichia coli Strains with Uropathogenic Virulence Characteristics in Sewage Treatment Plants▿

    PubMed Central

    Anastasi, E. M.; Matthews, B.; Gundogdu, A.; Vollmerhausen, T. L.; Ramos, N. L.; Stratton, H.; Ahmed, W.; Katouli, M.

    2010-01-01

    We investigated the prevalence and persistence of Escherichia coli strains in four sewage treatment plants (STPs) in a subtropical region of Queensland, Australia. In all, 264 E. coli strains were typed using a high-resolution biochemical fingerprinting method and grouped into either a single or a common biochemical phenotype (S-BPT and C-BPT, respectively). These strains were also tested for their phylogenetic groups and 12 virulence genes associated with intestinal and extraintestinal E. coli strains. Comparison of BPTs at various treatment stages indicated that certain BPTs were found in two or all treatment stages. These BPTs constituted the highest proportion of E. coli strains in each STP and belonged mainly to phylogenetic group B2 and, to a lesser extent, group D. No virulence genes associated with intestinal E. coli were found among the strains, but 157 (59.5%) strains belonging to 14 C-BPTs carried one or more virulence genes associated with uropathogenic strains. Of these, 120 (76.4%) strains belonged to seven persistent C-BPTs and were found in all four STPs. Our results indicate that certain clonal groups of E. coli with virulence characteristics of uropathogenic strains can survive the treatment processes of STPs. These strains were common to all STPs and constituted the highest proportion of the strains in different treatment tanks of each STP. PMID:20622128

  9. Inverse relation between disease severity and expression of the streptococcal cysteine protease, SpeB, among clonal M1T1 isolates recovered from invasive group A streptococcal infection cases.

    PubMed

    Kansal, R G; McGeer, A; Low, D E; Norrby-Teglund, A; Kotb, M

    2000-11-01

    The streptococcal cysteine protease (SpeB) is one of the major virulence factors produced by group A streptococci (GAS). In this study we investigated if differences exist in SpeB production by clonally related M1T1 clinical isolates derived from patients with invasive infections. Twenty-nine of these isolates were from nonsevere cases and 48 were from severe cases, including streptococcal toxic shock syndrome (STSS) and necrotizing fasciitis (NF) cases. The expression and amount of the 28-kDa SpeB protein produced were determined by quantitative Western blotting, and protease activity was measured by a fluorescent enzymatic assay. A high degree of variation in SpeB expression was seen among the isolates, and this variation seemed to correlate with the severity and/or clinical manifestation of the invasive infection. The mean amount of 28-kDa SpeB protein and cysteine protease activity produced by isolates from nonsevere cases was significantly higher than that from STSS cases (P = 0.001). This difference was partly due to the fact that 41% of STSS isolates produced little or no SpeB compared to only 14% of isolates recovered in nonsevere cases. Moreover, the cysteine protease activity among those isolates that expressed SpeB was significantly lower for STSS isolates than for isolates from nonsevere cases (P = 0.001). Increased SpeB production was also inversely correlated with intact M protein expression, and inhibition of cysteine protease activity blocked the cleavage of the surface M protein. Together, the data support the existence of both an "on-off" and a posttranslational regulatory mechanism(s) controlling SpeB production, and they suggest that isolates with the speB gene in the "off" state are more likely to spare the surface M protein and to be isolated from cases of severe rather than nonsevere invasive infection. These findings may have important implications for the role of SpeB in host-pathogen interactions via regulation of the expression of GAS

  10. Inverse Relation between Disease Severity and Expression of the Streptococcal Cysteine Protease, SpeB, among Clonal M1T1 Isolates Recovered from Invasive Group A Streptococcal Infection Cases

    PubMed Central

    Kansal, Rita G.; McGeer, Allison; Low, Donald E.; Norrby-Teglund, Anna; Kotb, Malak

    2000-01-01

    The streptococcal cysteine protease (SpeB) is one of the major virulence factors produced by group A streptococci (GAS). In this study we investigated if differences exist in SpeB production by clonally related M1T1 clinical isolates derived from patients with invasive infections. Twenty-nine of these isolates were from nonsevere cases and 48 were from severe cases, including streptococcal toxic shock syndrome (STSS) and necrotizing fasciitis (NF) cases. The expression and amount of the 28-kDa SpeB protein produced were determined by quantitative Western blotting, and protease activity was measured by a fluorescent enzymatic assay. A high degree of variation in SpeB expression was seen among the isolates, and this variation seemed to correlate with the severity and/or clinical manifestation of the invasive infection. The mean amount of 28-kDa SpeB protein and cysteine protease activity produced by isolates from nonsevere cases was significantly higher than that from STSS cases (P = 0.001). This difference was partly due to the fact that 41% of STSS isolates produced little or no SpeB compared to only 14% of isolates recovered in nonsevere cases. Moreover, the cysteine protease activity among those isolates that expressed SpeB was significantly lower for STSS isolates than for isolates from nonsevere cases (P = 0.001). Increased SpeB production was also inversely correlated with intact M protein expression, and inhibition of cysteine protease activity blocked the cleavage of the surface M protein. Together, the data support the existence of both an “on-off” and a posttranslational regulatory mechanism(s) controlling SpeB production, and they suggest that isolates with the speB gene in the “off” state are more likely to spare the surface M protein and to be isolated from cases of severe rather than nonsevere invasive infection. These findings may have important implications for the role of SpeB in host-pathogen interactions via regulation of the expression of

  11. Dissemination of multidrug-resistant Escherichia coli in Korean veterinary hospitals.

    PubMed

    So, Jeong Hwa; Kim, Juwon; Bae, Il Kwon; Jeong, Seok Hoon; Kim, So Hyun; Lim, Suk-kyung; Park, Yong Ho; Lee, Kyungwon

    2012-06-01

    This study was performed to investigate the prevalence of rectal colonization with multidrug-resistant Escherichia coli in dogs hospitalized at veterinary hospitals in Korea and to assess the molecular epidemiologic traits of this organism. A total of 63 unique E. coli isolates obtained from the rectal swabs of hospitalized dogs were analyzed. Genes encoding CTX-M extended-spectrum β-lactamases (ESBLs) and AmpC enzymes were detected in 21 (33.3%) and 15 (23.8%) canine E. coli isolates, respectively. Twelve canine E. coli isolates harbored both the genes encoding the CTX-M and AmpC enzymes. Six ESBL-producing E. coli isolates also carried the rmtB gene. All 24 E. coli isolates producing CTX-M ESBL and/or CMY-2 were resistant to ciprofloxacin. Furthermore, mutations were found in the gyrA and the parC genes. In most cases, the bla genes of the CTX-M ESBL and AmpC enzymes and the rmtB gene were localized to incompatibility group F (IncF) plasmids. Possible small clonal outbreaks are suggested because some E. coli isolates recovered in the same veterinary hospital were identified as identical sequence types and showed identical banding patterns in repetitive sequence-based polymerase chain reaction. The horizontal transfer of IncF plasmids and the clonal transfer of E. coli strains are suggested to play a role in the dissemination of antimicrobial resistance genes, and this transfer may occur across host species (i.e., between humans and dogs). PMID:22516765

  12. Molecular Epidemiology of Ceftiofur-Resistant Escherichia coli Isolates from Dairy Calves

    PubMed Central

    Donaldson, Sarah C.; Straley, Beth A.; Hegde, Narasimha V.; Sawant, Ashish A.; DebRoy, Chitrita; Jayarao, Bhushan M.

    2006-01-01

    Healthy calves (n = 96, 1 to 9 weeks old) from a dairy herd in central Pennsylvania were examined each month over a five-month period for fecal shedding of ceftiofur-resistant gram-negative bacteria. Ceftiofur-resistant Escherichia coli isolates (n = 122) were characterized by antimicrobial resistance (disk diffusion and MIC), serotype, pulsed-field gel electrophoresis subtypes, beta-lactamase genes, and virulence genes. Antibiotic disk diffusion assays showed that the isolates were resistant to ampicillin (100%), ceftiofur (100%), chloramphenicol (94%), florfenicol (93%), gentamicin (89%), spectinomycin (72%), tetracycline (98%), ticarcillin (99%), and ticarcillin-clavulanic acid (99%). All isolates were multidrug resistant and displayed elevated MICs. The E. coli isolates belonged to 42 serotypes, of which O8:H25 was the predominant serotype (49.2%). Pulsed-field gel electrophoresis classified the E. coli isolates into 27 profiles. Cluster analysis showed that 77 isolates (63.1%) belonged to one unique group. The prevalence of pathogenic E. coli was low (8%). A total of 117 ceftiofur-resistant E. coli isolates (96%) possessed the blaCMY2 gene. Based on phenotypic and genotypic characterization, the ceftiofur-resistant E. coli isolates belonged to 59 clonal types. There was no significant relationship between calf age and clonal type. The findings of this study revealed that healthy dairy calves were rapidly colonized by antibiotic-resistant strains of E. coli shortly after birth. The high prevalence of multidrug-resistant nonpathogenic E. coli in calves could be a significant source of resistance genes to other bacteria that share the same environment. PMID:16751500

  13. Capsular polysaccharide vaccine for Group B Neisseria meningitidis, Escherichia coli K1, and Pasteurella haemolytica A2

    PubMed Central

    Robbins, John B.; Schneerson, Rachel; Xie, Guilin; Hanson, Lars Å.; Miller, Mark A.

    2011-01-01

    We reviewed the literature that is the basis for our proposal that (2→8)-α-Neu5Ac conjugates will be safe and effective vaccines for Group B meningococci (GBMs), Escherichia coli K1, and Pasteurella haemolytica A2. Although (2→8)-α-Neu5Ac is a virulence factor and a protective antigen of these three pathogens, it is also a component of normal tissues (neural cell adhesion molecule). Natural, anti–(2→8)-α-Neu5Ac present in most adults, vaccine-induced antibodies, and even high levels of spontaneously appearing monoclonal anti–(2→8)-α-Neu5Ac did not cause autoimmunity. Although it is not possible to prove a null hypothesis, there are no epidemiologic, serologic, immunologic, or clinical data to indicate that (2→8)-α-Neu5Ac antibodies will induce pathology or an autoimmune disease. No increased pathology caused by these antibodies was found, even in neonates and infants of mothers recovered from GBM meningitis. The lack of pathology mediated by anti–(2→8)-α-Neu5Ac may be explained by different presentations of (2→8)-α-Neu5Ac on bacterial and mammalian cells and by the unusual physicochemical properties of anti–(2→8)-α-Neu5Ac. Based on clinical and experimental data collected over 30 y and because (2→8)-α-Neu5Ac is an essential virulence factor and a protective antigen for GBM, E. coli K1, and P. haemolytica A2, protein conjugates of it are easy to prepare using inexpensive and plentiful ingredients, and they would be compatible with routinely administered infant vaccines, clinical studies of these conjugates should proceed. PMID:22025709

  14. Pretransplant cytotoxic conditioning produces effects consistent with clonal deletion mechanisms.

    PubMed

    Zheng, T L; Johnson, C P; Sutherland, D E

    1987-05-01

    A rat cardiac allograft model (ACl to Lewis) was used to investigate the clonal deletion theory. Twelve groups of Lewis recipients received various combinations of donor-specific blood transfusions (DSTs), immediate post-DST immunosuppression with azathioprine/prednisone, and low-dose cyclosporine (1 mg/kg/day) posttransplant. DSTs and cyclosporine together gave modest prolongation of graft survival (from 6.0 to 17 days). DSTs plus immediate post-DST immunosuppression followed by low-dose cyclosporine prolonged graft survival to an average of 45 days. Third-party transfusions alone and in combination with immunosuppression did not significantly prolong allograft survival. Postoperative cyclosporine was required for the expression of this effect suggesting that clonal depression rather than clonal deletion had occurred. Combining DSTs with brief but intense preoperative immunosuppression may be a more effective method of pretransplant conditioning than DSTs alone. PMID:3295388

  15. Enhanced group II intron retrohoming in magnesium-deficient Escherichia coli via selection of mutations in the ribozyme core

    PubMed Central

    Truong, David M.; Sidote, David J.; Russell, Rick; Lambowitz, Alan M.

    2013-01-01

    Mobile group II introns are bacterial retrotransposons thought to be evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes. They consist of a catalytically active intron RNA (“ribozyme”) and an intron-encoded reverse transcriptase, which function together to promote RNA splicing and intron mobility via reverse splicing of the intron RNA into new DNA sites (“retrohoming”). Although group II introns are active in bacteria, their natural hosts, they function inefficiently in eukaryotes, where lower free Mg2+ concentrations decrease their ribozyme activity and constitute a natural barrier to group II intron proliferation within nuclear genomes. Here, we show that retrohoming of the Ll.LtrB group II intron is strongly inhibited in an Escherichia coli mutant lacking the Mg2+ transporter MgtA, and we use this system to select mutations in catalytic core domain V (DV) that partially rescue retrohoming at low Mg2+ concentrations. We thus identified mutations in the distal stem of DV that increase retrohoming efficiency in the MgtA mutant up to 22-fold. Biochemical assays of splicing and reverse splicing indicate that the mutations increase the fraction of intron RNA that folds into an active conformation at low Mg2+ concentrations, and terbium-cleavage assays suggest that this increase is due to enhanced Mg2+ binding to the distal stem of DV. Our findings indicate that DV is involved in a critical Mg2+-dependent RNA folding step in group II introns and demonstrate the feasibility of selecting intron variants that function more efficiently at low Mg2+ concentrations, with implications for evolution and potential applications in gene targeting. PMID:24043808

  16. Clonal Origin of Hepatocellular Carcinoma and Recurrence After Liver Transplantation.

    PubMed

    Wang, Zhenglu; Gong, Weihua; Shou, Dawei; Zhang, Luzhou; Gu, Xiangqian; Wang, Yuliang; Teng, Dahong; Zheng, Hong

    2016-01-01

    BACKGROUND This study aimed to determine whether patterns of tumor clonal origin in pluri-nodular hepatocellular carcinoma (PNHC) could serve as an indicator of tumor recurrence following liver transplantation. MATERIAL AND METHODS Tumor tissue samples from 60 PNHC patients who underwent liver transplantation were examined. The diagnosis of patients conformed to the University of California San Francisco (UCSF) standards for pluri-nodular hepatocellular carcinoma. We performed loss of heterozygosity tests at multiple microsatellite sites to determine the clonal origins of the tumors. Clinical information, pathological data, preoperative serum alpha-feto protein (AFP) and postoperative follow-ups were obtained and correlations between the clonal origin of the tumor, tumor-free survival, pathological characteristics, and AFP levels in serum were studied. RESULTS A total of 165 tumor nodules were collected. Tumor clonal origins were identified as intrahepatic metastasis (IM; 41.67%), multicentric occurrence (MO; 55%) or unidentified (3.33%). Three-year tumor-free survival for the IM group was 48% compared to 75.76% in the MO group (p<0.05), while the occurrence of microscopic tumor thrombus was 100% and 3.03% (p<0.05) for these groups, respectively. The degree of tumor differentiation was 80% for the IM group and 18.18% for the MO group (p<0.05), while the mean AFP concentration for these groups was 226.80 μg/L (2.78-3000 μg/L) and 24.59 μg/L (1.16-531. 30 μg/L; p<0.05), respectively. CONCLUSIONS Clonal origin patterns can serve as important indicators to predict the recurrence of PNHC following liver transplantation. Taken together with pathological characteristics and preoperative serum AFP levels, the risk of recurrence can be established in advance. PMID:27487734

  17. The population structure of Escherichia coli isolated from subtropical and temperate soils

    USGS Publications Warehouse

    Byappanahalli, Muruleedhara N.; Yan, Tao; Hamilton, Matthew J.; Ishii, Satoshi; Fujioka, Roger S.; Whitman, Richard L.; Sadowsky, Michael J.

    2012-01-01

    While genotypically-distinct naturalized Escherichia coli strains have been shown to occur in riparian soils of Lake Michigan and Lake Superior watersheds, comparative analyses of E. coli populations in diverse soils across a range of geographic and climatic conditions have not been investigated. The main objectives of this study were to: (a) examine the population structure and genetic relatedness of E. coli isolates collected from different soil types on a tropical island (Hawaii), and (b) determine if E. coli populations from Hawaii and temperate soils (Indiana, Minnesota) shared similar genotypes that may be reflective of biome-related soil conditions. DNA fingerprint and multivariate statistical analyses were used to examine the population structure and genotypic characteristics of the E. coli isolates. About 33% (98 of 293) of the E. coli from different soil types and locations on the island of Oahu, Hawaii, had unique DNA fingerprints, indicating that these bacteria were relatively diverse; the Shannon diversity index for the population was 4.03. Nearly 60% (171 of 293) of the E. coli isolates from Hawaii clustered into two major groups and the rest, with two or more isolates, fell into one of 22 smaller groups, or individual lineages. Multivariate analysis of variance of 89, 21, and 106 unique E. coli DNA fingerprints for Hawaii, Indiana, and Minnesota soils, respectively, showed that isolates formed tight cohesive groups, clustering mainly by location. However, there were several instances of clonal isolates being shared between geographically different locations. Thus, while nearly identical E. coli strains were shared between disparate climatologically- and geographically-distinct locations, a vast majority of the soil E. coli strains were genotypically diverse and were likely derived from separate lineages. This supports the hypothesis that these bacteria are not unique and multiple genotypes can readily adapt to become part of the soil autochthonous

  18. A Multi-Country Cross-Sectional Study of Vaginal Carriage of Group B Streptococci (GBS) and Escherichia coli in Resource-Poor Settings: Prevalences and Risk Factors

    PubMed Central

    Cools, Piet; Jespers, Vicky; Hardy, Liselotte; Crucitti, Tania; Delany-Moretlwe, Sinead; Mwaura, Mary; Ndayisaba, Gilles F.; van de Wijgert, Janneke H. H. M.; Vaneechoutte, Mario

    2016-01-01

    Background One million neonates die each year in low- and middle-income countries because of neonatal sepsis; group B Streptococcus (GBS) and Escherichia coli are the leading causes. In sub-Saharan Africa, epidemiological data on vaginal GBS and E. coli carriage, a prerequisite for GBS and E. coli neonatal sepsis, respectively, are scarce but necessary to design and implement prevention strategies. Therefore, we assessed vaginal GBS and E. coli carriage rates and risk factors and the GBS serotype distribution in three sub-Saharan countries. Methods A total of 430 women from Kenya, Rwanda and South Africa were studied cross-sectionally. Vaginal carriage of GBS and E. coli, and GBS serotype were assessed using molecular techniques. Risk factors for carriage were identified using multivariable logistic regression analysis. Results Vaginal carriage rates in reference groups from Kenya and South Africa were 20.2% (95% CI, 13.7–28.7%) and 23.1% (95% CI, 16.2–31.9%), respectively for GBS; and 25.0% (95% CI, 17.8–33.9%) and 27.1% (95% CI, 19.6–36.2%), respectively for E. coli. GBS serotypes Ia (36.8%), V (26.3%) and III (14.0%) were most prevalent. Factors independently associated with GBS and E. coli carriage were Candida albicans, an intermediate vaginal microbiome, bacterial vaginosis, recent vaginal intercourse, vaginal washing, cervical ectopy and working as a sex worker. GBS and E. coli carriage were positively associated. Conclusions Reduced vaginal GBS carriage rates might be accomplished by advocating behavioral changes such as abstinence from sexual intercourse and by avoidance of vaginal washing during late pregnancy. It might be advisable to explore the inclusion of vaginal carriage of C. albicans, GBS, E. coli and of the presence of cervical ectopy in a risk- and/or screening-based administration of antibiotic prophylaxis. Current phase II GBS vaccines (a trivalent vaccine targeting serotypes Ia, Ib, and III, and a conjugate vaccine targeting serotype

  19. High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease

    PubMed Central

    Kotlowski, Roman; Bernstein, Charles N; Sepehri, Shadi; Krause, Denis O

    2007-01-01

    Background It is not clear which species of bacteria may be involved in inflammatory bowel disease (IBD). One way of determining which bacteria might be likely candidates is to use culture‐independent methods to identify microorganisms that are present in diseased tissues but not in controls. Aims (1) To assess the diversity of microbial communities of biopsy tissue using culture‐independent methods; (2) to culture the bacteria found in the tissues of patients with IBD but not in the controls; (3) to identify potential virulence factors associated with cultured bacteria. Methods 84 biopsy specimens were collected from 15 controls, 13 patients with Crohn's disease (CD) and 19 patients with ulcerative colitis (UC) from a population‐based case–control study. Ribosomal intergenic spacer analysis (RISA) was conducted to identify unique DNA bands in tissues from patients with CD and UC that did not appear in controls. Results RISA followed by DNA sequencing identified unique bands in biopsy specimens from patients with IBD that were classified as Escherichia coli. Targeted culture showed a significantly (p<0.05) higher number of Enterobacteriaceae in specimens from patients with IBD. The B2+D phylogenetic group, serine protease autotransporters (SPATE) and adherence factors were more likely to be associated with tissues from patients with UC and CD than with controls. Conclusions The abundance of Enterobacteriaceae is 3–4 logs higher in tissues of patients with IBD and the B2+D phylogenetic groups are more prevalent in patients with UC and CD. The B2+D phylogenetic groups are associated with SPATE and adherence factors and may have a significant role in disease aetiology. PMID:17028128

  20. Feeding the Probiotic Enterococcus faecium Strain NCIMB 10415 to Piglets Specifically Reduces the Number of Escherichia coli Pathotypes That Adhere to the Gut Mucosa

    PubMed Central

    Guenther, Sebastian; Oelgeschläger, Kathrin; Kinnemann, Bianca; Pieper, Robert; Hartmann, Susanne; Tedin, Karsten; Semmler, Torsten; Neumann, Konrad; Schierack, Peter; Bethe, Astrid; Wieler, Lothar H.

    2013-01-01

    Feed supplementation with the probiotic Enterococcus faecium for piglets has been found to reduce pathogenic gut microorganisms. Since Escherichia coli is among the most important pathogens in pig production, we performed comprehensive analyses to gain further insight into the influence of E. faecium NCIMB 10415 on porcine intestinal E. coli. A total of 1,436 E. coli strains were isolated from three intestinal habitats (mucosa, digesta, and feces) of probiotic-supplemented and nonsupplemented (control) piglets. E. coli bacteria were characterized via pulsed-field gel electrophoresis (PFGE) for clonal analysis. The high diversity of E. coli was reflected by 168 clones. Multilocus sequence typing (MLST) was used to determine the phylogenetic backgrounds, revealing 79 sequence types (STs). Pathotypes of E. coli were further defined using multiplex PCR for virulence-associated genes. While these analyses discerned only a few significant differences in the E. coli population between the feeding groups, analyses distinguishing clones that were uniquely isolated in either the probiotic group only, the control group only, or both groups (shared group) revealed clear effects at the habitat level. Interestingly, extraintestinal pathogenic E. coli (ExPEC)-typical clones adhering to the mucosa were significantly reduced in the probiotic group. Our data show a minor influence of E. faecium on the overall population of E. coli in healthy piglets. In contrast, this probiotic has a profound effect on mucosa-adherent E. coli. This finding further substantiates a specific effect of E. faecium strain NCIMB 10415 in piglets against pathogenic E. coli in the intestine. In addition, these data question the relevance of data based on sampling fecal E. coli only. PMID:24123741

  1. Comparative Genomic Indexing Reveals the Phylogenomics of Escherichia coli Pathogens

    PubMed Central

    Anjum, Muna F.; Lucchini, Sacha; Thompson, Arthur; Hinton, Jay C. D.; Woodward, Martin J.

    2003-01-01

    The Escherichia coli O26 serogroup includes important food-borne pathogens associated with human and animal diarrheal disease. Current typing methods have revealed great genetic heterogeneity within the O26 group; the data are often inconsistent and focus only on verotoxin (VT)-positive O26 isolates. To improve current understanding of diversity within this serogroup, the genomic relatedness of VT-positive and -negative O26 strains was assessed by comparative genomic indexing. Our results clearly demonstrate that irrespective of virulence characteristics and pathotype designation, the O26 strains show greater genomic similarity to each other than to any other strain included in this study. Our data suggest that enteropathogenic and VT-expressing E. coli O26 strains represent the same clonal lineage and that VT-expressing E. coli O26 strains have gained additional virulence characteristics. Using this approach, we established the core genes which are central to the E. coli species and identified regions of variation from the E. coli K-12 chromosomal backbone. PMID:12874348

  2. Extended spectrum beta-lactamase and fluoroquinolone resistance genes and plasmids among Escherichia coli isolates from zoo animals, Czech Republic.

    PubMed

    Dobiasova, Hana; Dolejska, Monika; Jamborova, Ivana; Brhelova, Eva; Blazkova, Lucie; Papousek, Ivo; Kozlova, Marketa; Klimes, Jiri; Cizek, Alois; Literak, Ivan

    2013-09-01

    Commensal Escherichia coli isolates from healthy zoo animals kept in Ostrava Zoological Garden, Czech Republic, were investigated to evaluate the dissemination of extended-spectrum beta-lactamase (ESBL) and plasmid-mediated quinolone resistance (PMQR) genes. A total of 160 faecal samples of various animal species were inoculated onto MacConkey agar with cefotaxime (2 mg L(-1)) or ciprofloxacin (0.05 mg L(-1)) to obtain ESBL- or PMQR-positive E. coli isolates. Clonality of E. coli isolates was investigated by multilocus sequence typing and pulsed-field gel electrophoresis. Plasmids carrying ESBL or PMQR genes were typed by PCR-based replicon typing, plasmid multilocus sequence typing and restriction fragment length polymorphism. Forty-nine (71%, n = 69) cefotaxime-resistant and 15 (16%, n = 94) ciprofloxacin-resistant E. coli isolates harboured ESBL or PMQR genes. Isolates were assigned to 18 sequence types (ST) and 20 clusters according to their macrorestriction patterns by pulsed-field gel electrophoresis. The genes blaCTX -M-1 and qnrS1 were detected on highly related IncI1 plasmids assigned to clonal complex 3 (ST3, ST38) and on non-related IncN plasmids of ST1 and ST3, respectively. The gene qnrS1 was located on related IncX1 plasmids. Dissemination of antibiotic resistance is associated with spreading of particular E. coli clones and plasmids of specific incompatibility groups among various animal species. PMID:23679004

  3. The Widespread Presence of a Multidrug-Resistant Escherichia coli ST131 Clade among Community-Associated and Hospitalized Patients

    PubMed Central

    den Reijer, P. Martijn; van Burgh, Sebastian; Burggraaf, Arjan; Ossewaarde, Jacobus M.; van der Zee, Anneke

    2016-01-01

    Background & Aims The extent of entry of multidrug-resistant Escherichia coli from the community into the hospital and subsequent clonal spread amongst patients is unclear. To investigate the extent and direction of clonal spread of these bacteria within a large teaching hospital, we prospectively genotyped multidrug-resistant E. coli obtained from community- and hospital associated patient groups and compared the distribution of diverse genetic markers. Methods A total of 222 E. coli, classified as multi-drug resistant according to national guidelines, were retrieved from both screening (n = 184) and non-screening clinical cultures (n = 38) from outpatients and patients hospitalized for various periods. All isolates were routinely genotyped using an amplified fragment length polymorphism (AFLP) assay and real-time PCR for CTX-M genes. Multi-locus sequence typing was additionally performed to confirm clusters. Based on demographics, patients were categorized into two groups: patients that were not hospitalized or less than 72 hours at time of strain isolation (group I) and patients that were hospitalized for at least 72 hours (group II). Results Genotyping showed that most multi-drug resistant E. coli either had unique AFLP profiles or grouped in small clusters of maximally 8 isolates. We identified one large ST131 clade comprising 31% of all isolates, containing several AFLP clusters with similar profiles. Although different AFLP clusters were found in the two patient groups, overall genetic heterogeneity was similar (35% vs 28% of isolates containing unique AFLP profiles, respectively). In addition, similar distributions of CTX-M groups, including CTX-M 15 (40% and 44% of isolates in group I and II, respectively) and ST131 (32% and 30% of isolates, respectively) were found. Conclusion We conclude that multi-drug resistant E. coli from the CTX-M 15 associated lineage ST131 are widespread amongst both community- and hospital associated patient groups, with similar

  4. Recurrent Escherichia coli bacteremia.

    PubMed Central

    Maslow, J N; Mulligan, M E; Arbeit, R D

    1994-01-01

    Escherichia coli is the most common gram-negative organism associated with bacteremia. While recurrent E. coli urinary tract infections are well-described, recurrent E. coli bacteremia appears to be uncommon, with no episodes noted in multiple series of patients with gram-negative bacteremias. We report on 5 patients with recurrent bloodstream infections identified from a series of 163 patients with E. coli bacteremia. For each patient, the isolates from each episode were analyzed by pulsed-field gel electrophoresis (PFGE) and ribotyping and for the presence of E. coli virulence factors. For each of four patients, the index and recurrent episodes of bacteremia represented the same strain as defined by PFGE, and the strains were found to carry one or more virulence factors. The remaining patient, with two episodes of bloodstream infection separated by a 4-year interval, was infected with two isolates that did not carry any virulence factors and that were clonally related by ribotype analysis but differed by PFGE. All five patients had either a local host defense defect (three patients) or impaired systemic defenses (one patient) or both (one patient). Thus, recurrent E. coli bacteremia is likely to represent a multifactorial process that occurs in patients with impaired host defenses who are infected with virulent isolates. Images PMID:7910828

  5. Characteristics of CTX-M Extended-Spectrum β-Lactamase-Producing Escherichia coli Strains Isolated from Multiple Rivers in Southern Taiwan.

    PubMed

    Chen, Po-An; Hung, Chih-Hsin; Huang, Ping-Chih; Chen, Jung-Ren; Huang, I-Fei; Chen, Wan-Ling; Chiou, Yee-Hsuan; Hung, Wan-Yu; Wang, Jiun-Ling; Cheng, Ming-Fang

    2016-03-01

    Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli sequence type ST131 has emerged as the leading cause of community-acquired urinary tract infections and bacteremia worldwide. Whether environmental water is a potential reservoir of these strains remains unclear. River water samples were collected from 40 stations in southern Taiwan from February to August 2014. PCR assay and multilocus sequence typing (MLST) analysis were conducted to determine the CTX-M group and sequence type, respectively. In addition, we identified the seasonal frequency of ESBL-producing E. coli strains and their geographical relationship with runoffs from livestock and poultry farms between February and August 2014. ESBL-producing E. coli accounted for 30% of the 621 E. coli strains isolated from river water in southern Taiwan. ESBL-producing E. coli ST131 was not detected among the isolates. The most commonly detected strain was E. coli CTX-M group 9. Among the 92 isolates selected for MLST analysis, the most common ESBL-producing clonal complexes were ST10 and ST58. The proportion of ESBL-producing E. coli was significantly higher in areas with a lower river pollution index (P = 0.025) and regions with a large number of chickens being raised (P = 0.013). ESBL-producing E. coli strains were commonly isolated from river waters in southern Taiwan. The most commonly isolated ESBL-producing clonal complexes were ST10 and ST58, which were geographically related to chicken farms. ESBL-producing E. coli ST131, the major clone causing community-acquired infections in Taiwan and worldwide, was not detected in river waters. PMID:26773082

  6. How clonal are bacteria over time?

    PubMed

    Shapiro, B Jesse

    2016-06-01

    Bacteria and archaea reproduce clonally (vertical descent), but exchange genes by recombination (horizontal transfer). Recombination allows adaptive mutations or genes to spread rapidly within (or even between) species, and reduces the burden of deleterious mutations. Clonality-defined here as the balance between vertical and horizontal inheritance-is therefore a key microbial trait, determining how quickly a population can adapt and the size of its gene pool. Here, I discuss whether clonality varies over time and if it can be considered a stable trait of a given population. I show that, in some cases, clonality is clearly not static. For example, non-clonal (highly recombining) populations can give rise to clonal expansions, often of pathogens. However, an analysis of time-course metagenomic data from a lake suggests that a bacterial population's past clonality (as measured by its genetic diversity) is a good predictor of its future clonality. Clonality therefore appears to be relatively-but not completely-stable over evolutionary time. PMID:27057964

  7. Generation of clonal zebrafish line by androgenesis without egg irradiation.

    PubMed

    Hou, Jilun; Fujimoto, Takafumi; Saito, Taiju; Yamaha, Etsuro; Arai, Katsutoshi

    2015-01-01

    Generation of clonal zebrafish will facilitate large-scale genetic screening and help us to overcome other biological and biotechnological challenges due to their isogenecity. However, protocols for the development of clonal lines have not been optimized. Here, we sought to develop a novel method for generation of clonal zebrafish by androgenesis induced by cold shock. Androgenetic zebrafish doubled haploids (DHs) were induced by cold shock of just-fertilized eggs, and the eggs were then heat shocked to double the chromosome set. The yield rate of putative DHs relative to the total number of eggs used was 1.10% ± 0.19%. Microsatellite genotyping of the putative DHs using 30 loci that covered all 25 linkage groups detected no heterozygous loci, confirming the homozygosity of the DHs. Thus, a clonal line was established from sperm of a DH through a second cycle of cold-shock androgenesis and heat-shock chromosome doubling, followed by genetic verification of the isogenic rate confirming the presence of identical DNA fingerprints by using amplified fragment length polymorphism markers. In addition, our data provided important insights into the cytological mechanisms of cold-shock-induced androgenesis. PMID:26289165

  8. Generation of clonal zebrafish line by androgenesis without egg irradiation

    PubMed Central

    Hou, Jilun; Fujimoto, Takafumi; Saito, Taiju; Yamaha, Etsuro; Arai, Katsutoshi

    2015-01-01

    Generation of clonal zebrafish will facilitate large-scale genetic screening and help us to overcome other biological and biotechnological challenges due to their isogenecity. However, protocols for the development of clonal lines have not been optimized. Here, we sought to develop a novel method for generation of clonal zebrafish by androgenesis induced by cold shock. Androgenetic zebrafish doubled haploids (DHs) were induced by cold shock of just-fertilized eggs, and the eggs were then heat shocked to double the chromosome set. The yield rate of putative DHs relative to the total number of eggs used was 1.10% ± 0.19%. Microsatellite genotyping of the putative DHs using 30 loci that covered all 25 linkage groups detected no heterozygous loci, confirming the homozygosity of the DHs. Thus, a clonal line was established from sperm of a DH through a second cycle of cold-shock androgenesis and heat-shock chromosome doubling, followed by genetic verification of the isogenic rate confirming the presence of identical DNA fingerprints by using amplified fragment length polymorphism markers. In addition, our data provided important insights into the cytological mechanisms of cold-shock–induced androgenesis. PMID:26289165

  9. A New Clone Sweeps Clean: the Enigmatic Emergence of Escherichia coli Sequence Type 131

    PubMed Central

    Johnson, James R.

    2014-01-01

    Escherichia coli sequence type 131 (ST131) is an extensively antimicrobial-resistant E. coli clonal group that has spread explosively throughout the world. Recent molecular epidemiologic and whole-genome phylogenetic studies have elucidated the fine clonal structure of ST131, which comprises multiple ST131 subclones with distinctive resistance profiles, including the (nested) H30, H30-R, and H30-Rx subclones. The most prevalent ST131 subclone, H30, arose from a single common fluoroquinolone (FQ)-susceptible ancestor containing allele 30 of fimH (type 1 fimbrial adhesin gene). An early H30 subclone member acquired FQ resistance and launched the rapid expansion of the resulting FQ-resistant subclone, H30-R. Subsequently, a member of H30-R acquired the CTX-M-15 extended-spectrum beta-lactamase and launched the rapid expansion of the CTX-M-15-containing subclone within H30-R, H30-Rx. Clonal expansion clearly is now the dominant mechanism for the rising prevalence of both FQ resistance and CTX-M-15 production in ST131 and in E. coli generally. Reasons for the successful dissemination and expansion of the key ST131 subclones remain undefined but may include increased transmissibility, greater ability to colonize and/or persist in the intestine or urinary tract, enhanced virulence, and more-extensive antimicrobial resistance compared to other E. coli. Here we discuss the epidemiology and molecular phylogeny of ST131 and its key subclones, possible mechanisms for their ecological success, implications of their widespread dissemination, and future research needs. PMID:24867985

  10. Molecular characterization of multiresistant Escherichia coli producing or not extended-spectrum β-lactamases

    PubMed Central

    2013-01-01

    Background The prevalence and type of plasmids, resistance genes and integrons carried by two collections of multiresistant E. coli producing or not extended-spectrum β-lactamases have been compared. Rep-PCR was used to determine the clonal relationship of the organisms. Plasmids were classified according to their incompatibility. Class 1 and Class 2 integrons and antibiotic resistance genes were analysed by PCR and sequencing. Results Both collections of organisms contained a large diversity of unrelated strains with some clones distributed in both groups of isolates. Large plasmids were identified in the two groups of organisms. Plasmids with replicons repK and repColE were more frequent among ESBL-producing isolates, while repFIA, repFII and repA/C replicons were more frequent in isolates lacking ESBL. Conjugative plasmids with repK and repA/C replicons coded for CTX-M-14 and CMY-2 β-lactamases, respectively. No significant differences were observed in the distribution of class 1 and class 2 integrons among multiresistant E. coli producing or not ESBL, and dfrA17-ant(3″)-Ie was the cassette arrangement most commonly found. Conclusions In the concrete temporal and geographical context of this study, multiresistant E. coli producing ESBL or other mechanisms of resistance were largely clonally diverse and present some differences in the types of harboured plasmids. Still, some clones were found in both ESBL-producing and –lacking isolates. PMID:23586437

  11. Clonal Dissemination of Enterobacter cloacae Harboring blaKPC-3 in the Upper Midwestern United States

    PubMed Central

    Hargreaves, Melissa L.; Shaw, Kristin M.; Dobbins, Ginette; Snippes Vagnone, Paula M.; Harper, Jane E.; Boxrud, Dave; Lynfield, Ruth; Aziz, Maliha; Price, Lance B.; Silverstein, Kevin A. T.; Danzeisen, Jessica L.; Youmans, Bonnie; Case, Kyle; Sreevatsan, Srinand

    2015-01-01

    Carbapenemase-producing, carbapenem-resistant Enterobacteriaceae, or CP-CRE, are an emerging threat to human and animal health, because they are resistant to many of the last-line antimicrobials available for disease treatment. Carbapenemase-producing Enterobacter cloacae harboring blaKPC-3 recently was reported in the upper midwestern United States and implicated in a hospital outbreak in Fargo, North Dakota (L. M. Kiedrowski, D. M. Guerrero, F. Perez, R. A. Viau, L. J. Rojas, M. F. Mojica, S. D. Rudin, A. M. Hujer, S. H. Marshall, and R. A. Bonomo, Emerg Infect Dis 20:1583–1585, 2014, http://dx.doi.org/10.3201/eid2009.140344). In early 2009, the Minnesota Department of Health began collecting and screening CP-CRE from patients throughout Minnesota. Here, we analyzed a retrospective group of CP-E. cloacae isolates (n = 34) collected between 2009 and 2013. Whole-genome sequencing and analysis revealed that 32 of the strains were clonal, belonging to the ST171 clonal complex and differing collectively by 211 single-nucleotide polymorphisms, and it revealed a dynamic clone under positive selection. The phylogeography of these strains suggests that this clone existed in eastern North Dakota and western Minnesota prior to 2009 and subsequently was identified in the Minneapolis and St. Paul metropolitan area. All strains harbored identical IncFIA-like plasmids conferring a CP-CRE phenotype and an additional IncX3 plasmid. In a single patient with multiple isolates submitted over several months, we found evidence that these plasmids had transferred from the E. cloacae clone to an Escherichia coli ST131 bacterium, rendering it as a CP-CRE. The spread of this clone throughout the upper midwestern United States is unprecedented for E. cloacae and highlights the importance of continued surveillance to identify such threats to human health. PMID:26438492

  12. Ecological Consequences of Clonal Integration in Plants

    PubMed Central

    Liu, Fenghong; Liu, Jian; Dong, Ming

    2016-01-01

    Clonal plants are widespread throughout the plant kingdom and dominate in diverse habitats. Spatiotemporal heterogeneity of environment is pervasive at multiple scales, even at scales relevant to individual plants. Clonal integration refers to resource translocation and information communication among the ramets of clonal plants. Due to clonal integration, clonal plant species possess a series of peculiar attributes: plasticity in response to local and non-local conditions, labor division with organ specialization for acquiring locally abundant resources, foraging behavior by selective placement of ramets in resource-rich microhabitats, and avoidance of intraclonal competition. Clonal integration has very profound ecological consequences for clonal plants. It allows them to efficiently cope with environmental heterogeneity, by alleviating local resource shortages, buffering environmental stresses and disturbances, influencing competitive ability, increasing invasiveness, and altering species composition and invasibility at the community level. In this paper, we present a comprehensive review of research on the ecological consequences of plant clonal integration based on a large body of literature. We also attempt to propose perspectives for future research. PMID:27446093

  13. African 2, a Clonal Complex of Mycobacterium bovis Epidemiologically Important in East Africa▿ †

    PubMed Central

    Berg, Stefan; Garcia-Pelayo, M. Carmen; Müller, Borna; Hailu, Elena; Asiimwe, Benon; Kremer, Kristin; Dale, James; Boniotti, M. Beatrice; Rodriguez, Sabrina; Hilty, Markus; Rigouts, Leen; Firdessa, Rebuma; Machado, Adelina; Mucavele, Custodia; Ngandolo, Bongo Nare Richard; Bruchfeld, Judith; Boschiroli, Laura; Müller, Annélle; Sahraoui, Naima; Pacciarini, Maria; Cadmus, Simeon; Joloba, Moses; van Soolingen, Dick; Michel, Anita L.; Djønne, Berit; Aranaz, Alicia; Zinsstag, Jakob; van Helden, Paul; Portaels, Françoise; Kazwala, Rudovick; Källenius, Gunilla; Hewinson, R. Glyn; Aseffa, Abraham; Gordon, Stephen V.; Smith, Noel H.

    2011-01-01

    We have identified a clonal complex of Mycobacterium bovis isolated at high frequency from cattle in Uganda, Burundi, Tanzania, and Ethiopia. We have named this related group of M. bovis strains the African 2 (Af2) clonal complex of M. bovis. Af2 strains are defined by a specific chromosomal deletion (RDAf2) and can be identified by the absence of spacers 3 to 7 in their spoligotype patterns. Deletion analysis of M. bovis isolates from Algeria, Mali, Chad, Nigeria, Cameroon, South Africa, and Mozambique did not identify any strains of the Af2 clonal complex, suggesting that this clonal complex of M. bovis is localized in East Africa. The specific spoligotype pattern of the Af2 clonal complex was rarely identified among isolates from outside Africa, and the few isolates that were found and tested were intact at the RDAf2 locus. We conclude that the Af2 clonal complex is localized to cattle in East Africa. We found that strains of the Af2 clonal complex of M. bovis have, in general, four or more copies of the insertion sequence IS6110, in contrast to the majority of M. bovis strains isolated from cattle, which are thought to carry only one or a few copies. PMID:21097608

  14. Characterization of Two New CTX-M-25-Group Extended-Spectrum β-Lactamase Variants Identified in Escherichia coli Isolates from Israel

    PubMed Central

    Vervoort, Jascha; Baraniak, Anna; Gazin, Muriel; Sabirova, Julia; Lammens, Christine; Kazma, Meital; Grabowska, Anna; Izdebski, Radosław; Carmeli, Yehuda; Kumar-Singh, Samir; Gniadkowski, Marek; Goossens, Herman; Malhotra-Kumar, Surbhi

    2012-01-01

    Objectives We characterized two new CTX-M-type extended-spectrum β-lactamase (ESBL) variants in Escherichia coli isolates from stool samples of two elderly patients admitted at the Tel Aviv Sourasky Medical Center, Israel. Both patients underwent treatment with cephalosporins prior to isolation of the E. coli strains. Methods ESBLs were detected by the double-disk synergy test and PCR-sequencing of β-lactamase genes. The blaCTX-M genes were cloned into the pCR-BluntII-TOPO vector in E. coli TOP10. The role of amino-acid substitutions V77A and D240G was analyzed by site-directed mutagenesis of the blaCTX-M-94 and blaCTX-M-100 genes and comparative characterization of the resulting E. coli recombinants. MICs of β-lactams were determined by Etest. Plasmid profiling, mating experiments, replicon typing and sequencing of blaCTX-M flanking regions were performed to identify the genetic background of the new CTX-M variants. Results The novel CTX-M β-lactamases, CTX-M-94 and -100, belonged to the CTX-M-25-group. Both variants differed from CTX-M-25 by the substitution V77A, and from CTX-M-39 by D240G. CTX-M-94 differed from all CTX-M-25-group enzymes by the substitution F119L. Glycine-240 was associated with reduced susceptibility to ceftazidime and leucine-119 with increased resistance to ceftriaxone. blaCTX-M-94 and blaCTX-M-100 were located within ISEcp1 transposition units inserted into ∼93 kb non-conjugative IncFI and ∼130 kb conjugative IncA/C plasmids, respectively. The plasmids carried also different class 1 integrons. Conclusions This is the first report on CTX-M-94 and -100 ESBLs, novel members of the CTX-M-25-group. PMID:23050014

  15. In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles.

    PubMed

    Bielecki, Piotr; Muthukumarasamy, Uthayakumar; Eckweiler, Denitsa; Bielecka, Agata; Pohl, Sarah; Schanz, Ansgar; Niemeyer, Ute; Oumeraci, Tonio; von Neuhoff, Nils; Ghigo, Jean-Marc; Häussler, Susanne

    2014-01-01

    mRNA profiling of pathogens during the course of human infections gives detailed information on the expression levels of relevant genes that drive pathogenicity and adaptation and at the same time allows for the delineation of phylogenetic relatedness of pathogens that cause specific diseases. In this study, we used mRNA sequencing to acquire information on the expression of Escherichia coli pathogenicity genes during urinary tract infections (UTI) in humans and to assign the UTI-associated E. coli isolates to different phylogenetic groups. Whereas the in vivo gene expression profiles of the majority of genes were conserved among 21 E. coli strains in the urine of elderly patients suffering from an acute UTI, the specific gene expression profiles of the flexible genomes was diverse and reflected phylogenetic relationships. Furthermore, genes transcribed in vivo relative to laboratory media included well-described virulence factors, small regulatory RNAs, as well as genes not previously linked to bacterial virulence. Knowledge on relevant transcriptional responses that drive pathogenicity and adaptation of isolates to the human host might lead to the introduction of a virulence typing strategy into clinical microbiology, potentially facilitating management and prevention of the disease. Importance: Urinary tract infections (UTI) are very common; at least half of all women experience UTI, most of which are caused by pathogenic Escherichia coli strains. In this study, we applied massive parallel cDNA sequencing (RNA-seq) to provide unbiased, deep, and accurate insight into the nature and the dimension of the uropathogenic E. coli gene expression profile during an acute UTI within the human host. This work was undertaken to identify key players in physiological adaptation processes and, hence, potential targets for new infection prevention and therapy interventions specifically aimed at sabotaging bacterial adaptation to the human host. PMID:25096872

  16. Clonal Integration Enhances the Performance of a Clonal Plant Species under Soil Alkalinity Stress

    PubMed Central

    Sun, Juanjuan; Chen, Jishan; Zhang, Yingjun

    2015-01-01

    Clonal plants have been shown to successfully survive in stressful environments, including salinity stress, drought and depleted nutrients through clonal integration between original and subsequent ramets. However, relatively little is known about whether clonal integration can enhance the performance of clonal plants under alkalinity stress. We investigated the effect of clonal integration on the performance of a typical rhizomatous clonal plant, Leymus chinensis, using a factorial experimental design with four levels of alkalinity and two levels of rhizome connection treatments, connected (allowing integration) and severed (preventing integration). Clonal integration was estimated by comparing physiological and biomass features between the rhizome-connected and rhizome-severed treatments. We found that rhizome-connected treatment increased the biomass, height and leaf water potential of subsequent ramets at highly alkalinity treatments but did not affect them at low alkalinity treatments. However, rhizome-connected treatment decreased the root biomass of subsequent ramets and did not influence the photosynthetic rates of subsequent ramets. The biomass of original ramets was reduced by rhizome-connected treatment at the highest alkalinity level. These results suggest that clonal integration can increase the performance of clonal plants under alkalinity stress. Rhizome-connected plants showed dramatically increased survival of buds with negative effects on root weight, indicating that clonal integration influenced the resource allocation pattern of clonal plants. A cost-benefit analysis based on biomass measures showed that original and subsequent ramets significantly benefited from clonal integration in highly alkalinity stress, indicating that clonal integration is an important adaptive strategy by which clonal plants could survive in local alkalinity soil. PMID:25790352

  17. Clonal growth and plant species abundance

    PubMed Central

    Herben, Tomáš; Nováková, Zuzana; Klimešová, Jitka

    2014-01-01

    Background and Aims Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf–height–seed) traits and by actual performance in the botanical garden. Methods Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area – height – seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. Key Results After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. Conclusions Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially

  18. PyClone: Statistical inference of clonal population structure in cancer

    PubMed Central

    Roth, Andrew; Khattra, Jaswinder; Yap, Damian; Wan, Adrian; Laks, Emma; Biele, Justina; Ha, Gavin; Aparicio, Samuel; Bouchard-Côté, Alexandre; Shah, Sohrab P.

    2016-01-01

    We introduce a novel statistical method, PyClone, for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy number changes and normal cell contamination. Single cell sequencing validation demonstrates that PyClone infers accurate clustering of mutations that co-occur in individual cells. PMID:24633410

  19. Clonal Evolution in Multiple Myeloma.

    PubMed

    Fakhri, Bita; Vij, Ravi

    2016-08-01

    Multiple myeloma (MM) is the second most common hematologic malignancy encountered among patients in the United States. The last decade has seen incremental improvements in the survival of patients with MM. These advances are, to a large extent, attributable to the addition of proteasome inhibitors and immunomodulatory drugs to the armamentarium of treatment options. The adoption of these drug classes was the result of an empiric research paradigm. However, with the application of next generation sequencing technologies, we are now starting to unravel the genomic landscape of MM. It is hoped that this will allow us to better disentangle the biology of the disease and allow for identification of new therapeutic targets. In this article, we review what we have learned to date about the mutational profile, clonal architecture, and evolution of the disease, and discuss the potential clinical implications of these findings. PMID:27521309

  20. Polymorphism, duplication, and IS1-mediated rearrangement in the chromosomal his-rfb-gnd region of Escherichia coli strains with group IA and capsular K antigens.

    PubMed

    Drummelsmith, J; Amor, P A; Whitfield, C

    1997-05-01

    Individual Escherichia coli strains produce several cell surface polysaccharides. In E. coli E69, the his region of the chromosome contains the rfb (serotype O9 lipopolysaccharide O-antigen biosynthesis) and cps (serotype K30 group IA capsular polysaccharide biosynthesis) loci. Polymorphisms in this region of the Escherichia coli chromosome reflect extensive antigenic diversity in the species. Previously, we reported a duplication of the manC-manB genes, encoding enzymes involved in GDP-mannose formation, upstream of rfb in strain E69 (P. Jayaratne et al., J. Bacteriol. 176:3126-3139, 1994). Here we show that one of the manC-manB copies is flanked by IS1 elements, providing a potential mechanism for the gene duplication. Adjacent to manB1 on the IS1-flanked segment is a further open reading frame (ugd), encoding uridine-5'-diphosphoglucose dehydrogenase. The Ugd enzyme is responsible for the production of UDP-glucuronic acid, a precursor required for K30 antigen synthesis. Construction of a chromosomal ugd::Gm(r) insertion mutation demonstrated the essential role for Ugd in the biosynthesis of the K30 antigen and confirmed that there is no additional functional ugd copy in strain E69. PCR amplification and Southern hybridization were used to examine the distribution of IS1 elements and ugd genes in the vicinity of rfb in other E. coli strains, producing different group IA K antigens. The relative order of genes and, where present, IS1 elements was established in these strains. The regions adjacent to rfb in these strains are highly variable in both size and gene order, but in all cases where a ugd homolog was present, it was found near rfb. The presence of IS1 elements in the rfb regions of several of these strains provides a potential mechanism for recombination and deletion events which could contribute to the antigenic diversity seen in surface polysaccharides. PMID:9150218

  1. Extraintestinal Pathogenic and Antimicrobial-Resistant Escherichia coli Contamination of 56 Public Restrooms in the Greater Minneapolis-St. Paul Metropolitan Area.

    PubMed

    Mohamed, Muhanad; Owens, Kris; Gajewski, Abby; Clabots, Connie; Johnston, Brian; Thuras, Paul; Kuskowski, Michael A; Johnson, James R

    2015-07-01

    How extraintestinal pathogenic Escherichia coli (ExPEC) and antimicrobial-resistant E. coli disseminate through the population is undefined. We studied public restrooms for contamination with E. coli and ExPEC in relation to source and extensively characterized the E. coli isolates. For this, we cultured 1,120 environmental samples from 56 public restrooms in 33 establishments (obtained from 10 cities in the greater Minneapolis-St. Paul, MN, metropolitan area in 2003) for E. coli and compared ecological data with culture results. Isolates underwent virulence genotyping, phylotyping, clonal typing, pulsed-field gel electrophoresis (PFGE), and disk diffusion antimicrobial susceptibility testing. Overall, 168 samples (15% from 89% of restrooms) fluoresced, indicating presumptive E. coli: 25 samples (2.2% from 32% of restrooms) yielded E. coli isolates, and 10 samples (0.9% from 16% of restrooms) contained ExPEC. Restroom category and cleanliness level significantly predicted only fluorescence, gender predicted fluorescence and E. coli, and feces-like material and toilet-associated sites predicted all three endpoints. Of the 25 E. coli isolates, 7 (28%) were from phylogenetic group B2(virulence-associated), and 8 (32%) were ExPEC. ExPEC isolates more commonly represented group B2 (50% versus 18%) and had significantly higher virulence gene scores than non-ExPEC isolates. Six isolates (24%) exhibited ≥3-class antibiotic resistance, 10 (40%) represented classic human-associated sequence types, and one closely resembled reference human clinical isolates by pulsed-field gel electrophoresis. Thus, E. coli, ExPEC, and antimicrobial-resistant E. coli sporadically contaminate public restrooms, in ways corresponding with restroom characteristics and within-restroom sites. Such restroom-source E. coli strains likely reflect human fecal contamination, may pose a health threat, and may contribute to population-wide dissemination of such strains. PMID:25911488

  2. Extraintestinal Pathogenic and Antimicrobial-Resistant Escherichia coli Contamination of 56 Public Restrooms in the Greater Minneapolis-St. Paul Metropolitan Area

    PubMed Central

    Owens, Kris; Gajewski, Abby; Clabots, Connie; Johnston, Brian; Thuras, Paul; Kuskowski, Michael A.; Johnson, James R.

    2015-01-01

    How extraintestinal pathogenic Escherichia coli (ExPEC) and antimicrobial-resistant E. coli disseminate through the population is undefined. We studied public restrooms for contamination with E. coli and ExPEC in relation to source and extensively characterized the E. coli isolates. For this, we cultured 1,120 environmental samples from 56 public restrooms in 33 establishments (obtained from 10 cities in the greater Minneapolis-St. Paul, MN, metropolitan area in 2003) for E. coli and compared ecological data with culture results. Isolates underwent virulence genotyping, phylotyping, clonal typing, pulsed-field gel electrophoresis (PFGE), and disk diffusion antimicrobial susceptibility testing. Overall, 168 samples (15% from 89% of restrooms) fluoresced, indicating presumptive E. coli: 25 samples (2.2% from 32% of restrooms) yielded E. coli isolates, and 10 samples (0.9% from 16% of restrooms) contained ExPEC. Restroom category and cleanliness level significantly predicted only fluorescence, gender predicted fluorescence and E. coli, and feces-like material and toilet-associated sites predicted all three endpoints. Of the 25 E. coli isolates, 7 (28%) were from phylogenetic group B2(virulence-associated), and 8 (32%) were ExPEC. ExPEC isolates more commonly represented group B2 (50% versus 18%) and had significantly higher virulence gene scores than non-ExPEC isolates. Six isolates (24%) exhibited ≥3-class antibiotic resistance, 10 (40%) represented classic human-associated sequence types, and one closely resembled reference human clinical isolates by pulsed-field gel electrophoresis. Thus, E. coli, ExPEC, and antimicrobial-resistant E. coli sporadically contaminate public restrooms, in ways corresponding with restroom characteristics and within-restroom sites. Such restroom-source E. coli strains likely reflect human fecal contamination, may pose a health threat, and may contribute to population-wide dissemination of such strains. PMID:25911488

  3. Escherichia coli (E. coli)

    MedlinePlus

    ... so you might hear about E. coli being found in drinking water, which are not themselves harmful, but indicate the ... at CDC Foodborne disease Travelers' Health: Safe Food & Water Healthy Swimming E. coli Infection & Farm ... Word file Microsoft Excel file Audio/Video file Apple ...

  4. Epigenetic Memory as a Basis for Intelligent Behavior in Clonal Plants

    PubMed Central

    Latzel, Vít; Rendina González, Alejandra P.; Rosenthal, Jonathan

    2016-01-01

    Environmentally induced epigenetic change enables plants to remember past environmental interactions. If this memory capability is exploited to prepare plants for future challenges, it can provide a basis for highly sophisticated behavior, considered intelligent by some. Against the backdrop of an overview of plant intelligence, we hypothesize: (1) that the capability of plants to engage in such intelligent behavior increases with the additional level of complexity afforded by clonality, and; (2) that more faithful inheritance of epigenetic information in clonal plants, in conjunction with information exchange and coordination between connected ramets, is likely to enable especially advanced intelligent behavior in this group. We therefore further hypothesize that this behavior provides ecological and evolutionary advantages to clonal plants, possibly explaining, at least in part, their widespread success. Finally, we suggest avenues of inquiry to enable assessing intelligent behavior and the role of epigenetic memory in clonal species.

  5. In Vivo mRNA Profiling of Uropathogenic Escherichia coli from Diverse Phylogroups Reveals Common and Group-Specific Gene Expression Profiles

    PubMed Central

    Bielecki, Piotr; Muthukumarasamy, Uthayakumar; Eckweiler, Denitsa; Bielecka, Agata; Pohl, Sarah; Schanz, Ansgar; Niemeyer, Ute; Oumeraci, Tonio; von Neuhoff, Nils; Ghigo, Jean-Marc

    2014-01-01

    ABSTRACT mRNA profiling of pathogens during the course of human infections gives detailed information on the expression levels of relevant genes that drive pathogenicity and adaptation and at the same time allows for the delineation of phylogenetic relatedness of pathogens that cause specific diseases. In this study, we used mRNA sequencing to acquire information on the expression of Escherichia coli pathogenicity genes during urinary tract infections (UTI) in humans and to assign the UTI-associated E. coli isolates to different phylogenetic groups. Whereas the in vivo gene expression profiles of the majority of genes were conserved among 21 E. coli strains in the urine of elderly patients suffering from an acute UTI, the specific gene expression profiles of the flexible genomes was diverse and reflected phylogenetic relationships. Furthermore, genes transcribed in vivo relative to laboratory media included well-described virulence factors, small regulatory RNAs, as well as genes not previously linked to bacterial virulence. Knowledge on relevant transcriptional responses that drive pathogenicity and adaptation of isolates to the human host might lead to the introduction of a virulence typing strategy into clinical microbiology, potentially facilitating management and prevention of the disease. PMID:25096872

  6. Cloning and expression of an afimbrial adhesin (AFA-I) responsible for P blood group-independent, mannose-resistant hemagglutination from a pyelonephritic Escherichia coli strain.

    PubMed Central

    Labigne-Roussel, A F; Lark, D; Schoolnik, G; Falkow, S

    1984-01-01

    The uropathogenic Escherichia coli KS52 strain expresses a mannose-resistant hemagglutinin involving an erythrocyte recognition site distinct from the alpha-digalactoside glycosphingolipid receptor identified for the uropathogenic E. coli strains specifying a P adhesin. The KS52 strain showed three major properties. (i) It agglutinated human erythrocytes of all tested blood groups. (ii) Hemagglutinin activity was found both in the supernatant fluid L-broth cultures and in cells grown on L-agar plates. (iii) No fimbriae in organisms grown on L-agar plates were detected by electron microscopy. Whole-cell DNA from the KS52 strain was size fractionated and cloned into the pHC79 cosmid vector. Three recombinant cosmids expressing a mannose-resistant hemagglutination (MRHA) phenotype were characterized and used to subclone the smallest DNA fragment able to confer the same MRHA properties as the parent strain. A 6.7-kilobase chromosomal DNA fragment cloned in pBR322 (pIL14) was shown to be necessary for host-cell MRHA expression and uroepithelial cell adherence. The insert encoded the production of a 16,000-dalton hemagglutinin. This polypeptide could be detected in culture supernatant fluids, in E. coli minicells harboring the pIL14 plasmid, and, by immunoblotting, in the KS52 strain and E. coli whole cells harboring the pIL14 plasmid. No homology was detected by Southern hybridization between the cloned insert and the DNA of the operon responsible for MRHA in the P-specifying, fimbriate strains (pap operon). Images PMID:6148308

  7. Dissimilar Fitness Associated with Resistance to Fluoroquinolones Influences Clonal Dynamics of Various Multiresistant Bacteria

    PubMed Central

    Fuzi, Miklos

    2016-01-01

    Fitness cost associated with resistance to fluoroquinolones was recently shown to vary across clones of methicillin-resistant Staphylococcus aureus and extended-spectrum β-lactamase-producing Klebsiella pneumoniae. The resulting dissimilar fitness should have influenced the clonal dynamics and thereby the rates of resistance for these pathogens. Moreover, a similar mechanism was recently proposed for the emergence of the H30 and H30R lineages of ESBL-producing E. coli and the major international clone (ribotype 027) of Clostridium difficile. Furthermore, several additional international clones of various multiresistant bacteria are suspect to have been selected by an analogous process. An ability to develop favorable mutations in the gyrase and topoisomerase IV genes seems to be a prerequisite for pathogens to retain fitness while showing high-level resistance to fluoroquinolones. Since, the consumption of other “non-fluoroquinolone” groups of antibiotics have also contributed to the rise in resistance rates a more judicious use of antibiotics in general and of fluoroquinolones in particular could ameliorate the international resistance situation. PMID:27458434

  8. Dissimilar Fitness Associated with Resistance to Fluoroquinolones Influences Clonal Dynamics of Various Multiresistant Bacteria.

    PubMed

    Fuzi, Miklos

    2016-01-01

    Fitness cost associated with resistance to fluoroquinolones was recently shown to vary across clones of methicillin-resistant Staphylococcus aureus and extended-spectrum β-lactamase-producing Klebsiella pneumoniae. The resulting dissimilar fitness should have influenced the clonal dynamics and thereby the rates of resistance for these pathogens. Moreover, a similar mechanism was recently proposed for the emergence of the H30 and H30R lineages of ESBL-producing E. coli and the major international clone (ribotype 027) of Clostridium difficile. Furthermore, several additional international clones of various multiresistant bacteria are suspect to have been selected by an analogous process. An ability to develop favorable mutations in the gyrase and topoisomerase IV genes seems to be a prerequisite for pathogens to retain fitness while showing high-level resistance to fluoroquinolones. Since, the consumption of other "non-fluoroquinolone" groups of antibiotics have also contributed to the rise in resistance rates a more judicious use of antibiotics in general and of fluoroquinolones in particular could ameliorate the international resistance situation. PMID:27458434

  9. Two distinct groups of porcine enteropathogenic Escherichia coli strains of serogroup O45 are revealed by comparative genomic hybridization and virulence gene microarray

    PubMed Central

    Bruant, Guillaume; Zhang, Yongxiang; Garneau, Philippe; Wong, Justin; Laing, Chad; Fairbrother, John M; Gannon, Victor PJ; Harel, Josée

    2009-01-01

    Background Porcine enteropathogenic Escherichia coli (PEPEC) strains of serogroup O45 cause post-weaning diarrhea and produce characteristic attaching and effacing (A/E) lesions. Most O45 PEPEC strains possess the locus of enterocyte effacement (LEE), encoding the virulence factors required for production of A/E lesions, and often possess the paa gene, which is thought to contribute to the early stages of PEPEC pathogenicity. In this study, nine O45 PEPEC strains and a rabbit enteropathogenic (REPEC) strain, known to produce A/E lesions in vivo, were characterized using an E. coli O157-E. coli K12 whole genome microarray and a virulence gene-specific microarray, and by PCR experiments. Results Based on their virulence gene profiles, the 10 strains were considered to be atypical EPEC. The differences in their genomes pointed to the identification of two distinct evolutionary groups of O45 PEPEC, Groups I and II, and provided evidence for a contribution of these genetic differences to their virulence in pigs. Group I included the REPEC strain and four O45 PEPEC strains known to induce severe A/E lesions in challenged pigs whereas Group II was composed of the five other O45 PEPEC strains, which induced less severe or no A/E lesions in challenged pigs. Significant differences between Groups I and II were found with respect to the presence or absence of 50 O-Islands (OIs) or S-loops and 13 K-islands (KIs) or K-loops, including the virulence-associated islands OI#1 (S-loop#1), OI#47 (S-loop#71), OI#57 (S-loop#85), OI#71 (S-loop#108), OI#115, OI#122, and OI#154 (S-loop#253). Conclusion We have genetically characterized a collection of O45 PEPEC strains and classified them into two distinct groups. The differences in their virulence gene and genomic island content may influence the pathogenicity of O45 PEPEC strains, and explain why Group I O45 PEPEC strains induced more severe A/E lesions in explants and challenged pigs than Group II strains. PMID:19709428

  10. Enforced Clonality Confers a Fitness Advantage

    PubMed Central

    Martínková, Jana; Klimešová, Jitka

    2016-01-01

    In largely clonal plants, splitting of a maternal plant into potentially independent plants (ramets) is usually spontaneous; however, such fragmentation also occurs in otherwise non-clonal species due to application of external force. This process might play an important yet largely overlooked role for otherwise non-clonal plants by providing a mechanism to regenerate after disturbance. Here, in a 5-year garden experiment on two short-lived, otherwise non-clonal species, Barbarea vulgaris and Barbarea stricta, we compared the fitness of plants fragmented by simulated disturbance (“enforced ramets”) both with plants that contemporaneously originate in seed and with individuals unscathed by the disturbance event. Because the ability to regrow from fragments is related to plant age and stored reserves, we compared the effects of disturbance applied during three different ontogenetic stages of the plants. In B. vulgaris, enforced ramet fitness was higher than the measured fitness values of both uninjured plants and plants established from seed after the disturbance. This advantage decreased with increasing plant age at the time of fragmentation. In B. stricta, enforced ramet fitness was lower than or similar to fitness of uninjured plants and plants grown from seed. Our results likely reflect the habitat preferences of the study species, as B. vulgaris occurs in anthropogenic, disturbed habitats where body fragmentation is more probable and enforced clonality thus more advantageous than in the more natural habitats preferred by B. stricta. Generalizing from our results, we see that increased fitness yielded by enforced clonality would confer an evolutionary advantage in the face of disturbance, especially in habitats where a seed bank has not been formed, e.g., during invasion or colonization. Our results thus imply that enforced clonality should be taken into account when studying population dynamics and life strategies of otherwise non-clonal species in disturbed

  11. E. Coli

    MedlinePlus

    ... E. coli is short for the medical term Escherichia coli . The strange thing about these bacteria — and lots ... cause a very serious infection. Someone who has E. coli infection may have these symptoms: bad stomach cramps and ...

  12. B-cell clonality and infection with Helicobacter pylori: implications for development of gastric lymphoma.

    PubMed Central

    Sorrentino, D; Ferraccioli, G F; DeVita, S; Avellini, C; Beltrami, C A; Labombarda, A; Bernardis, V; De Biase, F; Trevisi, A; Pivetta, B; Boiocchi, M; Bartoli, E

    1996-01-01

    BACKGROUND: Although Helicobacter pylori has been implicated in the pathogenesis of gastric mucosa associated lymphoid tissue (MALT) and MALT lymphoma, it is not known how it may trigger these lesions and whether there is an identifiable pre-neoplastic stage. AIMS: To investigate the relation between MALT, H pylori infection, and B-cell clonality (a potential marker of pre-neoplastic lesions). PATIENTS: 141 subjects with simple dyspepsia. METHODS: Gastric biopsy specimens from all patients were examined for MALT and H pylori. Of these, 25 consecutive MALT positive specimens were scored for features of MALT lymphoma and VDJ clonality studied by polymerase chain reaction. RESULTS: Overall, prevalence was 62% for H pylori and 46% for MALT. VDJ clonality was frequent in the sub-group studied (nine of 25), mostly associated with lymphoid follicles (eight of nine or 89%), and with a high scoring for MALT lymphoma. VDJ clonality was equally frequent in patients with and without H pylori (seven of 20 and two of five or 35% and 40% respectively). CONCLUSIONS: B-cell clonality is unexpectedly common in subjects with simple dyspepsia and MALT raising clinical management questions. These findings also suggest that the cascade MALT formation--B-cell clonality--MALT lymphoma may not be uniquely associated with H pylori infection. PMID:8984020

  13. Enhancing cancer clonality analysis with integrative genomics

    PubMed Central

    2015-01-01

    Introduction It is understood that cancer is a clonal disease initiated by a single cell, and that metastasis, which is the spread of cancer from the primary site, is also initiated by a single cell. The seemingly natural capability of cancer to adapt dynamically in a Darwinian manner is a primary reason for therapeutic failures. Survival advantages may be induced by cancer therapies and also occur as a result of inherent cell and microenvironmental factors. The selected "more fit" clones outmatch their competition and then become dominant in the tumor via propagation of progeny. This clonal expansion leads to relapse, therapeutic resistance and eventually death. The goal of this study is to develop and demonstrate a more detailed clonality approach by utilizing integrative genomics. Methods Patient tumor samples were profiled by Whole Exome Sequencing (WES) and RNA-seq on an Illumina HiSeq 2500 and methylation profiling was performed on the Illumina Infinium 450K array. STAR and the Haplotype Caller were used for RNA-seq processing. Custom approaches were used for the integration of the multi-omic datasets. Results Reported are major enhancements to CloneViz, which now provides capabilities enabling a formal tumor multi-dimensional clonality analysis by integrating: i) DNA mutations, ii) RNA expressed mutations, and iii) DNA methylation data. RNA and DNA methylation integration were not previously possible, by CloneViz (previous version) or any other clonality method to date. This new approach, named iCloneViz (integrated CloneViz) employs visualization and quantitative methods, revealing an integrative genomic mutational dissection and traceability (DNA, RNA, epigenetics) thru the different layers of molecular structures. Conclusion The iCloneViz approach can be used for analysis of clonal evolution and mutational dynamics of multi-omic data sets. Revealing tumor clonal complexity in an integrative and quantitative manner facilitates improved mutational

  14. Abrupt Emergence of a Single Dominant Multidrug-Resistant Strain of Escherichia coli

    PubMed Central

    Johnson, James R.; Tchesnokova, Veronika; Johnston, Brian; Clabots, Connie; Roberts, Pacita L.; Billig, Mariya; Riddell, Kim; Rogers, Peggy; Qin, Xuan; Butler-Wu, Susan; Price, Lance B.; Aziz, Maliha; Nicolas-Chanoine, Marie-Hélène; DebRoy, Chitrita; Robicsek, Ari; Hansen, Glen; Urban, Carl; Platell, Joanne; Trott, Darren J.; Zhanel, George; Weissman, Scott J.; Cookson, Brad T.; Fang, Ferric C.; Limaye, Ajit P.; Scholes, Delia; Chattopadhyay, Sujay; Hooper, David C.; Sokurenko, Evgeni V.

    2013-01-01

    Background. Fluoroquinolone-resistant Escherichia coli are increasingly prevalent. Their clonal origins—potentially critical for control efforts—remain undefined. Methods. Antimicrobial resistance profiles and fine clonal structure were determined for 236 diverse-source historical (1967–2009) E. coli isolates representing sequence type ST131 and 853 recent (2010–2011) consecutive E. coli isolates from 5 clinical laboratories in Seattle, Washington, and Minneapolis, Minnesota. Clonal structure was resolved based on fimH sequence (fimbrial adhesin gene: H subclone assignments), multilocus sequence typing, gyrA and parC sequence (fluoroquinolone resistance-determining loci), and pulsed-field gel electrophoresis. Results. Of the recent fluoroquinolone-resistant clinical isolates, 52% represented a single ST131 subclonal lineage, H30, which expanded abruptly after 2000. This subclone had a unique and conserved gyrA/parC allele combination, supporting its tight clonality. Unlike other ST131 subclones, H30 was significantly associated with fluoroquinolone resistance and was the most prevalent subclone among current E. coli clinical isolates, overall (10.4%) and within every resistance category (11%–52%). Conclusions. Most current fluoroquinolone-resistant E. coli clinical isolates, and the largest share of multidrug-resistant isolates, represent a highly clonal subgroup that likely originated from a single rapidly expanded and disseminated ST131 strain. Focused attention to this strain will be required to control the fluoroquinolone and multidrug-resistant E. coli epidemic. PMID:23288927

  15. Multicenter Study of the Mechanisms of Resistance and Clonal Relationships of Streptococcus agalactiae Isolates Resistant to Macrolides, Lincosamides, and Ketolides in Spain

    PubMed Central

    Gonzalez, J. J.; Andreu, A.

    2005-01-01

    Macrolide, lincosamide, and ketolide mechanisms of resistance and clonal relationships were characterized in a collection of 79 resistant group B streptococcus isolates obtained from neonates or pregnant women. The erm(B), erm(TR), and mef(A) genes were present in 62%, 30.4%, and 3.8% of the isolates, respectively. There was considerable clonal diversity among them. PMID:15917563

  16. Evolutionary perspectives on clonal reproduction in vertebrate animals

    PubMed Central

    Avise, John C.

    2015-01-01

    A synopsis is provided of different expressions of whole-animal vertebrate clonality (asexual organismal-level reproduction), both in the laboratory and in nature. For vertebrate taxa, such clonal phenomena include the following: human-mediated cloning via artificial nuclear transfer; intergenerational clonality in nature via parthenogenesis and gynogenesis; intergenerational hemiclonality via hybridogenesis and kleptogenesis; intragenerational clonality via polyembryony; and what in effect qualifies as clonal replication via self-fertilization and intense inbreeding by simultaneous hermaphrodites. Each of these clonal or quasi-clonal mechanisms is described, and its evolutionary genetic ramifications are addressed. By affording an atypical vantage on standard vertebrate reproduction, clonality offers fresh perspectives on the evolutionary and ecological significance of recombination-derived genetic variety. PMID:26195735

  17. Guanosine 2-NH2 groups of Escherichia coli RNase P RNA involved in intramolecular tertiary contacts and direct interactions with tRNA.

    PubMed Central

    Heide, C; Pfeiffer, T; Nolan, J M; Hartmann, R K

    1999-01-01

    We have identified by nucleotide analog interference mapping (NAIM) exocyclic NH2 groups of guanosines in RNase P RNA from Escherichia coli that are important for tRNA binding. The majority of affected guanosines represent phylogenetically conserved nucleotides. Several sites of interference could be assigned to direct contacts with the tRNA moiety, whereas others were interpreted as reflecting indirect effects on tRNA binding due to the disruption of tertiary contacts within the catalytic RNA. Our results support the involvement of the 2-NH2 groups of G292/G293 in pairing with C74 and C75 of tRNA CCA-termini, as well as formation of two consecutive base triples involving C75 and A76 of CCA-ends interacting with G292/A258 and G291/G259, respectively. Moreover, we present first biochemical evidence for two tertiary contacts (L18/P8 and L8/P4) within the catalytic RNA, whose formation has been postulated previously on the basis of phylogenetic comparative analyses. The tRNA binding interference data obtained in this and our previous studies are consistent with the formation of a consecutive nucleotide triple and quadruple between the tetraloop L18 and helix P8. Formation of the nucleotide triple (G316 and A94:U104 in wild-type E. coli RNase P RNA) is also supported by mutational analysis. For the mutant RNase P RNA carrying a G94:C104 double mutation, an additional G316-to-A mutation resulted in a restoration of binding affinity for mature and precursor tRNA. PMID:9917070

  18. Clonal deletion and clonal anergy in the thymus induced by cellular elements with different radiation sensitivities

    SciTech Connect

    Roberts, J.L.; Sharrow, S.O.; Singer, A. )

    1990-03-01

    The present study demonstrates that immune tolerance can be achieved in the thymus both by clonal deletion and by clonal inactivation, but that the two tolerant states are induced by cellular elements with different radiation sensitivities. TCR engagement of self antigens on bone marrow-derived, radiation-sensitive (presumably dendritic) cells induces clonal deletion of developing thymocytes, whereas TCR engagement of self antigens on radiation-resistant cellular elements, such as thymic epithelium, induces clonal anergy. The nondeleted, anergic thymocytes can express IL-2-Rs but are unable to proliferate in response to either specific antigen or anti-TCR antibodies, and do develop into phenotypically mature cells that emigrate out of the thymus and into the periphery.

  19. Quality improvement in Vignoles through clonal selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our goal is to select an improved, loose-clustered clone of Vignoles that will contribute to an integrated approach to disease control. Clonal selection has historically proven useful in reducing cluster compactness through a variety of mechanisms, including decreased berry size, lengthening of the ...

  20. Plant Diseases Impact USDA Clonal Vaccinium Genebank

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA Agricultural Research Service maintains a diverse collection of Vaccinium genotypes at the National Clonal Germplasm Repository, a temperate fruit and nut genebank in Corvallis, Oregon. Vaccinium species are hosts for two emerging diseases in the U.S. Pacific Northwest that impact the colle...

  1. 'Sharpe', a clonal plum rootstock for peach

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sharpe clonal rootstock for peach is jointly released for grower trial by the U.S. Department of Agriculture, Agricultural Research Service (Byron, GA), and Florida Agricultural Experiment Station. Sharpe, previously tested as FLA1-1, was discovered in the wild and appears to be a hybrid of Chickas...

  2. HIV genetic information and clonal growth

    Cancer.gov

    Based on an analysis of blood cells from five HIV-infected individuals, NCI researchers have identified more than 2,400 HIV DNA insertion sites. Analysis of these sites showed that there is extensive clonal expansion (growth) of HIV infected cells.

  3. TNFα facilitates clonal expansion of JAK2V617F positive cells in myeloproliferative neoplasms

    PubMed Central

    Aichberger, Karl J.; Luty, Samuel B.; Bumm, Thomas G.; Petersen, Curtis L.; Doratotaj, Shirin; Vasudevan, Kavin B.; LaTocha, Dorian H.; Yang, Fei; Press, Richard D.; Loriaux, Marc M.; Pahl, Heike L.; Silver, Richard T.; Agarwal, Anupriya; O'Hare, Thomas; Druker, Brian J.; Bagby, Grover C.

    2011-01-01

    Proinflammatory cytokines such as TNFα are elevated in patients with myeloproliferative neoplasms (MPN), but their contribution to disease pathogenesis is unknown. Here we reveal a central role for TNFα in promoting clonal dominance of JAK2V617F expressing cells in MPN. We show that JAK2V617F kinase regulates TNFα expression in cell lines and primary MPN cells and TNFα expression is correlated with JAK2V617F allele burden. In clonogenic assays, normal controls show reduced colony formation in the presence of TNFα while colony formation by JAK2V617F-positive progenitor cells is resistant or stimulated by exposure to TNFα. Ectopic JAK2V617F expression confers TNFα resistance to normal murine progenitor cells and overcomes inherent TNFα hypersensitivity of Fanconi anemia complementation group C deficient progenitors. Lastly, absence of TNFα limits clonal expansion and attenuates disease in a murine model of JAK2V617F-positive MPN. Altogether our data are consistent with a model where JAK2V617F promotes clonal selection by conferring TNFα resistance to a preneoplastic TNFα sensitive cell, while simultaneously generating a TNFα-rich environment. Mutations that confer resistance to environmental stem cell stressors are a recognized mechanism of clonal selection and leukemogenesis in bone marrow failure syndromes and our data suggest that this mechanism is also critical to clonal selection in MPN. PMID:21860020

  4. Clonal hematopoiesis in acquired aplastic anemia.

    PubMed

    Ogawa, Seishi

    2016-07-21

    Clonal hematopoiesis (CH) in aplastic anemia (AA) has been closely linked to the evolution of late clonal disorders, including paroxysmal nocturnal hemoglobinuria and myelodysplastic syndromes (MDS)/acute myeloid leukemia (AML), which are common complications after successful immunosuppressive therapy (IST). With the advent of high-throughput sequencing of recent years, the molecular aspect of CH in AA has been clarified by comprehensive detection of somatic mutations that drive clonal evolution. Genetic abnormalities are found in ∼50% of patients with AA and, except for PIGA mutations and copy-neutral loss-of-heterozygosity, or uniparental disomy (UPD) in 6p (6pUPD), are most frequently represented by mutations involving genes commonly mutated in myeloid malignancies, including DNMT3A, ASXL1, and BCOR/BCORL1 Mutations exhibit distinct chronological profiles and clinical impacts. BCOR/BCORL1 and PIGA mutations tend to disappear or show stable clone size and predict a better response to IST and a significantly better clinical outcome compared with mutations in DNMT3A, ASXL1, and other genes, which are likely to increase their clone size, are associated with a faster progression to MDS/AML, and predict an unfavorable survival. High frequency of 6pUPD and overrepresentation of PIGA and BCOR/BCORL1 mutations are unique to AA, suggesting the role of autoimmunity in clonal selection. By contrast, DNMT3A and ASXL1 mutations, also commonly seen in CH in the general population, indicate a close link to CH in the aged bone marrow, in terms of the mechanism for selection. Detection and close monitoring of somatic mutations/evolution may help with prediction and diagnosis of clonal evolution of MDS/AML and better management of patients with AA. PMID:27121470

  5. Consequences of clonality for sexual fitness: Clonal expansion enhances fitness under spatially restricted dispersal

    PubMed Central

    Van Drunen, Wendy E.; van Kleunen, Mark; Dorken, Marcel E.

    2015-01-01

    Clonality is a pervasive feature of sessile organisms, but this form of asexual reproduction is thought to interfere with sexual fitness via the movement of gametes among the modules that comprise the clone. This within-clone movement of gametes is expected to reduce sexual fitness via mate limitation of male reproductive success and, in some cases, via the production of highly inbred (i.e., self-fertilized) offspring. However, clonality also results in the spatial expansion of the genetic individual (i.e., genet), and this should decrease distances gametes and sexually produced offspring must travel to avoid competing with other gametes and offspring from the same clone. The extent to which any negative effects of clonality on mating success might be offset by the positive effects of spatial expansion is poorly understood. Here, we develop spatially explicit models in which fitness was determined by the success of genets through their male and female sex functions. Our results indicate that clonality serves to increase sexual fitness when it is associated with the outward expansion of the genet. Our models further reveal that the main fitness benefit of clonal expansion might occur through the dispersal of offspring over a wider area compared with nonclonal phenotypes. We conclude that, instead of interfering with sexual reproduction, clonal expansion should often serve to enhance sexual fitness. PMID:26195748

  6. Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality

    PubMed Central

    Laskey, Sarah B.; Pohlmeyer, Christopher W.; Bruner, Katherine M.; Siliciano, Robert F.

    2016-01-01

    In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings. PMID:27494508

  7. Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality.

    PubMed

    Laskey, Sarah B; Pohlmeyer, Christopher W; Bruner, Katherine M; Siliciano, Robert F

    2016-08-01

    In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings. PMID:27494508

  8. Fluoroquinolone-resistant Escherichia coli carriage in long-term care facility.

    PubMed

    Maslow, Joel N; Lee, Betsy; Lautenbach, Ebbing

    2005-06-01

    We conducted a cross-sectional study to determine the prevalence of, and risk factors for, colonization with fluoroquinolone (FQ)-resistant Escherichia coli in residents in a long-term care facility. FQ-resistant E. coli were identified from rectal swabs for 25 (51%) of 49 participants at study entry. On multivariable analyses, prior FQ use was the only independent risk factor for FQ-resistant E. coli carriage and was consistent for FQ exposures in the previous 3, 6, 9, or 12 months. Pulsed-field gel electrophoresis of FQ-resistant E. coli identified clonal spread of 1 strain among 16 residents. Loss (6 residents) or acquisition (7 residents) of FQ-resistant E. coli was documented and was associated with de novo colonization with genetically distinct strains. Unlike the case in the hospital setting, FQ-resistant E. coli carriage in long-term care facilities is associated with clonal spread. PMID:15963284

  9. Fluoroquinolone-resistant Escherichia coli Carriage in Long-Term Care Facility

    PubMed Central

    Lee, Betsy; Lautenbach, Ebbing

    2005-01-01

    We conducted a cross-sectional study to determine the prevalence of, and risk factors for, colonization with fluoroquinolone (FQ)-resistant Escherichia coli in residents in a long-term care facility. FQ-resistant E. coli were identified from rectal swabs for 25 (51%) of 49 participants at study entry. On multivariable analyses, prior FQ use was the only independent risk factor for FQ-resistant E. coli carriage and was consistent for FQ exposures in the previous 3, 6, 9, or 12 months. Pulsed-field gel electrophoresis of FQ-resistant E. coli identified clonal spread of 1 strain among 16 residents. Loss (6 residents) or acquisition (7 residents) of FQ-resistant E. coli was documented and was associated with de novo colonization with genetically distinct strains. Unlike the case in the hospital setting, FQ-resistant E. coli carriage in long-term care facilities is associated with clonal spread. PMID:15963284

  10. Large scale analysis of virulence genes in Escherichia coli strains isolated from Avalon Bay, CA.

    PubMed

    Hamilton, Matthew J; Hadi, Asbah Z; Griffith, John F; Ishii, Satoshi; Sadowsky, Michael J

    2010-10-01

    Contamination of recreational waters with Escherichia coli and Enterococcus sp. is a widespread problem resulting in beach closures and loss of recreational activity. While E. coli is frequently used as an indicator of fecal contamination, and has been extensively measured in waterways, few studies have examined the presence of potentially pathogenic E. coli strains in beach waters. In this study, a combination of high-throughput, robot-assisted colony hybridization and PCR-based analyses were used to determine the genomic composition and frequency of virulence genes present in E. coli isolated from beach water in Avalon Bay, Santa Catalina Island, CA. A total of 24,493 E. coli isolates were collected from two sites at a popular swimming beach between August through September 2007 and from July through August 2008. All isolates were examined for the presence of shiga-like toxins (stx1/stx2), intimin (eaeA), and enterotoxins (ST/LT). Of the 24,493 isolates examined, 3.6% contained the eaeA gene, indicating that these isolates were potential EPEC strains. On five dates, however, greater than 10% of the strains were potential EPEC, suggesting that incidence of virulence genes at this beach has a strong temporal component. No STEC or ETEC isolates were detected, and only eight (<1.0%) of the potential EPEC isolates were found to carry the EAF plasmid. The potential EPEC isolates mainly belonged to E. coli phylogenetic groups B1 or B2, and carried the β intimin subtype. DNA fingerprint analyses of the potential EPEC strains indicated that the isolates belonged to several genetically diverse groups, although clonal isolates were frequently detected. While the presence of virulence genes alone cannot be used to determine the pathogenicity of strains, results from this study show that potential EPEC strains can be found in marine beach water and their presence needs to be considered as one of the factors used in decisions concerning beach closures. PMID:20643468

  11. Characterization of cellulose production in Escherichia coli Nissle 1917 and its biological consequences.

    PubMed

    Monteiro, Cláudia; Saxena, Inder; Wang, Xiaoda; Kader, Abdul; Bokranz, Werner; Simm, Roger; Nobles, David; Chromek, Milan; Brauner, Annelie; Brown, R Malcolm; Römling, Ute

    2009-05-01

    Bacterial species of the Enterobacteriaceae family produce cellulose and curli fimbriae as extracellular matrix components, and their synthesis is positively regulated by the transcriptional activator CsgD. In this group of bacteria, cellulose biosynthesis is commonly regulated by CsgD via the GGDEF domain protein AdrA, a diguanylate cyclase that produces cyclic-diguanylic acid (c-di-GMP), an allosteric activator of cellulose synthase. In the probiotic Escherichia coli strain Nissle 1917 and its recent clonal isolates, CsgD activates the production of curli fimbriae at 28 degrees C, but neither CsgD nor AdrA is required for the c-di-GMP-dependent biosynthesis of cellulose at 28 degrees C and 37 degrees C. In these strains, the GGDEF domain protein YedQ, a diguanylate cyclase that activates cellulose biosynthesis in certain E. coli strains, is not required for cellulose biosynthesis and it has in fact evolved into a novel protein. Cellulose production in Nissle 1917 is required for adhesion of bacteria to the gastrointestinal epithelial cell line HT-29, to the mouse epithelium in vivo, and for enhanced cytokine production. The role of cellulose in this strain is in contrast to the role of cellulose in the commensal strain E. coli TOB1. Consequently, the role of cellulose in bacterial-host interaction is dependent on the E. coli strain background. PMID:19175667

  12. Emergence of uropathogenic extended-spectrum beta lactamases-producing Escherichia coli strains in the community.

    PubMed

    Marijan, Tatjana; Vranes, Jasmina; Bedenić, Branka; Mlinarić-Dzepina, Ana; Plecko, Vanda; Kalenić, Smilja

    2007-03-01

    The aim of this study was to determine the virulence characteristics and resistance pattern of the extended-spectrum/lactamases (ESBLs)-producing Escherichia coli strains isolated from urine of outpatients in the Zagreb region during a five-month period, and to compare them with the non ESBLs-producing E. coli strains isolated in the same period. Out of 2451 E. coli strains isolated from urine of nonhospitalized patients with significant bacteriuria, a total of 39 ESBLs-producing strains (1.59%) were detected by a double-disk diffusion technique and by the broth-dilution minimal inhibitory concentration reduction method. The 45 non ESBLs-producing strains were randomly chosen, and phenotype of the two groups of strains was characterized and compared. Serogroup O4, hemolysin production, expression of P- and type 1 fimbriae as well as resistance to gentamicin and amikacin were significantly more prevalent characteristics among the ESBLs-producing strains than among non ESBLs-producing strains (p < 0.01), while higher prevalence of trimethoprim-sulfamethoxazole resistance among ESBLs-producing strains was not statistically significant (p > 0.05). Chromosomal DNA analysis by pulsed-field gel electrophoresis exhibited a great genomic similarity among ESBLs-producing strains and revealed that those highly virulent and resistant E. coli strains isolated from urine of outpatients in the Zagreb region had a clonal propagation. PMID:17598406

  13. The impact of category, cytopathology and cytogenetics on development and progression of clonal and malignant myeloid transformation in inherited bone marrow failure syndromes

    PubMed Central

    Cada, Michaela; Segbefia, Catherin I.; Klaassen, Robert; Fernandez, Conrad V.; Yanofsky, Rochelle A.; Wu, John; Pastore, Yves; Silva, Mariana; Lipton, Jeffrey H.; Brossard, Josee; Michon, Bruno; Abish, Sharon; Steele, MacGregor; Sinha, Roona; Belletrutti, Mark; Breakey, Vicky; Jardine, Lawrence; Goodyear, Lisa; Sung, Lillian; Shago, Mary; Beyene, Joseph; Sharma, Preeti; Zlateska, Bozana; Dror, Yigal

    2015-01-01

    Inherited bone marrow failure syndromes are a group of rare, heterogeneous genetic disorders with a risk of clonal and malignant myeloid transformation including clonal marrow cytogenetic abnormalities, myelodysplastic syndrome and acute myeloid leukemia. The clinical characteristics, risk classification, prognostic factors and outcome of clonal and malignant myeloid transformation associated with inherited bone marrow failure syndromes are largely unknown. The aims of this study were to determine the impact of category, cytopathology and cytogenetics, the three components of the “Category Cytology Cytogenetics” classification of pediatric myelodysplastic syndrome, on the outcome of clonal and malignant myeloid transformation associated with inherited bone marrow failure. We used data from the Canadian Inherited Marrow Failure Registry. Among 327 patients with inherited bone marrow failure syndrome enrolled in the registry, the estimated risk of clonal and malignant myeloid transformation by the age of 18 years was 37%. The risk of clonal and malignant myeloid transformation varied according to the type of inherited bone marrow failure syndrome but was highest in Fanconi anemia. The development of clonal and malignant myeloid transformation significantly affected overall survival. Mortality varied based on cytopathological group. The largest group of patients had refractory cytopenia. Clonal marrow cytogenetic abnormalities were identified in 87% of patients with clonal and malignant myeloid transformation, and different cytogenetic groups had different impacts on disease progression. We conclude that category, cytopathology and cytogenetics in cases of clonal and malignant myeloid transformation associated with inherited bone marrow failure syndromes have an important impact on outcome and that the classification of such cases should incorporate these factors. PMID:25682607

  14. Occurrence of weak mutators among avian pathogenic Escherichia coli (APEC) isolates causing salpingitis and peritonitis in broiler breeders.

    PubMed

    Pires-dos-Santos, Teresa; Bisgaard, Magne; Kyvsgaard, Niels; Christensen, Henrik

    2014-01-10

    A collection of 46 avian pathogenic Escherichia coli (APEC) isolates was examined for the presence of mutators by determining the rate of mutation to rifampicin resistance. The collection included 34 E. coli isolates obtained in pure culture from chronic lesions of salpingitis and peritonitis in 34 broiler breeders, of which 12 were associated with the development of secondary septicemia. Twelve additional isolates were obtained from a clonal outbreak (ST95) of E. coli peritonitis syndrome (EPS), the lesions of which changed gradually over time into a subacute/chronic form. The hypothesis of the present study was that mutation rates would be higher for chronic infection isolates than for isolates from acute infections/exacerbations. The distribution of mutation rates followed a pattern similar to that found for other clinical isolates of E. coli, with a modal/median value of 1.47 × 10(-8). Of the 46 isolates, 24% (n=11) were weakly hypermutable (2.00 × 10(-8) ≤ μ<2.00 × 10(-7)), however, no strong mutators were detected (μ ≥ 2.00 × 10(-7)). Chronic salpingitis isolates had the highest proportion (45%, P=0.001) of weak mutators and also, significantly higher mutation rates (P=0.003) compared to isolates that caused septicemia (4%). In addition, mutation rates were significantly lower among ST95 isolates (P<0.0005), and among isolates from the same clonal group as ST95 (P=0.027), when compared to isolates from other groups. Although a clear association with the time phase of infection (as lesions of EPS became more chronic) could not be observed (ρ=0.523, P=0.081), a higher frequency of weak mutators among chronic infection isolates suggests that increased mutation rates play a role in adaptation of APEC to long-term persistence in an infected host environment. PMID:24230977

  15. The crystal structure of Escherichia coli group 4 capsule protein GfcC reveals a domain organization resembling that of Wza.

    PubMed

    Sathiyamoorthy, Karthik; Mills, Erez; Franzmann, Titus M; Rosenshine, Ilan; Saper, Mark A

    2011-06-21

    We report the 1.9 Å resolution crystal structure of enteropathogenic Escherichia coli GfcC, a periplasmic protein encoded by the gfc operon, which is essential for assembly of group 4 polysaccharide capsule (O-antigen capsule). Presumed gene orthologs of gfcC are present in capsule-encoding regions of at least 29 genera of Gram-negative bacteria. GfcC, a member of the DUF1017 family, is comprised of tandem β-grasp (ubiquitin-like) domains (D2 and D3) and a carboxyl-terminal amphipathic helix, a domain arrangement reminiscent of that of Wza that forms an exit pore for group 1 capsule export. Unlike the membrane-spanning C-terminal helix from Wza, the GfcC C-terminal helix packs against D3. Previously unobserved in a β-grasp domain structure is a 48-residue helical hairpin insert in D2 that binds to D3, constraining its position and sequestering the carboxyl-terminal amphipathic helix. A centrally located and invariant Arg115 not only is essential for proper localization but also forms one of two mostly conserved pockets. Finally, we draw analogies between a GfcC protein fused to an outer membrane β-barrel pore in some species and fusion proteins necessary for secreting biofilm-forming exopolysaccharides. PMID:21449614

  16. The Crystal Structure of Escherichia coli Group 4 Capsule Protein GfcC Reveals a Domain Organization Resembling That of Wza

    SciTech Connect

    Sathiyamoorthy, Karthik; Mills, Erez; Franzmann, Titus M.; Rosenshine, Ilan; Saper, Mark A.

    2012-03-15

    We report the 1.9 {angstrom} resolution crystal structure of enteropathogenic Escherichia coli GfcC, a periplasmic protein encoded by the gfc operon, which is essential for assembly of group 4 polysaccharide capsule (O-antigen capsule). Presumed gene orthologs of gfcC are present in capsule-encoding regions of at least 29 genera of Gram-negative bacteria. GfcC, a member of the DUF1017 family, is comprised of tandem {beta}-grasp (ubiquitin-like) domains (D2 and D3) and a carboxyl-terminal amphipathic helix, a domain arrangement reminiscent of that of Wza that forms an exit pore for group 1 capsule export. Unlike the membrane-spanning C-terminal helix from Wza, the GfcC C-terminal helix packs against D3. Previously unobserved in a {beta}-grasp domain structure is a 48-residue helical hairpin insert in D2 that binds to D3, constraining its position and sequestering the carboxyl-terminal amphipathic helix. A centrally located and invariant Arg115 not only is essential for proper localization but also forms one of two mostly conserved pockets. Finally, we draw analogies between a GfcC protein fused to an outer membrane {beta}-barrel pore in some species and fusion proteins necessary for secreting biofilm-forming exopolysaccharides.

  17. A Novel 7-Single Nucleotide Polymorphism-Based Clonotyping Test Allows Rapid Prediction of Antimicrobial Susceptibility of Extraintestinal Escherichia coli Directly From Urine Specimens

    PubMed Central

    Tchesnokova, Veronika; Avagyan, Hovhannes; Billig, Mariya; Chattopadhyay, Sujay; Aprikian, Pavel; Chan, Diana; Pseunova, Julietta; Rechkina, Elena; Riddell, Kim; Scholes, Delia; Fang, Ferric C.; Johnson, James R.; Sokurenko, Evgeni V.

    2016-01-01

    Background. Escherichia coli is a highly clonal pathogen. Extraintestinal isolates belong to a limited number of genetically related groups, which often exhibit characteristic antimicrobial resistance profiles. Methods. We developed a rapid clonotyping method for extraintestinal E coli based on detection of the presence or absence of 7 single nucleotide polymorphisms (SNPs) within 2 genes (fumC and fimH). A reference set of 2559 E coli isolates, primarily of urinary origin, was used to predict the resolving power of the 7-SNP-based typing method, and 582 representative strains from this set were used to evaluate test robustness. Results. Fifty-four unique SNP combinations (“septatypes”) were identified in the reference strains. These septatypes yielded a clonal group resolution power on par with that of traditional multilocus sequence typing. In 72% of isolates, septatype identity predicted sequence type identity with at least 90% (mean, 97%) accuracy. Most septatypes exhibited highly distinctive antimicrobial susceptibility profiles. The 7-SNP-based test could be performed with high specificity and sensitivity using single or multiplex conventional polymerase chain reaction (PCR) and quantitative PCR. In the latter format, E coli presence and septatype identity were determined directly in urine specimens within 45 minutes with bacterial loads as low as 102 colony-forming units/mL and, at clinically significant bacterial loads, with 100% sensitivity and specificity. Conclusions. 7-SNP-based typing of E coli can be used for both epidemiological studies and clinical diagnostics, which could greatly improve the empirical selection of antimicrobial therapy. PMID:26925427

  18. Molecular typing of avian pathogenic Escherichia coli colonies originating from outbreaks of E. coli peritonitis syndrome in chicken flocks.

    PubMed

    Landman, W J M; Buter, G J; Dijkman, R; van Eck, J H H

    2014-01-01

    Escherichia coli colonies isolated from the bone marrow of fresh dead hens of laying flocks with the E. coli peritonitis syndrome (EPS) were genotyped using pulsed-field gel electrophoresis (PFGE). Typing is important from an epidemiological point of view and also if the use of autogenous (auto)vaccines is considered. Birds with EPS originated from one house of each of three layer farms and one broiler breeder farm. Farms were considered as separate epidemiological units. In total, six flocks were examined including two successive flocks of one layer farm and the broiler breeder farm. E. coli colonies (one per bird) from nine to 16 hens of each flock were genotyped. The clonality of E. coli within birds was studied using five colonies of each of nine to 14 birds per flock. E. coli genotypes, which totalled 15, differed between farms and flocks except for two successive layer flocks that shared three genotypes. One to five genotypes were found per flock with one or two genotypes dominating each outbreak. Within hens, E. coli bacteria were always clonal. Colonies of the same PFGE type always had the same multilocus sequence type. However, four PFGE types shared sequence type 95. Neither PFGE types nor multilocus sequence types were unambiguously related to avian pathogenic E. coli from EPS. In cases where persistence of E. coli strains associated with EPS is found to occur frequently, routine genotyping to select strains for autovaccines should be considered. PMID:24944080

  19. Clonal Evolution Revealed by Whole Genome Sequencing in a Case of Primary Myelofibrosis Transformed to Secondary Acute Myeloid Leukemia

    PubMed Central

    Engle, Elizabeth K.; Fisher, Daniel A.C.; Miller, Christopher A.; McLellan, Michael D.; Fulton, Robert S.; Moore, Deborah M.; Wilson, Richard K.; Ley, Timothy J.; Oh, Stephen T.

    2014-01-01

    Clonal architecture in myeloproliferative neoplasms (MPNs) is poorly understood. Here we report genomic analyses of a patient with primary myelofibrosis (PMF) transformed to secondary acute myeloid leukemia (sAML). Whole genome sequencing (WGS) was performed on PMF and sAML diagnosis samples, with skin included as a germline surrogate. Deep sequencing validation was performed on the WGS samples and an additional sample obtained during sAML remission/relapsed PMF. Clustering analysis of 649 validated somatic single nucleotide variants revealed four distinct clonal groups, each including putative driver mutations. The first group (including JAK2 and U2AF1), representing the founding clone, included mutations with high frequency at all three disease stages. The second clonal group (including MYB) was present only in PMF, suggesting the presence of a clone that was dispensable for transformation. The third group (including ASXL1) contained mutations with low frequency in PMF and high frequency in subsequent samples, indicating evolution of the dominant clone with disease progression. The fourth clonal group (including IDH1 and RUNX1) was acquired at sAML transformation and was predominantly absent at sAML remission/relapsed PMF. Taken together, these findings illustrate the complex clonal dynamics associated with disease evolution in MPNs and sAML. PMID:25252869

  20. Detectable Clonal Mosaicism in the Human Genome

    PubMed Central

    Machiela, Mitchell J.; Chanock, Stephen J.

    2013-01-01

    Human genetic mosaicism is the presence of two or more cellular populations with distinct genotypes in an individual who developed from a single fertilized ovum. While initially observed across a spectrum of rare genetic disorders, detailed assessment of data from genome-wide association studies now reveal that detectable clonal mosaicism involving large structural alterations (> 2 Mb) can also be seen in populations of apparently healthy individuals. The first generation of descriptive studies have generated new interest in understanding the molecular basis of the affected genomic regions, percent of the cellular subpopulation involved, and developmental timing of the underlying mutational event, which could reveal new insights into the initiation, clonal expansion and phenotypic manifestations of mosaic events. Early evidence indicates detectable clonal mosaicism increases in frequency with age and could preferentially occur in males. The observed pattern of recurrent events affecting specific chromosomal regions indicates some regions are more susceptible to these events, which could reflect inter-individual differences in genomic stability. Moreover, it is also plausible that the presence of large structural events could be associated with cancer risk. The characterization of detectable genetic mosaicism reveals that there could be important dynamic changes in the human genome associated with the aging process, which could be associated with risk for common disorders, such as cancer, cardiovascular disease, diabetes, and neurological disorders. PMID:24246702

  1. Prevalence and Antimicrobial Resistance in Escherichia coli from Food Animals in Lagos, Nigeria.

    PubMed

    Adenipekun, Eyitayo O; Jackson, Charlene R; Oluwadun, Afolabi; Iwalokun, Bamidele A; Frye, Jonathan G; Barrett, John B; Hiott, Lari M; Woodley, Tiffanie A

    2015-06-01

    Foodborne bacteria are often associated with human infections; these infections can become more complicated to treat if the bacteria are also resistant to antimicrobials. In this study, prevalence, antimicrobial resistance, and genetic relatedness of Escherichia coli among food producing animals from Lagos, Nigeria, was investigated. From December 2012 to June 2013, E. coli were isolated from fecal samples of healthy cattle, chicken, and swine. Antimicrobial susceptibility testing against 22 antimicrobials was performed using broth microdilution with the Sensititre™ system. Clonal types were determined by pulsed-field gel electrophoresis (PFGE). From the analysis, 211/238 (88.7%), 170/210 (81%), and 136/152 (89.5%) samples from cattle, chicken, and swine, respectively, were positive for E. coli. A subset of those isolates (n=211) selected based on β-lactamase production was chosen for further study. Overall, E. coli exhibited the highest resistance to tetracycline (124/211; 58.8%), trimethoprim/sulfamethoxazole (84/211; 39.8%), and ampicillin (72/211; 34.1%). Approximately 40% of the isolates were pan-susceptible, and none of the isolates were resistant to amikacin, cefepime, ceftazidime, ertapenem, meropenem, or tigecycline. Among the resistant isolates, 28 different resistance patterns were observed; 26 of those were characterized as multi-drug resistant (MDR; resistance to ≥2 antimicrobials). One isolate was resistant to 13 different antimicrobials representing five different antimicrobial classes. Using PFGE, MDR E. coli were genetically diverse and overall did not group based on source; identical PFGE patterns were detected among isolates from different sources. These results suggest that isolates cannot be attributed to specific sources, and some may be present across all of the sources. Results from this study indicate that food-producing animals in Nigeria are a reservoir of MDR E. coli that may be transferred to humans via the food chain. PMID

  2. Frequency of Plasmid-Mediated AmpC β-Lactamases in Escherichia coli Isolates from Urine Samples in São Paulo, Brazil.

    PubMed

    Rocha, Darlan Augusto Costa; Campos, Juliana Coutinho; Passadore, Lilian Ferri; Sampaio, Suely Carlos Ferreira; Nicodemo, Antonio Carlos; Sampaio, Jorge Luiz Mello

    2016-06-01

    Plasmid-mediated AmpC β-lactamases (PMACBLs) in Enterobacteriaceae encode resistance to third-generation cephalosporins, and these can mediate carbapenem resistance when associated with porin loss. However, no standardized phenotypic method is available for detecting these enzymes in the clinical microbiology laboratory. Limited data are available concerning the frequency of PMACBLs in Enterobacteriaceae in Brazil. This study was conducted in response to an increased cefoxitin (CFO) resistance rate of 3.7% in Escherichia coli isolates from urine samples from patients with suspected urinary tract infections during 2010. We collected 2,266 E. coli isolates prospectively during January 2012. A total of 109 (4.8%) isolates were nonsusceptible to CFO. These strains were further examined using multiplex PCR for the presence of genes encoding PMACBLs and using inhibitor assays with CFO and ceftazidime (CAZ) disks with and without phenylboronic acid. Pulsed-field gel electrophoresis was used to evaluate clonal dissemination. Genes encoding PMACBLs were detected in 1.8% of the isolates from inpatients and 0.46% of isolates from outpatients. The most prevalent gene was blaCMY-2 and blaCMY-4 was also detected. The phenotypic analysis showed 100% sensitivity and specificity for CMY-2 and CMY-4 when CFO-resistant isolates with a minimum zone diameter difference of 5 mm for CAZ or CAZ and CFO were considered positive. Although most of the isolates were nonclonal, one clonal group with two isolates was observed. Thus, the most frequent PMACBL in E. coli from São Paulo, Brazil is CMY-2, and both clonal and plasmid-mediated dissemination occur. PMID:26670152

  3. In vitro and in vivo comparison of human Escherichia coli heat-stable peptide analogues incorporating the 111In-DOTA group and distinct linker moieties.

    PubMed

    Giblin, Michael F; Gali, Hariprasad; Sieckman, Gary L; Owen, Nellie K; Hoffman, Timothy J; Forte, Leonard R; Volkert, Wynn A

    2004-01-01

    Three human Escherichia coli heat-stable peptide (STh) analogues, each containing a DOTA chelating group, were synthesized by SPPS and oxidative refolding and compared in in vitro and in vivo systems. One analogue, DOTA-F19-STh(1-19), contains an N-terminal DOTA group attached via an amide bond linkage to an STh moiety which is essentially wild-type except for a Tyr to Phe alteration at position 19 of the molecule. A second analogue, DOTA-R1,4,F19-STh(1-19), differs from the first in that asparagine residues in positions 1 and 4 have been altered to arginine residues in order to examine the effect of positively charged groups in the linker domain. A third analogue, DOTA-11AUN-F19-STh(1-19), differs from the first in that it incorporates an 11-aminoundecanoic acid spacer group between the DOTA group and the first asparagine residue. In vitro competitive binding assays utilizing T-84 human colon cancer cells demonstrated that significant alterations to the N-terminal region of the STh molecule were well tolerated and did not significantly affect binding affinity of STh for the guanylyl cyclase C (GC-C) receptor. Internalization and efflux studies of the indium-labeled species demonstrated that inclusion of positive charge in the linker moiety inhibits internalization of the compound within tumor cells. The characteristics of the three analogues were compared in an in vivo model utilizing T-84 human colon cancer cell xenografts in SCID mice. Clearance of all analogues was rapid, primarily via renal excretion into the urine, with >89% ID excreted into the urine at 1 h pi for all analogues. The 111In-DOTA-R1,4,F19-STh(1-19) and 111In-DOTA-11AUN-F19-STh(1-19) analogues both had longer residence times in the blood than did the 111In-DOTA-F19-STh(1-19) analogue, probably accounting for increased %ID/g values for tumors and nontarget tissues at 1 h pi. At 4 h pi, significant differences between analogues were only seen with respect to metabolic routes of excretion

  4. Phenotypic and genotypic characterization of enterotoxigenic Escherichia coli clinical isolates from northern Colombia, South America.

    PubMed

    Guerra, Julio A; Romero-Herazo, Yesenia C; Arzuza, Octavio; Gómez-Duarte, Oscar G

    2014-01-01

    Enterotoxigenic Escherichia coli (ETEC) are major causes of childhood diarrhea in low and middle income countries including Colombia, South America. To understand the diversity of ETEC strains in the region, clinical isolates obtained from northern Colombia children were evaluated for multiple locus sequencing typing, serotyping, classical and nonclassical virulence genes, and antibiotic susceptibility. Among 40 ETEC clinical isolates evaluated, 21 (52.5%) were positive for LT gene, 13 (32.5%) for ST gene, and 6 (15%) for both ST and LT. The most prevalent colonization surface antigens (CS) were CS21 and CFA/I identified in 21 (50%) and 13 (32.5%) isolates, respectively. The eatA, irp2, and fyuA were the most common nonclassical virulence genes present in more than 60% of the isolates. Ampicillin resistance (80% of the strains) was the most frequent phenotype among ETEC strains followed by trimethoprim-sulfamethoxazole resistance (52.5%). Based on multiple locus sequencing typing (MLST), we recognize that 6 clonal groups of ETEC clinical isolates circulate in Colombia. ETEC clinical isolates from children in northern Colombia are highly diverse, yet some isolates circulating in the community belong to well-defined clonal groups that share a unique set of virulence factors, serotypes, and MLST sequence types. PMID:24877071

  5. Phenotypic and Genotypic Characterization of Enterotoxigenic Escherichia coli Clinical Isolates from Northern Colombia, South America

    PubMed Central

    Guerra, Julio A.; Romero-Herazo, Yesenia C.; Arzuza, Octavio; Gómez-Duarte, Oscar G.

    2014-01-01

    Enterotoxigenic Escherichia coli (ETEC) are major causes of childhood diarrhea in low and middle income countries including Colombia, South America. To understand the diversity of ETEC strains in the region, clinical isolates obtained from northern Colombia children were evaluated for multiple locus sequencing typing, serotyping, classical and nonclassical virulence genes, and antibiotic susceptibility. Among 40 ETEC clinical isolates evaluated, 21 (52.5%) were positive for LT gene, 13 (32.5%) for ST gene, and 6 (15%) for both ST and LT. The most prevalent colonization surface antigens (CS) were CS21 and CFA/I identified in 21 (50%) and 13 (32.5%) isolates, respectively. The eatA, irp2, and fyuA were the most common nonclassical virulence genes present in more than 60% of the isolates. Ampicillin resistance (80% of the strains) was the most frequent phenotype among ETEC strains followed by trimethoprim-sulfamethoxazole resistance (52.5%). Based on multiple locus sequencing typing (MLST), we recognize that 6 clonal groups of ETEC clinical isolates circulate in Colombia. ETEC clinical isolates from children in northern Colombia are highly diverse, yet some isolates circulating in the community belong to well-defined clonal groups that share a unique set of virulence factors, serotypes, and MLST sequence types. PMID:24877071

  6. Multi-scale temporal and spatial variation in genotypic composition of Cladophora-borne Escherichia coli populations in Lake Michigan

    USGS Publications Warehouse

    Badgley, B.D.; Ferguson, J.; Heuvel, A.V.; Kleinheinz, G.T.; McDermott, C.M.; Sandrin, T.R.; Kinzelman, J.; Junion, E.A.; Byappanahalli, M.N.; Whitman, R.L.; Sadowsky, M.J.

    2011-01-01

    High concentrations of Escherichia coli in mats of Cladophora in the Great Lakes have raised concern over the continued use of this bacterium as an indicator of microbial water quality. Determining the impacts of these environmentally abundant E. coli, however, necessitates a better understanding of their ecology. In this study, the population structure of 4285 Cladophora-borne E. coli isolates, obtained over multiple three day periods from Lake Michigan Cladophora mats in 2007-2009, was examined by using DNA fingerprint analyses. In contrast to previous studies that have been done using isolates from attached Cladophora obtained over large time scales and distances, the extensive sampling done here on free-floating mats over successive days at multiple sites provided a large dataset that allowed for a detailed examination of changes in population structure over a wide range of spatial and temporal scales. While Cladophora-borne E. coli populations were highly diverse and consisted of many unique isolates, multiple clonal groups were also present and accounted for approximately 33% of all isolates examined. Patterns in population structure were also evident. At the broadest scales, E. coli populations showed some temporal clustering when examined by year, but did not show good spatial distinction among sites. E. coli population structure also showed significant patterns at much finer temporal scales. Populations were distinct on an individual mat basis at a given site, and on individual days within a single mat. Results of these studies indicate that Cladophora-borne E. coli populations consist of a mixture of stable, and possibly naturalized, strains that persist during the life of the mat, and more unique, transient strains that can change over rapid time scales. It is clear that further study of microbial processes at fine spatial and temporal scales is needed, and that caution must be taken when interpolating short term microbial dynamics from results obtained

  7. Extended-Spectrum-β-Lactamase-Producing Escherichia coli as a Cause of Pediatric Infections: Report of a Neonatal Intensive Care Unit Outbreak Due to a CTX-M-14-Producing Strain

    PubMed Central

    Oteo, Jesús; Cercenado, Emilia; Fernández-Romero, Sara; Saéz, David; Padilla, Belén; Zamora, Elena; Cuevas, Oscar; Bautista, Verónica

    2012-01-01

    Little information is available about pediatric infections caused by extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli. We characterized an outbreak caused by a CTX-M-14-producing E. coli isolate in a neonatal intensive care unit (NICU) and studied other infections caused by ESBL-producing E. coli in non-NICU pediatric units. All children ≤4 years old who were infected or colonized by ESBL-producing E. coli isolates between January 2009 and September 2010 were included. Molecular epidemiology was studied by phylogroup analysis, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing. Antibiotic resistance genes were analyzed by PCR and sequencing. Plasmids were studied by PFGE with S1 nuclease digestion and by incompatibility group analysis using a PCR-based replicon-typing scheme. Of the ESBL-producing E. coli isolates colonizing or infecting the 30 newborns, identical PFGE results were observed for 21 (70%) isolates, which were classified as CTX-M-14-producing E. coli of ST23 phylogroup A. blaCTX-M-14a was linked to ISEcp1 and was carried on an ∼80-bp IncK plasmid. A smaller ongoing outbreak due to SHV-12-producing ST131 E. coli was also identified in the same NICU. Fifteen additional infections with ESBL-producing E. coli were identified in non-NICU pediatric units, but none was caused by the CTX-M-14-producing E. coli epidemic clone. Overall, CTX-M-14 (71.1%), CTX-M-15 (13.3%), and SHV-12 (13.3%) were the most important ESBLs causing pediatric infections in this study. Infections of newborns with CTX-M-14-producing E. coli were caused by both clonal and nonclonal isolates. PMID:21986825

  8. Assessment of clonality and serotypes of Streptococcus mutans among children by multilocus sequence typing.

    PubMed

    Momeni, Stephanie S; Whiddon, Jennifer; Cheon, Kyounga; Moser, Stephen A; Childers, Noel K

    2015-12-01

    Studies using multilocus sequence typing (MLST) have demonstrated that Streptococcus mutans isolates are genetically diverse. Our laboratory previously demonstrated clonality of S. mutans using MLST but could not discount the possibility of sampling bias. In this study, the clonality of randomly selected S. mutans plaque isolates from African-American children was examined using MLST. Serotype and the presence of collagen-binding proteins (CBPs) encoded by cnm/cbm were also assessed. One-hundred S. mutans isolates were randomly selected for MLST analysis. Sequence analysis was performed and phylogenetic trees were generated using start2 and mega. Thirty-four sequence types were identified, of which 27 were unique to this population. Seventy-five per cent of the isolates clustered into 16 clonal groups. The serotypes observed were c (n = 84), e (n = 3), and k (n = 11). The prevalence of S. mutans isolates of serotype k was notably high, at 17.5%. All isolates were cnm/cbm negative. The clonality of S. mutans demonstrated in this study illustrates the importance of localized population studies and are consistent with transmission. The prevalence of serotype k, a recently proposed systemic pathogen, observed in this study, is higher than reported in most populations and is the first report of S. mutans serotype k in a United States population. PMID:26443288

  9. Molecular Characterization of the Multidrug Resistant Escherichia coli ST131 Clone

    PubMed Central

    Schembri, Mark A.; Ben Zakour, Nouri L.; Phan, Minh-Duy; Forde, Brian M.; Stanton-Cook, Mitchell; Beatson, Scott A.

    2015-01-01

    Escherichia coli ST131 is a recently emerged and globally disseminated multidrug resistant clone associated with urinary tract and bloodstream infections in both community and clinical settings. The most common group of ST131 strains are defined by resistance to fluoroquinolones and possession of the type 1 fimbriae fimH30 allele. Here we provide an update on our recent work describing the globally epidemiology of ST131. We review the phylogeny of ST131 based on whole genome sequence data and highlight the important role of recombination in the evolution of this clonal lineage. We also summarize our findings on the virulence of the ST131 reference strain EC958, and highlight the use of transposon directed insertion-site sequencing to define genes associated with serum resistance and essential features of its large antibiotic resistance plasmid pEC958. PMID:26131613

  10. Multidrug-resistant and epidemic clones of Escherichia coli from natural beds of Venus clam.

    PubMed

    Vignaroli, C; Di Sante, L; Leoni, F; Chierichetti, S; Ottaviani, D; Citterio, B; Biavasco, F

    2016-10-01

    Epidemic Escherichia coli clones have been recovered in marine sediment along the coast of Marche, an Adriatic region in central Italy. In the present study, E. coli strains from the clam Chamelea gallina, sampled from seven natural beds in the same area, were detected. Selected E. coli isolates from all sampling sites were screened for antimicrobial susceptibility, genetic diversity and correlation. The majority (60%) belonged to phylogroups A or B1, 31% to the other groups (B2, C, D, E, F), 8% to cryptic clades, and 1% were untypable. Moreover, 33.3% of isolates were resistant to at least one drug and 11% were multidrug resistant (MDR). The most common resistance was to tetracycline, ampicillin, and streptomycin. No clonality was detected, but the strains' high genetic heterogeneity pointed at multiple sources of microbiological contamination. MLST analysis found potentially pathogenic and even epidemic MDR strains in clams collected in class A (ST746 and ST46) and class B (ST393, ST58 and ST131) areas, indicating that strains of clinical origin are detectable in clams. These data highlight that eating raw or lightly cooked clams may pose a health risk if purification is not performed or is ineffective. PMID:27375238

  11. Inferring Clonal Composition from Multiple Sections of a Breast Cancer

    PubMed Central

    Hu, Alex; Weber, Kris; Smith, Josh; Nickerson, Debbie; Song, ChaoZhong; Witten, Daniela; Blau, C. Anthony; Noble, William Stafford

    2014-01-01

    Cancers arise from successive rounds of mutation and selection, generating clonal populations that vary in size, mutational content and drug responsiveness. Ascertaining the clonal composition of a tumor is therefore important both for prognosis and therapy. Mutation counts and frequencies resulting from next-generation sequencing (NGS) potentially reflect a tumor's clonal composition; however, deconvolving NGS data to infer a tumor's clonal structure presents a major challenge. We propose a generative model for NGS data derived from multiple subsections of a single tumor, and we describe an expectation-maximization procedure for estimating the clonal genotypes and relative frequencies using this model. We demonstrate, via simulation, the validity of the approach, and then use our algorithm to assess the clonal composition of a primary breast cancer and associated metastatic lymph node. After dividing the tumor into subsections, we perform exome sequencing for each subsection to assess mutational content, followed by deep sequencing to precisely count normal and variant alleles within each subsection. By quantifying the frequencies of 17 somatic variants, we demonstrate that our algorithm predicts clonal relationships that are both phylogenetically and spatially plausible. Applying this method to larger numbers of tumors should cast light on the clonal evolution of cancers in space and time. PMID:25010360

  12. Clonality Testing in Veterinary Medicine: A Review With Diagnostic Guidelines.

    PubMed

    Keller, S M; Vernau, W; Moore, P F

    2016-07-01

    The accurate distinction of reactive and neoplastic lymphoid proliferations can present challenges. Given the different prognoses and treatment strategies, a correct diagnosis is crucial. Molecular clonality assays assess rearranged lymphocyte antigen receptor gene diversity and can help differentiate reactive from neoplastic lymphoid proliferations. Molecular clonality assays are commonly used to assess atypical, mixed, or mature lymphoid proliferations; small tissue fragments that lack architecture; and fluid samples. In addition, clonality testing can be utilized to track neoplastic clones over time or across anatomic sites. Molecular clonality assays are not stand-alone tests but useful adjuncts that follow clinical, morphologic, and immunophenotypic assessment. Even though clonality testing provides valuable information in a variety of situations, the complexities and pitfalls of this method, as well as its dependency on the experience of the interpreter, are often understated. In addition, a lack of standardized terminology, laboratory practices, and interpretational guidelines hinders the reproducibility of clonality testing across laboratories in veterinary medicine. The objectives of this review are twofold. First, the review is intended to familiarize the diagnostic pathologist or interested clinician with the concepts, potential pitfalls, and limitations of clonality testing. Second, the review strives to provide a basis for future harmonization of clonality testing in veterinary medicine by providing diagnostic guidelines. PMID:26933096

  13. Distribution and molecular characterization of genes encoding CTX-M and AmpC β-lactamases in Escherichia coli isolated from an Indian urban aquatic environment.

    PubMed

    Bajaj, Priyanka; Singh, Nambram Somendro; Kanaujia, Pawan Kumar; Virdi, Jugsharan Singh

    2015-02-01

    Aquatic environments harboring antibiotic resistant Escherichia coli constitute an important public health concern. Thus, it is important to characterize the resistance genetic elements of waterborne E. coli. It is also important to identify the predominant clonal groups/phylogroups represented by resistant strains to understand the epidemiology of antibiotic resistant E. coli in natural environments, and to identify the role of well-established genotypes in the spread of resistance in a particular geographical area through natural environments. In the present investigation, E. coli strains (n=126) isolated from various points along the river Yamuna traversing through the National Capital Territory of Delhi (India) were grouped phylogenetically. A collection of 61 strains representing all phylogroups was investigated for extended-spectrum β-lactamase (ESBL) and AmpC production. blaTEM, blaSHV and blaCTX-M genes were detected and analyzed, promoter/attenuator mutations associated with chromosomally-mediated AmpC overexpression were identified, and plasmid-mediated ampC was determined. blaTEM was the most widespread (100%) gene followed by bla(CTX-M) (16%), and plasmid-mediated ampC (3%). bla(CTX-M-15) and bla(CMY-42) were identified as the genes encoding CTX-M type ESBL and CIT type AmpC β-lactamases, respectively. CTX-M-15 ESBL phenotype was most common in phylogroup D (50%), followed by phylogroups B1 (30%), and A (20%). E. coli that produce plasmid-mediated AmpC were rare and present only in phylogroup D. Presence of multi β-lactam resistance, bla(CTX-M-15) and bla(CMY-42) in waterborne E. coli belonging to virulence-associated phylogroup D highlights the need for routine surveillance of resistance determinants in aquatic environments. This is also the first report for the presence of bla(CMY-42) in waterborne E. coli. PMID:25461036

  14. Clonal Non-Malignant Hematological Disorders: Unraveling Molecular Pathogenic Mechanisms to Develop Novel Targeted Therapeutics

    PubMed Central

    Risitano, Antonio M.; Selleri, Carmine

    2014-01-01

    Clonal non-malignant hematological disorders are a heterogeneous group of diseases that are particularly challenging for hematologists. Indeed, most obvious and frequent hematological diseases include a broad spectrum of malignancies, such as leukemias, lymphomas, myeloma, and other myeloproliferative or lymphoproliferative disorders. In recent years, all these diseases have been categorized by the WHO according to a novel classification of myeloid and lymphoid malignancies, which takes in account the outstanding progress in our understanding of molecular defects underlying hematological malignancies. Regardless of a number of novel technologies, hematologists continue to deal daily with conditions where a clear diagnosis of a malignancy is missing: this is the case of several clonal hematological disorders, which are considered bona fide non-malignant. Some myelodysplastic syndromes, chronic T and NK disorders of granular lymphocytes, myelofibrosis, monoclonal gammopathies, monoclonal B-cel lymphocytosis, mastocytosis and paroxysmal nocturnal hemoglobinuria are paradigmatic examples of how clonal disorders are clearly different from cancers, even if they may share with hematological malignancies similar molecular, genetic, epigenetic and immunological processes. Indeed, it is not entirely clear whether in individual conditions such pathogenic mechanisms may represent initial step(s) of malignant transformation, making a bridge between these clonal non-malignant disorders and typical hematological cancers. Some of these non-malignant disorders imply specific pathogenic mechanisms and/or clinical course, and so they have been definitely established with their own biological and clinical identity. However, the obvious question whether some of these clonal non-malignant hematological diseases form some a kind of disease-continuum with their corresponding malignant counterpart is still to be answered. PMID:24778992

  15. Intracavernous delivery of clonal mesenchymal stem cells rescues erectile function in the streptozotocin-induced diabetic mouse.

    PubMed

    Ryu, J-K; Kim, D-H; Song, K-M; Ryu, D-S; Kim, S-N; Shin, D-H; Yi, T; Suh, J-K; Song, S U

    2016-01-01

    The major hurdle for the clinical application of stem cell therapy is the heterogeneous nature of the isolated cells, which may cause different treatment outcomes. The aim of this study was to examine the effectiveness of mouse clonal bone marrow-derived stem cells (BMSCs) obtained from a single colony by using subfractionation culturing method for erectile function in diabetic animals. Twelve-week-old C57BL/6J mice were divided into four groups: controls, diabetic mice, and diabetic mice treated with a single intracavernous injection of PBS (20 μL) or clonal BMSCs (3 × 10(5) cells/20 μL). Clonal BMSCs were isolated from 5-week-old C3H mice. Two weeks after treatment, erectile function was measured by electrical stimulation of the cavernous nerve. The penis was stained with antibodies to PECAM-1, smooth muscle α-actin, neuronal nitric oxide synthase (nNOS), neurofilament, and phosphorylated endothelial NOS (phospho-eNOS). We also performed Western blot for phospho-eNOS, and eNOS in the corpus cavernosum tissue. Local delivery of clonal BMSCs significantly restored cavernous endothelial and smooth muscle cell contents, and penile nNOS and neurofilament contents, and induced eNOS phosphorylation (Ser1177) in diabetic mice. Intracavernous injection of clonal BMSCs induced significant recovery of erectile function, which reached 80-90% of the control values. Clonal BMSCs successfully restored erectile function through dual angiogenic and neurotrophic effects in diabetic mice. The homogenous nature of clonal mesenchymal stem cells may allow their clinical applications and open a new avenue through which to treat diabetic erectile dysfunction. PMID:26711324

  16. Kin Recognition in a Clonal Fish, Poecilia formosa.

    PubMed

    Makowicz, Amber M; Tiedemann, Ralph; Steele, Rachel N; Schlupp, Ingo

    2016-01-01

    Relatedness strongly influences social behaviors in a wide variety of species. For most species, the highest typical degree of relatedness is between full siblings with 50% shared genes. However, this is poorly understood in species with unusually high relatedness between individuals: clonal organisms. Although there has been some investigation into clonal invertebrates and yeast, nothing is known about kin selection in clonal vertebrates. We show that a clonal fish, the Amazon molly (Poecilia formosa), can distinguish between different clonal lineages, associating with genetically identical, sister clones, and use multiple sensory modalities. Also, they scale their aggressive behaviors according to the relatedness to other females: they are more aggressive to non-related clones. Our results demonstrate that even in species with very small genetic differences between individuals, kin recognition can be adaptive. Their discriminatory abilities and regulation of costly behaviors provides a powerful example of natural selection in species with limited genetic diversity. PMID:27483372

  17. Kin Recognition in a Clonal Fish, Poecilia formosa

    PubMed Central

    Makowicz, Amber M.; Tiedemann, Ralph; Schlupp, Ingo

    2016-01-01

    Relatedness strongly influences social behaviors in a wide variety of species. For most species, the highest typical degree of relatedness is between full siblings with 50% shared genes. However, this is poorly understood in species with unusually high relatedness between individuals: clonal organisms. Although there has been some investigation into clonal invertebrates and yeast, nothing is known about kin selection in clonal vertebrates. We show that a clonal fish, the Amazon molly (Poecilia formosa), can distinguish between different clonal lineages, associating with genetically identical, sister clones, and use multiple sensory modalities. Also, they scale their aggressive behaviors according to the relatedness to other females: they are more aggressive to non-related clones. Our results demonstrate that even in species with very small genetic differences between individuals, kin recognition can be adaptive. Their discriminatory abilities and regulation of costly behaviors provides a powerful example of natural selection in species with limited genetic diversity. PMID:27483372

  18. Correlation between the genomic o454-nlpD region polymorphisms, virulence gene equipment and phylogenetic group of extraintestinal Escherichia coli (ExPEC) enables pathotyping irrespective of host, disease and source of isolation

    PubMed Central

    2014-01-01

    Background The mutS-rpoS intergenic region in E. coli displays a mosaic structure which revealed pathotype specific patterns. To assess the importance of this region as a surrogate marker for the identification of highly virulent extraintestinal pathogenic E. coli (ExPEC) strains we aimed to: (i) characterize the genetic diversity of the mutS gene and the o454-nlpD genomic region among 510 E. coli strains from animals and humans; (ii) delineate associations between the polymorphism of this region and features such as phylogenetic background of E. coli, pathotype, host species, clinical condition, serogroup and virulence associated genes (VAG)s; and (iii) identify the most important VAGs for classification of the o454-nlpD region. Methods Size variation in the o454-nlpD region was investigated by PCR amplification and sequencing. Phylogenetic relationships were assessed by Ecor- and Multilocus sequence- typing (MLST), and a comparative analysis between mutS gene phylogenetic tree obtained with RAxML and the MLST grouping method was performed. Correlation between o454-nlpD patterns and the features described above were analysed. In addition, the importance of 47 PCR-amplified ExPEC-related VAGs for classification of o454-nlpD patterns was investigated by means of Random Forest algorithm. Results Four main structures (patterns I-IV) of the o454-nlpD region among ExPEC and commensal E. coli strains were identified. Statistical analysis showed a positive and exclusive association between pattern III and the ExPEC strains. A strong association between pattern III and either the Ecor group B2 or the sequence type complexes known to represent the phylogenetic background of highly virulent ExPEC strains (such as STC95, STC73 and STC131) was found as well. RF analyses determined five genes (csgA, malX, chuA, sit, and vat) to be suitable to predict pattern III strains. Conclusion The significant association between pattern III and group B2 strains suggested the o454-nlp

  19. Multidrug resistance dissemination by extended-spectrum β-lactamase-producing Escherichia coli causing community-acquired urinary tract infection in the Central-Western Region, Brazil.

    PubMed

    Gonçalves, Laura Fernandes; de Oliveira Martins-Júnior, Paulo; de Melo, Ana Beatriz Fabrício; da Silva, Rafaella Christina Rocha Moreira; de Paulo Martins, Vicente; Pitondo-Silva, André; de Campos, Tatiana Amabile

    2016-09-01

    The aim of this work was to analyse extended-spectrum β-lactamase (ESBL)-producing Escherichia coli strains isolated from outpatients with signs of cystitis in Hospital Universitário de Brasília (Brasília, Brazil) during the period July 2013 to April 2014. E. coli isolated from urine culture were identified and their antibiotic susceptibility profile was determined by VITEK 2. ESBL-producing strains identified were submitted to PCR for Clermont phylotyping, CTX-M group typing and virulence determinant detection, and clonal relationships were determined by enterobacterial repetitive intergenic consensus (ERIC)-PCR. One strain belonging to each cluster of the dendrogram obtained by ERIC-PCR was selected for multilocus sequence typing (MLST). Among 324 uropathogenic E. coli (UPEC) analysed, 23 (7.1%) were identified as producing ESBL. All ESBL-producing strains were multidrug-resistant (MDR), i.e. presented non-susceptibility to at least one agent in three or more antimicrobial categories. Of the 23 ESBL-producing UPEC strains, 9 were assigned to phylogenetic group B2 and 7 each belonged to phylogenetic groups D and A. Virulence genotyping showed that aer was the most prevalent gene observed among the strains (21/23), followed by traT (18/23), pap (5/23), afa (5/23), PAI (5/23), cnf (3/23) and sfa (1/23). Analysis of the dendrogram showed that multidrug resistance and CTX-M ESBL groups were distributed among all strains, independent of clonality and phylogroup. Sequence types (STs) associated with pandemic resistance clones, such as B2-ST131 and D-ST648, were observed among the isolates. In conclusion, the results showed worrisome evidence of the potential for antibiotic multiresistant dissemination among community-acquired urinary tract infection caused by UPEC. PMID:27530830

  20. Characterization of WbiQ: An {alpha}1,2-fucosyltransferase from Escherichia coli O127:K63(B8), and synthesis of H-type 3 blood group antigen

    SciTech Connect

    Pettit, Nicholas; Styslinger, Thomas; Mei, Zhen; Han, Weiqing; Zhao, Guohui; Wang, Peng George

    2010-11-12

    Research highlights: {yields} WbiQ is an {alpha}1,2-fucosyltransferase from Escherichia coli O127. {yields} WbiQ demonstrates strict substrate specificity for the Gal-{beta}1,3-GalNAc acceptor. {yields} WbiQ was used to synthesize milligram scale of the H-type 3 blood group antigen. -- Abstract: Escherichia coli O127:K63(B8) possesses high human blood group H (O) activity due to its O-antigen repeating unit structure. In this work, the wbiQ gene from E. coli O127:K63(B8) was expressed in E. coli BL21 (DE3) and purified as a fusion protein containing an N-terminal GST affinity tag. Using the GST-WbiQ fusion protein, the wbiQ gene was identified to encode an {alpha}1,2-fucosyltransferase using a radioactivity based assay, thin-layer chromatography assay, as well confirming product formation by using mass spectrometry and NMR spectroscopy. The fused enzyme (GST-WbiQ) has an optimal pH range from 6.5 to 7.5 and does not require the presence of a divalent metal to be enzymatically active. WbiQ displays strict substrate specificity, displaying activity only towards acceptors that contain Gal-{beta}1,3-GalNAc-{alpha}-OR linkages; indicating that both the Gal and GalNAc residues are vital for enzymatic activity. In addition, WbiQ was used to prepare the H-type 3 blood group antigen, Fuc-{alpha}1,2-Gal-{beta}1,3-GalNAc-{alpha}-OMe, on a milligram scale.

  1. Variable region sequences and idiotypic expression of a protective human immunoglobulin M antibody to capsular polysaccharides of Neisseria meningitidis group B and Escherichia coli K1.

    PubMed Central

    Azmi, F H; Lucas, A H; Raff, H V; Granoff, D M

    1994-01-01

    We determined the heavy (H)- and light (L)-chain variable (V) region nucleotide and translated amino acid sequences of the human immunoglobulin M(kappa) monoclonal antibody (MAb) 5E1, which is specific for the polysaccharide capsule of Escherichia coli K1 and Neisseria meningitidis group B (poly[alpha(2-->8)-N-acetylneuraminic acid]) and which is protective in animal models of infection. The 5E1 VH gene is a member of the VHIIIb family and is 97% homologous to the 9.1 germ line gene. The 5E1 VL gene is a member of the kappa I subgroup and is 98% homologous to the germ line gene, 15A, also known as KLO12. The VL and/or VH genes used by 5E1 are highly homologous to the V genes encoding antibodies to the Haemophilus influenzae type b polysaccharide and to antibodies reactive with self-antigens such as erythrocyte "i," DNA, and thyroid peroxidase. We also produced three murine anti-idiotype (Id) MAbs against 5E1. All three anti-Ids recognize a minor subset of antimeningococcal B polysaccharide antibodies present in serum from normal adults. Two of the anti-Ids define distinct Ids associated with antibodies having kappa I-15A V regions. These 15A-associated Ids are expressed by some heterologous human antimeningococcal B polysaccharide MAbs, and they also are independently expressed by two human MAbs that are specific for either the H. influenzae b polysaccharide or the i erythrocyte antigen and that utilize the kappa I-15A V region. Taken together, these data indicate that the 5E1 antibody uses V regions that recur in the human antibody repertoires to this polysaccharide and to structurally dissimilar polysaccharides and autoantigens. Thus, the poor immunogenicity of poly[alpha(2-->8)-N-acetylneuraminic acid] cannot be explained by the unavailability of certain critical VH and VL genes required for generation of antibody response. PMID:8168940

  2. Antioxidant activities from different rosemary clonal lines.

    PubMed

    Ban, Lan; Narasimhamoorthy, Brindha; Zhao, Liuqing; Greaves, John A; Schroeder, William D

    2016-06-15

    Rosemary extract is widely used in food industry and carnosic acid is reported to be the major component that is responsible for its antioxidant activities. However, it is unclear how the numerous plant metabolites interact and contribute to the overall antioxidant activity. In this study, with poultry fat as the model food system, rosemary extract from six clonal lines were evaluated that each represented a different genetic variant. As expected, rosemary extract with higher carnosic acid content had higher antioxidant activity. However, rosemary extract which had carnosic acid removed retained a significant amount of activity. Furthermore, when the individual contributions of carnosic acid and the portion without carnosic acid were evaluated separately, neither was shown to be responsible for the overall level of its stabilization effect from rosemary extract as a whole entity. The interactions among different plant metabolites have a major impact on the overall antioxidant capabilities of rosemary extract. PMID:26868574

  3. Isolation and Characterization of Potentially Pathogenic Antimicrobial-Resistant Escherichia coli Strains from Chicken and Pig Farms in Spain▿ †

    PubMed Central

    Cortés, Pilar; Blanc, Vanessa; Mora, Azucena; Dahbi, Ghizlane; Blanco, Jesús E.; Blanco, Miguel; López, Cecilia; Andreu, Antonia; Navarro, Ferran; Alonso, María Pilar; Bou, Germán; Blanco, Jorge; Llagostera, Montserrat

    2010-01-01

    To ascertain whether on animal farms there reside extended-spectrum β-lactamase (ESBL) and plasmidic class C β-lactamase-producing Escherichia coli isolates potentially pathogenic for humans, phylogenetic analyses, pulsed-field gel electrophoresis (PFGE) typing, serotyping, and virulence genotyping were performed for 86 isolates from poultry (57 isolates) and pig (29 isolates) farms. E. coli isolates from poultry farms carried genes encoding enzymes of the CTX-M-9 group as well as CMY-2, whereas those from pig farms mainly carried genes encoding CTX-M-1 enzymes. Poultry and pig isolates differed significantly in their phylogenetic group assignments, with phylogroup A predominating in pig isolates and phylogroup D predominating in avian isolates. Among the 86 farm isolates, 23 (26.7%) carried two or more virulence genes typical of extraintestinal pathogenic E. coli (ExPEC). Of these, 20 were isolated from poultry farms and only 3 from pig farms. Ten of the 23 isolates belonged to the classic human ExPEC serotypes O2:H6, O2:HNM, O2:H7, O15:H1, and O25:H4. Despite the high diversity of serotypes and pulsotypes detected among the 86 farm isolates, 13 PFGE clusters were identified. Four of these clusters contained isolates with two or more virulence genes, and two clusters exhibited the classic human ExPEC serotypes O2:HNM (ST10) and O2:H6 (ST115). Although O2:HNM and O2:H6 isolates of human and animal origins differed with respect to their virulence genes and PFGE pulsotypes, the O2:HNM isolates from pigs showed the same sequence type (ST10) as those from humans. The single avian O15:H1 isolate was compared with human clinical isolates of this serotype. Although all were found to belong to phylogroup D and shared the same virulence gene profile, they differed in their sequence types (ST362-avian and ST393-human) and PFGE pulsotypes. Noteworthy was the detection, for the first time, in poultry farms of the clonal groups O25b:H4-ST131-B2, producing CTX-M-9, and O25a

  4. Multi-jet propulsion organized by clonal development in a colonial siphonophore

    NASA Astrophysics Data System (ADS)

    Costello, John; Colin, Sean; Gemmell, Brad; Dabiri, John; Sutherland, Kelly

    2015-11-01

    Physonect siphonophores are colonial cnidarians that are pervasive predators in many neritic and oceanic ecosystems. Physonects employ multiple, clonal medusan individuals, termed nectophores, to propel an aggregate colony. Here we show that developmental differences between clonal nectophores of the physonect Nanomia bijuga produce a division of labor in thrust and torque production that controls direction and magnitude of whole colony swimming. Although smaller and less powerful, the position of young nectophores near the apex of the nectosome allows them to dominate torque production for turning whereas older, larger and more powerful individuals near the base of the nectosome contribute predominantly to forward thrust production. The patterns we describe offer insight into the biomechanical success of an ecologically important and widespread colonial animal group, but more broadly, provide basic physical understanding of a natural solution to multi-engine organization that may contribute to the expanding field of underwater distributed propulsion vehicle design.

  5. The coelomic epithelium transcriptome from a clonal sea star, Coscinasterias muricata.

    PubMed

    Gabre, Jonatan L; Martinez, Pedro; Nilsson Sköld, Helen; Ortega-Martinez, Olga; Abril, Josep F

    2015-12-01

    Coscinasterias is a cosmopolitan genus of large asteroid sea stars with the ability of somatic fission as a clonal reproductive strategy. During fission, the animals tear themselves apart across their central disc, where the lost body parts are regenerated afterwards. Here, we have sequenced and subsequently analysed the transcriptome of the coelomic epithelium of a clonal Coscinasterias muricata specimen from New Zealand. Out of the total 389,768 raw reads, 11,344 contigs were assembled and grouped into functions. Raw read and assembled contig sequences are available at NCBI (BioSample: SAMN03371637), while the annotated assembly can be accessed through the project transcriptome browser (compgen.bio.ub.edu/gbrowse/starfish_transcriptome/). Our data is valuable for future detailed exploration of the coelomic epithelium functions as well as for a better understanding of sea star physiology. PMID:26321383

  6. Multi-jet propulsion organized by clonal development in a colonial siphonophore.

    PubMed

    Costello, John H; Colin, Sean P; Gemmell, Brad J; Dabiri, John O; Sutherland, Kelly R

    2015-01-01

    Physonect siphonophores are colonial cnidarians that are pervasive predators in many neritic and oceanic ecosystems. Physonects employ multiple, clonal medusan individuals, termed nectophores, to propel an aggregate colony. Here we show that developmental differences between clonal nectophores of the physonect Nanomia bijuga produce a division of labour in thrust and torque production that controls direction and magnitude of whole-colony swimming. Although smaller and less powerful, the position of young nectophores near the apex of the nectosome allows them to dominate torque production for turning, whereas older, larger and more powerful individuals near the base of the nectosome contribute predominantly to forward thrust production. The patterns we describe offer insight into the biomechanical success of an ecologically important and widespread colonial animal group, but, more broadly, provide basic physical understanding of a natural solution to multi-engine organization that may contribute to the expanding field of underwater-distributed propulsion vehicle design. PMID:26327286

  7. Multi-jet propulsion organized by clonal development in a colonial siphonophore

    PubMed Central

    Costello, John H.; Colin, Sean P.; Gemmell, Brad J.; Dabiri, John O.; Sutherland, Kelly R.

    2015-01-01

    Physonect siphonophores are colonial cnidarians that are pervasive predators in many neritic and oceanic ecosystems. Physonects employ multiple, clonal medusan individuals, termed nectophores, to propel an aggregate colony. Here we show that developmental differences between clonal nectophores of the physonect Nanomia bijuga produce a division of labour in thrust and torque production that controls direction and magnitude of whole-colony swimming. Although smaller and less powerful, the position of young nectophores near the apex of the nectosome allows them to dominate torque production for turning, whereas older, larger and more powerful individuals near the base of the nectosome contribute predominantly to forward thrust production. The patterns we describe offer insight into the biomechanical success of an ecologically important and widespread colonial animal group, but, more broadly, provide basic physical understanding of a natural solution to multi-engine organization that may contribute to the expanding field of underwater-distributed propulsion vehicle design. PMID:26327286

  8. Coexistence of normal and clonal haemopoiesis in aplastic anaemia patients treated with immunosuppressive therapy.

    PubMed

    Piaggio, G; Podestà, M; Pitto, A; Sessarego, M; Figari, O; Fugazza, G; Benvenuto, F; Bruno, B; Van Lint, M T; Truini, M; Frassoni, F; Bacigalupo, A

    1999-12-01

    Cytogenetic abnormalities and paroxysmal nocturnal haemoglobinuria (PNH) phenotype are frequent findings in aplastic anaemia patients treated with immunosuppressive therapy (IST). In this study we investigated whether the appearance of clonal haemopoiesis influences patient outcome and survival. 97 patients entered this study and were followed from the onset of the disease for a median follow-up (FU) of 53 months. 93% are alive, 56% achieved complete remission, 30% partial remission, both transfusion independent, and 14% did not respond. Three groups were identified: (A) patients without evidence of emerging clones (71/97); (B) patients who acquired chromosomal abnormalities (13/97); (C) patients who showed low expression of glycosyl phosphatidylinositol anchored proteins (GPI-AP) (PNH phenotype) at presentation or later (16/97). Three patients showed both PIG-AP deficiency and chromosomal abnormalities. The actuarial survival of patients without clonal haemopoiesis (n = 71) at 6 years was 95%, for patients with chromosomal abnormalities (n = 13), 88%, and for patients with PIG-AP deficiency (n = 16), 89%. There was no difference in the probability of becoming transfusion independent in the three groups (93%, 92% and 88% respectively). This study confirmed that a proportion of severe aplastic anaemia (SAA) patients exhibit clonal markers during the time after IST, often coexisting with cytogenetically or phenotypically normal haemopoiesis. There was no significant clinical impact of these abnormalities on transfusion independence and survival at the median follow-up of 4 years. PMID:10583249

  9. Effects of clonal integration on the invasive clonal plant Alternanthera philoxeroides under heterogeneous and homogeneous water availability

    PubMed Central

    You, Wen-Hua; Han, Cui-Min; Liu, Chun-Hua; Yu, Dan

    2016-01-01

    Many notorious invasive plants are clonal, living in heterogeneous or homogeneous habitats. To understand how clonal integration affects the performance of these plants in different habitat conditions, an 8-week greenhouse experiment was conducted: ramet pairs of A. philoxeroides were grown in two habitats, either heterogeneous or homogeneous in water availability, with the stolon connections either severed or kept intact. Under heterogeneous water availability, compared with ramets in homogeneous habitats, clonal integration significantly promoted the growth and photosynthetic performance of water-stressed apical ramets, whereas it only increased the photosynthetic performance but did not affect the growth of water-stressed basal ramets. Moreover, clonal integration markedly increased the root/shoot ratios of ramets grown in habitats with high water supply but decreased it under low water availability. Under homogeneous water availability, stolon connection (clonal integration) did not influence the growth, photosynthetic performance and biomass allocation of water-stressed ramets, but it significantly promoted the growth of well-watered ramets in both apical and basal sections. These findings deepen our understanding of the bidirectional and differentiated (mainly acropetal) clonal integration of A. philoxeroides, suggesting that the invasive plant A. philoxeroides can benefit from clonal integration in both heterogeneous and homogeneous habitats. PMID:27416868

  10. Effects of clonal integration on the invasive clonal plant Alternanthera philoxeroides under heterogeneous and homogeneous water availability.

    PubMed

    You, Wen-Hua; Han, Cui-Min; Liu, Chun-Hua; Yu, Dan

    2016-01-01

    Many notorious invasive plants are clonal, living in heterogeneous or homogeneous habitats. To understand how clonal integration affects the performance of these plants in different habitat conditions, an 8-week greenhouse experiment was conducted: ramet pairs of A. philoxeroides were grown in two habitats, either heterogeneous or homogeneous in water availability, with the stolon connections either severed or kept intact. Under heterogeneous water availability, compared with ramets in homogeneous habitats, clonal integration significantly promoted the growth and photosynthetic performance of water-stressed apical ramets, whereas it only increased the photosynthetic performance but did not affect the growth of water-stressed basal ramets. Moreover, clonal integration markedly increased the root/shoot ratios of ramets grown in habitats with high water supply but decreased it under low water availability. Under homogeneous water availability, stolon connection (clonal integration) did not influence the growth, photosynthetic performance and biomass allocation of water-stressed ramets, but it significantly promoted the growth of well-watered ramets in both apical and basal sections. These findings deepen our understanding of the bidirectional and differentiated (mainly acropetal) clonal integration of A. philoxeroides, suggesting that the invasive plant A. philoxeroides can benefit from clonal integration in both heterogeneous and homogeneous habitats. PMID:27416868

  11. E. Coli and Pregnancy

    MedlinePlus

    ... care provider. What is E. coli? E. coli (Escherichia coli) is a bacterium that lives in your colon ( ... 10):1411-1413. Jones B, et al. 2004. Escherichia coli: a growing problem in early onset neonatal sepsis. ...

  12. E. Coli Infection

    MedlinePlus

    ... is E. coli? E. coli is short for Escherichia coli -- bacteria (germs) that cause severe cramps and diarrhea. E. ... and especially in people who have another illness. E. coli infection is more common during the summer months and ...

  13. NSAIDs modulate clonal evolution in Barrett's esophagus.

    PubMed

    Kostadinov, Rumen L; Kuhner, Mary K; Li, Xiaohong; Sanchez, Carissa A; Galipeau, Patricia C; Paulson, Thomas G; Sather, Cassandra L; Srivastava, Amitabh; Odze, Robert D; Blount, Patricia L; Vaughan, Thomas L; Reid, Brian J; Maley, Carlo C

    2013-06-01

    Cancer is considered an outcome of decades-long clonal evolution fueled by acquisition of somatic genomic abnormalities (SGAs). Non-steroidal anti-inflammatory drugs (NSAIDs) have been shown to reduce cancer risk, including risk of progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EA). However, the cancer chemopreventive mechanisms of NSAIDs are not fully understood. We hypothesized that NSAIDs modulate clonal evolution by reducing SGA acquisition rate. We evaluated thirteen individuals with BE. Eleven had not used NSAIDs for 6.2±3.5 (mean±standard deviation) years and then began using NSAIDs for 5.6±2.7 years, whereas two had used NSAIDs for 3.3±1.4 years and then discontinued use for 7.9±0.7 years. 161 BE biopsies, collected at 5-8 time points over 6.4-19 years, were analyzed using 1Million-SNP arrays to detect SGAs. Even in the earliest biopsies there were many SGAs (284±246 in 10/13 and 1442±560 in 3/13 individuals) and in most individuals the number of SGAs changed little over time, with both increases and decreases in SGAs detected. The estimated SGA rate was 7.8 per genome per year (95% support interval [SI], 7.1-8.6) off-NSAIDs and 0.6 (95% SI 0.3-1.5) on-NSAIDs. Twelve individuals did not progress to EA. In ten we detected 279±86 SGAs affecting 53±30 Mb of the genome per biopsy per time point and in two we detected 1,463±375 SGAs affecting 180±100 Mb. In one individual who progressed to EA we detected a clone having 2,291±78 SGAs affecting 588±18 Mb of the genome at three time points in the last three of 11.4 years of follow-up. NSAIDs were associated with reduced rate of acquisition of SGAs in eleven of thirteen individuals. Barrett's cells maintained relative equilibrium level of SGAs over time with occasional punctuations by expansion of clones having massive amount of SGAs. PMID:23785299

  14. NSAIDs Modulate Clonal Evolution in Barrett's Esophagus

    PubMed Central

    Kostadinov, Rumen L.; Kuhner, Mary K.; Li, Xiaohong; Sanchez, Carissa A.; Galipeau, Patricia C.; Paulson, Thomas G.; Sather, Cassandra L.; Srivastava, Amitabh; Odze, Robert D.; Blount, Patricia L.; Vaughan, Thomas L.; Reid, Brian J.; Maley, Carlo C.

    2013-01-01

    Cancer is considered an outcome of decades-long clonal evolution fueled by acquisition of somatic genomic abnormalities (SGAs). Non-steroidal anti-inflammatory drugs (NSAIDs) have been shown to reduce cancer risk, including risk of progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EA). However, the cancer chemopreventive mechanisms of NSAIDs are not fully understood. We hypothesized that NSAIDs modulate clonal evolution by reducing SGA acquisition rate. We evaluated thirteen individuals with BE. Eleven had not used NSAIDs for 6.2±3.5 (mean±standard deviation) years and then began using NSAIDs for 5.6±2.7 years, whereas two had used NSAIDs for 3.3±1.4 years and then discontinued use for 7.9±0.7 years. 161 BE biopsies, collected at 5–8 time points over 6.4–19 years, were analyzed using 1Million-SNP arrays to detect SGAs. Even in the earliest biopsies there were many SGAs (284±246 in 10/13 and 1442±560 in 3/13 individuals) and in most individuals the number of SGAs changed little over time, with both increases and decreases in SGAs detected. The estimated SGA rate was 7.8 per genome per year (95% support interval [SI], 7.1–8.6) off-NSAIDs and 0.6 (95% SI 0.3–1.5) on-NSAIDs. Twelve individuals did not progress to EA. In ten we detected 279±86 SGAs affecting 53±30 Mb of the genome per biopsy per time point and in two we detected 1,463±375 SGAs affecting 180±100 Mb. In one individual who progressed to EA we detected a clone having 2,291±78 SGAs affecting 588±18 Mb of the genome at three time points in the last three of 11.4 years of follow-up. NSAIDs were associated with reduced rate of acquisition of SGAs in eleven of thirteen individuals. Barrett's cells maintained relative equilibrium level of SGAs over time with occasional punctuations by expansion of clones having massive amount of SGAs. PMID:23785299

  15. Molecular Mimicry and Clonal Deletion: A Fresh Look

    PubMed Central

    Rose, Noel R.

    2014-01-01

    In this article, I trace the historic background of clonal deletion and molecular mimicry, two major pillars underlying our present understanding of autoimmunity and autoimmune disease. Clonal deletion originated as a critical element of the clonal selection theory of antibody formation in order to explain tolerance of self. If we did have complete clonal deletion, there would be major voids, the infamous “black holes”, in our immune repertoire. For comprehensive, protective adaptive immunity, full deletion is necessarily a rare event. Molecular mimicry, the sharing of epitopes among self and non-self antigens, is extraordinary common and provides the evidence that complete deletion of self-reactive clones is rare. If molecular mimicry were not common, protective adaptive immunity could not be all-encompassing. By taking a fresh look at these two processes together we can envision their evolutionary basis and understand the need for regulatory devices to prevent molecular mimicry from progressing to autoimmune disease. PMID:25172771

  16. GENETIC VARIATION IN CLONAL VERTEBRATES DETECTED BY SIMPLE SEQUENCE FINGERPRINTING

    EPA Science Inventory

    Measurement of clonal heterogeneity is central to understanding evolutionary and population genetics of roughly 50 species of vertebrates lack effective genetic recombination. imple-sequence DNA fingerprinting with oligonucleotide probes (CAG)5 and (GACA)4 was used to detect hete...

  17. Molecular mimicry and clonal deletion: A fresh look.

    PubMed

    Rose, Noel R

    2015-06-21

    In this article, I trace the historic background of clonal deletion and molecular mimicry, two major pillars underlying our present understanding of autoimmunity and autoimmune disease. Clonal deletion originated as a critical element of the clonal selection theory of antibody formation in order to explain tolerance of self. If we did have complete clonal deletion, there would be major voids, the infamous "black holes", in our immune repertoire. For comprehensive, protective adaptive immunity, full deletion is necessarily a rare event. Molecular mimicry, the sharing of epitopes among self and non-self antigens, is extraordinary common and provides the evidence that complete deletion of self-reactive clones is rare. If molecular mimicry were not common, protective adaptive immunity could not be all-encompassing. By taking a fresh look at these two processes together we can envision their evolutionary basis and understand the need for regulatory devices to prevent molecular mimicry from progressing to autoimmune disease. PMID:25172771

  18. Clonal Expansion (CE) Models in Cancer Risk Assessment

    EPA Science Inventory

    Cancer arises when cells accumulate sufficient critical mutations. Carcinogens increase the probability of mutation during cell division or promote clonal expansion within stages. Multistage CE models recapitulate this process and provide a framework for incorporating relevant da...

  19. Clonal integration in Ludwigia hexapetala under different light regimes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Physiological integration among ramets of invasive plant species may support their colonization and spread in novel aquatic environments where growth-limiting resources are spatially heterogeneous. Under contrasting light conditions, we investigated how clonal integration influences growth, biomass...

  20. Roles of Clonal Integration in both Heterogeneous and Homogeneous Habitats

    PubMed Central

    Zhang, Haijie; Liu, Fenghong; Wang, Renqing; Liu, Jian

    2016-01-01

    Many studies have shown that clonal integration can promote the performance of clonal plants in heterogeneous habitats, but the roles of clonal integration in both heterogeneous and homogeneous habitats were rarely studied simultaneously. Ramet pairs of Alternanthera philoxeroides (Mart.) Griseb were placed in two habitats either heterogeneous or homogeneous in soil nutrient availability, with stolon connections left intact or severed. Total biomass, total length of stolons, and number of new ramets of distal (relatively young) ramets located in low-nutrient environments were significantly greater when the distal ramets were connected to than when they were disconnected from proximal (relatively old) ramets located in high-nutrient environments. Total length of stolons of proximal ramets growing in low-nutrient environments was significantly higher when the proximal ramets were connected to than when they were disconnected from the distal ramets growing in high-nutrient environments, but stolon connection did not affect total biomass or number of new ramets of the proximal ramets. Stolon severing also did not affect the growth of the whole ramet pairs in heterogeneous environments. In homogeneous high-nutrient environments stolon severing promoted the growth of the proximal ramets and the ramet pairs, but in homogeneous low-nutrient environments it did not affect the growth of the proximal or distal ramets. Hence, for A. philoxeroides, clonal fragmentation appears to be more advantageous than clonal integration in resource-rich homogeneous habitats, and clonal integration becomes beneficial in heterogeneous habitats. Our study contributes to revealing roles of clonal integration in both heterogeneous and homogeneous habitats and expansion patterns of invasive clonal plants such as A. philoxeroides in multifarious habitats. PMID:27200026

  1. Roles of Clonal Integration in both Heterogeneous and Homogeneous Habitats.

    PubMed

    Zhang, Haijie; Liu, Fenghong; Wang, Renqing; Liu, Jian

    2016-01-01

    Many studies have shown that clonal integration can promote the performance of clonal plants in heterogeneous habitats, but the roles of clonal integration in both heterogeneous and homogeneous habitats were rarely studied simultaneously. Ramet pairs of Alternanthera philoxeroides (Mart.) Griseb were placed in two habitats either heterogeneous or homogeneous in soil nutrient availability, with stolon connections left intact or severed. Total biomass, total length of stolons, and number of new ramets of distal (relatively young) ramets located in low-nutrient environments were significantly greater when the distal ramets were connected to than when they were disconnected from proximal (relatively old) ramets located in high-nutrient environments. Total length of stolons of proximal ramets growing in low-nutrient environments was significantly higher when the proximal ramets were connected to than when they were disconnected from the distal ramets growing in high-nutrient environments, but stolon connection did not affect total biomass or number of new ramets of the proximal ramets. Stolon severing also did not affect the growth of the whole ramet pairs in heterogeneous environments. In homogeneous high-nutrient environments stolon severing promoted the growth of the proximal ramets and the ramet pairs, but in homogeneous low-nutrient environments it did not affect the growth of the proximal or distal ramets. Hence, for A. philoxeroides, clonal fragmentation appears to be more advantageous than clonal integration in resource-rich homogeneous habitats, and clonal integration becomes beneficial in heterogeneous habitats. Our study contributes to revealing roles of clonal integration in both heterogeneous and homogeneous habitats and expansion patterns of invasive clonal plants such as A. philoxeroides in multifarious habitats. PMID:27200026

  2. First Description of an Extended-Spectrum Cephalosporin- and Fluoroquinolone- Resistant Avian Pathogenic Escherichia coli Clone in Algeria.

    PubMed

    Meguenni, Nacima; Le Devendec, Laetitia; Jouy, Eric; Le Corvec, Maena; Bounar-Kechih, Saliha; Rabah Bakour, D; Kempf, Isabelle

    2015-03-01

    Eleven avian pathogenic Escherichia coli (APEC) strains isolated from 2006 to 2010 from different farms in Algeria and resistant to cephalosporins were studied. Their susceptibility to antimicrobials was determined by disk diffusion, and the genes responsible for resistance to critical antimicrobials were studied by PCR, sequencing, and conjugation. Their genetic profiles were compared by pulsed-field gel electrophoresis (PFGE). All strains were resistant to extended-spectrum cephalosporins, ciprofloxacin, tetracycline, trimethoprim-sulfamethoxazole, and neomycin and showed the same PFGE profile. For most of them, resistance was encoded by a nontransferable group 1 bla(CTX-M) gene, and multiple mutations were detected in the quinolone resistance-determining regions. The clonal dissemination of this resistant APEC is worrying for animal and public health. PMID:26292529

  3. Dynamics of extended-spectrum cephalosporin resistance in pathogenic Escherichia coli isolated from diseased pigs in Quebec, Canada.

    PubMed

    Jahanbakhsh, Seyedehameneh; Smith, Matthew G; Kohan-Ghadr, Hamid-Reza; Letellier, Ann; Abraham, Sam; Trott, Darren J; Fairbrother, John Morris

    2016-08-01

    The aim of this study was to investigate the evolution with time of ceftiofur-resistant Escherichia coli clinical isolates from pigs in Québec, Canada, between 1997 and 2012 with respect to pathotypes, clones and antimicrobial resistance. Eighty-five ceftiofur-resistant E. coli isolates were obtained from the OIE (World Organisation for Animal Health) Reference Laboratory for Escherichia coli. The most prevalent pathovirotypes were enterotoxigenic E. coli (ETEC):F4 (40%), extraintestinal pathogenic E. coli (ExPEC) (16.5%) and Shiga toxin-producing E. coli (STEC):F18 (8.2%). Susceptibility testing to 15 antimicrobial agents revealed a high prevalence of resistance to 13 antimicrobials, with all isolates being multidrug-resistant. blaCMY-2 (96.5%) was the most frequently detected β-lactamase gene, followed by blaTEM (49.4%) and blaCTX-M (3.5%). Pulsed-field gel electrophoresis (PFGE) applied to 45 representative E. coli isolates revealed that resistance to ceftiofur is spread both horizontally and clonally. In addition, the emergence of extended-spectrum β-lactamase-producing E. coli isolates carrying blaCTX-M was observed in 2011 and 2012 in distinct clones. The most predominant plasmid incompatibility (Inc) groups were IncFIB, IncI1, IncA/C and IncFIC. Resistance to gentamicin, kanamycin and chloramphenicol as well as the frequency of blaTEM and IncA/C significantly decreased over the study period, whereas the frequency of IncI1 and multidrug resistance to seven antimicrobial categories significantly increased. These findings reveal that extended-spectrum cephalosporin-resistant porcine E. coli isolates in Québec belong to several different clones with diverse antimicrobial resistance patterns and plasmids. Furthermore, blaCMY-2 was the major β-lactamase gene in these isolates. From 2011, we report the emergence of blaCTX-M in distinct clones. PMID:27286922

  4. Escherichia Coli

    ERIC Educational Resources Information Center

    Goodsell, David S.

    2009-01-01

    Diverse biological data may be used to create illustrations of molecules in their cellular context. I describe the scientific results that support a recent textbook illustration of an "Escherichia coli cell". The image magnifies a portion of the bacterium at one million times, showing the location and form of individual macromolecules. Results…

  5. E. coli

    MedlinePlus

    ... sure that ground beef has reached a safe internal temperature of 160° F. Wash hands before preparing food, after diapering infants, and after contact with cows, sheep, or goats, their food or treats, or their living environment . General Information E. coli Infections (NIH MedlinePlus) Trusted ...

  6. Divergent clonal selection dominates medulloblastoma at recurrence

    PubMed Central

    Morrissy, A. Sorana; Garzia, Livia; Shih, David J. H.; Zuyderduyn, Scott; Huang, Xi; Skowron, Patryk; Remke, Marc; Cavalli, Florence M. G.; Ramaswamy, Vijay; Lindsay, Patricia E.; Jelveh, Salomeh; Donovan, Laura K.; Wang, Xin; Luu, Betty; Zayne, Kory; Li, Yisu; Mayoh, Chelsea; Thiessen, Nina; Mercier, Eloi; Mungall, Karen L.; Ma, Yusanne; Tse, Kane; Zeng, Thomas; Shumansky, Karey; Roth, Andrew J. L.; Shah, Sohrab; Farooq, Hamza; Kijima, Noriyuki; Holgado, Borja L.; Lee, John J. Y.; Matan-Lithwick, Stuart; Liu, Jessica; Mack, Stephen C.; Manno, Alex; Michealraj, K. A.; Nor, Carolina; Peacock, John; Qin, Lei; Reimand, Juri; Rolider, Adi; Thompson, Yuan Y.; Wu, Xiaochong; Pugh, Trevor; Ally, Adrian; Bilenky, Mikhail; Butterfield, Yaron S. N.; Carlsen, Rebecca; Cheng, Young; Chuah, Eric; Corbett, Richard D.; Dhalla, Noreen; He, An; Lee, Darlene; Li, Haiyan I.; Long, William; Mayo, Michael; Plettner, Patrick; Qian, Jenny Q.; Schein, Jacqueline E.; Tam, Angela; Wong, Tina; Birol, Inanc; Zhao, Yongjun; Faria, Claudia C.; Pimentel, José; Nunes, Sofia; Shalaby, Tarek; Grotzer, Michael; Pollack, Ian F.; Hamilton, Ronald L.; Li, Xiao-Nan; Bendel, Anne E.; Fults, Daniel W.; Walter, Andrew W.; Kumabe, Toshihiro; Tominaga, Teiji; Collins, V. Peter; Cho, Yoon-Jae; Hoffman, Caitlin; Lyden, David; Wisoff, Jeffrey H.; Garvin, James H.; Stearns, Duncan S.; Massimi, Luca; Schüller, Ulrich; Sterba, Jaroslav; Zitterbart, Karel; Puget, Stephanie; Ayrault, Olivier; Dunn, Sandra E.; Tirapelli, Daniela P. C.; Carlotti, Carlos G.; Wheeler, Helen; Hallahan, Andrew R.; Ingram, Wendy; MacDonald, Tobey J.; Olson, Jeffrey J.; Van Meir, Erwin G.; Lee, Ji-Yeoun; Wang, Kyu-Chang; Kim, Seung-Ki; Cho, Byung-Kyu; Pietsch, Torsten; Fleischhack, Gudrun; Tippelt, Stephan; Ra, Young Shin; Bailey, Simon; Lindsey, Janet C.; Clifford, Steven C.; Eberhart, Charles G.; Cooper, Michael K.; Packer, Roger J.; Massimino, Maura; Garre, Maria Luisa; Bartels, Ute; Tabori, Uri; Hawkins, Cynthia E.; Dirks, Peter; Bouffet, Eric; Rutka, James T.; Wechsler-Reya, Robert J.; Weiss, William A.; Collier, Lara S.; Dupuy, Adam J.; Korshunov, Andrey; Jones, David T. W.; Kool, Marcel; Northcott, Paul A.; Pfister, Stefan M.; Largaespada, David A.; Mungall, Andrew J.; Moore, Richard A.; Jabado, Nada; Bader, Gary D.; Jones, Steven J. M.; Malkin, David; Marra, Marco A.; Taylor, Michael D.

    2016-01-01

    The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon–driven, functional genomic mouse model of medulloblastoma with ‘humanized’ in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (<5%). Whole-genome sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (<12% diagnostic events were retained at recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy. PMID:26760213

  7. Divergent clonal selection dominates medulloblastoma at recurrence.

    PubMed

    Morrissy, A Sorana; Garzia, Livia; Shih, David J H; Zuyderduyn, Scott; Huang, Xi; Skowron, Patryk; Remke, Marc; Cavalli, Florence M G; Ramaswamy, Vijay; Lindsay, Patricia E; Jelveh, Salomeh; Donovan, Laura K; Wang, Xin; Luu, Betty; Zayne, Kory; Li, Yisu; Mayoh, Chelsea; Thiessen, Nina; Mercier, Eloi; Mungall, Karen L; Ma, Yusanne; Tse, Kane; Zeng, Thomas; Shumansky, Karey; Roth, Andrew J L; Shah, Sohrab; Farooq, Hamza; Kijima, Noriyuki; Holgado, Borja L; Lee, John J Y; Matan-Lithwick, Stuart; Liu, Jessica; Mack, Stephen C; Manno, Alex; Michealraj, K A; Nor, Carolina; Peacock, John; Qin, Lei; Reimand, Juri; Rolider, Adi; Thompson, Yuan Y; Wu, Xiaochong; Pugh, Trevor; Ally, Adrian; Bilenky, Mikhail; Butterfield, Yaron S N; Carlsen, Rebecca; Cheng, Young; Chuah, Eric; Corbett, Richard D; Dhalla, Noreen; He, An; Lee, Darlene; Li, Haiyan I; Long, William; Mayo, Michael; Plettner, Patrick; Qian, Jenny Q; Schein, Jacqueline E; Tam, Angela; Wong, Tina; Birol, Inanc; Zhao, Yongjun; Faria, Claudia C; Pimentel, José; Nunes, Sofia; Shalaby, Tarek; Grotzer, Michael; Pollack, Ian F; Hamilton, Ronald L; Li, Xiao-Nan; Bendel, Anne E; Fults, Daniel W; Walter, Andrew W; Kumabe, Toshihiro; Tominaga, Teiji; Collins, V Peter; Cho, Yoon-Jae; Hoffman, Caitlin; Lyden, David; Wisoff, Jeffrey H; Garvin, James H; Stearns, Duncan S; Massimi, Luca; Schüller, Ulrich; Sterba, Jaroslav; Zitterbart, Karel; Puget, Stephanie; Ayrault, Olivier; Dunn, Sandra E; Tirapelli, Daniela P C; Carlotti, Carlos G; Wheeler, Helen; Hallahan, Andrew R; Ingram, Wendy; MacDonald, Tobey J; Olson, Jeffrey J; Van Meir, Erwin G; Lee, Ji-Yeoun; Wang, Kyu-Chang; Kim, Seung-Ki; Cho, Byung-Kyu; Pietsch, Torsten; Fleischhack, Gudrun; Tippelt, Stephan; Ra, Young Shin; Bailey, Simon; Lindsey, Janet C; Clifford, Steven C; Eberhart, Charles G; Cooper, Michael K; Packer, Roger J; Massimino, Maura; Garre, Maria Luisa; Bartels, Ute; Tabori, Uri; Hawkins, Cynthia E; Dirks, Peter; Bouffet, Eric; Rutka, James T; Wechsler-Reya, Robert J; Weiss, William A; Collier, Lara S; Dupuy, Adam J; Korshunov, Andrey; Jones, David T W; Kool, Marcel; Northcott, Paul A; Pfister, Stefan M; Largaespada, David A; Mungall, Andrew J; Moore, Richard A; Jabado, Nada; Bader, Gary D; Jones, Steven J M; Malkin, David; Marra, Marco A; Taylor, Michael D

    2016-01-21

    The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon-driven, functional genomic mouse model of medulloblastoma with 'humanized' in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (<5%). Whole-genome sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (<12% diagnostic events were retained at recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy. PMID:26760213

  8. Lineage and clonal development of gastric glands.

    PubMed

    Nomura, S; Esumi, H; Job, C; Tan, S S

    1998-12-01

    Individual gastric glands of the stomach are composed of cells of different phenotypes. These are derived from multipotent progenitor stem cells located at the isthmus region of the gland. Previous cell lineage analyses suggest that gastric glands, as in the colon and small intestine, are invariably monoclonal by adult stages. However, little is known about the ontogenetic progression of glandular clonality in the stomach. To examine this issue, we employed an in situ cell lineage marker in female mice heterozygous for an X-linked transgene. We found that stomach glands commence development as polyclonal units, but by adulthood (6 weeks), the majority progressed to monoclonal units. Our analysis suggests that at least three progenitor cells are required to initiate the development of individual gastric glands if they are analyzed just after birth. Hence, unlike the colon and small intestine, stomachs showed a significant fraction (10-25%) of polyclonal glands at adult stages. We suggest that these glands persist from polyclonal glands present in the embryonic stomach and hypothesize that they represent a subpopulation of glands with larger numbers of self-renewing stem cells. PMID:9851847

  9. Clonal complex Pseudomonas aeruginosa in horses.

    PubMed

    Kidd, Timothy J; Gibson, Justine S; Moss, Susan; Greer, Ristan M; Cobbold, Rowland N; Wright, John D; Ramsay, Kay A; Grimwood, Keith; Bell, Scott C

    2011-05-01

    Pseudomonas aeruginosa is associated with infectious endometritis in horses. Although infectious endometritis is often considered a venereal infection, there is relatively limited genotypic-based evidence to support this mode of transmission. The study sought to determine the relatedness between genital P. aeruginosa isolates collected from a limited geographical region using molecular strain typing. Enterobacterial repetitive intergenic consensus PCR typing was performed on 93 isolates collected between 2005 and 2009 from 2058 thoroughbred horses (including 18 stallions) at 66 studs. While P. aeruginosa was not detected in the stallions, 53/93 (57%) mares harbouring P. aeruginosa had clonally related strains, which included a single dominant genotype detected in 42 (45%) mares from 13 different studs. These novel findings suggest that most equine genital P. aeruginosa infections in this region may have been acquired from mechanisms other than direct horse to horse transmission. Instead, other potential acquisition pathways, as well as strain specific adaptation to the equine genital tract, should be investigated. PMID:21183294

  10. Disturbance and clonal reproduction determine liana distribution and maintain liana diversity in a tropical forest.

    PubMed

    Ledo, Alicia; Schnitzer, Stefan A

    2014-08-01

    Negative density dependence (NDD) and habitat specialization have received strong empirical support as mechanisms that explain tree species diversity maintenance and distribution in tropical forests. In contrast, disturbance appears to play only a minor role. Previous studies have rarely examined the relative strengths of these diversity maintenance mechanisms concurrently, and few studies have included plant groups other than trees. Here we used a large, spatially explicit data set from Barro Colorado Island, Panama (BCI) to test whether liana and tree species distribution patterns are most consistent with NDD, habitat specialization, or disturbance. We found compelling evidence that trees responded to habitat specialization and NDD; however, only disturbance explained the distribution of the majority of liana species and maintained liana diversity. Lianas appear to respond to disturbance with high vegetative (clonal) reproduction, and liana species' ability to produce clonal stems following disturbance results in a clumped spatial distribution. Thus, clonal reproduction following disturbance explains local liana spatial distribution and diversity maintenance on BCI, whereas negative density dependence and habitat specialization, two prominent mechanisms contributing to tree species diversity and distribution, do not. PMID:25230468

  11. Clonality analysis of combined Brenner and mucinous tumours of the ovary reveals their monoclonal origin.

    PubMed

    Wang, Yihong; Wu, Ren-chin; Shwartz, Lauren Ende; Haley, Lisa; Lin, Ming-tse; Shih, Ie-ming; Kurman, Robert J

    2015-10-01

    The derivation of ovarian intestinal-type mucinous tumours is not well established. Some are derived from teratomas but the origin of the majority is not clear. It has been recently proposed that the non-germ cell group may be derived from Brenner tumours, as the association of a mucinous tumour with a Brenner tumour is frequently observed. In order to explore the histogenesis of these neoplasms, we undertook a clonality analysis of the two components of ten combined Brenner and mucinous tumours using a human androgen receptor gene (HUMARA) assay. All eight informative cases of ten showed a concordant X-chromosome inactivation pattern between the two tumour components, indicative of a shared clonal origin (p = 0.0039). Microsatellite genotyping in five of the combined tumours displayed an identical heterozygous pattern with paired Fallopian tube tissue, indicative of a somatic cell origin. In addition, paired box protein 8, a highly sensitive Müllerian epithelial marker, was not detected by immunohistochemistry in either tumour component in any of the ten tumours, suggesting that this subset of mucinous tumours does not originate from Müllerian-derived epithelium. In conclusion, this study demonstrates that in combined mucinous and Brenner tumours, there is a shared clonal relationship between the two different tumour components and suggests that some pure mucinous tumours may develop from a Brenner tumour in which the Brenner tumour component becomes compressed and obliterated by an expanding mucinous neoplasm. PMID:26095692

  12. Multilocus sequence typing analysis of Staphylococcus lugdunensis implies a clonal population structure.

    PubMed

    Chassain, Benoît; Lemée, Ludovic; Didi, Jennifer; Thiberge, Jean-Michel; Brisse, Sylvain; Pons, Jean-Louis; Pestel-Caron, Martine

    2012-09-01

    Staphylococcus lugdunensis is recognized as one of the major pathogenic species within the genus Staphylococcus, even though it belongs to the coagulase-negative group. A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 87 S. lugdunensis isolates from various clinical and geographic sources by DNA sequence analysis of seven housekeeping genes (aroE, dat, ddl, gmk, ldh, recA, and yqiL). The number of alleles ranged from four (gmk and ldh) to nine (yqiL). Allelic profiles allowed the definition of 20 different sequence types (STs) and five clonal complexes. The 20 STs lacked correlation with geographic source. Isolates recovered from hematogenic infections (blood or osteoarticular isolates) or from skin and soft tissue infections did not cluster in separate lineages. Penicillin-resistant isolates clustered mainly in one clonal complex, unlike glycopeptide-tolerant isolates, which did not constitute a distinct subpopulation within S. lugdunensis. Phylogenies from the sequences of the seven individual housekeeping genes were congruent, indicating a predominantly mutational evolution of these genes. Quantitative analysis of the linkages between alleles from the seven loci revealed a significant linkage disequilibrium, thus confirming a clonal population structure for S. lugdunensis. This first MLST scheme for S. lugdunensis provides a new tool for investigating the macroepidemiology and phylogeny of this unusually virulent coagulase-negative Staphylococcus. PMID:22785196

  13. Multilocus Sequence Typing Analysis of Staphylococcus lugdunensis Implies a Clonal Population Structure

    PubMed Central

    Chassain, Benoît; Lemée, Ludovic; Didi, Jennifer; Thiberge, Jean-Michel; Brisse, Sylvain; Pons, Jean-Louis

    2012-01-01

    Staphylococcus lugdunensis is recognized as one of the major pathogenic species within the genus Staphylococcus, even though it belongs to the coagulase-negative group. A multilocus sequence typing (MLST) scheme was developed to study the genetic relationships and population structure of 87 S. lugdunensis isolates from various clinical and geographic sources by DNA sequence analysis of seven housekeeping genes (aroE, dat, ddl, gmk, ldh, recA, and yqiL). The number of alleles ranged from four (gmk and ldh) to nine (yqiL). Allelic profiles allowed the definition of 20 different sequence types (STs) and five clonal complexes. The 20 STs lacked correlation with geographic source. Isolates recovered from hematogenic infections (blood or osteoarticular isolates) or from skin and soft tissue infections did not cluster in separate lineages. Penicillin-resistant isolates clustered mainly in one clonal complex, unlike glycopeptide-tolerant isolates, which did not constitute a distinct subpopulation within S. lugdunensis. Phylogenies from the sequences of the seven individual housekeeping genes were congruent, indicating a predominantly mutational evolution of these genes. Quantitative analysis of the linkages between alleles from the seven loci revealed a significant linkage disequilibrium, thus confirming a clonal population structure for S. lugdunensis. This first MLST scheme for S. lugdunensis provides a new tool for investigating the macroepidemiology and phylogeny of this unusually virulent coagulase-negative Staphylococcus. PMID:22785196

  14. β-Lactamases Encoded by blaCTX-M Group I Genes as Determinants of Resistance of Esbl-Positive Enterobacteriaceae in European Soldiers in Tropical Mali

    PubMed Central

    Hagen, Ralf Matthias; Hinz, Rebecca; Frickmann, Hagen

    2015-01-01

    ESBL (extended-spectrum-β-lactamase)-positive Enterobacteriaceae, which colonized European soldiers in tropical Western African Mali, were subjected to a molecular assessment of their resistance determinants. By doing so, a better insight into the locally endemic pattern of ESBL-associated β-lactamase genes was aspired. From a previous study on diarrhea in European soldiers on deployment in tropical Mali, 15 ESBL-positive Escherichia coli with demonstrated high clonal diversity and one positive Klebsiella pneumoniae were assessed. Polymerase chain reactions (PCRs) for blaTEM and blaSHV β-lactamase genes with subsequent sequencing for the discrimination of ESBL- and non-ESBL variants were performed, followed by four group-specific PCRs for blaCTX-M genes. Non-ESBL-associated blaTEM-1 was identified in six out of 15 (40%) E. coli strains, while 100% of the assessed strains were positive for group I blaCTX-M. Considering the known clonal diversity of the assessed strains, the striking restriction to one group of blaCTX-M genes accounting for the ESBL phenotypes of the isolates suggests little genetic exchange in the local setting. Under such circumstances of restricted numbers of locally endemic target genes, PCR-based screening approaches for ESBL colonization might be promising. PMID:26716016

  15. Clonally diverse rfb gene clusters are involved in expression of a family of related D-galactan O antigens in Klebsiella species.

    PubMed Central

    Kelly, R F; Whitfield, C

    1996-01-01

    Klebsiella species express a family of structurally related lipopolysaccharide O antigens which share a common backbone known as D-galactan I. Serotype specificity results from modification of D-galactan I by addition of domains of altered structure or by substitution with O-acetyl and/or alpha-D-Galp side groups with various linkages and stoichiometries. In the prototype, Klebsiella serotype O1, the his-linked rfb gene cluster is required for synthesis of D-galactan I, but genes conferring serotype specificity are unlinked. The D-galactan I part of the O polysaccharide is O acetylated in Klebsiella serotype O8. By cloning the rfb region from Klebsiella serotype O8 and analyzing the O polysaccharide synthesized in Escherichia coli K-12 hosts, we show that, like rfbO1, the rfbO8 region directs formation of unmodified D-galactan I. The rfbAB genes encode an ATP-binding cassette transporter required for export of polymeric D-galactan I across the plasma membrane prior to completion of the lipopolysaccharide molecule by ligation of the O polysaccharide to lipid A-core. Complementation experiments show that the rfbAB gene products in serotypes O1 and O8 are functionally equivalent and interchangeable. Hybridization experiments and physical mapping of the rfb regions in related Klebsiella serotypes suggest the existence of shared rfb genes with a common organization. However, despite the functional equivalence of these rfb gene clusters, at least three distinct clonal groups were detected in different Klebsiella species and subspecies, on the basis of Southern hybridization experiments carried out under high-stringency conditions. The clonal groups cannot be predicted by features of the O-antigen structure. To examine the relationships in more detail, the complete nucleotide sequence of the serotype O8 rfb cluster was determined and compared with that of the serotype O1 prototype. The nucleotide sequences for the six rfb genes showed variations in moles percent G

  16. An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers.

    PubMed

    Wang, Rang Jian; Gao, Xiang Feng; Kong, Xiang Rui; Yang, Jun

    2016-01-01

    Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property. PMID:27504250

  17. IncN plasmids carrying bla CTX-M-1 in Escherichia coli isolates on a dairy farm.

    PubMed

    Dolejska, Monika; Jurcickova, Zuzana; Literak, Ivan; Pokludova, Lucie; Bures, Jiri; Hera, Alfred; Kohoutova, Ludmila; Smola, Jiri; Cizek, Alois

    2011-05-01

    The aim of the study was to compare the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli bovine isolates on a conventional dairy cattle farm with high consumption of parenteral and intramammary cephalosporins (farm A) and on an organic dairy farm with no cephalosporin use (farm B). ESBL-producing E. coli were isolated from rectal swabs and milk filters by selective cultivation on MacConkey agar with cefotaxime (2mg/l). ESBL genes were identified by polymerase chain reaction (PCR) and sequencing, and the genetic diversity of the isolates was determined by XbaI pulsed field gel electrophoresis (PFGE). Conjugative transfer, incompatibility group, and restriction fragment length polymorphism (RFLP) profiles of the ESBL-carrying plasmids were studied. Higher prevalence (39%, n(rectal samples in cows)=309) of CTX-M-1-producing E. coli isolates was found on farm A compared to farm B (<1%, n(rectal samples in cows)=154; 0%, n(rectal samples in calves)=46). Using PFGE, the isolates from farm A were divided into nine pulsotypes. In all ESBL-positive isolates, the bla(CTX-M-1) gene was carried on 40 kb IncN conjugative plasmids of three related HincII restriction profiles. Horizontal gene transfer through transmission of IncN plasmids harboring bla(CTX-M-1) as well as clonal dissemination of a particular clone seems to be involved in dissemination of CTX-M-1-producing E. coli isolates in cows on the farm using cephalosporins in treating bacterial infections. The study demonstrates a possible role of cephalosporin use in the widespread occurrence of CTX-M-1-producing E. coli on the conventional dairy cattle farm compared to the organic farm. PMID:21276666

  18. Clonal Structure and Characterization of Staphylococcus aureus Strains from Invasive Infections in Paediatric Patients from South Poland: Association between Age, spa Types, Clonal Complexes, and Genetic Markers.

    PubMed

    Ilczyszyn, Weronika M; Sabat, Artur J; Akkerboom, Viktoria; Szkarlat, Anna; Klepacka, Joanna; Sowa-Sierant, Iwona; Wasik, Barbara; Kosecka-Strojek, Maja; Buda, Aneta; Miedzobrodzki, Jacek; Friedrich, Alexander W

    2016-01-01

    The aim of current study was to examine clonal structure and genetic profile of invasive Staphylococcus aureus isolates recovered from infants and children treated at the Jagiellonian University Children's Hospital of Krakow, Poland. The 107 invasive S. aureus isolates, collected between February 2012 and August 2014, were analysed retrospectively. Antimicrobial susceptibility testing, spa typing and DNA microarray analysis were performed to determine clonal distribution, diversity and gene content in regard to patients characteristics. In total, 107 isolates were recovered from 88 patients with clinical symptoms of invasive bacterial infection. The final set of 92 non-duplicate samples included 38 MRSA isolates. Additionally, a set of 54 S. aureus isolates collected during epidemiological screening was genotyped and analysed. There were 72 healthcare-associated (HCA) and 20 community-onset (CO) infection events caused by 33 and 5 MRSA isolates, respectively. The majority of isolates were affiliated with the major European clonal complexes CC5 (t003, spa-CC 002), CC45 (spa-CC 015), CC7 or CC15 (t084, t091, spa-CC 084). Two epidemic clones (CC5-MRSA-II or CC45-MRSA-IV) dominated among MRSA isolates, while MSSA population contained 15 different CCs. The epidemiological screening isolates belonged to similar genetic lineages as those collected from invasive infection cases. The HCA infection events, spa types t003, t2642 or CC5 were significantly associated with infections occurring in neonates and children under 5 years of age. Moreover, carriage of several genetic markers, including erm(A), sea (N315), egc-cluster, chp was significantly higher in isolates obtained from children in this age group. The spa types t091 and t008 were underrepresented among patients aged 5 years or younger, whereas spa type t008, CC8 and presence of splE was associated with infection in children aged 10 years or older. The HCA-MRSA strains were most frequently found in children under 5

  19. Clonal Structure and Characterization of Staphylococcus aureus Strains from Invasive Infections in Paediatric Patients from South Poland: Association between Age, spa Types, Clonal Complexes, and Genetic Markers

    PubMed Central

    Ilczyszyn, Weronika M.; Sabat, Artur J.; Akkerboom, Viktoria; Szkarlat, Anna; Klepacka, Joanna; Sowa-Sierant, Iwona; Wasik, Barbara; Kosecka-Strojek, Maja; Buda, Aneta; Miedzobrodzki, Jacek; Friedrich, Alexander W.

    2016-01-01

    The aim of current study was to examine clonal structure and genetic profile of invasive Staphylococcus aureus isolates recovered from infants and children treated at the Jagiellonian University Children’s Hospital of Krakow, Poland. The 107 invasive S. aureus isolates, collected between February 2012 and August 2014, were analysed retrospectively. Antimicrobial susceptibility testing, spa typing and DNA microarray analysis were performed to determine clonal distribution, diversity and gene content in regard to patients characteristics. In total, 107 isolates were recovered from 88 patients with clinical symptoms of invasive bacterial infection. The final set of 92 non-duplicate samples included 38 MRSA isolates. Additionally, a set of 54 S. aureus isolates collected during epidemiological screening was genotyped and analysed. There were 72 healthcare-associated (HCA) and 20 community-onset (CO) infection events caused by 33 and 5 MRSA isolates, respectively. The majority of isolates were affiliated with the major European clonal complexes CC5 (t003, spa-CC 002), CC45 (spa-CC 015), CC7 or CC15 (t084, t091, spa-CC 084). Two epidemic clones (CC5-MRSA-II or CC45-MRSA-IV) dominated among MRSA isolates, while MSSA population contained 15 different CCs. The epidemiological screening isolates belonged to similar genetic lineages as those collected from invasive infection cases. The HCA infection events, spa types t003, t2642 or CC5 were significantly associated with infections occurring in neonates and children under 5 years of age. Moreover, carriage of several genetic markers, including erm(A), sea (N315), egc-cluster, chp was significantly higher in isolates obtained from children in this age group. The spa types t091 and t008 were underrepresented among patients aged 5 years or younger, whereas spa type t008, CC8 and presence of splE was associated with infection in children aged 10 years or older. The HCA-MRSA strains were most frequently found in children under 5

  20. Diversity of Multi-Drug Resistant Avian Pathogenic Escherichia coli (APEC) Causing Outbreaks of Colibacillosis in Broilers during 2012 in Spain.

    PubMed

    Solà-Ginés, Marc; Cameron-Veas, Karla; Badiola, Ignacio; Dolz, Roser; Majó, Natalia; Dahbi, Ghizlane; Viso, Susana; Mora, Azucena; Blanco, Jorge; Piedra-Carrasco, Nuria; González-López, Juan José; Migura-Garcia, Lourdes

    2015-01-01

    Avian pathogenic Escherichia coli (APEC) are the major cause of colibacillosis in poultry production. In this study, a total of 22 E. coli isolated from colibacillosis field cases and 10 avian faecal E. coli (AFEC) were analysed. All strains were characterised phenotypically by susceptibility testing and molecular typing methods such as pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The presence of 29 virulence genes associated to APEC and human extraintestinal pathogenic E. coli (ExPEC) was also evaluated. For cephalosporin resistant isolates, cephalosporin resistance genes, plasmid location and replicon typing was assessed. Avian isolates belonged to 26 O:H serotypes and 24 sequence types. Out of 22 APEC isolates, 91% contained the virulence genes predictors of APEC; iutA, hlyF, iss, iroN and ompT. Of all strains, 34% were considered ExPEC. PFGE analysis demonstrated a high degree of genetic polymorphism. All strains were multi-resistant, including those isolated from healthy animals. Eleven strains were resistant to cephalosporins; six contained blaCTX-M-14, two blaSHV-12, two blaCMY-2 and one blaSHV-2. Two strains harboured qnrA, and two qnrA together with aac(6')-Ib-cr. Additionally, the emergent clone O25b:H4-B2-ST131 was isolated from a healthy animal which harboured blaCMY-2 and qnrS genes. Cephalosporin resistant genes were mainly associated to the presence of IncK replicons. This study demonstrates a very diverse population of multi-drug resistant E. coli containing a high number of virulent genes. The E. coli population among broilers is a reservoir of resistance and virulence-associated genes that could be transmitted into the community through the food chain. More epidemiological studies are necessary to identify clonal groups and resistance mechanisms with potential relevance to public health. PMID:26600205

  1. Occurrence and growth characteristics of Escherichia coli and enterococci within the accumulated fluid of the northern pitcher plant (Sarracenia purpurea L.)

    USGS Publications Warehouse

    Whitman, Richard L.; Byers, Stacey E.; Shively, Dawn A.; Ferguson, Donna M.; Byappanahalli, Muruleedhara N.

    2005-01-01

    Sarracenia purpurea L., a carnivorous bog plant (also known as the pitcher plant), represents an excellent model of a well-defined, self-contained ecosystem; the individual pitchers of the plant serve as a microhabitat for a variety of micro- and macro-organisms. Previously, fecal indicator bacteria (Escherichia coli and enterococci) were shown as incidental contaminants in pitcher fluid; however, whether their occurrence in pitcher fluid is incidental or common has not been established. The purpose of this study was to investigate the occurrence, distribution, and growth potential of E. coli and enterococci in pitcher plant fluid from a protected bog in northwest Indiana. Escherichia coli and enterococci were recovered in pitcher fluids (n = 43 plants), with mean densities (log CFU mL-1) of 1.28 ± 0.23 and 1.97 ± 0.27, respectively. In vitro experiments showed that E. coli growth in fluid not containing insects or indigenous organisms was directly proportional to the fluid concentration (growth was 10-fold in 24 h in 100% fluid); however, in the presence of other indigenous organisms, E. coli and enterococci were only sustained for 5 days at 26 °C. Pulsed-field gel electrophoresis (PFGE) analysis showed that the plant Enterococcus faecalis isolates were genetically distinct from the human isolates; identical PFGE patterns were observed among plant isolates that fell into one of six clonal groups. These findings suggest that (i) E. coli and enterococci occurrence in pitcher plants is rather common in the bog studied, although their originating source is unclear, and (ii) the pitcher fluid contains adequate nutrients, especially carbon and energy sources, to promote the growth of indicator bacteria; however, under natural conditions, the biotic factors (e.g., competition for nutrients) may restrict their growth.

  2. Occurrence and growth characteristics of Escherichia coli and enterococci within the accumulated fluid of the northern pitcher plant (Sarracenia purpurea L.).

    PubMed

    Whitman, Richard L; Byers, Stacey E; Shively, Dawn A; Ferguson, Donna M; Byappanahalli, Muruleedhara

    2005-12-01

    Sarracenia purpurea L., a carnivorous bog plant (also known as the pitcher plant), represents an excellent model of a well-defined, self-contained ecosystem; the individual pitchers of the plant serve as a microhabitat for a variety of micro- and macro-organisms. Previously, fecal indicator bacteria (Escherichia coli and enterococci) were shown as incidental contaminants in pitcher fluid; however, whether their occurrence in pitcher fluid is incidental or common has not been established. The purpose of this study was to investigate the occurrence, distribution, and growth potential of E. coli and enterococci in pitcher plant fluid from a protected bog in northwest Indiana. Escherichia coli and enterococci were recovered in pitcher fluids (n=43 plants), with mean densities (log CFU mL-1) of 1.28+/-0.23 and 1.97+/-0.27, respectively. In vitro experiments showed that E. coli growth in fluid not containing insects or indigenous organisms was directly proportional to the fluid concentration (growth was 10-fold in 24 h in 100% fluid); however, in the presence of other indigenous organisms, E. coli and enterococci were only sustained for 5 days at 26 degrees C. Pulsed-field gel electrophoresis (PFGE) analysis showed that the plant Enterococcus faecalis isolates were genetically distinct from the human isolates; identical PFGE patterns were observed among plant isolates that fell into one of six clonal groups. These findings suggest that (i) E. coli and enterococci occurrence in pitcher plants is rather common in the bog studied, although their originating source is unclear, and (ii) the pitcher fluid contains adequate nutrients, especially carbon and energy sources, to promote the growth of indicator bacteria; however, under natural conditions, the biotic factors (e.g., competition for nutrients) may restrict their growth. PMID:16462861

  3. Diversity of Multi-Drug Resistant Avian Pathogenic Escherichia coli (APEC) Causing Outbreaks of Colibacillosis in Broilers during 2012 in Spain

    PubMed Central

    Solà-Ginés, Marc; Cameron-Veas, Karla; Badiola, Ignacio; Dolz, Roser; Majó, Natalia; Dahbi, Ghizlane; Viso, Susana; Mora, Azucena; Blanco, Jorge; Piedra-Carrasco, Nuria; González-López, Juan José; Migura-Garcia, Lourdes

    2015-01-01

    Avian pathogenic Escherichia coli (APEC) are the major cause of colibacillosis in poultry production. In this study, a total of 22 E. coli isolated from colibacillosis field cases and 10 avian faecal E. coli (AFEC) were analysed. All strains were characterised phenotypically by susceptibility testing and molecular typing methods such as pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The presence of 29 virulence genes associated to APEC and human extraintestinal pathogenic E. coli (ExPEC) was also evaluated. For cephalosporin resistant isolates, cephalosporin resistance genes, plasmid location and replicon typing was assessed. Avian isolates belonged to 26 O:H serotypes and 24 sequence types. Out of 22 APEC isolates, 91% contained the virulence genes predictors of APEC; iutA, hlyF, iss, iroN and ompT. Of all strains, 34% were considered ExPEC. PFGE analysis demonstrated a high degree of genetic polymorphism. All strains were multi-resistant, including those isolated from healthy animals. Eleven strains were resistant to cephalosporins; six contained blaCTX-M-14, two blaSHV-12, two blaCMY-2 and one blaSHV-2. Two strains harboured qnrA, and two qnrA together with aac(6’)-Ib-cr. Additionally, the emergent clone O25b:H4-B2-ST131 was isolated from a healthy animal which harboured blaCMY-2 and qnrS genes. Cephalosporin resistant genes were mainly associated to the presence of IncK replicons. This study demonstrates a very diverse population of multi-drug resistant E. coli containing a high number of virulent genes. The E. coli population among broilers is a reservoir of resistance and virulence-associated genes that could be transmitted into the community through the food chain. More epidemiological studies are necessary to identify clonal groups and resistance mechanisms with potential relevance to public health. PMID:26600205

  4. An invasive clonal plant benefits from clonal integration more than a co-occurring native plant in nutrient-patchy and competitive environments.

    PubMed

    You, Wenhua; Fan, Shufeng; Yu, Dan; Xie, Dong; Liu, Chunhua

    2014-01-01

    Many notorious invasive plants are clonal, however, little is known about the different roles of clonal integration effects between invasive and native plants. Here, we hypothesize that clonal integration affect growth, photosynthetic performance, biomass allocation and thus competitive ability of invasive and native clonal plants, and invasive clonal plants benefit from clonal integration more than co-occurring native plants in heterogeneous habitats. To test these hypotheses, two stoloniferous clonal plants, Alternanthera philoxeroides (invasive), Jussiaea repens (native) were studied in China. The apical parts of both species were grown either with or without neighboring vegetation and the basal parts without competitors were in nutrient- rich or -poor habitats, with stolon connections were either severed or kept intact. Competition significantly reduced growth and photosynthetic performance of the apical ramets in both species, but not the biomass of neighboring vegetation. Without competition, clonal integration greatly improved the growth and photosynthetic performance of both species, especially when the basal parts were in nutrient-rich habitats. When grown with neighboring vegetation, growth of J. repens and photosynthetic performance of both species were significantly enhanced by clonal integration with the basal parts in both nutrient-rich and -poor habitats, while growth and relative neighbor effect (RNE) of A. philoxeroides were greatly improved by clonal integration only when the basal parts were in nutrient-rich habitats. Moreover, clonal integration increased A. philoxeroides's biomass allocation to roots without competition, but decreased it with competition, especially when the basal ramets were in nutrient-rich sections. Effects of clonal integration on biomass allocation of J. repens was similar to that of A. philoxeroides but with less significance. These results supported our hypothesis that invasive clonal plants A. philoxeroides benefits

  5. An Invasive Clonal Plant Benefits from Clonal Integration More than a Co-Occurring Native Plant in Nutrient-Patchy and Competitive Environments

    PubMed Central

    You, Wenhua; Fan, Shufeng; Yu, Dan; Xie, Dong; Liu, Chunhua

    2014-01-01

    Many notorious invasive plants are clonal, however, little is known about the different roles of clonal integration effects between invasive and native plants. Here, we hypothesize that clonal integration affect growth, photosynthetic performance, biomass allocation and thus competitive ability of invasive and native clonal plants, and invasive clonal plants benefit from clonal integration more than co-occurring native plants in heterogeneous habitats. To test these hypotheses, two stoloniferous clonal plants, Alternanthera philoxeroides (invasive), Jussiaea repens (native) were studied in China. The apical parts of both species were grown either with or without neighboring vegetation and the basal parts without competitors were in nutrient- rich or -poor habitats, with stolon connections were either severed or kept intact. Competition significantly reduced growth and photosynthetic performance of the apical ramets in both species, but not the biomass of neighboring vegetation. Without competition, clonal integration greatly improved the growth and photosynthetic performance of both species, especially when the basal parts were in nutrient-rich habitats. When grown with neighboring vegetation, growth of J. repens and photosynthetic performance of both species were significantly enhanced by clonal integration with the basal parts in both nutrient-rich and -poor habitats, while growth and relative neighbor effect (RNE) of A. philoxeroides were greatly improved by clonal integration only when the basal parts were in nutrient-rich habitats. Moreover, clonal integration increased A. philoxeroides's biomass allocation to roots without competition, but decreased it with competition, especially when the basal ramets were in nutrient-rich sections. Effects of clonal integration on biomass allocation of J. repens was similar to that of A. philoxeroides but with less significance. These results supported our hypothesis that invasive clonal plants A. philoxeroides benefits

  6. Comparative study of the coupling between topoisomerase I activity and high-mobility group proteins in E. coli and mammalian cells.

    PubMed

    Veilleux, S; Caron, N; Boissonneault, G

    2000-07-01

    It is now well established that the HMG box DNA-binding motif can alter the topology of double-stranded DNA in several ways. Using the spermatid-specific tsHMG as a model protein of the HMG-1/-2 family, we have demonstrated that its expression in E. coli produces an increase in plasmid supercoiling density that is likely a consequence of its ability to constrain free supercoils in vivo. As demonstrated in vitro, stabilization of free DNA supercoils by tsHMG prevents topoisomerase I from gaining access to the template and could represent a mechanism for the apparent inhibition of topoisomerase I in bacteria. A similar modulation of eukaryotic topoisomerase I activity was not detected after expression of the tsHMG in mammalian cells. This differential response is discussed in terms of the marked difference in DNA packaging and accessibility of free supercoils in prokaryotic vs. eukaryotic cells. PMID:10945232

  7. Tyr254 hydroxyl group acts as a two-way switch mechanism in the coupling of heterotropic and homotropic effects in Escherichia coli glucosamine-6-phosphate deaminase.

    PubMed

    Montero-Morán, G M; Horjales, E; Calcagno, M L; Altamirano, M M

    1998-05-26

    The involvement of tyrosine residues in the allosteric function of the enzyme glucosamine 6-phosphate deaminase from Escherichia coli was first proposed on the basis of a theoretical analysis of the sequence and demonstrated by spectrophotometric experiments. Two tyrosine residues, Tyr121 and Tyr254, were indicated as involved in the mechanism of cooperativity and in the allosteric regulation of the enzyme [Altamirano et al. (1994) Eur. J. Biochem. 220, 409-413]. Tyr121 replacement by threonine or tryptophan altered the symmetric character of the T --> R transition [Altamirano et al. (1995) Biochemistry 34, 6074-6082]. From crystallographic data of the R allosteric conformer, Tyr254 has been shown to be part of the allosteric pocket [Oliva et al. (1995) Structure 3, 1323-1332]. Although it is not directly involved in binding the allosteric activator, N-acetylglucosamine 6-phosphate, Tyr 254 is hydrogen bonded through its phenolic hydroxyl to the backbone carbonyl from residue 161 in the neighboring polypeptide chain. Kinetic and binding experiments with the mutant form Tyr254-Phe of the enzyme reveal that this replacement caused an uncoupling of the homotropic and heterotropic effects. Homotropic cooperativity diminished and the allosteric activation pattern changed from one of the K-type in the wild-type deaminase to a mixed K-V pattern. On the other hand, Tyr254-Trp deaminase is kinetically closer to a K-type enzyme and it has a higher catalytic efficiency than the wild-type protein. These results show that the interactions of Tyr254 are fundamental in coupling binding in the active site to events occurring in the allosteric pocket of E. coli glucosamine 6-P deaminase. PMID:9601045

  8. PM2, a group 3 LEA protein from soybean, and its 22-mer repeating region confer salt tolerance in Escherichia coli

    SciTech Connect

    Yun Liu; Zheng Yizhi . E-mail: yzzheng@szu.edu.cn

    2005-05-27

    To have knowledge of the effect of soybean PM2 protein in protecting dehydrated cells and its functional region, PM2 cDNA was isolated from soybean immature seeds. The recombinants expressing full-length PM2, truncated polypeptides of PM2A (aa 1-262) or PM2B (aa 129-262, 22-mer repeating region), or artificial polypeptide PM2C (duplication of 22-mer repeating region) were constructed. By using SDS-PAGE and mass spectrometry approaches, these fusion polypeptides were identified and proved to be hydrophilic and heat-stable. Spot assays of BL/PM2 and BL/pET28 (as control) showed that protein PM2 increased salt tolerance (500 mM NaCl or 500 mM KCl) of Escherichia coli, rather than osmotic tolerance (1100 mM sorbitol). In addition, comparing the survival ratios of the transformants under 500 mM NaCl or 500 mM KCl stresses, the results showed that: (1) the survival ratios of BL/PM2 and BL/PM2B were quite similar, both showing much higher values than those of BL/pET28. (2) The survival ratios of BL/PM2C were much higher than those of BL/PM2, BL/PM2A, and BL/PM2B. This provides the first experimental evidence that PM2 polypeptide enhances salt tolerance of E. coli cells, and the 22-mer repeat region is an important functional region.

  9. Comparative epidemiology of CTX-M-14 and CTX-M-15 producing Escherichia coli: association with distinct demographic groups in the community in New Zealand.

    PubMed

    Freeman, J T; Williamson, D A; Heffernan, H; Smith, M; Bower, J E; Roberts, S A

    2012-08-01

    Extended spectrum beta-lactamase producing E. coli (ESBL-EC) are an emerging public health issue. In New Zealand (NZ), bla (CTX-M-14) and bla (CTX-M-15) are the most common ESBL genes. Although many studies describe risk factors for ESBL-EC, few describe risk factors for specific ESBL genes. Between January 2006 and December 2007, we characterized 108 consecutive, non-duplicate isolates of ESBL-EC at the Auckland Hospital laboratory. Demographic and clinical data were recorded. Of the 108, 54.6% (59) were CTX-M-15-EC, 26.9% (29) were CTX-M-14-EC and 12.09% were CTX-M-9 (13). The remaining seven isolates carried CTX-M-3 (3; 2.7%), CTX-M-65 (2; 1.8%), CTX-M-27 (1; 0.9%) and CTX-M-57 (1; 0.9%). CTX-M-15-EC were more likely than CTX-M-14-EC to be fluoroquinolone-resistant (86.4% versus 32.4%; p=0.006) and to be non-susceptible to amoxicillin-clavulanate (84.7% versus 41.4%; p=0.0001). Patients with CTX-M-15-EC were more likely to be of Indian ethnicity (34.5% versus 0%; p=0.0012) and to have travelled recently (31.6% versus 4%; p=0.0088). Patients with CTX-M-14-EC were more likely to have Chinese or South-East Asian ethnicity (48.1% versus 5.2%; p<0.0001) and to have no history of either travel or prior hospital admission (44% versus 8.9%; p=0.0006). These data imply that CTX-M-15 and CTX-M-14 producing E. coli are associated with distinct demographic subgroups in NZ. PMID:22271302

  10. How Clonal Is Clonal? Genome Plasticity across Multicellular Segments of a "Candidatus Marithrix sp." Filament from Sulfidic, Briny Seafloor Sediments in the Gulf of Mexico.

    PubMed

    Salman-Carvalho, Verena; Fadeev, Eduard; Joye, Samantha B; Teske, Andreas

    2016-01-01

    "Candidatus Marithrix" is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria). This genus of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 μm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, "Candidatus Marithrix" was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the "Candidatus Marithrix" genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98 and 100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes-the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs) between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or "intrasegmental sequence heterogeneity" (ISH) events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament. PMID:27536274

  11. Label-free isolation and deposition of single bacterial cells from heterogeneous samples for clonal culturing.

    PubMed

    Riba, J; Gleichmann, T; Zimmermann, S; Zengerle, R; Koltay, P

    2016-01-01

    The isolation and analysis of single prokaryotic cells down to 1 μm and less in size poses a special challenge and requires micro-engineered devices to handle volumes in the picoliter to nanoliter range. Here, an advanced Single-Cell Printer (SCP) was applied for automated and label-free isolation and deposition of bacterial cells encapsulated in 35 pl droplets by inkjet-like printing. To achieve this, dispenser chips to generate micro droplets have been fabricated with nozzles 20 μm in size. Further, the magnification of the optical system used for cell detection was increased. Redesign of the optical path allows for collision-free addressing of any flat substrate since no compartment protrudes below the nozzle of the dispenser chip anymore. The improved system allows for deterministic isolation of individual bacterial cells. A single-cell printing efficiency of 93% was obtained as shown by printing fluorescent labeled E. coli. A 96-well plate filled with growth medium is inoculated with single bacteria cells on average within about 8 min. Finally, individual bacterial cells from a heterogeneous sample of E. coli and E. faecalis were isolated for clonal culturing directly on agar plates in user-defined array geometry. PMID:27596612

  12. Label-free isolation and deposition of single bacterial cells from heterogeneous samples for clonal culturing

    PubMed Central

    Riba, J.; Gleichmann, T.; Zimmermann, S.; Zengerle, R.; Koltay, P.

    2016-01-01

    The isolation and analysis of single prokaryotic cells down to 1 μm and less in size poses a special challenge and requires micro-engineered devices to handle volumes in the picoliter to nanoliter range. Here, an advanced Single-Cell Printer (SCP) was applied for automated and label-free isolation and deposition of bacterial cells encapsulated in 35 pl droplets by inkjet-like printing. To achieve this, dispenser chips to generate micro droplets have been fabricated with nozzles 20 μm in size. Further, the magnification of the optical system used for cell detection was increased. Redesign of the optical path allows for collision-free addressing of any flat substrate since no compartment protrudes below the nozzle of the dispenser chip anymore. The improved system allows for deterministic isolation of individual bacterial cells. A single-cell printing efficiency of 93% was obtained as shown by printing fluorescent labeled E. coli. A 96-well plate filled with growth medium is inoculated with single bacteria cells on average within about 8 min. Finally, individual bacterial cells from a heterogeneous sample of E. coli and E. faecalis were isolated for clonal culturing directly on agar plates in user-defined array geometry. PMID:27596612

  13. Propagule Pressure, Habitat Conditions and Clonal Integration Influence the Establishment and Growth of an Invasive Clonal Plant, Alternanthera philoxeroides

    PubMed Central

    You, Wen-Hua; Han, Cui-Min; Fang, Long-Xiang; Du, Dao-Lin

    2016-01-01

    Many notorious invasive plants are clonal, spreading mainly by vegetative propagules. Propagule pressure (the number of propagules) may affect the establishment, growth, and thus invasion success of these clonal plants, and such effects may also depend on habitat conditions. To understand how propagule pressure, habitat conditions and clonal integration affect the establishment and growth of the invasive clonal plants, an 8-week greenhouse with an invasive clonal plant, Alternanthera philoxeroides was conducted. High (five fragments) or low (one fragment) propagule pressure was established either in bare soil (open habitat) or dense native vegetation of Jussiaea repens (vegetative habitat), with the stolon connections either severed from or connected to the relatively older ramets. High propagule pressure greatly increased the establishment and growth of A. philoxeroides, especially when it grew in vegetative habitats. Surprisingly, high propagule pressure significantly reduced the growth of individual plants of A. philoxeroides in open habitats, whereas it did not affect the individual growth in vegetative habitats. A shift in the intraspecific interaction on A. philoxeroides from competition in open habitats to facilitation in vegetative habitats may be the main reason. Moreover, clonal integration significantly improved the growth of A. philoxeroides only in open habitats, especially with low propagule pressure, whereas it had no effects on the growth and competitive ability of A. philoxeroides in vegetative habitats, suggesting that clonal integration may be of most important for A. philoxeroides to explore new open space and spread. These findings suggest that propagule pressure may be crucial for the invasion success of A. philoxeroides, and such an effect also depends on habitat conditions. PMID:27200041

  14. Propagule Pressure, Habitat Conditions and Clonal Integration Influence the Establishment and Growth of an Invasive Clonal Plant, Alternanthera philoxeroides.

    PubMed

    You, Wen-Hua; Han, Cui-Min; Fang, Long-Xiang; Du, Dao-Lin

    2016-01-01

    Many notorious invasive plants are clonal, spreading mainly by vegetative propagules. Propagule pressure (the number of propagules) may affect the establishment, growth, and thus invasion success of these clonal plants, and such effects may also depend on habitat conditions. To understand how propagule pressure, habitat conditions and clonal integration affect the establishment and growth of the invasive clonal plants, an 8-week greenhouse with an invasive clonal plant, Alternanthera philoxeroides was conducted. High (five fragments) or low (one fragment) propagule pressure was established either in bare soil (open habitat) or dense native vegetation of Jussiaea repens (vegetative habitat), with the stolon connections either severed from or connected to the relatively older ramets. High propagule pressure greatly increased the establishment and growth of A. philoxeroides, especially when it grew in vegetative habitats. Surprisingly, high propagule pressure significantly reduced the growth of individual plants of A. philoxeroides in open habitats, whereas it did not affect the individual growth in vegetative habitats. A shift in the intraspecific interaction on A. philoxeroides from competition in open habitats to facilitation in vegetative habitats may be the main reason. Moreover, clonal integration significantly improved the growth of A. philoxeroides only in open habitats, especially with low propagule pressure, whereas it had no effects on the growth and competitive ability of A. philoxeroides in vegetative habitats, suggesting that clonal integration may be of most important for A. philoxeroides to explore new open space and spread. These findings suggest that propagule pressure may be crucial for the invasion success of A. philoxeroides, and such an effect also depends on habitat conditions. PMID:27200041

  15. Phylogenetic and Molecular Analysis of Food-Borne Shiga Toxin-Producing Escherichia coli

    PubMed Central

    Hauser, Elisabeth; Mellmann, Alexander; Semmler, Torsten; Stoeber, Helen; Wieler, Lothar H.; Karch, Helge; Kuebler, Nikole; Fruth, Angelika; Harmsen, Dag; Weniger, Thomas; Tietze, Erhard

    2013-01-01

    Seventy-five food-associated Shiga toxin-producing Escherichia coli (STEC) strains were analyzed by molecular and phylogenetic methods to describe their pathogenic potential. The presence of the locus of proteolysis activity (LPA), the chromosomal pathogenicity island (PAI) PAI ICL3, and the autotransporter-encoding gene sabA was examined by PCR. Furthermore, the occupation of the chromosomal integration sites of the locus of enterocyte effacement (LEE), selC, pheU, and pheV, as well as the Stx phage integration sites yehV, yecE, wrbA, z2577, and ssrA, was analyzed. Moreover, the antibiotic resistance phenotypes of all STEC strains were determined. Multilocus sequence typing (MLST) was performed, and sequence types (STs) and sequence type complexes (STCs) were compared with those of 42 hemolytic-uremic syndrome (HUS)-associated enterohemorrhagic E. coli (HUSEC) strains. Besides 59 STs and 4 STCs, three larger clusters were defined in this strain collection. Clusters A and C consist mostly of highly pathogenic eae-positive HUSEC strains and some related food-borne STEC strains. A member of a new O26 HUS-associated clone and the 2011 outbreak strain E. coli O104:H4 were found in cluster A. Cluster B comprises only eae-negative food-borne STEC strains as well as mainly eae-negative HUSEC strains. Although food-borne strains of cluster B were not clearly associated with disease, serotypes of important pathogens, such as O91:H21 and O113:H21, were in this cluster and closely related to the food-borne strains. Clonal analysis demonstrated eight closely related genetic groups of food-borne STEC and HUSEC strains that shared the same ST and were similar in their virulence gene composition. These groups should be considered with respect to their potential for human infection. PMID:23417002

  16. Phylogenetic and molecular analysis of food-borne shiga toxin-producing Escherichia coli.

    PubMed

    Hauser, Elisabeth; Mellmann, Alexander; Semmler, Torsten; Stoeber, Helen; Wieler, Lothar H; Karch, Helge; Kuebler, Nikole; Fruth, Angelika; Harmsen, Dag; Weniger, Thomas; Tietze, Erhard; Schmidt, Herbert

    2013-04-01

    Seventy-five food-associated Shiga toxin-producing Escherichia coli (STEC) strains were analyzed by molecular and phylogenetic methods to describe their pathogenic potential. The presence of the locus of proteolysis activity (LPA), the chromosomal pathogenicity island (PAI) PAI ICL3, and the autotransporter-encoding gene sabA was examined by PCR. Furthermore, the occupation of the chromosomal integration sites of the locus of enterocyte effacement (LEE), selC, pheU, and pheV, as well as the Stx phage integration sites yehV, yecE, wrbA, z2577, and ssrA, was analyzed. Moreover, the antibiotic resistance phenotypes of all STEC strains were determined. Multilocus sequence typing (MLST) was performed, and sequence types (STs) and sequence type complexes (STCs) were compared with those of 42 hemolytic-uremic syndrome (HUS)-associated enterohemorrhagic E. coli (HUSEC) strains. Besides 59 STs and 4 STCs, three larger clusters were defined in this strain collection. Clusters A and C consist mostly of highly pathogenic eae-positive HUSEC strains and some related food-borne STEC strains. A member of a new O26 HUS-associated clone and the 2011 outbreak strain E. coli O104:H4 were found in cluster A. Cluster B comprises only eae-negative food-borne STEC strains as well as mainly eae-negative HUSEC strains. Although food-borne strains of cluster B were not clearly associated with disease, serotypes of important pathogens, such as O91:H21 and O113:H21, were in this cluster and closely related to the food-borne strains. Clonal analysis demonstrated eight closely related genetic groups of food-borne STEC and HUSEC strains that shared the same ST and were similar in their virulence gene composition. These groups should be considered with respect to their potential for human infection. PMID:23417002

  17. Clonal integration in homogeneous environments increases performance of Alternanthera philoxeroides.

    PubMed

    Dong, Bi-Cheng; Alpert, Peter; Zhang, Qian; Yu, Fei-Hai

    2015-10-01

    Physiological integration between connected ramets can increase the performance of clonal plants when ramets experience contrasting levels of resource availabilities in heterogeneous environments. It has generally been shown or assumed that clonal integration has little effect on clonal performance in homogeneous environments. However, a conceptual model suggests that integration could increase performance in a homogeneous environment when connected ramets differ in uptake ability and external resource supply is high. We tested this hypothesis in a greenhouse experiment with the amphibious plant Alternanthera philoxeroides. Ramets in clonal fragments containing three rooted and two unrooted ramets were either left connected or divided into a basal part with two rooted ramets and an apical part with the other ramets. To simulate realistic, homogeneous environments of the species with different levels of resource supply, plants were grown at 0, 20, or 40 cm of water depth. Water depth had a positive effect on most measures of growth, indicating that resource supply increased with depth. Connection had negative to neutral effects on total growth of fragments at a water depth of 0 cm, and neutral to positive effects at 20- and 40-cm depths; effects on the apical part were generally positive and larger at greater depth; effects on the basal part were generally negative and smaller at greater depth. Results largely supported the hypothesis and further suggest that clonal integration of allocation and reproduction may modify benefits of resource sharing in homogeneous environments. PMID:26009243

  18. Multiple disturbances accelerate clonal growth in a potentially monodominant bamboo.

    PubMed

    Gagnon, Paul R; Platt, William J

    2008-03-01

    Organisms capable of rapid clonal growth sometimes monopolize newly freed space and resources. We hypothesize that sequential disturbances might change short-term clonal demography of these organisms in ways that promote formation of monotypic stands. We examined this hypothesis by studying the clonal response of Arundinaria gigantea (giant cane, a bamboo) to windstorm and fire. We studied giant cane growing in both a large tornado-blowdown gap and under forest canopy, in burned and unburned plots, using a split-block design. We measured density of giant cane ramets (culms) and calculated finite rates of increase (lamda) for populations of ramets over three years. Ramet density nearly doubled in stands subjected to both windstorm and fire; the high ramet densities that resulted could inhibit growth in other plants. In comparison, ramet density increased more slowly after windstorm alone, decreased after fire alone, and remained in stasis in controls. We predict that small, sparse stands of giant cane could spread and amalgamate to form dense, monotypic stands (called "canebrakes") that might influence fire return intervals and act as an alternative state to bottomland forest. Other clonal species may similarly form monotypic stands following successive disturbances via rapid clonal growth. PMID:18459325

  19. The Complex, Clonal, and Controversial Nature of Barrett's Esophagus.

    PubMed

    Evans, James A; McDonald, Stuart A C

    2016-01-01

    Barrett's esophagus (BO) is a preneoplastic condition described as the replacement of the stratified squamous epithelium of the distal esophagus with one that histologically presents as a diverse mixture of metaplastic glands resembling gastric or intestinal-type columnar epithelium. The clonal origins of BO are still unclear. More recently, we have begun to investigate the relationship between the various metaplastic gland phenotypes observed in BO, how they evolve, and the cancer risk they bestow. Studies have revealed that glands along the BO segment are clonal units containing a single stem cell clone that can give rise to all the differentiated epithelial cell types in glands. Clonal lineage tracing analysis has revealed that Barrett's glands are capable of bifurcation and this facilitates clonal expansion and competition. In fact, BO in some patients appears to consist of multiple, independently initiated clones that compete with each other for space and possibly resources. This chapter discusses the concepts of clonal competition and expansion in BO and sets out to query what we know about the role of gland diversity and phenotypic evolution within this complex columnar metaplasia. PMID:27573766

  20. Molecular epidemiology of clonal diploids: a quick overview and a short DIY (do it yourself) notice.

    PubMed

    De Meeûs, Thierry; Lehmann, Laurent; Balloux, François

    2006-03-01

    In this short review we report the basic notions needed for understanding the population genetics of clonal diploids. We focus on the consequences of clonality on the distribution of genetic diversity within individuals, between individuals and between populations. We then summarise how to detect clonality in mainly sexual populations, conversely, how to detect sexuality in mainly clonal populations and also how genetic differentiation between populations is affected by clonality in diploids. This information is then used for building recipes on how to analyse and interpret genetic polymorphism data in molecular epidemiology studies of clonal diploids. PMID:16290062

  1. SNP markers identify widely distributed clonal lineages of Phytophthora colocasiae in Vietnam, Hawaii and Hainan Island, China.

    PubMed

    Shrestha, Sandesh; Hu, Jian; Fryxell, Rebecca Trout; Mudge, Joann; Lamour, Kurt

    2014-01-01

    Taro (Colocasia esculenta) is an important food crop, and taro leaf blight caused by Phytophthora colocasiae can significantly affect production. Our objectives were to develop single nucleotide polymorphism (SNP) markers for P. colocasiae and characterize populations in Hawaii (HI), Vietnam (VN) and Hainan Island, China (HIC). In total, 379 isolates were analyzed for mating type and multilocus SNP profiles including 214 from HI, 97 from VN and 68 from HIC. A total of 1152 single nucleotide variant (SNV) sites were identified via restriction site-associated DNA (RAD) sequencing of two field isolates. Genotyping with 27 SNPs revealed 41 multilocus SNP genotypes grouped into seven clonal lineages containing 2-232 members. Three clonal lineages were shared among countries. In addition, five SNP markers had a low incidence of loss of heterozygosity (LOH) during asexual laboratory growth. For HI and VN, >95% of isolates were the A2 mating type. On HIC, isolates within single clonal lineages had A1, A2 and A0 (neuter) isolates. The implications for the wide dispersal of clonal lineages are discussed. PMID:24895424

  2. Physiological Integration Ameliorates Negative Effects of Drought Stress in the Clonal Herb Fragaria orientalis

    PubMed Central

    Zhang, Yunchun; Zhang, Qiaoying; Sammul, Marek

    2012-01-01

    Clonal growth allows plants to spread horizontally and to establish ramets in sites of contrasting resource status. If ramets remain physiologically integrated, clones in heterogeneous environments can act as cooperative systems – effects of stress on one ramet can be ameliorated by another connected ramet inhabiting benign conditions. But little is known about the effects of patch contrast on physiological integration of clonal plants and no study has addressed its effects on physiological traits like osmolytes, reactive oxygen intermediates and antioxidant enzymes. We examined the effect of physiological integration on survival, growth and stress indicators such as osmolytes, reactive oxygen intermediates (ROIs) and antioxidant enzymes in a clonal plant, Fragaria orientalis, growing in homogenous and heterogeneous environments differing in patch contrast of water availability (1 homogeneous (no contrast) group; 2 low contrast group; 3 high contrast group). Drought stress markedly reduced the survival and growth of the severed ramets of F. orientalis, especially in high contrast treatments. Support from a ramet growing in benign patch considerably reduced drought stress and enhanced growth of ramets in dry patches. The larger the contrast between water availability, the larger the amount of support the depending ramet received from the supporting one. This support strongly affected the growth of the supporting ramet, but not to an extent to cause increase in stress indicators. We also found indication of costs related to maintenance of physiological connection between ramets. Thus, the net benefit of physiological integration depends on the environment and integration between ramets of F. orientalis could be advantageous only in heterogeneous conditions with a high contrast. PMID:22957054

  3. Fructose-6-phosphate aldolase is a novel class I aldolase from Escherichia coli and is related to a novel group of bacterial transaldolases.

    PubMed

    Schurmann, M; Sprenger, G A

    2001-04-01

    We have cloned an open reading frame from the Escherichia coli K-12 chromosome that had been assumed earlier to be a transaldolase or a transaldolase-related protein, termed MipB. Here we show that instead a novel enzyme activity, fructose-6-phosphate aldolase, is encoded by this open reading frame, which is the first report of an enzyme that catalyzes an aldol cleavage of fructose 6-phosphate from any organism. We propose the name FSA (for fructose-six phosphate aldolase; gene name fsa). The recombinant protein was purified to apparent homogeneity by anion exchange and gel permeation chromatography with a yield of 40 mg of protein from 1 liter of culture. By using electrospray tandem mass spectroscopy, a molecular weight of 22,998 per subunit was determined. From gel filtration a size of 257,000 (+/- 20,000) was calculated. The enzyme most likely forms either a decamer or dodecamer of identical subunits. The purified enzyme displayed a V(max) of 7 units mg(-)1 of protein for fructose 6-phosphate cleavage (at 30 degrees C, pH 8.5 in 50 mm glycylglycine buffer). For the aldolization reaction a V(max) of 45 units mg(-)1 of protein was found; K(m) values for the substrates were 9 mm for fructose 6-phosphate, 35 mm for dihydroxyacetone, and 0.8 mm for glyceraldehyde 3-phosphate. FSA did not utilize fructose, fructose 1-phosphate, fructose 1,6-bisphosphate, or dihydroxyacetone phosphate. FSA is not inhibited by EDTA which points to a metal-independent mode of action. The lysine 85 residue is essential for its action as its exchange to arginine (K85R) resulted in complete loss of activity in line with the assumption that the reaction mechanism involves a Schiff base formation through this lysine residue (class I aldolase). Another fsa-related gene, talC of Escherichia coli, was shown to also encode fructose-6-phosphate aldolase activity and not a transaldolase as proposed earlier. PMID:11120740

  4. Improved detection of extended spectrum beta-lactamase (ESBL)-producing Escherichia coli in input and output samples of German biogas plants by a selective pre-enrichment procedure.

    PubMed

    Schauss, Thorsten; Glaeser, Stefanie P; Gütschow, Alexandra; Dott, Wolfgang; Kämpfer, Peter

    2015-01-01

    The presence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli was investigated in input (manure from livestock husbandry) and output samples of six German biogas plants in 2012 (one sampling per biogas plant) and two German biogas plants investigated in an annual cycle four times in 2013/2014. ESBL-producing Escherichia coli were cultured by direct plating on CHROMagar ESBL from input samples in the range of 100 to 104 colony forming units (CFU) per g dry weight but not from output sample. This initially indicated a complete elimination of ESBL-producing E. coli by the biogas plant process. Detected non target bacteria were assigned to the genera Acinetobacter, Pseudomonas, Bordetella, Achromobacter, Castellaniella, and Ochrobactrum. A selective pre-enrichment procedure increased the detection efficiency of ESBL-producing E. coli in input samples and enabled the detection in five of eight analyzed output samples. In total 119 ESBL-producing E. coli were isolated from input and 46 from output samples. Most of the E. coli isolates carried CTX-M-type and/or TEM-type beta lactamases (94%), few SHV-type beta lactamase (6%). Sixty-four blaCTX-M genes were characterized more detailed and assigned mainly to CTX-M-groups 1 (85%) and 9 (13%), and one to group 2. Phylogenetic grouping of 80 E. coli isolates showed that most were assigned to group A (71%) and B1 (27%), only one to group D (2%). Genomic fingerprinting and multilocus sequence typing (MLST) showed a high clonal diversity with 41 BOX-types and 19 ST-types. The two most common ST-types were ST410 and ST1210. Antimicrobial susceptibility testing of 46 selected ESBL-producing E. coli revealed that several isolates were additionally resistant to other veterinary relevant antibiotics and some grew on CHROMagar STEC but shiga-like toxine (SLT) genes were not detected. Resistance to carbapenems was not detected. In summary the study showed for the first time the presence of ESBL-producing E. coli in

  5. Improved Detection of Extended Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli in Input and Output Samples of German Biogas Plants by a Selective Pre-Enrichment Procedure

    PubMed Central

    Schauss, Thorsten; Glaeser, Stefanie P.; Gütschow, Alexandra; Dott, Wolfgang; Kämpfer, Peter

    2015-01-01

    The presence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli was investigated in input (manure from livestock husbandry) and output samples of six German biogas plants in 2012 (one sampling per biogas plant) and two German biogas plants investigated in an annual cycle four times in 2013/2014. ESBL-producing Escherichia coli were cultured by direct plating on CHROMagar ESBL from input samples in the range of 100 to 104 colony forming units (CFU) per g dry weight but not from output sample. This initially indicated a complete elimination of ESBL-producing E. coli by the biogas plant process. Detected non target bacteria were assigned to the genera Acinetobacter, Pseudomonas, Bordetella, Achromobacter, Castellaniella, and Ochrobactrum. A selective pre-enrichment procedure increased the detection efficiency of ESBL-producing E. coli in input samples and enabled the detection in five of eight analyzed output samples. In total 119 ESBL-producing E. coli were isolated from input and 46 from output samples. Most of the E. coli isolates carried CTX-M-type and/or TEM-type beta lactamases (94%), few SHV-type beta lactamase (6%). Sixty-four blaCTX-M genes were characterized more detailed and assigned mainly to CTX-M-groups 1 (85%) and 9 (13%), and one to group 2. Phylogenetic grouping of 80 E. coli isolates showed that most were assigned to group A (71%) and B1 (27%), only one to group D (2%). Genomic fingerprinting and multilocus sequence typing (MLST) showed a high clonal diversity with 41 BOX-types and 19 ST-types. The two most common ST-types were ST410 and ST1210. Antimicrobial susceptibility testing of 46 selected ESBL-producing E. coli revealed that several isolates were additionally resistant to other veterinary relevant antibiotics and some grew on CHROMagar STEC but shiga-like toxine (SLT) genes were not detected. Resistance to carbapenems was not detected. In summary the study showed for the first time the presence of ESBL-producing E. coli in

  6. Dynamic clonal equilibrium and predetermined cancer risk in Barrett's oesophagus.

    PubMed

    Martinez, Pierre; Timmer, Margriet R; Lau, Chiu T; Calpe, Silvia; Sancho-Serra, Maria Del Carmen; Straub, Danielle; Baker, Ann-Marie; Meijer, Sybren L; Kate, Fiebo J W Ten; Mallant-Hent, Rosalie C; Naber, Anton H J; van Oijen, Arnoud H A M; Baak, Lubbertus C; Scholten, Pieter; Böhmer, Clarisse J M; Fockens, Paul; Bergman, Jacques J G H M; Maley, Carlo C; Graham, Trevor A; Krishnadath, Kausilia K

    2016-01-01

    Surveillance of Barrett's oesophagus allows us to study the evolutionary dynamics of a human neoplasm over time. Here we use multicolour fluorescence in situ hybridization on brush cytology specimens, from two time points with a median interval of 37 months in 195 non-dysplastic Barrett's patients, and a third time point in a subset of 90 patients at a median interval of 36 months, to study clonal evolution at single-cell resolution. Baseline genetic diversity predicts progression and remains in a stable dynamic equilibrium over time. Clonal expansions are rare, being detected once every 36.8 patient years, and growing at an average rate of 1.58 cm(2) (95% CI: 0.09-4.06) per year, often involving the p16 locus. This suggests a lack of strong clonal selection in Barrett's and that the malignant potential of 'benign' Barrett's lesions is predetermined, with important implications for surveillance programs. PMID:27538785

  7. Dynamic clonal equilibrium and predetermined cancer risk in Barrett's oesophagus

    PubMed Central

    Martinez, Pierre; Timmer, Margriet R.; Lau, Chiu T.; Calpe, Silvia; Sancho-Serra, Maria del Carmen; Straub, Danielle; Baker, Ann-Marie; Meijer, Sybren L.; Kate, Fiebo J. W. ten; Mallant-Hent, Rosalie C.; Naber, Anton H. J.; van Oijen, Arnoud H. A. M.; Baak, Lubbertus C.; Scholten, Pieter; Böhmer, Clarisse J. M.; Fockens, Paul; Bergman, Jacques J. G. H. M.; Maley, Carlo C.; Graham, Trevor A.; Krishnadath, Kausilia K

    2016-01-01

    Surveillance of Barrett's oesophagus allows us to study the evolutionary dynamics of a human neoplasm over time. Here we use multicolour fluorescence in situ hybridization on brush cytology specimens, from two time points with a median interval of 37 months in 195 non-dysplastic Barrett's patients, and a third time point in a subset of 90 patients at a median interval of 36 months, to study clonal evolution at single-cell resolution. Baseline genetic diversity predicts progression and remains in a stable dynamic equilibrium over time. Clonal expansions are rare, being detected once every 36.8 patient years, and growing at an average rate of 1.58 cm2 (95% CI: 0.09–4.06) per year, often involving the p16 locus. This suggests a lack of strong clonal selection in Barrett's and that the malignant potential of ‘benign' Barrett's lesions is predetermined, with important implications for surveillance programs. PMID:27538785

  8. [Clonal eosinophilia revealed by recurrent Staphylococcus aureus infection].

    PubMed

    Vandenbos, F; Figueredo, M; Dumon-Gubeno, M-C; Nicolle, I; Tarhini, A; Medioni, L-D; Naman, H; Mouroux, J

    2011-06-01

    Acquired eosinophilia is currently classified into secondary (reactional to underlying diseases), clonal (presence of a bone marrow histological, cytogenetic or molecular marker of a myeloid malignancy) and idiopathic (neither secondary nor clonal) categories. We report the case of a 47-year-old male who was admitted to the hospital for Staphylococcus aureus recurring infections. An hypereosinophilia was discovered and led to molecular analysis. The identification of FIP1L1-PDGFRA fusion gene permitted the diagnostic of clonal eosinophilia. Treatment by imatinib mesylate induced an haematological remission, the control of the infection and thoracotomy cicatrization. This case is original because of its infectious presentation and the efficacy of imatinib mesylate to control the infectious process. PMID:21665081

  9. Female and male fitness consequences of clonal growth in a dwarf bamboo population with a high degree of clonal intermingling

    PubMed Central

    Matsuo, Ayumi; Tomimatsu, Hiroshi; Suzuki, Jun-Ichirou; Saitoh, Tomoyuki; Shibata, Shozo; Makita, Akifumi; Suyama, Yoshihisa

    2014-01-01

    Background and Aims Although many studies have reported that clonal growth interferes with sexual reproduction as a result of geitonogamous self-pollination and inbreeding depression, the mating costs of clonal growth are expected to be reduced when genets are spatially intermingled with others. This study examined how clonal growth affects both female and male reproductive success by studying a population of a mass-flowering plant, Sasa veitchii var. hirsuta, with a high degree of clonal intermingling. Methods In a 10 × 10 m plot, genets were discriminated based on the multilocus genotypes of 11 nuclear microsatellite loci. The relationships between genet size and the components of reproductive success were then investigated. Male siring success and female and male selfing rates were assessed using paternity analysis. Key Results A total of 111 genets were spatially well intermingled with others. In contrast to previous studies with species forming distinct monoclonal patches, seed production linearly increased with genet size. While male siring success was a decelerating function of genet size, selfing rates were relatively low and not related to genet size. Conclusions The results, in conjunction with previous studies, emphasize the role of the spatial arrangement of genets on both the quantity and quality of offpsring, and suggest that an intermingled distribution of genets can reduce the mating costs of clonal growth and enhance overall fitness, particularly female fitness. PMID:25228034

  10. Pathology and Molecular Characterization of Escherichia Coli Associated With the Avian Salpingitis-Peritonitis Disease Syndrome.

    PubMed

    Heidemann Olsen, Rikke; Bisgaard, Magne; Christensen, Jens Peter; Kabell, Susanne; Christensen, Henrik

    2016-03-01

    Outbreaks of salpingitis and peritonitis cause major economic losses due to high mortality, reduced egg-production, and culling. The aim of the present study was to characterize, in detail, lesions associated with increased mortality in layers due to avianpathogenic Escherichia coli (APEC) and to investigate the population structure of the E. coli involved, which is important for selection of optimal treatment and prophylactic strategies. Among 322 layers received from eight farms with increased mortality due to E. coli, three lesion types were observed; sepsis-like lesions, chronic salpingitis and peritonitis, and chronic salpingitis and peritonitis associated with sepsis-like lesions. One hundred isolates of E. coli obtained in pure culture from the different lesion types were selected for genetic characterization. Six out of 10 submissions (two farms with two submissions) were considered clonal as defined by more than 85% of the typed isolates of E. coli belonging to the same sequence-type (ST). B2 was the most-prevalent phylogroup, including the clonal complex of ST95. The most-important virulence genes of E. coli were demonstrated from both clonal and nonclonal outbreaks, and major differences as to phylogeny and virulence genes were not observed between the lesion types. Cannibalism was more-often observed during polyclonal outbreaks. A new pathotype of APEC is suggested based upon lesions and route of infection, high similarity of virulence genes including plasmid-associated genes, and high frequency of ST95 and other isolates belonging to phylogroup B2. Compared to the best-known pathotypes of E. coli, this needs further investigations, including infection experiments to show if single virulence factors can be pointed out that are specific for the salpingitis-peritonitis pathotype and possibly not found in other pathotypes of E. coli. PMID:26953937

  11. E. coli enteritis

    MedlinePlus

    Traveler's diarrhea - E. coli ; Food poisoning - E. coli ; E. coli diarrhea; Hamburger disease ... infected. The most common symptom is sudden, severe diarrhea that is often bloody. Other symptoms may include: ...

  12. Clinical Clostridium difficile: clonality and pathogenicity locus diversity.

    PubMed

    Dingle, Kate E; Griffiths, David; Didelot, Xavier; Evans, Jessica; Vaughan, Alison; Kachrimanidou, Melina; Stoesser, Nicole; Jolley, Keith A; Golubchik, Tanya; Harding, Rosalind M; Peto, Tim E; Fawley, Warren; Walker, A Sarah; Wilcox, Mark; Crook, Derrick W

    2011-01-01

    Clostridium difficile infection (CDI) is an important cause of mortality and morbidity in healthcare settings. The major virulence determinants are large clostridial toxins, toxin A (tcdA) and toxin B (tcdB), encoded within the pathogenicity locus (PaLoc). Isolates vary in pathogenicity from hypervirulent PCR-ribotypes 027 and 078 with high mortality, to benign non-toxigenic strains carried asymptomatically. The relative pathogenicity of most toxigenic genotypes is still unclear, but may be influenced by PaLoc genetic variant. This is the largest study of C. difficile molecular epidemiology performed to date, in which a representative collection of recent isolates (n = 1290) from patients with CDI in Oxfordshire, UK, was genotyped by multilocus sequence typing. The population structure was described using NeighborNet and ClonalFrame. Sequence variation within toxin B (tcdB) and its negative regulator (tcdC), was mapped onto the population structure. The 69 Sequence Types (ST) showed evidence for homologous recombination with an effect on genetic diversification four times lower than mutation. Five previously recognised genetic groups or clades persisted, designated 1 to 5, each having a strikingly congruent association with tcdB and tcdC variants. Hypervirulent ST-11 (078) was the only member of clade 5, which was divergent from the other four clades within the MLST loci. However, it was closely related to the other clades within the tcdB and tcdC loci. ST-11 (078) may represent a divergent formerly non-toxigenic strain that acquired the PaLoc (at least) by genetic recombination. This study focused on human clinical isolates collected from a single geographic location, to achieve a uniquely high density of sampling. It sets a baseline of MLST data for future comparative studies investigating genotype virulence potential (using clinical severity data for these isolates), possible reservoirs of human CDI, and the evolutionary origins of hypervirulent strains

  13. Effect of rearing environment and dietary zinc oxide on the response of group-housed weaned pigs to enterotoxigenic Escherichia coli O149 challenge.

    PubMed

    Slade, R D; Kyriazakis, I; Carroll, S M; Reynolds, F H; Wellock, I J; Broom, L J; Miller, H M

    2011-06-01

    A 2 × 2 factorial experiment was conducted to determine the effects of rearing environment (indoor (In) v. outdoor (Out)) and dietary zinc oxide (ZnO) supplementation (0 (-Zn) v. 3100 (+Zn) mg/kg feed) on the response of weaned pigs to a challenge infection with enterotoxigenic Escherichia coli (ETEC). Pigs from the two rearing environments were weaned onto trial diets at 4 weeks of age, moved into conventional accommodation and infected 3 days later with 109 CFU ETEC per os. Faecal ETEC shedding was determined before and after challenge. After 7 days of ETEC infection, all pigs were euthanized for gut lactic acid bacteria (LAB)-to-coliform ratio, pH and small intestine morphological measurements. Both ZnO and outdoor rearing reduced ETEC excretion, and these effects were additive. Outdoor rearing increased small intestine and colon tissue weight. ZnO increased villus height and goblet cell number in the upper small intestine, LAB-to-coliform ratio (through reduced coliforms) in the lower small intestine and proximal colon, and improved growth performance. There were interactive effects of rearing environment and ZnO supplementation on upper small intestine villus height and daily gain, as outdoor rearing conferred advantages on these variables only with ZnO dietary supplementation. Daily gains were 233, 174, 277 and 347 (s.e.m. 27.2) g/day for the In - Zn, Out - Zn, In + Zn and Out + Zn, respectively. These results suggest different, but complementary mechanisms of intestinal health and performance in outdoor-reared pigs and those offered ZnO supplemented diets. The results indicate that the benefits of ZnO to the weaned pig extend beyond suppression of ETEC and appear mediated through altered development of the small intestine mucosa. PMID:22440169

  14. Assignment of function to Histidines 260 and 298 by engineering the E1 component of the Escherichia coli 2-oxoglutarate dehydrogenase complex; substitutions that lead to acceptance of substrates lacking the 5-carboxyl group.†

    PubMed Central

    Shim, Da Jeong; Nemeria, Natalia S.; Balakrishnan, Anand; Patel, Hetalben; Song, Jaeyoung; Wang, Junjie; Jordan, Frank; Farinas, Edgardo T.

    2011-01-01

    The first component (E1o) of the Escherichia coli 2-oxoglutarate dehydrogenase complex (OGDHc) was engineered to accept substrates lacking the 5-carboxylate group by subjecting H260 and H298 to saturation mutagenesis. Apparently, H260 is required for substrate recognition, but H298 could be replaced by hydrophobic residues of similar molecular volume. To interrogate whether the second component would enable synthesis of acyl-coenzymeA derivatives, hybrid complexes consisting of recombinant components of OGDHc (o) and pyruvate dehydrogenase (p) enzymes were constructed, suggesting that a different component is the ‘gatekeeper’ for specificity for these two multienzyme complexes in bacteria, E1p for pyruvate, but E2o for 2-oxoglutarate. PMID:21809826

  15. Genetic Diversity and Virulence Potential of Shiga Toxin-Producing Escherichia coli O113:H21 Strains Isolated from Clinical, Environmental, and Food Sources

    PubMed Central

    Delannoy, Sabine; Lacher, David W.; dos Santos, Luis Fernando; Beutin, Lothar; Fach, Patrick; Rivas, Marta; Hartland, Elizabeth L.; Paton, Adrienne W.; Guth, Beatriz E. C.

    2014-01-01

    Shiga toxin-producing Escherichia coli strains of serotype O113:H21 have caused severe human diseases, but they are unusual in that they do not produce adherence factors coded by the locus of enterocyte effacement. Here, a PCR microarray was used to characterize 65 O113:H21 strains isolated from the environment, food, and clinical infections from various countries. In comparison to the pathogenic strains that were implicated in hemolytic-uremic syndrome in Australia, there were no clear differences between the pathogens and the environmental strains with respect to the 41 genetic markers tested. Furthermore, all of the strains carried only Shiga toxin subtypes associated with human infections, suggesting that the environmental strains have the potential to cause disease. Most of the O113:H21 strains were closely related and belonged in the same clonal group (ST-223), but CRISPR analysis showed a great degree of genetic diversity among the O113:H21 strains. PMID:24858089

  16. Specific Strains of Escherichia coli Are Pathogenic for the Endometrium of Cattle and Cause Pelvic Inflammatory Disease in Cattle and Mice

    PubMed Central

    Sheldon, I. Martin; Rycroft, Andrew N.; Dogan, Belgin; Craven, Melanie; Bromfield, John J.; Chandler, Alyssa; Roberts, Mark H.; Price, Sian B.; Gilbert, Robert O.; Simpson, Kenneth W.

    2010-01-01

    Background Escherichia coli are widespread in the environment and pathogenic strains cause diseases of mucosal surfaces including the female genital tract. Pelvic inflammatory disease (PID; metritis) or endometritis affects ∼40% of cattle after parturition. We tested the expectation that multiple genetically diverse E. coli from the environment opportunistically contaminate the uterine lumen after parturition to establish PID. Methodology/Principal Findings Distinct clonal groups of E. coli were identified by Random Amplification of Polymorphic DNA (RAPD) and Multilocus sequence typing (MLST) from animals with uterine disease and these differed from known diarrhoeic or extra-intestinal pathogenic E. coli. The endometrial pathogenic E. coli (EnPEC) were more adherent and invasive for endometrial epithelial and stromal cells, compared with E. coli isolated from the uterus of clinically unaffected animals. The endometrial epithelial and stromal cells produced more prostaglandin E2 and interleukin-8 in response to lipopolysaccharide (LPS) purified from EnPEC compared with non-pathogenic E. coli. The EnPEC or their LPS also caused PID when infused into the uterus of mice with accumulation of neutrophils and macrophages in the endometrium. Infusion of EnPEC was only associated with bacterial invasion of the endometrium and myometrium. Despite their ability to invade cultured cells, elicit host cell responses and establish PID, EnPEC lacked sixteen genes commonly associated with adhesion and invasion by enteric or extraintestinal pathogenic E. coli, though the ferric yersiniabactin uptake gene (fyuA) was present in PID-associated EnPEC. Endometrial epithelial or stromal cells from wild type but not Toll-like receptor 4 (TLR4) null mice secreted prostaglandin E2 and chemokine (C-X-C motif) ligand 1 (CXCL1) in response to LPS from EnPEC, highlighting the key role of LPS in PID. Conclusions/Significance The implication arising from the discovery of EnPEC is that

  17. Comparison of ruminant and human attaching and effacing Escherichia coli (AEEC) strains.

    PubMed

    Horcajo, Pilar; Domínguez-Bernal, Gustavo; de la Fuente, Ricardo; Ruiz-Santa-Quiteria, José A; Blanco, Jesús E; Blanco, Miguel; Mora, Azucena; Dahbi, Ghizlane; López, Cecilia; Puentes, Beatriz; Alonso, María Pilar; Blanco, Jorge; Orden, José A

    2012-03-23

    The presence of 12 genes associated with virulence in human attaching and effacing Escherichia coli (AEEC) was studied within a collection of 20 enterohemorrhagic E. coli (EHEC) and 206 atypical enteropathogenic E. coli (EPEC) isolated from ruminants. In addition, virulence genes and the clonal relationship of 49 atypical EPEC O26 strains isolated from humans and ruminants were compared to clarify whether ruminants serve as a reservoir of atypical EPEC for humans. A great diversity in the content of virulence gene was found. Thus, the espH, espG and map genes were detected in more than 85% of ruminant AEEC strains; the tccP2, espI, efa1/lifA, ehxA and paa genes were present in 50-70% of strains; and other genes such as tccP, espP, katP and toxB were detected in <25% of strains. EHEC strains contained more virulence genes than atypical EPEC strains. Our results suggest for the first time that the efa1/lifA gene is associated with diarrhea in newborn ruminants and that the AEEC strains with the H11 flagellar antigen are potentially more virulent than the non-H11 AEEC strains. Importantly, we identified a new intimin variant gene, eaeρ, in three ruminant atypical EPEC strains. The comparison of ruminant and human EPEC O26 strains showed that some ruminant strains possess virulence gene profiles and pulse-field gel electrophoresis pulsotypes similar to those of human strains. In conclusion, our data suggest that atypical EPEC is a heterogeneous group with different pathogenic potential and that ruminants could serve as a reservoir of atypical EPEC for humans. PMID:21958746

  18. An epidemiologically successful Escherichia coli sequence type modulates Plasmodium falciparum infection in the mosquito midgut.

    PubMed

    Tchioffo, Majoline T; Abate, Luc; Boissière, Anne; Nsango, Sandrine E; Gimonneau, Geoffrey; Berry, Antoine; Oswald, Eric; Dubois, Damien; Morlais, Isabelle

    2016-09-01

    Malaria transmission relies on the successful development of Plasmodium parasites in the Anopheles mosquito vector. Within the mosquito midgut, malaria parasites encounter a resident bacterial flora and parasite-bacteria interactions modulate Plasmodium development. The mechanisms by which the bacteria interact with malaria parasites are still unknown. The intestinal microbiota could regulate immune signaling pathways or produce bacterial compounds that block Plasmodium development. In this study, we characterized Escherichia coli strains previously isolated from the Anopheles mosquito midgut and investigated the putative role of two E. coli clones, 444ST95 and 351ST73, on parasite development. Sporogonic development was significantly impacted by exposure to clone 444ST95 whereas prevalence and intensity of infection were not different in mosquitoes challenged with 351ST73 as compared to control mosquitoes. This result indicates midgut bacteria exhibit intra-specific variation in their ability to inhibit Plasmodium development. Expression patterns of immune genes differed between mosquitoes challenged with 444ST95 and 351ST73 and examination of the luminal midgut surface by transmission electron microscopy revealed distinct effects of bacterial exposure on midgut epithelial cells. The 444ST95 clone strongly affected mosquito survival and parasite development and this could be associated to the Hemolysin F or other toxins released by the bacteria. Further studies will be needed to decipher the virulence factors and to determine their contribution to the observed phenotype of the 444ST95E. coli strain that belongs to the epidemiological ST95 clonal group responsible for extra intestinal infections in human and other animals. PMID:27154329

  19. Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

    PubMed Central

    Sheppard, Anna E.; Pankhurst, Louise; De Maio, Nicola; Moore, Catrin E.; Sebra, Robert; Turner, Paul; Anson, Luke W.; Kasarskis, Andrew; Batty, Elizabeth M.; Kos, Veronica; Wilson, Daniel J.; Phetsouvanh, Rattanaphone; Wyllie, David; Sokurenko, Evgeni; Manges, Amee R.; Johnson, Timothy J.; Price, Lance B.; Peto, Timothy E. A.; Johnson, James R.; Didelot, Xavier; Walker, A. Sarah; Crook, Derrick W.

    2016-01-01

    ABSTRACT Escherichia coli sequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. This study of the largest worldwide collection (n = 215) of sequenced ST131 E. coli isolates to date demonstrates that the clonal expansion of two previously recognized antimicrobial-resistant clades, C1/H30R and C2/H30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/H30Rx clade driven by the acquisition of a blaCTX-M-15-containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids and chromosomal integration of blaCTX-M within subclusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed among ST131, the blaCTX-M-14/14-like group. The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages of E. coli. These data also highlight the global imperative to reduce specific antibiotic selection pressures and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages. PMID:27006459

  20. Intrafamilial cluster of pulmonary tuberculosis due to Mycobacterium bovis of the African 1 clonal complex.

    PubMed

    Godreuil, S; Jeziorski, E; Bañuls, A L; Fraisse, T; Van de Perre, P; Boschiroli, M L

    2010-12-01

    A new clonal complex of Mycobacterium bovis present at high frequency in cattle from west central African countries has been described as the African 1 (Af1) clonal complex. Here, the first intrafamilial cluster of human tuberculosis cases due to M. bovis Af1 clonal complex strains is reported. We discuss hypotheses regarding modes of transmission. PMID:20980573

  1. Clonal Outbreak of Plasmodium falciparum Infection in Eastern Panama

    PubMed Central

    Obaldia, Nicanor; Baro, Nicholas K.; Calzada, Jose E.; Santamaria, Ana M.; Daniels, Rachel; Wong, Wesley; Chang, Hsiao-Han; Hamilton, Elizabeth J.; Arevalo-Herrera, Myriam; Herrera, Socrates; Wirth, Dyann F.; Hartl, Daniel L.; Marti, Matthias; Volkman, Sarah K.

    2015-01-01

    Identifying the source of resurgent parasites is paramount to a strategic, successful intervention for malaria elimination. Although the malaria incidence in Panama is low, a recent outbreak resulted in a 6-fold increase in reported cases. We hypothesized that parasites sampled from this epidemic might be related and exhibit a clonal population structure. We tested the genetic relatedness of parasites, using informative single-nucleotide polymorphisms and drug resistance loci. We found that parasites were clustered into 3 clonal subpopulations and were related to parasites from Colombia. Two clusters of Panamanian parasites shared identical drug resistance haplotypes, and all clusters shared a chloroquine-resistance genotype matching the pfcrt haplotype of Colombian origin. Our findings suggest these resurgent parasite populations are highly clonal and that the high clonality likely resulted from epidemic expansion of imported or vestigial cases. Malaria outbreak investigations that use genetic tools can illuminate potential sources of epidemic malaria and guide strategies to prevent further resurgence in areas where malaria has been eliminated. PMID:25336725

  2. The role of plant propagation at clonal genebanks

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Clonal genebanks utilize both seed and vegetative propagation techniques. Seed propagation is important for the introduction of new genotypes (accessions), especially crop wild relatives. Additionally, seed may be produced by breeding or to otherwise support research. Temperate tree fruit and nut c...

  3. Clonal diversity of recurrently mutated genes in myelodysplastic syndromes

    PubMed Central

    Walter, MJ; Shen, D; Shao, J; Ding, L; White, BS; Kandoth, C; Miller, CA; Niu, B; McLellan, MD; Dees, ND; Fulton, R; Elliot, K; Heath, S; Grillot, M; Westervelt, P; Link, DC; DiPersio, JF; Mardis, E; Ley, TJ; Wilson, RK; Graubert, TA

    2013-01-01

    Recent studies suggest that most cases of myelodysplastic syndrome (MDS) are clonally heterogeneous, with a founding clone and multiple subclones. It is not known whether specific gene mutations typically occur in founding clones or subclones. We screened a panel of 94 candidate genes in a cohort of 157 patients with MDS or secondary acute myeloid leukemia (sAML). This included 150 cases with samples obtained at MDS diagnosis and 15 cases with samples obtained at sAML transformation (8 were also analyzed at the MDS stage). We performed whole-genome sequencing (WGS) to define the clonal architecture in eight sAML genomes and identified the range of variant allele frequencies (VAFs) for founding clone mutations. At least one mutation or cytogenetic abnormality was detected in 83% of the 150 MDS patients and 17 genes were significantly mutated (false discovery rate ≤0.05). Individual genes and patient samples displayed a wide range of VAFs for recurrently mutated genes, indicating that no single gene is exclusively mutated in the founding clone. The VAFs of recurrently mutated genes did not fully recapitulate the clonal architecture defined by WGS, suggesting that comprehensive sequencing may be required to accurately assess the clonal status of recurrently mutated genes in MDS. PMID:23443460

  4. Quantification of Clonal Circulating Plasma cells in Relapsed Multiple Myeloma

    PubMed Central

    Gonsalves, Wilson I; Morice, William G; Rajkumar, S. Vincent; Gupta, Vinay; Timm, Michael M; Dispenzieri, Angela; Buadi, Francis K; Lacy, Martha Q; Singh, Preet P; Kapoor, Prashant; Gertz, Morie A; Kumar, Shaji K

    2014-01-01

    The presence of clonal circulating plasma cells (cPCs) remains a marker of high-risk disease in newly diagnosed multiple myeloma (MM) patients. However, its prognostic utility in MM patients with previously treated disease is unknown. We studied 647 consecutive patients with previously treated MM seen at the Mayo Clinic, Rochester who had their peripheral blood evaluated for cPCs by multi-parameter flow cytometry. Of these patients, 145 had actively relapsing disease while the remaining 502 had disease that was in a plateau and included 68 patients in complete remission (CR) and 434 patients with stable disease. Patients with actively relapsing disease were more likely to have clonal cPCs than those in a plateau (P < 0.001). None of the patients in CR had any clonal cPCs detected. Among patients whose disease was in a plateau, the presence of clonal cPCs predicted for a worse median survival (22 months vs. not reached; P=0.004). Among actively relapsing patients, the presence of ≥100 cPCs predicted for a worse survival after flow cytometry analysis (12 months vs. 33 months; P<0.001). Future studies are needed to determine the role of these findings in developing a risk-adapted treatment approach in MM patients with actively relapsing disease. PMID:25113422

  5. Genomic Aberrations Drive Clonal Evolution of Neuroendocrine Tumors.

    PubMed

    Kaushik, Akash Kumar; Sreekumar, Arun

    2016-05-01

    Molecular features of castration-resistant neuroendocrine prostate cancer (CRPC-NE) are not well characterized. A recent study that investigated genomic aberrations of CRPC-NE tumors suggests their clonal evolution from CRPC adenocarcinoma. Furthermore, the existence of a distinct DNA methylation profile in CRPC-NE implicates a critical role for epigenetic modification in the development of CRPC-NE. PMID:27037211

  6. Phenotypic differences among three clonal lineages of Phytophthora ramorum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are three major clonal lineages of Phytophthora ramorum present in North America and Europe named NA1, NA2, and EU1. Twenty-three isolates representing all three lineages were evaluated for phenotype including (i) aggressiveness on detached Rhododendron leaves and (ii) growth rate at minimum, ...

  7. Comparative organogenic responses of six clonal apple rootstock cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The organogenesis potential is different among cultivars and must be optimized for individual genotypes. Shoot organogenesis capacity from leaf explants and root organogenesis capacity of in vitro shoots in six clonal apple rootstock cultivars were compared. The shoot organogenesis capacity was hi...

  8. Extended Virulence Genotype of Pathogenic Escherichia coli Isolates Carrying the afa-8 Operon: Evidence of Similarities between Isolates from Humans and Animals with Extraintestinal Infections

    PubMed Central

    Girardeau, Jean Pierre; Lalioui, Lila; Said, A. Mohamed Ou; De Champs, Christophe; Le Bouguénec, Chantal

    2003-01-01

    The afimbrial AfaE-VIII adhesin is common among Escherichia coli isolates from calves with intestinal and/or extraintestinal infections and from humans with sepsis or pyelonephritis. The virulence genotypes of 77 Escherichia coli afa-8 isolates from farm animals and humans were compared to determine whether any trait of commonality exists between isolates of the different host species. Over half of the extraintestinal afa-8 isolates were associated with pap and f17Ac adhesin genes and contained virulence genes (pap, hly, and cnf1) which are characteristic of human extraintestinal pathogenic E. coli (ExPEC). PapG, which occurs as three known variants (variants I to III), is encoded by the corresponding three alleles of papG. Among the pap-positive strains, new papG variants (papGrs) that differed from the isolates with genes for the three adhesin classes predominated over isolates with papG allele III, which in turn were more prevalent than those with allele II. The data showed the substantial prevalence of the enteroaggregative E. coli heat-stable enterotoxin gene (east1) among afa-8 isolates. Most of the afa-8 isolates harbored the high-pathogenicity island (HPI) present in pathogenic Yersinia; however, two-thirds of the HPI-positive strains shared a truncated HPI integrase gene. The presence of ExPEC-associated virulence factors (VFs) in extraintestinal isolates that carry genes typical of enteric strains and that express O antigens associated with intestinal E. coli is consistent with transfer of VFs and O-antigen determinants between ExPEC and enteric strains. The similarities between animal and human ExPEC strains support the hypothesis of overlapping populations, with members of certain clones or clonal groups including animal and human strains. The presence of multiple-antibiotic-resistant bovine afa-8 strains among such clones may represent a potential public health risk. PMID:12517852

  9. Genetic Diversity of the fliC Genes Encoding the Flagellar Antigen H19 of Escherichia coli and Application to the Specific Identification of Enterohemorrhagic E. coli O121:H19

    PubMed Central

    Beutin, Lothar; Delannoy, Sabine

    2015-01-01

    Enterohemorrhagic Escherichia coli (EHEC) O121:H19 belong to a specific clonal type distinct from other classical EHEC and major enteropathogenic E. coli groups and is regarded as one of the major EHEC serogroups involved in severe infections in humans. Sequencing of the fliC genes associated with the flagellar antigen H19 (fliCH19) revealed the genetic diversity of the fliCH19 gene sequences in E. coli. A cluster analysis of 12 fliCH19 sequences, 4 from O121 and 8 from non-O121 E. coli strains, revealed five different genotypes. All O121:H19 strains fell into one cluster, whereas a second cluster was formed by five non-O121:H19 strains. Cluster 1 and cluster 2 strains differ by 27 single nucleotide exchanges in their fliCH19 genes (98.5% homology). Based on allele discrimination of the fliCH19 genes, a real-time PCR test was designed for specific identification of EHEC O121:H19. The O121 fliCH19 PCR tested negative in 73 E. coli H19 strains that belonged to serogroups other than O121, including 28 different O groups, O-nontypeable H19, and O-rough:H19 strains. The O121 fliCH19 PCR reacted with all 16 tested O121:H19 strains and 1 O-rough:H19 strain which was positive for the O121 wzx gene. A cross-reaction was observed only with E. coli H32 strains which share sequence similarities in the target region of the O121 fliCH19 PCR. The combined use of O-antigen genotyping (O121 wzx) and the detection of O121 fliCH19 allele type contributes to improving the identification and molecular serotyping of EHEC O121:H19 motile and nonmotile strains and variants of these strains lacking stx genes. PMID:25862232

  10. Molecular characterization of bacteremic Escherichia coli isolates in Romania.

    PubMed

    Usein, Codruţa-Romaniţa; Papagheorghe, Raluca; Oprea, Mihaela; Condei, Maria; Strãuţ, Monica

    2016-05-01

    The increasing prevalence of invasive infections caused by antibiotic resistant Escherichia coli strains in Romanian patients, already mentioned in the European reports, requires better knowledge of their specific traits. Thus, a set of 38 E. coli blood isolates, collected between 2010 and 2012 at one of the local hospitals participating into the European Antimicrobial Resistance Surveillance Network, was investigated retrospectively with respect to the phylogenetic origin, extraintestinal virulence-associated markers (i.e. fimH, papC, papG alleles, sfa/foc, afa/dra, hly, cnf1, sat, iucC, fyuA, ibeA), and beta-lactamase encoding genes (i.e. bla CTX-M, bla TEM, and bla SHV alleles). The isolates with extended-spectrum beta-lactamase (ESBL) phenotypes were further characterized using PCR-based replicon typing and multilocus sequencing typing. For ST131 members, pulsed-field gel electrophoresis (PFGE) and PCR-based detection of fimH30 allele were performed. Overall, the isolates were more likely members of the major phylogenetic group A (53 %) and to a lesser extent of groups B2 (29 %), D (10 %), and B1 (8 %). All but three of the virulence markers sought (i.e. papGI, hly, cnf1) were detected with prevalence ranging from 3 % (i.e. ibeA, papGIII) to 87 % (fimH). As expected, the most complex genotypes (four to seven virulence markers) defined the isolates derived from phylogenetic groups B2 and D. ESBL producers were bla CTX-M-15-positive, mostly of phylogroup A (67 %), harboured IncF multireplicon plasmids, and belonged to six sequence types (i.e. ST10, ST131, ST167, ST410, ST540, ST1275). Members of ST10 clonal complex (i.e. ST10, ST167) were the most common. The ST131 isolates belonged to H30 subclone and displayed 74 % similarity at PFGE analysis. PMID:26452764

  11. Clonal Diversity of Nosocomial Epidemic Acinetobacter baumannii Strains Isolated in Spain▿

    PubMed Central

    Villalón, Pilar; Valdezate, Sylvia; Medina-Pascual, Maria J.; Rubio, Virginia; Vindel, Ana; Saez-Nieto, Juan A.

    2011-01-01

    Acinetobacter baumannii is one of the major pathogens involved in nosocomial outbreaks. The clonal diversity of 729 epidemic strains isolated from 19 Spanish hospitals (mainly from intensive care units) was analyzed over an 11-year period. Pulsed-field gel electrophoresis (PFGE) identified 58 PFGE types that were subjected to susceptibility testing, rpoB gene sequencing, and multilocus sequence typing (MLST). All PFGE types were multidrug resistant; colistin was the only agent to which all pathogens were susceptible. The 58 PFGE types were grouped into 16 clones based on their genetic similarity (cutoff of 80%). These clones were distributed into one major cluster (cluster D), three medium clusters (clusters A, B, and C), and three minor clusters (clusters E, F, and G). The rpoB gene sequencing and MLST results reflected a clonal distribution, in agreement with the PFGE results. The MLST sequence types (STs) (and their percent distributions) were as follows: ST-2 (47.5%), ST-3 (5.1%), ST-15 (1.7%), ST-32 (1.7%), ST-79 (13.6%), ST-80 (20.3%), and ST-81 (10.2%). ST-79, ST-80, and ST-81 and the alleles cpn60-26 and recA29 are described for the first time. International clones I, II, and III were represented by ST-81, ST-2, and ST-3, respectively. ST-79 and ST-80 could be novel emerging clones. This work confirms PFGE and MLST to be complementary tools in clonality studies. Here PFGE was able to demonstrate the monoclonal pattern of most outbreaks, the inter- and intrahospital transmission of bacteria, and their endemic persistence in some wards. MLST allowed the temporal evolution and spatial distribution of Spanish clones to be monitored and permitted international comparisons to be made. PMID:21177889

  12. Shiga Toxin Producing Escherichia coli.

    PubMed

    Bryan, Allen; Youngster, Ilan; McAdam, Alexander J

    2015-06-01

    Shiga toxin-producing Escherichia coli (STEC) is among the common causes of foodborne gastroenteritis. STEC is defined by the production of specific toxins, but within this pathotype there is a diverse group of organisms. This diversity has important consequences for understanding the pathogenesis of the organism, as well as for selecting the optimum strategy for diagnostic testing in the clinical laboratory. This review includes discussions of the mechanisms of pathogenesis, the range of manifestations of infection, and the several different methods of laboratory detection of Shiga toxin-producing E coli. PMID:26004641

  13. Diarrheagenic Escherichia coli

    PubMed Central

    Nataro, James P.; Kaper, James B.

    1998-01-01

    Escherichia coli is the predominant nonpathogenic facultative flora of the human intestine. Some E. coli strains, however, have developed the ability to cause disease of the gastrointestinal, urinary, or central nervous system in even the most robust human hosts. Diarrheagenic strains of E. coli can be divided into at least six different categories with corresponding distinct pathogenic schemes. Taken together, these organisms probably represent the most common cause of pediatric diarrhea worldwide. Several distinct clinical syndromes accompany infection with diarrheagenic E. coli categories, including traveler’s diarrhea (enterotoxigenic E. coli), hemorrhagic colitis and hemolytic-uremic syndrome (enterohemorrhagic E. coli), persistent diarrhea (enteroaggregative E. coli), and watery diarrhea of infants (enteropathogenic E. coli). This review discusses the current level of understanding of the pathogenesis of the diarrheagenic E. coli strains and describes how their pathogenic schemes underlie the clinical manifestations, diagnostic approach, and epidemiologic investigation of these important pathogens. PMID:9457432

  14. Fixed nuclei as alternative template of BIOMED-2 multiplex polymerase chain reaction for immunoglobulin gene clonality testing in B-cell malignancies

    PubMed Central

    Tang, Yuan; Chen, Jie; Wang, Jianchao; Zheng, Ke; Liao, Dianying; Liao, Xiaomei; Liu, Weiping; Wang, Lin

    2015-01-01

    Evaluation of immunoglobulin (Ig) gene rearrangements with BIOMED-2 multiplex PCR has become a standard detection of clonality in mature B cell malignancies. Conventionally, this method is relatively labor-intensive and time-consuming, as it requires DNA isolation from bone marrow aspirates (BM) or peripheral blood (PB) in patients with BM or PB involvement. On the other hand, fluorescence in situ hybridization (FISH) is routinely used as genetic screening in B cell malignancies, but the surplus fixed nuclei initially prepared for FISH usually turn useless afterwards. We sought to use these surplus nuclei after FISH as a template to perform PCR-based Ig gene clonality testing. Templates of 12 patients with mature B cell malignancies, which consisted of both DNA isolated with commercial DNA isolation kit from fresh BM or PB (DNA group) and the fixed nuclei initially prepared for FISH (nuclei group) from the same individuals, were subjected to PCR with BIOMED-2 primer sets for immunoglobulin heavy chain and kappa light chain under recommended conditions. Our result, for the first time, showed a high consistency between the two groups in detecting B cell clonality, which indicates that nuclei for FISH can function as a reliable template comparable to fresh tissue-isolated DNA in PCR based Ig clonality testing. This offers a simple, rapid and more economical alternative to standard Ig testing based on regular DNA. PMID:27069754

  15. Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics

    PubMed Central

    Gawad, Charles; Koh, Winston; Quake, Stephen R.

    2014-01-01

    Many cancers have substantial genomic heterogeneity within a given tumor, and to fully understand that diversity requires the ability to perform single cell analysis. We performed targeted sequencing of a panel of single nucleotide variants (SNVs), deletions, and IgH sequences in 1,479 single tumor cells from six acute lymphoblastic leukemia (ALL) patients. By accurately segregating groups of cooccurring mutations into distinct clonal populations, we identified codominant clones in the majority of patients. Evaluation of intraclonal mutation patterns identified clone-specific punctuated cytosine mutagenesis events, showed that most structural variants are acquired before SNVs, determined that KRAS mutations occur late in disease development but are not sufficient for clonal dominance, and identified clones within the same patient that are arrested at varied stages in B-cell development. Taken together, these data order the sequence of genetic events that underlie childhood ALL and provide a framework for understanding the development of the disease at single-cell resolution. PMID:25425670

  16. Clonal Analysis of Newborn Hippocampal Dentate Granule Cell Proliferation and Development in Temporal Lobe Epilepsy123

    PubMed Central

    LaSarge, Candi L.; McAuliffe, John J.

    2015-01-01

    Abstract Hippocampal dentate granule cells are among the few neuronal cell types generated throughout adult life in mammals. In the normal brain, new granule cells are generated from progenitors in the subgranular zone and integrate in a typical fashion. During the development of epilepsy, granule cell integration is profoundly altered. The new cells migrate to ectopic locations and develop misoriented “basal” dendrites. Although it has been established that these abnormal cells are newly generated, it is not known whether they arise ubiquitously throughout the progenitor cell pool or are derived from a smaller number of “bad actor” progenitors. To explore this question, we conducted a clonal analysis study in mice expressing the Brainbow fluorescent protein reporter construct in dentate granule cell progenitors. Mice were examined 2 months after pilocarpine-induced status epilepticus, a treatment that leads to the development of epilepsy. Brain sections were rendered translucent so that entire hippocampi could be reconstructed and all fluorescently labeled cells identified. Our findings reveal that a small number of progenitors produce the majority of ectopic cells following status epilepticus, indicating that either the affected progenitors or their local microenvironments have become pathological. By contrast, granule cells with “basal” dendrites were equally distributed among clonal groups. This indicates that these progenitors can produce normal cells and suggests that global factors sporadically disrupt the dendritic development of some new cells. Together, these findings strongly predict that distinct mechanisms regulate different aspects of granule cell pathology in epilepsy. PMID:26756038

  17. Clonality of T cell and phenotypically undefined lymphoid neoplasms: the value of genotypic analyses.

    PubMed Central

    Hodges, E; Stacey, G N; Howell, W M; Jones, D B; Smith, J L

    1990-01-01

    The value of genotypic analysis for routine assessment of leukaemia and lymphoma was shown by the findings in a selected series of 30 cases. T cell receptor (TcR) gene rearrangements were observed in six out of nine cases of CD3+ CD8+ lymphocytoses and provided clear evidence for clonality in this group. The T cell proliferations in two of the remaining cases masked B cell lymphocytic leukaemia and hairy cell leukaemia, while in the third case no cause was found for the polyclonal proliferation. Heterogeneity of phenotype and genotype were observed in peripheral T cell lymphomas: one out of six cases showed TcR gene rearrangement, one case retained its germline configuration, a further case masked B cell lymphoma and the remainder were polyclonal. Genotypic analysis was helpful in the analysis of a tumour of mixed T cell and myeloid phenotype which was shown to be germline for TcR and immunoglobulin genes, consistent with a myeloid origin. Two histiocytic tumours were found to have clonal rearrangement of TcR genes. Nine out of 11 B cell tumours showed immunoglobulin gene rearrangement. It is concluded that genetic analyses are useful in the analysis of T cell, histiocytic, and B cell tumours in which an immunoglobulin phenotype cannot be defined. Images PMID:2143202

  18. Wide Dispersion and Diversity of Clonally Related Inhibitory Interneurons

    PubMed Central

    Harwell, Corey C.; Fuentealba, Luis C.; Gonzalez-Cerrillo, Adrian; Parker, Phillip R.L.; Gertz, Caitlyn C.; Mazzola, Emanuele; Turrero Garcia, Miguel; Alvarez-Buylla, Arturo; Cepko, Constance L.; Kriegstein, Arnold

    2015-01-01

    The mammalian neocortex is composed of two major neuronal cell types with distinct origins: excitatory pyramidal neurons and inhibitory interneurons, generated in dorsal and ventral progenitor zones of the embryonic telencephalon respectively. Thus, inhibitory neurons migrate relatively long distances to reach their destination in the developing forebrain. The role of lineage in the organization and circuitry of interneurons is still not well understood. Utilizing a combination of genetics, retroviral fate mapping and lineage-specific retroviral barcode labeling, we find that clonally related interneurons can be widely dispersed while unrelated interneurons can be closely clustered. These data suggest that migratory mechanisms related to the clustering of interneurons occur largely independent of their clonal origin. PMID:26299474

  19. Improved Clonal Selection Algorithm Combined with Ant Colony Optimization

    NASA Astrophysics Data System (ADS)

    Gao, Shangce; Wang, Wei; Dai, Hongwei; Li, Fangjia; Tang, Zheng

    Both the clonal selection algorithm (CSA) and the ant colony optimization (ACO) are inspired by natural phenomena and are effective tools for solving complex problems. CSA can exploit and explore the solution space parallely and effectively. However, it can not use enough environment feedback information and thus has to do a large redundancy repeat during search. On the other hand, ACO is based on the concept of indirect cooperative foraging process via secreting pheromones. Its positive feedback ability is nice but its convergence speed is slow because of the little initial pheromones. In this paper, we propose a pheromone-linker to combine these two algorithms. The proposed hybrid clonal selection and ant colony optimization (CSA-ACO) reasonably utilizes the superiorities of both algorithms and also overcomes their inherent disadvantages. Simulation results based on the traveling salesman problems have demonstrated the merit of the proposed algorithm over some traditional techniques.

  20. Clonal forestry, heterosis and advanced-generation breeding

    SciTech Connect

    Tuskan, G.A.

    1997-08-01

    This report discusses the clonal planting stock offers many advantages to the forest products industry. Advanced-generation breeding strategies should be designed to maximize within-family variance and at the same time allow the capture of heterosis. Certainly there may be a conflict in the choice of breeding strategy based on the trait of interest. It may be that the majority of the traits express heterosis due to overdominance. Alternatively, disease resistance is expressed as the lack of a specific metabolite or infection court then the homozygous recessive genotype may be the most desirable. Nonetheless, as the forest products industry begins to utilize the economic advantages of clonal forestry, breeding strategies will have to be optimized for these commercial plant materials. Here, molecular markers can be used to characterize the nature of heterosis and therefore define the appropriate breeding strategy.

  1. Mechanisms of clonal evolution in childhood acute lymphoblastic leukemia

    PubMed Central

    Park, Eugene; Papaemmanuil, Elli; Ford, Anthony; Kweon, Soo-Mi; Trageser, Daniel; Hasselfeld, Brian; Henke, Nadine; Mooster, Jana; Geng, Huimin; Schwarz, Klaus; Kogan, Scott C.; Casellas, Rafael; Schatz, David G.; Lieber, Michael R; Greaves, Mel F.; Müschen, Markus

    2015-01-01

    Childhood acute lymphoblastic leukemia can often be retraced to a pre-leukemic clone carrying a prenatal genetic lesion. Postnatally acquired mutations then drive clonal evolution towards overt leukemia. RAG1-RAG2 and AID enzymes, the diversifiers of immunoglobulin genes, are strictly segregated to early and late stages of B-lymphopoiesis, respectively. Here, we identified small pre-BII cells as a natural subset of increased genetic vulnerability owing to concurrent activation of these enzymes. Consistent with epidemiological findings on childhood ALL etiology, susceptibility to genetic lesions during B-lymphopoiesis at the large to small pre-BII transition is exacerbated by abnormal cytokine signaling and repetitive inflammatory stimuli. We demonstrate that AID and RAG1-RAG2 drive leukemic clonal evolution with repeated exposure to inflammatory stimuli, paralleling chronic infections in childhood. PMID:25985233

  2. Distinguishing clonal apple rootstocks by isozymes banding patterns.

    PubMed

    Kaushal, K; Modgil, M; Sharma, D R

    2001-11-01

    Molecular characterisation of clonal apple rootstocks using isozymes was carried out to identify isozyme polymorphism in seven clonal apple rootstocks and to identify the most characteristic and stable enzyme markers for each individual rootstock. Five enzyme systems were studied out of which polyphenol oxidase, malate dehydrogenase, acid phosphatase and peroxidase were useful in discriminating among the rootstocks. The peroxidase enzyme system showed maximum variation and esterase showed the least variation among the rootstocks. Out of seven rootstocks, three were distinguished on the basis of one enzyme system only (M.3 with MDH or PER, M.7 with PPO or PER and MM. 111 with MDH). Out of the sixteen loci studied seven were found to be polymorphic. Genetic variation among the rootstocks was explained on the basis of various parameters. The percentage of polymorphic loci varied from 13.33 to 35.71 per cent. PMID:11906109

  3. Wide Dispersion and Diversity of Clonally Related Inhibitory Interneurons.

    PubMed

    Harwell, Corey C; Fuentealba, Luis C; Gonzalez-Cerrillo, Adrian; Parker, Phillip R L; Gertz, Caitlyn C; Mazzola, Emanuele; Garcia, Miguel Turrero; Alvarez-Buylla, Arturo; Cepko, Constance L; Kriegstein, Arnold R

    2015-09-01

    The mammalian neocortex is composed of two major neuronal cell types with distinct origins: excitatory pyramidal neurons and inhibitory interneurons, generated in dorsal and ventral progenitor zones of the embryonic telencephalon, respectively. Thus, inhibitory neurons migrate relatively long distances to reach their destination in the developing forebrain. The role of lineage in the organization and circuitry of interneurons is still not well understood. Utilizing a combination of genetics, retroviral fate mapping, and lineage-specific retroviral barcode labeling, we find that clonally related interneurons can be widely dispersed while unrelated interneurons can be closely clustered. These data suggest that migratory mechanisms related to the clustering of interneurons occur largely independent of their clonal origin. PMID:26299474

  4. Clonal analysis of limbal epithelial stem cell populations.

    PubMed

    Schlötzer-Schrehardt, Ursula

    2013-01-01

    While convincing data clearly suggest the presence of stem cells in the basal limbal epithelium in vivo, testing the proliferation, self-renewal, and differentiation capacity of stem cells relies on the development of methodologies that allow for their isolation and extensive propagation in vitro. Clonal analysis involving differentiation between short-lived transient cell clones and long-lived stem cell clones is an invaluable technique to identify stem cells in vitro, and allows cells to be expanded over multiple passages. This chapter describes a protocol for the isolation, expansion, and clonal analysis of limbal epithelial stem cells. The cultivation method described may be essential for long-term restoration of the damaged ocular surface in patients with limbal stem cell deficiency. PMID:23690004

  5. Clonal development and organization of the adult Drosophila central brain

    PubMed Central

    Yu, Hung-Hsiang; Awasaki, Takeshi; Schroeder, Mark David; Long, Fuhui; Yang, Jacob S.; He, Yisheng; Ding, Peng; Kao, Jui-Chun; Wu, Gloria Yueh-Yi; Peng, Hanchuan; Myers, Gene; Lee, Tzumin

    2013-01-01

    Summary Background The insect brain can be divided into neuropils that are formed by neurites of both local and remote origin. The complexity of the interconnections obscures how these neuropils are established and interconnected through development. The Drosophila central brain develops from a fixed number of neuroblasts (NBs) that deposit neurons in regional clusters. Results By determining individual NB clones and pursuing their projections into specific neuropils we unravel the regional development of the brain neural network. Exhaustive clonal analysis revealed 95 stereotyped neuronal lineages with characteristic cell body locations and neurite trajectories. Most clones show complex projection patterns, but despite the complexity, neighboring clones often co-innervate the same local neuropil(s) and further target a restricted set of distant neuropils. Conclusions These observations argue for regional clonal development of both neuropils and neuropil connectivity throughout the Drosophila central brain. PMID:23541733

  6. Complex Antigens Drive Permissive Clonal Selection in Germinal Centers.

    PubMed

    Kuraoka, Masayuki; Schmidt, Aaron G; Nojima, Takuya; Feng, Feng; Watanabe, Akiko; Kitamura, Daisuke; Harrison, Stephen C; Kepler, Thomas B; Kelsoe, Garnett

    2016-03-15

    Germinal center (GC) B cells evolve toward increased affinity by a Darwinian process that has been studied primarily in genetically restricted, hapten-specific responses. We explored the population dynamics of genetically diverse GC responses to two complex antigens-Bacillus anthracis protective antigen and influenza hemagglutinin-in which B cells competed both intra- and interclonally for distinct epitopes. Preferred VH rearrangements among antigen-binding, naive B cells were similarly abundant in early GCs but, unlike responses to haptens, clonal diversity increased in GC B cells as early "winners" were replaced by rarer, high-affinity clones. Despite affinity maturation, inter- and intraclonal avidities varied greatly, and half of GC B cells did not bind the immunogen but nonetheless exhibited biased VH use, V(D)J mutation, and clonal expansion comparable to antigen-binding cells. GC reactions to complex antigens permit a range of specificities and affinities, with potential advantages for broad protection. PMID:26948373

  7. Defining the clonal dynamics leading to mouse skin tumour initiation.

    PubMed

    Sánchez-Danés, Adriana; Hannezo, Edouard; Larsimont, Jean-Christophe; Liagre, Mélanie; Youssef, Khalil Kass; Simons, Benjamin D; Blanpain, Cédric

    2016-08-18

    The changes in cell dynamics after oncogenic mutation that lead to the development of tumours are currently unknown. Here, using skin epidermis as a model, we assessed the effect of oncogenic hedgehog signalling in distinct cell populations and their capacity to induce basal cell carcinoma, the most frequent cancer in humans. We found that only stem cells, and not progenitors, initiated tumour formation upon oncogenic hedgehog signalling. This difference was due to the hierarchical organization of tumour growth in oncogene-targeted stem cells, characterized by an increase in symmetric self-renewing divisions and a higher p53-dependent resistance to apoptosis, leading to rapid clonal expansion and progression into invasive tumours. Our work reveals that the capacity of oncogene-targeted cells to induce tumour formation is dependent not only on their long-term survival and expansion, but also on the specific clonal dynamics of the cancer cell of origin. PMID:27459053

  8. Local genetic structure in a clonal dioecious angiosperm.

    PubMed

    Ruggiero, M V; Reusch, T B H; Procaccini, G

    2005-04-01

    We used seven microsatellite loci to characterize genetic structure and clonal architecture at three different spatial scales (from meters to centimetres) of a Cymodocea nodosa population. C. nodosa exhibits both sexual reproduction and vegetative propagation by rhizome elongation. Seeds remain buried in the sediment nearby the mother plant in a dormant stage until germination. Seed dispersal potential is therefore expected to be extremely restricted. High clonal diversity (up to 67% of distinct genotypes) and a highly intermingled configuration of genets at different spatial scales were found. No significant differences in genetic structure were found among the three spatial scales, indicating that genetic diversity is evenly distributed along the meadow. Autocorrelation analyses of kinship estimates confirmed the absence of spatial clumping of genets at small spatial scale and the expectations of a very restricted seed dispersal (observed dispersal range 1-21 m) in this species. PMID:15773928

  9. Emergence and spread of O16-ST131 and O25b-ST131 clones among faecal CTX-M-producing Escherichia coli in healthy individuals in Hunan Province, China

    PubMed Central

    Zhong, Yi-Ming; Liu, Wen-En; Liang, Xiang-Hui; Li, Yan-Ming; Jian, Zi-Juan; Hawkey, Peter M.

    2015-01-01

    Objectives The objectives of this study were to determine CTX-M-producing Escherichia coli ST131 strain prevalence in stool specimens from healthy subjects in central China and to molecularly characterize clonal groups. Methods From November 2013 to January 2014, stool specimens from healthy individuals in Hunan Province were screened for ESBL-producing E. coli using chromogenic medium and CTX-M genotypes and phylogenetic groups were determined. ST131 clonal groups were detected by PCR and characterized for antibiotic resistance, fimH, gyrA and parC alleles, plasmid-mediated quinolone resistance determinants, virulence genotypes and PFGE patterns. Results Among 563 subjects, 287 (51.0%) exhibited the presence of faecal ESBL-producing E. coli, all of which produced CTX-M enzymes. The most common CTX-M genotypes were CTX-M-14 (48.4%), CTX-M-15 (27.5%) and CTX-M-27 (15.0%). Of the 287 CTX-M-producing isolates, 32 (11.1%) belonged to the ST131 clone. O16-ST131 isolates were dominant (75%) and contained the fimH41 allele. The remaining eight (25%) ST131 isolates were of the O25b subgroup and contained fimH30 or fimH41. Ciprofloxacin resistance was found in 100% of the O25b-ST131 isolates, whereas only 8% of the O16-ST131 isolates were resistant. All of the O25b-ST131 isolates except one showed gyrA1AB and parC1aAB mutations; most of the O16-ST131 isolates had gyrA1A and parC1b mutations. The virulence genotypes of O16-ST131 resembled those of the O25b-ST131 isolates. The 32 ST131 isolates formed one large group at the 64% similarity level. They comprised 15 PFGE groups (defined at ≥85% similarity). Conclusions O16-ST131 isolates have emerged as the predominant type of ST131 isolate in faecal CTX-M-producing E. coli in healthy individuals in China. PMID:25957581

  10. Molecular Markers Reveal Exclusively Clonal Reproduction in Trichophyton rubrum

    PubMed Central

    Gräser, Y.; Kühnisch, J.; Presber, W.

    1999-01-01

    Genotypic variability among 96 Trichophyton rubrum strains which displayed different colony morphologies and were collected from four continents was investigated. Twelve markers representing 57 loci were analyzed by PCR fingerprinting, amplified fragment length polymorphism, and random amplified monomorphic DNA markers. Interestingly, none of the methods used revealed any DNA polymorphism, indicating a strictly clonal mode of reproduction and a strong adaptation to human skin. PMID:10523582

  11. Comparative analysis of ESBL-positive Escherichia coli isolates from animals and humans from the UK, The Netherlands and Germany.

    PubMed

    Wu, Guanghui; Day, Michaela J; Mafura, Muriel T; Nunez-Garcia, Javier; Fenner, Jackie J; Sharma, Meenaxi; van Essen-Zandbergen, Alieda; Rodríguez, Irene; Dierikx, Cindy; Kadlec, Kristina; Schink, Anne-Kathrin; Chattaway, Marie; Wain, John; Helmuth, Reiner; Guerra, Beatriz; Schwarz, Stefan; Threlfall, John; Woodward, Martin J; Woodford, Neil; Coldham, Nick; Mevius, Dik

    2013-01-01

    The putative virulence and antimicrobial resistance gene contents of extended spectrum β-lactamase (ESBL)-positive E. coli (n=629) isolated between 2005 and 2009 from humans, animals and animal food products in Germany, The Netherlands and the UK were compared using a microarray approach to test the suitability of this approach with regard to determining their similarities. A selection of isolates (n=313) were also analysed by multilocus sequence typing (MLST). Isolates harbouring bla(CTX-M-group-1) dominated (66%, n=418) and originated from both animals and cases of human infections in all three countries; 23% (n=144) of all isolates contained both bla(CTX-M-group-1) and bla(OXA-1-like) genes, predominantly from humans (n=127) and UK cattle (n=15). The antimicrobial resistance and virulence gene profiles of this collection of isolates were highly diverse. A substantial number of human isolates (32%, n=87) did not share more than 40% similarity (based on the Jaccard coefficient) with animal isolates. A further 43% of human isolates from the three countries (n=117) were at least 40% similar to each other and to five isolates from UK cattle and one each from Dutch chicken meat and a German dog; the members of this group usually harboured genes such as mph(A), mrx, aac(6')-Ib, catB3, bla(OXA-1-like) and bla(CTX-M-group-1). forty-four per cent of the MLST-typed isolates in this group belonged to ST131 (n=18) and 22% to ST405 (n=9), all from humans. Among animal isolates subjected to MLST (n=258), only 1.2% (n=3) were more than 70% similar to human isolates in gene profiles and shared the same MLST clonal complex with the corresponding human isolates. The results suggest that minimising human-to-human transmission is essential to control the spread of ESBL-positive E. coli in humans. PMID:24086522

  12. Ubiquitylation of CD98 limits cell proliferation and clonal expansion.

    PubMed

    Ablack, Jailal N G; Metz, Patrick J; Chang, John T; Cantor, Joseph M; Ginsberg, Mark H

    2015-12-01

    CD98 heavy chain (SLC3A2) facilitates lymphocyte clonal expansion that enables adaptive immunity; however, increased expression of CD98 is also a feature of both lymphomas and leukemias and represents a potential therapeutic target in these diseases. CD98 is transcriptionally regulated and ectopic expression of the membrane-associated RING-CH (MARCH) E3 ubiquitin ligases MARCH1 or MARCH8 leads to ubiquitylation and lysosomal degradation of CD98. Here, we examined the potential role of ubiquitylation in regulating CD98 expression and cell proliferation. We report that blocking ubiquitylation by use of a catalytically inactive MARCH or by creating a ubiquitylation-resistant CD98 mutant, prevents MARCH-induced CD98 downregulation in HeLa cells. March1-null T cells display increased CD98 expression. Similarly, T cells expressing ubiquitylation-resistant CD98 manifest increased proliferation in vitro and clonal expansion in vivo. Thus, ubiquitylation and the resulting downregulation of CD98 can limit cell proliferation and clonal expansion. PMID:26493331

  13. Gene expression variability in clonal populations: Causes and consequences.

    PubMed

    Roberfroid, Stefanie; Vanderleyden, Jos; Steenackers, Hans

    2016-11-01

    During the last decade it has been shown that among cell variation in gene expression plays an important role within clonal populations. Here, we provide an overview of the different mechanisms contributing to gene expression variability in clonal populations. These are ranging from inherent variations in the biochemical process of gene expression itself, such as intrinsic noise, extrinsic noise and bistability to individual responses to variations in the local micro-environment, a phenomenon called phenotypic plasticity. Also genotypic variations caused by clonal evolution and phase variation can contribute to gene expression variability. Consequently, gene expression studies need to take these fluctuations in expression into account. However, frequently used techniques for expression quantification, such as microarrays, RNA sequencing, quantitative PCR and gene reporter fusions classically determine the population average of gene expression. Here, we discuss how these techniques can be adapted towards single cell analysis by integration with single cell isolation, RNA amplification and microscopy. Alternatively more qualitative selection-based techniques, such as mutant screenings, in vivo expression technology (IVET) and recombination-based IVET (RIVET) can be applied for detection of genes expressed only within a subpopulation. Finally, differential fluorescence induction (DFI), a protocol specially designed for single cell expression is discussed. PMID:26731119

  14. A Computational Clonal Analysis of the Developing Mouse Limb Bud

    PubMed Central

    Marcon, Luciano; Arqués, Carlos G.; Torres, Miguel S.; Sharpe, James

    2011-01-01

    A comprehensive spatio-temporal description of the tissue movements underlying organogenesis would be an extremely useful resource to developmental biology. Clonal analysis and fate mappings are popular experiments to study tissue movement during morphogenesis. Such experiments allow cell populations to be labeled at an early stage of development and to follow their spatial evolution over time. However, disentangling the cumulative effects of the multiple events responsible for the expansion of the labeled cell population is not always straightforward. To overcome this problem, we develop a novel computational method that combines accurate quantification of 2D limb bud morphologies and growth modeling to analyze mouse clonal data of early limb development. Firstly, we explore various tissue movements that match experimental limb bud shape changes. Secondly, by comparing computational clones with newly generated mouse clonal data we are able to choose and characterize the tissue movement map that better matches experimental data. Our computational analysis produces for the first time a two dimensional model of limb growth based on experimental data that can be used to better characterize limb tissue movement in space and time. The model shows that the distribution and shapes of clones can be described as a combination of anisotropic growth with isotropic cell mixing, without the need for lineage compartmentalization along the AP and PD axis. Lastly, we show that this comprehensive description can be used to reassess spatio-temporal gene regulations taking tissue movement into account and to investigate PD patterning hypothesis. PMID:21347315

  15. Stem Cell Hierarchy and Clonal Evolution in Acute Lymphoblastic Leukemia

    PubMed Central

    Lang, Fabian; Wojcik, Bartosch; Rieger, Michael A.

    2015-01-01

    Cancer is characterized by a remarkable intertumoral, intratumoral, and cellular heterogeneity that might be explained by the cancer stem cell (CSC) and/or the clonal evolution models. CSCs have the ability to generate all different cells of a tumor and to reinitiate the disease after remission. In the clonal evolution model, a consecutive accumulation of mutations starting in a single cell results in competitive growth of subclones with divergent fitness in either a linear or a branching succession. Acute lymphoblastic leukemia (ALL) is a highly malignant cancer of the lymphoid system in the bone marrow with a dismal prognosis after relapse. However, stabile phenotypes and functional data of CSCs in ALL, the so-called leukemia-initiating cells (LICs), are highly controversial and the question remains whether there is evidence for their existence. This review discusses the concepts of CSCs and clonal evolution in respect to LICs mainly in B-ALL and sheds light onto the technical controversies in LIC isolation and evaluation. These aspects are important for the development of strategies to eradicate cells with LIC capacity. Common properties of LICs within different subclones need to be defined for future ALL diagnostics, treatment, and disease monitoring to improve the patients' outcome in ALL. PMID:26236346

  16. Multiplexing clonality: combining RGB marking and genetic barcoding.

    PubMed

    Cornils, Kerstin; Thielecke, Lars; Hüser, Svenja; Forgber, Michael; Thomaschewski, Michael; Kleist, Nadja; Hussein, Kais; Riecken, Kristoffer; Volz, Tassilo; Gerdes, Sebastian; Glauche, Ingmar; Dahl, Andreas; Dandri, Maura; Roeder, Ingo; Fehse, Boris

    2014-04-01

    RGB marking and DNA barcoding are two cutting-edge technologies in the field of clonal cell marking. To combine the virtues of both approaches, we equipped LeGO vectors encoding red, green or blue fluorescent proteins with complex DNA barcodes carrying color-specific signatures. For these vectors, we generated highly complex plasmid libraries that were used for the production of barcoded lentiviral vector particles. In proof-of-principle experiments, we used barcoded vectors for RGB marking of cell lines and primary murine hepatocytes. We applied single-cell polymerase chain reaction to decipher barcode signatures of individual RGB-marked cells expressing defined color hues. This enabled us to prove clonal identity of cells with one and the same RGB color. Also, we made use of barcoded vectors to investigate clonal development of leukemia induced by ectopic oncogene expression in murine hematopoietic cells. In conclusion, by combining RGB marking and DNA barcoding, we have established a novel technique for the unambiguous genetic marking of individual cells in the context of normal regeneration as well as malignant outgrowth. Moreover, the introduction of color-specific signatures in barcodes will facilitate studies on the impact of different variables (e.g. vector type, transgenes, culture conditions) in the context of competitive repopulation studies. PMID:24476916

  17. Multiplexing clonality: combining RGB marking and genetic barcoding

    PubMed Central

    Cornils, Kerstin; Thielecke, Lars; Hüser, Svenja; Forgber, Michael; Thomaschewski, Michael; Kleist, Nadja; Hussein, Kais; Riecken, Kristoffer; Volz, Tassilo; Gerdes, Sebastian; Glauche, Ingmar; Dahl, Andreas; Dandri, Maura; Roeder, Ingo; Fehse, Boris

    2014-01-01

    RGB marking and DNA barcoding are two cutting-edge technologies in the field of clonal cell marking. To combine the virtues of both approaches, we equipped LeGO vectors encoding red, green or blue fluorescent proteins with complex DNA barcodes carrying color-specific signatures. For these vectors, we generated highly complex plasmid libraries that were used for the production of barcoded lentiviral vector particles. In proof-of-principle experiments, we used barcoded vectors for RGB marking of cell lines and primary murine hepatocytes. We applied single-cell polymerase chain reaction to decipher barcode signatures of individual RGB-marked cells expressing defined color hues. This enabled us to prove clonal identity of cells with one and the same RGB color. Also, we made use of barcoded vectors to investigate clonal development of leukemia induced by ectopic oncogene expression in murine hematopoietic cells. In conclusion, by combining RGB marking and DNA barcoding, we have established a novel technique for the unambiguous genetic marking of individual cells in the context of normal regeneration as well as malignant outgrowth. Moreover, the introduction of color-specific signatures in barcodes will facilitate studies on the impact of different variables (e.g. vector type, transgenes, culture conditions) in the context of competitive repopulation studies. PMID:24476916

  18. Antimicrobial resistance and genetic diversity of Escherichia coli isolated from humans and foods

    PubMed Central

    Melo, Daniela Benevides; Menezes, Ana Paula de Oliveira; Reis, Joice Neves; Guimarães, Alaíse Gil

    2015-01-01

    Antibiotic resistance has increased in recent years, raising the concern of public health authorities. We conducted a study of Escherichia coli isolates obtained from human and food samples to assess the prevalence of antimicrobial resistance and to determine the genotype and clonal relationship of 84 E. coli isolates (48 from humans and 36 from foods). An antimicrobial susceptibility test was performed using the disk diffusion method. Virulence factors were evaluated by multiplex PCR, and the clonal relationship among the resistant isolates was studied by Pulsed Field Gel Electrophoresis (PFGE). All isolates were susceptible to ceftriaxone. Overall, 26%, 20.2%, 15.4% and 6% of the isolates were resistant to tetracycline, ampicillin, sulfamethoxazole/trimethoprim and cephalotin, respectively. Twenty two percent of the isolates exhibited resistance to more than one antimicrobial agent. Multiple-drug resistance was mostly observed in the human isolates and involved the antibiotics ampicillin and tetracycline. None of the six virulence genes were identified among the isolates. Analysis of genetic diversity by PFGE of 31 resistant isolates, revealed 29 distinct restriction patterns. In conclusion, E. coli from humans and foods are resistant to commonly used antibiotics and are highly genetically diverse. In this setting, inappropriate use of antibiotics may be a cause of high resistance rate instead of clonal spread. PMID:26691477

  19. Characterization of Fosfomycin Resistant Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates from Human and Pig in Taiwan

    PubMed Central

    Tseng, Sung-Pin; Wang, Sheng-Fan; Kuo, Cheng-Yu; Huang, Jun-Wei; Hung, Wei-Chun; Ke, Guan-Ming; Lu, Po-Liang

    2015-01-01

    To investigate the efficacy of fosfomycin against extended-spectrum β-lactamases (ESBL) producing Escherichia coli in Taiwan and the resistance mechanisms and characterization of human and pig isolates, we analyzed 145 ESBL-producing isolates collected from two hospitals (n = 123) and five farms (n = 22) in Taiwan from February to May, 2013. Antimicrobial susceptibilities were determined. Clonal relatedness was determined by PFGE and multi-locus sequence typing. ESBLs, ampC, and fosfomycin resistant genes were detected by PCR, and their flanking regions were determined by PCR mapping and sequencing. The fosfomycin resistant mechanisms, including modification of the antibiotic target (MurA), functionless transporters (GlpT and UhpT) and their regulating genes such as uhpA, cyaA, and ptsI, and antibiotic inactivation by enzymes (FosA and FosC), were examined. The size and replicon type of plasmids carrying fosfomycin resistant genes were analyzed. Our results revealed the susceptibility rates of fosfomycin were 94% for human ESBL-producing E. coli isolates and 77% for pig isolates. The PFGE analysis revealed 79 pulsotypes. No pulsotype was found existing in both human and pig isolates. Three pulsotypes were distributed among isolates from two hospitals. ISEcp1 carrying blaCTX-M-group 9 was the predominant transposable elements of the ESBL genes. Among the thirteen fosfomycin resistant isolates, functionless transporters were identified in 9 isolates. Three isolates contained novel amino acid substitutions (Asn67Ile, Phe151Ser and Trp164Ser, Val146Ala and His159Tyr, respectively) in MurA (the target of fosfomycin). Four isolates had fosfomycin modified enzyme (fosA3) in their plasmids. The fosA3 gene was harboured in an IncN-type plasmid (101 kbp) in the three pig isolates and an IncB/O-type plasmid (113 kbp) in the human isolate. In conclusion, we identified that 6% and 23% of the ESBL-producing E. coli from human and pigs were resistant to fosfomycin, respectively

  20. Escherichia coli β-Lactamases: What Really Matters

    PubMed Central

    Bajaj, Priyanka; Singh, Nambram S.; Virdi, Jugsharan S.

    2016-01-01

    Escherichia coli strains belonging to diverse pathotypes have increasingly been recognized as a major public health concern. The β-lactam antibiotics have been used successfully to treat infections caused by pathogenic E. coli. However, currently, the utility of β-lactams is being challenged severely by a large number of hydrolytic enzymes – the β-lactamases expressed by bacteria. The menace is further compounded by the highly flexible genome of E. coli, and propensity of resistance dissemination through horizontal gene transfer and clonal spread. Successful management of infections caused by such resistant strains requires an understanding of the diversity of β-lactamases, their unambiguous detection, and molecular mechanisms underlying their expression and spread with regard to the most relevant information about individual bacterial species. Thus, this review comprises first such effort in this direction for E. coli, a bacterial species known to be associated with production of diverse classes of β-lactamases. The review also highlights the role of commensal E. coli as a potential but under-estimated reservoir of β-lactamases-encoding genes. PMID:27065978

  1. E. Coli Infections

    MedlinePlus

    ... adults with weak immune systems. You can get E. coli infections by eating foods containing the bacteria. Symptoms of ... pool contaminated with human waste. Most cases of E. coli infection get better without treatment in 5 to 10 ...

  2. Genetic and clonal diversity of the endemic ant-plant Humboldtia brunonis (Fabaceae) in the Western Ghats of India.

    PubMed

    Dev, Suma A; Shenoy, Megha; Borges, Renee M

    2010-06-01

    Humboldtia brunonis (Fabaceae, Caesalpinioideae) is a dominant self-incompatible ant-plant or myrmecophyte, growing as an understorey tree in high-density patches. It is endemic to the biodiversity hotspot of the southern Western Ghats of India and, besides ants, harbours many endemic invertebrate taxa, such as bees that pollinate it as well as arboreal earthworms, within swollen hollow stem internodes called domatia. Using inter simple sequence repeat (ISSR) markers, three geographically separated populations were found to be multiclonal, characterized by high levels of clonal diversity. Values for the Simpson diversity index ranged between 0.764 and 0.964, and for Fager's evenness index between 0.00 and 0.036 for neighbourhoods within populations. This myrmecophyte was found to combine sexual recruitment (66.7%) and clonal production (33.3%) as methods of reproduction. Moderate amounts of genetic diversity at the species level were observed, with 52.63% polymorphism, and moderate values of Shannon's diversity index (0.1895) as well as of Nei's gene diversity (0.1186). In each population, observed genotypic diversity was significantly lower than expected, indicating significant genetic structure. Neighbour-joining trees demonstrated that Agumbe, which is the most northern population examined and geographically twice as far away from the other two populations, grouped separately and with larger bootstrap support from a larger cluster consisting of the Sampaji and Solaikolli populations, which are closer to each other geographically. Some neighbourhoods within each population showed spatial genetic structure even at small spatial scales of less than 5 m. A combination of clonality and short-distance pollen movement by small pollinating bees (Braunsapis puangensis) coupled with primary ballistic seed dispersal, and possible secondary seed dispersal by rodents, may contribute to spatial genetic structure at such small scales. The clonality of H. brunonis may be a

  3. Presence of Shiga toxin-producing Escherichia coli O-groups in small and very-small beef-processing plants and resulting ground beef detected by a multiplex polymerase chain reaction assay.

    PubMed

    Svoboda, Amanda L; Dudley, Edward G; Debroy, Chitrita; Mills, Edward W; Cutter, Catherine N

    2013-09-01

    Shiga toxin-producing Escherichia coli (STEC) are associated with foodborne illnesses, including hemolytic uremic syndrome in humans. Cattle and consequently, beef products are considered a major source of STEC. E. coli O157:H7 has been regulated as an adulterant in ground beef since 1996. The United States Department of Agriculture Food Safety and Inspection Service began regulating six additional STEC (O145, O121, O111, O103, O45, and O26) as adulterants in beef trim and raw ground beef in June 2012. Little is known about the presence of STEC in small and very-small beef-processing plants. Therefore, we propose to determine whether small and very-small beef-processing plants are a potential source of non-O157:H7 STEC. Environmental swabs, carcass swabs, hide swabs, and ground beef from eight small and very-small beef-processing plants were obtained from October 2010 to December 2011. A multiplex polymerase chain reaction assay was used to determine the presence of STEC O-groups: O157, O145, O121, O113, O111, O103, O45, and O26 in the samples. Results demonstrated that 56.6% (154/272) of the environmental samples, 35.0% (71/203) of the carcass samples, 85.2% (23/27) of the hide samples, and 17.0% (20/118) of the ground beef samples tested positive for one or more of the serogroups. However, only 7.4% (20/272) of the environmental samples, 4.4% (9/203) of the carcass samples, and 0% (0/118) ground beef samples tested positive for both the serogroup and Shiga toxin genes. Based on this survey, small and very-small beef processors may be a source of non-O157:H7 STEC. The information from this study may be of interest to regulatory officials, researchers, public health personnel, and the beef industry that are interested in the presence of these pathogens in the beef supply. PMID:23742295

  4. Emergence of co-production of plasmid-mediated AmpC beta-lactamase and ESBL in cefoxitin-resistant uropathogenic Escherichia coli.

    PubMed

    Ghosh, B; Mukherjee, M

    2016-09-01

    Plasmid-mediated AmpC (pAmpC) and ESBL co-production was detected in Escherichia coli a major etiologic agent of urinary tract infection. Isolates resistant to cefoxitin by CLSI methodology were tested for pAmpC beta-lactamase using phenylboronic acid and ESBLs by combined disk diffusion method. pAmpC/ESBL genes were characterized by PCR and sequencing. Transconjugation experiments were done to study the transfer of pAmpC and ESBL production from clinical isolates as donor to E. coli J53 AziR as recipient. Incompatibility groups of transmissible plasmids were classified by PCR-based replicon typing (PBRT). Among 148 urine culture positive isolates, E. coli was reported in 39.86 % (59/148), with 93.22 % (55/59) of cefoxitin resistance. pAmpC production was detected in 25, with varied distribution of blaCMY-2 and blaDHA-1type genes alone (n = 13 and 7 respectively) or in combination (n = 5). ESBL co-production was observed in 88 % (22/25) of pAmpC producing isolates with predominance of blaTEM (n = 20). Twenty-three transconjugants showed transmission of pAmpC-and ESBL-resistant genes with co-carriage of blaCMY-2 and blaTEM (n = 15) in plasmids of IncF type (n = 9) being predominant, followed by IncI1 (n = 4) and IncH1 (n = 2) in combination. All clinical isolates were clonally diverse. Resistance against different beta-lactams in uropathogenic E. coli has been an emerging concern in resource- poor countries such as India. Knowledge on the occurrence of AmpC beta-lactamases and ESBL amongst this pathogen and its transmission dynamics may aid in hospital infection control. PMID:27250633

  5. Clonal Integration of Fragaria orientalis in Reciprocal and Coincident Patchiness Resources: Cost-Benefit Analysis

    PubMed Central

    Zhang, Yunchun; Zhang, Qiaoying

    2013-01-01

    Clonal growth allows plants to spread horizontally and to experience different levels of resources. If ramets remain physiologically integrated, clonal plants can reciprocally translocate resources between ramets in heterogeneous environments. But little is known about the interaction between benefits of clonal integration and patterns of resource heterogeneity in different patches, i.e., coincident patchiness or reciprocal patchiness. We hypothesized that clonal integration will show different effects on ramets in different patches and more benefit to ramets under reciprocal patchiness than to those under coincident patchiness, as well as that the benefit from clonal integration is affected by the position of proximal and distal ramets under reciprocal or coincident patchiness. A pot experiment was conducted with clonal fragments consisting of two interconnected ramets (proximal and distal ramet) of Fragaria orientalis. In the experiment, proximal and distal ramets were grown in high or low availability of resources, i.e., light and water. Resource limitation was applied either simultaneously to both ramets of a clonal fragment (coincident resource limitation) or separately to different ramets of the same clonal fragment (reciprocal resource limitation). Half of the clonal fragments were connected while the other half were severed. From the experiment, clonal fragments growing under coincident resource limitation accumulated more biomass than those under reciprocal resource limitation. Based on a cost-benefit analysis, the support from proximal ramets to distal ramets was stronger than that from distal ramets to proximal ramets. Through division of labour, clonal fragments of F. orientalis benefited more in reciprocal patchiness than in coincident patchiness. While considering biomass accumulation and ramets production, coincident patchiness were more favourable to clonal plant F. orientalis. PMID:24265832

  6. Invasive clonal plant species have a greater root-foraging plasticity than non-invasive ones.

    PubMed

    Keser, Lidewij H; Dawson, Wayne; Song, Yao-Bin; Yu, Fei-Hai; Fischer, Markus; Dong, Ming; van Kleunen, Mark

    2014-03-01

    Clonality is frequently positively correlated with plant invasiveness, but which aspects of clonality make some clonal species more invasive than others is not known. Due to their spreading growth form, clonal plants are likely to experience spatial heterogeneity in nutrient availability. Plasticity in allocation of biomass to clonal growth organs and roots may allow these plants to forage for high-nutrient patches. We investigated whether this foraging response is stronger in species that have become invasive than in species that have not. We used six confamilial pairs of native European clonal plant species differing in invasion success in the USA. We grew all species in large pots under homogeneous or heterogeneous nutrient conditions in a greenhouse, and compared their nutrient-foraging response and performance. Neither invasive nor non-invasive species showed significant foraging responses to heterogeneity in clonal growth organ biomass or in aboveground biomass of clonal offspring. Invasive species had, however, a greater positive foraging response in terms of root and belowground biomass than non-invasive species. Invasive species also produced more total biomass. Our results suggest that the ability for strong root foraging is among the characteristics promoting invasiveness in clonal plants. PMID:24352844

  7. Enterohemorrhagic Escherichia coli Hybrid Pathotype O80:H2 as a New Therapeutic Challenge.

    PubMed

    Soysal, Nurcan; Mariani-Kurkdjian, Patricia; Smail, Yasmine; Liguori, Sandrine; Gouali, Malika; Loukiadis, Estelle; Fach, Patrick; Bruyand, Mathias; Blanco, Jorge; Bidet, Philippe; Bonacorsi, Stéphane

    2016-09-01

    We describe the epidemiology, clinical features, and molecular characterization of enterohemorrhagic Escherichia coli (EHEC) infections caused by the singular hybrid pathotype O80:H2, and we examine the influence of antibiotics on Shiga toxin production. In France, during 2005-2014, a total of 54 patients were infected with EHEC O80:H2; 91% had hemolytic uremic syndrome. Two patients had invasive infections, and 2 died. All strains carried stx2 (variants stx2a, 2c, or 2d); the rare intimin gene (eae-ξ); and at least 4 genes characteristic of pS88, a plasmid associated with extraintestinal virulence. Similar strains were found in Spain. All isolates belonged to the same clonal group. At subinhibitory concentrations, azithromycin decreased Shiga toxin production significantly, ciprofloxacin increased it substantially, and ceftriaxone had no major effect. Antibiotic combinations that included azithromycin also were tested. EHEC O80:H2, which can induce hemolytic uremic syndrome complicated by bacteremia, is emerging in France. However, azithromycin might effectively combat these infections. PMID:27533474

  8. Enterohemorrhagic Escherichia coli Hybrid Pathotype O80:H2 as a New Therapeutic Challenge

    PubMed Central

    Soysal, Nurcan; Mariani-Kurkdjian, Patricia; Smail, Yasmine; Liguori, Sandrine; Gouali, Malika; Loukiadis, Estelle; Fach, Patrick; Bruyand, Mathias; Blanco, Jorge; Bidet, Philippe

    2016-01-01

    We describe the epidemiology, clinical features, and molecular characterization of enterohemorrhagic Escherichia coli (EHEC) infections caused by the singular hybrid pathotype O80:H2, and we examine the influence of antibiotics on Shiga toxin production. In France, during 2005–2014, a total of 54 patients were infected with EHEC O80:H2; 91% had hemolytic uremic syndrome. Two patients had invasive infections, and 2 died. All strains carried stx2 (variants stx2a, 2c, or 2d); the rare intimin gene (eae-ξ); and at least 4 genes characteristic of pS88, a plasmid associated with extraintestinal virulence. Similar strains were found in Spain. All isolates belonged to the same clonal group. At subinhibitory concentrations, azithromycin decreased Shiga toxin production significantly, ciprofloxacin increased it substantially, and ceftriaxone had no major effect. Antibiotic combinations that included azithromycin also were tested. EHEC O80:H2, which can induce hemolytic uremic syndrome complicated by bacteremia, is emerging in France. However, azithromycin might effectively combat these infections. PMID:27533474

  9. Clonal reproduction and population genetic structure of grape phylloxera, Daktulosphaira vitifoliae, in Australia.

    PubMed

    Corrie, A M; Crozier, R H; Van Heeswijck, R; Hoffmann, A A

    2002-03-01

    The grape phylloxera, Daktulosphaira vitifoliae, is a viticultural pest that in the past has devastated vineyards worldwide, yet little is known about this insect's biology. The genetic structure of Australian populations of grape phylloxera and its mode of reproduction were studied following the development of four polymorphic microsatellite loci. Insects were collected from 28 vineyards, with a total of 361 insects included in the study. The majority of vineyards were infested by functionally parthenogenetic lineages of grape phylloxera that inhabit the root system and there was little support for the traditionally described holocyclic life cycle for this species. Clonal diversity was limited in all of the vineyard regions, with the exception of the Rutherglen region. A multiple founder scenario or occasional sex may contribute to diversity within the Rutherglen region. Leaf galling populations comprised classes distinct from the common genotypic classes identified on the roots, suggesting limited exchange between these groups. Implications for the management of D. vitifoliae are discussed. PMID:11920122

  10. Molecular evolution of the Escherichia coli chromosome. IV. Sequence comparisons.

    PubMed

    Milkman, R; Bridges, M M

    1993-03-01

    DNA sequences have been compared in a 4,400-bp region for Escherichia coli K12 and 36 ECOR strains. Discontinuities in degree of similarity, previously inferred, are confirmed in detail. Three clonal frames are described on the basis of the present local high-resolution data, as well as previous analyses of restriction fragment length polymorphism (RFLP) and of multilocus enzyme electrophoresis (MLEE) covering small regions more widely dispersed on the chromosome. These three approaches show important consistency. The data illustrate the fact that, in the limited context of intraspecific genomic sequence variation, clonality and homology are synonymous. Two estimable quantitative properties are defined: recency of common ancestry (the reciprocal of the log10 of the number of generations since the most recent common ancestor), and the number of nucleotide pairs over which a given recency of common ancestry applies. In principle, these parameters are measures of the degree and physical extent of homology. The small size of apparent recombinational replacements, together with the observation that they occasionally occur in discontinuous series, raises the question of whether they result from the superimposition of replacements of much larger size (as expected from an elementary interpretation of conjugation and transduction in experimental E. coli systems) or via an alternative mechanism. Length polymorphisms of several sorts are described. PMID:8095913

  11. Emergence of Clonal Complex 17 Enterococcus faecium in The Netherlands▿

    PubMed Central

    Top, Janetta; Willems, Rob; van der Velden, Saskia; Asbroek, Miranda; Bonten, Marc

    2008-01-01

    The global emergence of vancomycin-resistant Enterococcus faecium has been characterized as the clonal spread of clonal complex 17 (CC17) E. faecium. CC17 was defined upon multilocus sequence typing and is characterized by resistance to quinolones and ampicillin and the presence of the enterococcal surface protein (Esp) in the majority of isolates. The recently noticed increased incidence of vancomycin-susceptible CC17 E. faecium infections in our hospital initiated a nationwide study to determine ecological changes among enterococcal infections. The data and strain collections were obtained from 26 (38%) and 9 (14%) of 66 microbiology laboratories in The Netherlands. E. faecium and E. faecalis were distinguished by multiplex PCR; all E. faecium isolates were genotyped by multiple-locus variable-number tandem-repeat analysis (MLVA), and the presence of esp was identified by PCR. Average numbers of ampicillin-resistant enterococcal isolates from normally sterile body sites per hospital increased from 5 ± 1 in 1994 to 25 ± 21 in 2005. Among all enterococcal bloodstream infections, the proportions of ampicillin-resistant E. faecium (AREF) increased from 4% in 1994 to 20% in 2005 (P < 0.001). All E. faecalis isolates were susceptible to ampicillin, whereas 78% of the E. faecium isolates were resistant (49% of these contained esp). Genotyping revealed that 86% of AREF isolates belonged to CC17, including four dominant MLVA types found in ≥3 hospitals, accounting for 64% of the AREF isolates. Infections caused by CC17 E. faecium has increased nationwide, especially in university hospitals due to the clonal spread of four MLVA types, and seems associated with acquisition of the esp gene. PMID:17977983

  12. Clonal architectures and driver mutations in metastatic melanomas.

    PubMed

    Ding, Li; Kim, Minjung; Kanchi, Krishna L; Dees, Nathan D; Lu, Charles; Griffith, Malachi; Fenstermacher, David; Sung, Hyeran; Miller, Christopher A; Goetz, Brian; Wendl, Michael C; Griffith, Obi; Cornelius, Lynn A; Linette, Gerald P; McMichael, Joshua F; Sondak, Vernon K; Fields, Ryan C; Ley, Timothy J; Mulé, James J; Wilson, Richard K; Weber, Jeffrey S

    2014-01-01

    To reveal the clonal architecture of melanoma and associated driver mutations, whole genome sequencing (WGS) and targeted extension sequencing were used to characterize 124 melanoma cases. Significantly mutated gene analysis using 13 WGS cases and 15 additional paired extension cases identified known melanoma genes such as BRAF, NRAS, and CDKN2A, as well as a novel gene EPHA3, previously implicated in other cancer types. Extension studies using tumors from another 96 patients discovered a large number of truncation mutations in tumor suppressors (TP53 and RB1), protein phosphatases (e.g., PTEN, PTPRB, PTPRD, and PTPRT), as well as chromatin remodeling genes (e.g., ASXL3, MLL2, and ARID2). Deep sequencing of mutations revealed subclones in the majority of metastatic tumors from 13 WGS cases. Validated mutations from 12 out of 13 WGS patients exhibited a predominant UV signature characterized by a high frequency of C->T transitions occurring at the 3' base of dipyrimidine sequences while one patient (MEL9) with a hypermutator phenotype lacked this signature. Strikingly, a subclonal mutation signature analysis revealed that the founding clone in MEL9 exhibited UV signature but the secondary clone did not, suggesting different mutational mechanisms for two clonal populations from the same tumor. Further analysis of four metastases from different geographic locations in 2 melanoma cases revealed phylogenetic relationships and highlighted the genetic alterations responsible for differential drug resistance among metastatic tumors. Our study suggests that clonal evaluation is crucial for understanding tumor etiology and drug resistance in melanoma. PMID:25393105

  13. Clonal Architectures and Driver Mutations in Metastatic Melanomas

    PubMed Central

    Dees, Nathan D.; Lu, Charles; Griffith, Malachi; Fenstermacher, David; Sung, Hyeran; Miller, Christopher A.; Goetz, Brian; Wendl, Michael C.; Griffith, Obi; Cornelius, Lynn A.; Linette, Gerald P.; McMichael, Joshua F.; Sondak, Vernon K.; Fields, Ryan C.; Ley, Timothy J.; Mulé, James J.; Wilson, Richard K.; Weber, Jeffrey S.

    2014-01-01

    To reveal the clonal architecture of melanoma and associated driver mutations, whole genome sequencing (WGS) and targeted extension sequencing were used to characterize 124 melanoma cases. Significantly mutated gene analysis using 13 WGS cases and 15 additional paired extension cases identified known melanoma genes such as BRAF, NRAS, and CDKN2A, as well as a novel gene EPHA3, previously implicated in other cancer types. Extension studies using tumors from another 96 patients discovered a large number of truncation mutations in tumor suppressors (TP53 and RB1), protein phosphatases (e.g., PTEN, PTPRB, PTPRD, and PTPRT), as well as chromatin remodeling genes (e.g., ASXL3, MLL2, and ARID2). Deep sequencing of mutations revealed subclones in the majority of metastatic tumors from 13 WGS cases. Validated mutations from 12 out of 13 WGS patients exhibited a predominant UV signature characterized by a high frequency of C->T transitions occurring at the 3′ base of dipyrimidine sequences while one patient (MEL9) with a hypermutator phenotype lacked this signature. Strikingly, a subclonal mutation signature analysis revealed that the founding clone in MEL9 exhibited UV signature but the secondary clone did not, suggesting different mutational mechanisms for two clonal populations from the same tumor. Further analysis of four metastases from different geographic locations in 2 melanoma cases revealed phylogenetic relationships and highlighted the genetic alterations responsible for differential drug resistance among metastatic tumors. Our study suggests that clonal evaluation is crucial for understanding tumor etiology and drug resistance in melanoma. PMID:25393105

  14. Clonal relationships in recurrent B-cell lymphomas.

    PubMed

    Lee, Seung Eun; Kang, So Young; Yoo, Hae Yong; Kim, Seok Jin; Kim, Won Seog; Ko, Young Hyeh

    2016-03-15

    Immunoglobulin (Ig) gene rearrangements remain largely unmodified during the clonal expansion of neoplastic cells. We investigated the clonal relationships between lymphoma components at diagnosis and at relapse by analyzing Ig gene rearrangements. A BIOMED-2 multiplex polymerase chain reaction (PCR) assay was performed in 27 patients using formalin-fixed paraffin embedded tissues, with subsequent cloning and sequencing of the amplified Ig genes in 17 patients. All 27 cases of primary and corresponding relapsed tumors showed monoclonal rearrangements of the Ig genes by BIOMED-2 PCR. Whereas IgVH or IgVK fragment lengths were identical in 8/27 pairs (30%), fragment lengths differed in 19/27 pairs (70%). In 17 cases analyzed by sequencing, an identical VDJ gene rearrangement was confirmed in 4/4 pairs (100%) with the same fragment lengths and in 10/13 pairs (77%) with different fragment lengths. Four of 17 primary lymphomas had multiple VDJ rearrangements, and three of them showed an unrelated relapse. Unrelated relapse was observed in 1/8 mantle cell lymphomas, 1/5 diffuse large B-cell lymphomas, and a large B cell lymphoma developed in a patient with a small lymphocytic lymphoma. Unrelated relapses developed after a longer disease-free interval and tended to show poorer outcome compared with related relapse. In summary, relapse of a lymphoma from an unrelated clone is uncommon, but can occur in B-cell lymphomas. Clonal relationships should be determined by sequencing of the Ig genes, and not just by comparing the PCR product size. PMID:26848863

  15. Clonal relationships in recurrent B-cell lymphomas

    PubMed Central

    Lee, Seung Eun; Kang, So Young; Yoo, Hae Yong; Kim, Seok Jin; Kim, Won Seog; Ko, Young Hyeh

    2016-01-01

    Immunoglobulin (Ig) gene rearrangements remain largely unmodified during the clonal expansion of neoplastic cells. We investigated the clonal relationships between lymphoma components at diagnosis and at relapse by analyzing Ig gene rearrangements. A BIOMED-2 multiplex polymerase chain reaction (PCR) assay was performed in 27 patients using formalin-fixed paraffin embedded tissues, with subsequent cloning and sequencing of the amplified Ig genes in 17 patients. All 27 cases of primary and corresponding relapsed tumors showed monoclonal rearrangements of the Ig genes by BIOMED-2 PCR. Whereas IgVH or IgVK fragment lengths were identical in 8/27 pairs (30%), fragment lengths differed in 19/27 pairs (70%). In 17 cases analyzed by sequencing, an identical VDJ gene rearrangement was confirmed in 4/4 pairs (100%) with the same fragment lengths and in 10/13 pairs (77%) with different fragment lengths. Four of 17 primary lymphomas had multiple VDJ rearrangements, and three of them showed an unrelated relapse. Unrelated relapse was observed in 1/8 mantle cell lymphomas, 1/5 diffuse large B-cell lymphomas, and a large B cell lymphoma developed in a patient with a small lymphocytic lymphoma. Unrelated relapses developed after a longer disease-free interval and tended to show poorer outcome compared with related relapse. In summary, relapse of a lymphoma from an unrelated clone is uncommon, but can occur in B-cell lymphomas. Clonal relationships should be determined by sequencing of the Ig genes, and not just by comparing the PCR product size. PMID:26848863

  16. [Phenomenon of the evolution of clonal chromosomal abnormalities in childhood acute myeloid leukemia].

    PubMed

    Andreeva, S V; Drozdova, V D; Kavardakova, N V

    2010-01-01

    Analysis of chromosomal abnormalities in bone marrow cells in 116 children with diagnosis of acute myeloid leukemia (AML) was performed. Frequency of evolution of clonal chromosome abnormalities in AML constituted 42,3%. The most abundant among them were numerical abnormalities of chromosomes 8, 9, and 21 as well as secondary structural abnormalities in region 12p12, 9p22, 9q22, 9q34, 11q14-23, and 16q22. Numerical abnormalities were registered in 26,7% cases. The basic mechanism of leukemic clone evolution was trisomy, deletion and monosomy. The frequency of evolution was 7 times higher in the age group up to 2 years and twice higher in the age group up to 5 years. The high frequency of evolution was established at t(15;17)(q22;q22) and the absence at inv(16)(p13q22). The patients with clonal evolution died earlier, before reaching remission, that can be connected with heavy initial state and high frequency of relapse. Conception of abnormality clone evolution was proposed at some stages: I--appearance of balanced rearrangement; II--trisomy; III--lose of chromosomal material. Appearance of unbalanced genome in evolution possess an advantage in proliferate activity and can be connected with the answer on chemotherapy. Identity of abnormal chromosome structure at diagnosis and relapse of disease can be an evidence of the influence of chemical agent on establishment of some types of evolution of chromosome abnormalities in leukemic cells in AML in children. PMID:20608159

  17. Inflammation as a Driver of Clonal Evolution in Myeloproliferative Neoplasm

    PubMed Central

    Fleischman, Angela G.

    2015-01-01

    Our understanding of inflammation's role in the pathogenesis of myeloproliferative neoplasm (MPN) is evolving. The impact of chronic inflammation, a characteristic feature of MPN, likely goes far beyond its role as a driver of constitutional symptoms. An inflammatory response to the neoplastic clone may be responsible for some pathologic aspects of MPN. Moreover, JAK2V617F mutated hematopoietic stem and progenitor cells are resistant to inflammation, and this gives the neoplastic clone a selective advantage allowing for its clonal expansion. Because inflammation plays a central role in MPN inflammation is a logical therapeutic target in MPN. PMID:26538830

  18. Pharmacokinetic and Pharmacodynamic Properties of Calaspargase Pegol Escherichia coli L-Asparaginase in the Treatment of Patients With Acute Lymphoblastic Leukemia: Results From Children's Oncology Group Study AALL07P4

    PubMed Central

    Angiolillo, Anne L.; Schore, Reuven J.; Devidas, Meenakshi; Borowitz, Michael J.; Carroll, Andrew J.; Gastier-Foster, Julie M.; Heerema, Nyla A.; Keilani, Taha; Lane, Ashley R.; Loh, Mignon L.; Reaman, Gregory H.; Adamson, Peter C.; Wood, Brent; Wood, Charlotte; Zheng, Hao W.; Raetz, Elizabeth A.; Winick, Naomi J.; Carroll, William L.; Hunger, Stephen P.

    2014-01-01

    Purpose Asparaginase is a critical agent used to treat acute lymphoblastic leukemia (ALL). Pegaspargase (SS-PEG), a pegylated form of Escherichia coli L-asparaginase with a succinimidyl succinate (SS) linker, is the first-line asparaginase product used in Children's Oncology Group (COG) ALL trials. Calaspargase pegol (SC-PEG) replaces the SS linker in SS-PEG with a succinimidyl carbamate linker, creating a more stable molecule. COG AALL07P4 was designed to determine the pharmacokinetic and pharmacodynamic comparability of SC-PEG to SS-PEG in patients with newly diagnosed high-risk (HR) B-cell ALL. Patients and Methods A total of 165 evaluable patients were randomly assigned at a 2:1 ratio to receive SC-PEG at 2,100 (SC-PEG2100; n = 69) or 2,500 IU/m2 (SC-PEG2500; n = 42) versus SS-PEG 2,500 IU/m2 (SS-PEG2500; n = 54) as part of an otherwise identical chemotherapy regimen. The groups were similar demographically, except more female patients received SC-PEG2500. Results The mean half-life of plasma asparaginase activity for both SC-PEG doses was approximately 2.5× longer than that of SS-PEG2500. The total systemic exposure, as defined by induction area under the curve from time 0 to 25 days, was greater with SC-PEG2500 than with SS-PEG2500 or SC-PEG2100. The proportion of patients with plasma asparaginase activity ≥ 100 mIU/mL and ≥ 400 mIU/mL was higher in patients who received SC-PEG as compared with SS-PEG2500. After one dose of pegylated asparaginase on induction day 4, plasma asparagine was undetectable for 11 days for SS-PEG2500 and 18 days for both SC-PEG groups. Conclusion SC-PEG2500 achieves a significantly longer period of asparaginase activity above defined thresholds and asparagine depletion compared with SS-PEG2500 and has a comparable toxicity profile in children with HR B-cell ALL. PMID:25348002

  19. Spread of blaCTX-M-14 Is Driven Mainly by IncK Plasmids Disseminated among Escherichia coli Phylogroups A, B1, and D in Spain▿

    PubMed Central

    Valverde, Aránzazu; Cantón, Rafael; Garcillán-Barcia, M. Pilar; Novais, Ângela; Galán, Juan Carlos; Alvarado, Andrés; de la Cruz, Fernando; Baquero, Fernando; Coque, Teresa M.

    2009-01-01

    Since its first description in 2000, CTX-M-14 has become one of the most widespread extended-spectrum β-lactamases in Spain. In the present Escherichia coli multilevel population genetic study involving the characterization of phylogroups, clones, plasmids, and genetic platforms, 61 isolates from 16 hospitalized patients and 40 outpatients and healthy volunteers recovered from 2000 to 2005 were analyzed. Clonal relatedness (XbaI pulsed-field gel electrophoresis [PFGE] type, phylogenetic group, multilocus sequence type [MLST]) was established by standard methods. Analysis of transferred plasmids (I-CeuI; S1 nuclease; restriction fragment length polymorphism analysis; and analysis of RNA interference, replicase, and relaxase) was performed by PCR, sequencing, and hybridization. The genetic environment of blaCTX-M-14 was characterized by PCR on the basis of known associated structures (ISEcp1, IS903, ISCR1). The isolates were mainly recovered from patients in the community (73.8%; 45/61) with urinary tract infections (62.2%; 28/45). They were clonally unrelated by PFGE and corresponded to phylogenetic groups A (36.1%), D (34.4%), and B1 (29.5%). MLST revealed a high degree of sequence type (ST) diversity among phylogroup D isolates and the overrepresentation of the ST10 complex among phylogroup A isolates and ST359/ST155 among phylogroup B1 isolates. Two variants of blaCTX-M-14 previously designated blaCTX-M-14a (n = 59/61) and blaCTX-M-14b (n = 2/61) were detected. blaCTX-M-14a was associated with either ISEcp1 within IncK plasmids (n = 27), ISCR1 linked to an IncHI2 plasmid (n = 1), or ISCR1 linked to IncI-like plasmids (n = 3). The blaCTX-M-14b identified was associated with an ISCR1 element located in an IncHI2 plasmid (n = 1) or with ISEcp1 located in IncK (n = 1). The CTX-M-14-producing E. coli isolates in our geographic area are frequent causes of community-acquired urinary tract infections. The increase in the incidence of such isolates is mostly due to the

  20. Plant traits and ecosystem effects of clonality: a new research agenda

    PubMed Central

    Cornelissen, Johannes H. C.; Song, Yao-Bin; Yu, Fei-Hai; Dong, Ming

    2014-01-01

    Background Clonal plants spread laterally by spacers between their ramets (shoot–root units); these spacers can transport and store resources. While much is known about how clonality promotes plant fitness, we know little about how different clonal plants influence ecosystem functions related to carbon, nutrient and water cycling. Approach The response–effect trait framework is used to formulate hypotheses about the impact of clonality on ecosystems. Central to this framework is the degree of correspondence between interspecific variation in clonal ‘response traits’ that promote plant fitness and interspecific variation in ‘effect traits’, which define a plant's potential effect on ecosystem functions. The main example presented to illustrate this concept concerns clonal traits of vascular plant species that determine their lateral extension patterns. In combination with the different degrees of decomposability of litter derived from their spacers, leaves, roots and stems, these clonal traits should determine associated spatial and temporal patterns in soil organic matter accumulation, nutrient availability and water retention. Conclusions This review gives some concrete pointers as to how to implement this new research agenda through a combination of (1) standardized screening of predominant species in ecosystems for clonal response traits and for effect traits related to carbon, nutrient and water cycling; (2) analysing the overlap between variation in these response traits and effect traits across species; (3) linking spatial and temporal patterns of clonal species in the field to those for soil properties related to carbon, nutrient and water stocks and dynamics; and (4) studying the effects of biotic interactions and feedbacks between resource heterogeneity and clonality. Linking these to environmental changes may help us to better understand and predict the role of clonal plants in modulating impacts of climate change and human activities on

  1. Changes in Enterococcal and E coli populations and related antibiotic resistance from medical center to receiving environment

    NASA Astrophysics Data System (ADS)

    Petit, F.; Berthe, T.; Oberle, K.; Denamur, E.; Clermont, O.; Leclercq, R.; Cattoir, V.; Budzinski, H.

    2013-12-01

    The spread of antibiotic-resistant faecal bacteria and their corresponding genes in water environment, as a result of the overuse of antibiotics, have become an ecological and a public problem. The aim of this multidisciplinary research program (FLASH) -associating chemists, hydrologists, clinical and environmental microbiologists- was to determine to what extent the hospital effluent have an ecological impact on the downstream aquatic environment. For this purpose, fate of Escherichia coli (distribution of phylogenetic groups, antibiotic resistance, integrons- 342 strains) and Enterococci (diversity, antibiotic resistance, genes ermB, mefA, clonal complex 17- 235 strains ) was analyzed in water and sediments along a medical center - WWTP - river - estuary continuum, during a high epidemiologic period in the North west of France. A multi-residue chemical methodology was developed in order to detect low levels of 34 antibiotics in water. To link occurrence of antibiotic-resistant bacteria in water and antibiotic prescription, we use the data collection from the hospital and the antibiotics sales information. In the medical center, the main prescribed antibiotic (amoxicillin) was weakly found in effluents. Along the continuum, contamination of water by antibiotics decreased from 160μg.L-1 (cefotaxim) in hospital effluents to 1ng.L-1 (ofloxacin) in the river. These concentrations were too low to exert a selective pressure (mg.L-1) on antibiotic-resistant bacteria. In same samples, occurrences of antibiotic-resistant E. coli and those harboring a class 1 integrons decreased significantly (p-value < 0.001) along the continuum and a lower survival of most of the E. coli isolates, multiresistant to antibiotic, was observed in water microcosm experiment (< 2days). Once in the estuary, E. coli and the corresponding antibiotic-resistance genes are submitted to the particle dynamics and are deposited on mudflats. Among Enterococcus populations, E. faecium was mainly isolated

  2. Genetic & virulence profiling of ESBL-positive E. coli from nosocomial & veterinary sources.

    PubMed

    Tyrrell, J M; Wootton, M; Toleman, M A; Howe, R A; Woodward, M; Walsh, T R

    2016-04-15

    CTX-M genes are the most prevalent ESBL globally, infiltrating nosocomial, community and environmental settings. Wild and domesticated animals may act as effective vectors for the dissemination of CTX-producing Enterobacteriaceae. This study aimed to contextualise blaCTX-M-14-positive, cephalosporin-resistant Enterobacteriaceae human infections and compared resistance and pathogenicity markers with veterinary isolates. Epidemiologically related human (n=18) and veterinary (n=4) blaCTX-M-14-positive E. coli were fully characterised. All were typed by XbaI pulsed field gel electrophoresis and ST. Chromosomal/plasmidic locations of blaCTX-M-14 were deduced by S1-nuclease digestion, and association with ISEcp1 was investigated by sequencing. Conjugation experiments assessed transmissibility of plasmids carrying blaCTX-M-14. Presence of virulence determinants was screened by PCR assay and pathogenicity potential was determined by in vitro Galleria mellonella infection models. 84% of clinical E. coli originated from community patients. blaCTX-M-14 was found ubiquitously downstream of ISEcp1 upon conjugative plasmids (25-150kb). blaCTX-M-14 was also found upon the chromosome of eight E. coli isolates. CTX-M-14-producing E. coli were found at multiple hospital sites. Clonal commonality between patient, hospitals and livestock microbial populations was found. In vivo model survival rates from clinical isolates (30%) and veterinary isolates (0%) were significantly different (p<0.05). Co-transfer of blaCTX-M-14 and virulence determinants was demonstrated. There is evidence of clonal spread of blaCTX-M-14-positive E. coli involving community patients and farm livestock. blaCTX-M-14 positive human clinical isolates carry a lower intrinsic pathogenic potential than veterinary E. coli highlighting the need for greater veterinary practices in preventing dissemination of MDR E. coli among livestock. PMID:27016755

  3. Divergent clonal evolution of castration resistant neuroendocrine prostate cancer

    PubMed Central

    Beltran, Himisha; Prandi, Davide; Mosquera, Juan Miguel; Benelli, Matteo; Puca, Loredana; Cyrta, Joanna; Marotz, Clarisse; Giannopoulou, Eugenia; Chakravarthi, Balabhadrapatruni V.S.K.; Varambally, Sooryanarayana; Tomlins, Scott A.; Nanus, David M.; Tagawa, Scott T.; Van Allen, Eliezer M.; Elemento, Olivier; Sboner, Andrea; Garraway, Levi A.; Rubin, Mark A.; Demichelis, Francesca

    2016-01-01

    An increasingly recognized resistance mechanism to androgen receptor (AR)-directed therapy in prostate cancer involves epithelial plasticity, wherein tumor cells demonstrate low to absent AR expression and often neuroendocrine features. The etiology and molecular basis for these “alternative” treatment-resistant cell states remain incompletely understood. Here, by analyzing whole exome sequencing data of metastatic biopsies from patients, we observed significant genomic overlap between castration resistant adenocarcinoma (CRPC-Adeno) and neuroendocrine histologies (CRPC-NE); analysis of serial progression samples points to a model most consistent with divergent clonal evolution. Genome-wide DNA methylation revealed marked epigenetic differences between CRPC-NE and CRPC-Adeno that also designated cases of CRPC-Adeno with clinical features of AR-independence as CRPC-NE, suggesting that epigenetic modifiers may play a role in the induction and/or maintenance of this treatment-resistant state. This study supports the emergence of an alternative, “AR-indifferent” cell state through divergent clonal evolution as a mechanism of treatment resistance in advanced prostate cancer. PMID:26855148

  4. Preventing clonal evolutionary processes in cancer: Insights from mathematical models

    PubMed Central

    Rodriguez-Brenes, Ignacio A.; Wodarz, Dominik

    2015-01-01

    Clonal evolutionary processes can drive pathogenesis in human diseases, with cancer being a prominent example. To prevent or treat cancer, mechanisms that can potentially interfere with clonal evolutionary processes need to be understood better. Mathematical modeling is an important research tool that plays an ever-increasing role in cancer research. This paper discusses how mathematical models can be useful to gain insights into mechanisms that can prevent disease initiation, help analyze treatment responses, and aid in the design of treatment strategies to combat the emergence of drug-resistant cells. The discussion will be done in the context of specific examples. Among defense mechanisms, we explore how replicative limits and cellular senescence induced by telomere shortening can influence the emergence and evolution of tumors. Among treatment approaches, we consider the targeted treatment of chronic lymphocytic leukemia (CLL) with tyrosine kinase inhibitors. We illustrate how basic evolutionary mathematical models have the potential to make patient-specific predictions about disease and treatment outcome, and argue that evolutionary models could become important clinical tools in the field of personalized medicine. PMID:26195751

  5. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer.

    PubMed

    Beltran, Himisha; Prandi, Davide; Mosquera, Juan Miguel; Benelli, Matteo; Puca, Loredana; Cyrta, Joanna; Marotz, Clarisse; Giannopoulou, Eugenia; Chakravarthi, Balabhadrapatruni V S K; Varambally, Sooryanarayana; Tomlins, Scott A; Nanus, David M; Tagawa, Scott T; Van Allen, Eliezer M; Elemento, Olivier; Sboner, Andrea; Garraway, Levi A; Rubin, Mark A; Demichelis, Francesca

    2016-03-01

    An increasingly recognized resistance mechanism to androgen receptor (AR)-directed therapy in prostate cancer involves epithelial plasticity, in which tumor cells demonstrate low to absent AR expression and often have neuroendocrine features. The etiology and molecular basis for this 'alternative' treatment-resistant cell state remain incompletely understood. Here, by analyzing whole-exome sequencing data of metastatic biopsies from patients, we observed substantial genomic overlap between castration-resistant tumors that were histologically characterized as prostate adenocarcinomas (CRPC-Adeno) and neuroendocrine prostate cancer (CRPC-NE); analysis of biopsy samples from the same individuals over time points to a model most consistent with divergent clonal evolution. Genome-wide DNA methylation analysis revealed marked epigenetic differences between CRPC-NE tumors and CRPC-Adeno, and also designated samples of CRPC-Adeno with clinical features of AR independence as CRPC-NE, suggesting that epigenetic modifiers may play a role in the induction and/or maintenance of this treatment-resistant state. This study supports the emergence of an alternative, 'AR-indifferent' cell state through divergent clonal evolution as a mechanism of treatment resistance in advanced prostate cancer. PMID:26855148

  6. Clonality of Bacterial Pathogens Causing Hospital-Acquired Pneumonia.

    PubMed

    Pudová, V; Htoutou Sedláková, M; Kolář, M

    2016-09-01

    Hospital-acquired pneumonia (HAP) is one of the most serious complications in patients staying in intensive care units. This multicenter study of Czech patients with HAP aimed at assessing the clonality of bacterial pathogens causing the condition. Bacterial isolates were compared using pulsed-field gel electrophoresis. Included in this study were 330 patients hospitalized between May 1, 2013 and December 31, 2014 at departments of anesthesiology and intensive care medicine of four big hospitals in the Czech Republic. A total of 531 bacterial isolates were obtained, of which 267 were classified as etiological agents causing HAP. Similarity or identity was assessed in 231 bacterial isolates most frequently obtained from HAP patients. Over the study period, no significant clonal spread was noted. Most isolates were unique strains, and the included HAP cases may therefore be characterized as mostly endogenous. Yet there were differences in species and potential identical isolates between the participating centers. In three hospitals, Gram-negative bacteria (Enterobacteriaceae and Pseudomonas aeruginosa) prevailed as etiological agents, and Staphylococcus aureus was most prevalent in the fourth center. PMID:27170306

  7. Clonality and intracellular polyploidy in virus evolution and pathogenesis.

    PubMed

    Perales, Celia; Moreno, Elena; Domingo, Esteban

    2015-07-21

    In the present article we examine clonality in virus evolution. Most viruses retain an active recombination machinery as a potential means to initiate new levels of genetic exploration that go beyond those attainable solely by point mutations. However, despite abundant recombination that may be linked to molecular events essential for genome replication, herein we provide evidence that generation of recombinants with altered biological properties is not essential for the completion of the replication cycles of viruses, and that viral lineages (near-clades) can be defined. We distinguish mechanistically active but inconsequential recombination from evolutionarily relevant recombination, illustrated by episodes in the field and during experimental evolution. In the field, recombination has been at the origin of new viral pathogens, and has conferred fitness advantages to some viruses once the parental viruses have attained a sufficient degree of diversification by point mutations. In the laboratory, recombination mediated a salient genome segmentation of foot-and-mouth disease virus, an important animal pathogen whose genome in nature has always been characterized as unsegmented. We propose a model of continuous mutation and recombination, with punctuated, biologically relevant recombination events for the survival of viruses, both as disease agents and as promoters of cellular evolution. Thus, clonality is the standard evolutionary mode for viruses because recombination is largely inconsequential, since the decisive events for virus replication and survival are not dependent on the exchange of genetic material and formation of recombinant (mosaic) genomes. PMID:26195777

  8. Synchronous Endometrial and Ovarian Carcinomas: Evidence of Clonality.

    PubMed

    Anglesio, Michael S; Wang, Yi Kan; Maassen, Madlen; Horlings, Hugo M; Bashashati, Ali; Senz, Janine; Mackenzie, Robertson; Grewal, Diljot S; Li-Chang, Hector; Karnezis, Anthony N; Sheffield, Brandon S; McConechy, Melissa K; Kommoss, Friedrich; Taran, Florin A; Staebler, Annette; Shah, Sohrab P; Wallwiener, Diethelm; Brucker, Sara; Gilks, C Blake; Kommoss, Stefan; Huntsman, David G

    2016-06-01

    Many women with ovarian endometrioid carcinoma present with concurrent endometrial carcinoma. Organ-confined and low-grade synchronous endometrial and ovarian tumors (SEOs) clinically behave as independent primary tumors rather than a single advanced-stage carcinoma. We used 18 SEOs to investigate the ancestral relationship between the endometrial and ovarian components. Based on both targeted and exome sequencing, 17 of 18 patient cases of simultaneous cancer of the endometrium and ovary from our series showed evidence of a clonal relationship, ie, primary tumor and metastasis. Eleven patient cases fulfilled clinicopathological criteria that would lead to classification as independent endometrial and ovarian primary carcinomas, including being of FIGO stage T1a/1A, with organ-restricted growth and without surface involvement; 10 of 11 of these cases showed evidence of clonality. Our observations suggest that the disseminating cells amongst SEOs are restricted to physically accessible and microenvironment-compatible sites yet remain indolent, without the capacity for further dissemination. PMID:26832771

  9. Differentiation of clonal complex 59 community-associated methicillin-resistant Staphylococcus aureus in Western Australia.

    PubMed

    Coombs, Geoffrey W; Monecke, Stefan; Ehricht, Ralf; Slickers, Peter; Pearson, Julie C; Tan, Hui-Leen; Christiansen, Keryn J; O'Brien, Frances G

    2010-05-01

    Clonal complex 59 (CC59) community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strains were characterized using pulsed-field gel electrophoresis, spa typing, multilocus sequence typing, diagnostic DNA microarrays, and PCRs targeting staphylococcal cassette chromosome mec (SCCmec) elements and Panton-Valentine leukocidin (PVL). Six distinct groups within CC59 were characterized. At least seven different variants of SCCmec elements were identified (IVa [2B], IVb [2B], IVd [2B], IV variant [2B], IVa [2B&5], V variant [5C2], and V [5C2&5]). (The structural type is indicated by a Roman numeral, with a lowercase letter indicating the subtype, and the ccr complex and the mec complex are indicated by an Arabic numeral and an uppercase letter, respectively. Where there is an extra ccr element, this is indicated by "&" and an Arabic numeral designating the ccr type.) The first group is similar to the American sequence type 59 (ST59) MRSA-IV CA-MRSA strain USA1000. The second group includes a PVL-negative ST87 strain with an SCCmec element of subtype IVb (2B). The third group comprises PVL-variable ST59 MRSA-IV strains harboring multiple SCCmec IV subtypes. PVL-negative ST59 MRSA strains with multiple or composite SCCmec elements (IVa [2B&5]) form the fourth group. Group 5 corresponds to the internationally known "Taiwan clone," a PVL-positive strain with a variant SCCmec element (V [5C2&5]). This strain proved to be the most common CC59 MRSA strain isolated in Western Australia. Finally, group 6 encompasses the ST59 MRSA-V variant (5C2). The differentiation of CC59 into groups and strains indicates a rapid evolution and spread of SCCmec elements. Observed differences between groups of strains as well as intrastrain variability within a group facilitate the tracing of their spread. PMID:20211891

  10. Clonal Characteristics of Circulating B Lymphocyte Repertoire in Primary Biliary Cholangitis.

    PubMed

    Tan, Yan-Guo; Wang, Yu-Qi; Zhang, Ming; Han, Ying-Xin; Huang, Chun-Yang; Zhang, Hai-Ping; Li, Zhuo-Min; Wu, Xiao-Lei; Wang, Xiao-Feng; Dong, Yan; Zhu, Hong-Mei; Zhu, Shi-da; Li, Hong-Mei; Li, Ning; Yan, Hui-Ping; Gao, Zu-Hua

    2016-09-01

    Primary biliary cholangitis (PBC) is an autoimmune liver disease characterized by elevated serum anti-mitochondrial Ab and lymphocyte-mediated bile duct damage. This study was designed to reveal the clonal characteristics of B lymphocyte repertoire in patients with PBC to facilitate better understanding of its pathogenesis and better management of these patients. Using high-throughput sequencing of Ig genes, we analyzed the repertoire of circulating B lymphocytes in 43 patients with PBC, and 34 age- and gender-matched healthy controls. Compared with healthy controls, PBC patients showed 1) a gain of 14 new clones and a loss of 8 clones; 2) a significant clonal expansion and increased relative IgM abundance, which corresponded with the elevated serum IgM level; 3) a significant reduction of clonal diversity and somatic hypermutations in class-switched sequences, which suggested a general immunocompromised status; 4) the reduction of clonal diversity and enhancement of clonal expansion were more obvious at the cirrhotic stage; and 5) treatment with ursodeoxycholic acid could increase the clonal diversity and reduce clonal expansion of the IgM repertoire, with no obvious effect on the somatic hypermutation level. Our data suggest that PBC is a complex autoimmune disease process with evidence of B lymphocyte clonal gains and losses, Ag-dependent ogligoclonal expansion, and a generally compromised immune reserve. This new insight into the pathogenesis of PBC opens up the prospect of studying disease-relevant B cells to better diagnose and treat this devastating disease. PMID:27430717

  11. Virulence, sporulation, and elicitin production in three clonal lineages of Phytophthora ramorum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phytophthora ramorum populations are clonal and consist of three lineages. Recent studies have shown that the clonal lineages may have varying degrees of aggressiveness on some host species, such as Quercus rubra. In this study, we examined virulence, sporulation and elicitin production of five P. ...

  12. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytica...

  13. Standardizing the Nomenclature for Clonal Lineages of the Sudden Oak Death Pathogen, Phytophthora ramorum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phytophthora ramorum, the causal agent of sudden oak death and ramorum blight, is known to exist as three distinct clonal lineages based on a range of molecular marker systems. However, in the recent literature there exists no consensus on naming of lineages. Here we name clonal lineages of P. ramor...

  14. Alternative end joining, clonal evolution, and escape from a telomere-driven crisis

    PubMed Central

    Hendrickson, Eric A; Baird, Duncan M

    2015-01-01

    Telomere dysfunction and fusion play key roles in driving genomic instability and clonal evolution in many tumor types. We have recently described a role for DNA ligase III (LIG3) in facilitating the escape of cells from crisis induced by telomere dysfunction. Our data indicate that LIG3-mediated telomere fusion is important in facilitating clonal evolution. PMID:27308409

  15. CYTOTOXICITY OF CHEMICAL CARCINOGENS TOWARDS HUMAN BRONCHIAL EPITHELIAL CELLS EVALUATED IN A CLONAL ASSAY

    EPA Science Inventory

    Survival of human bronchial epithelial cells after administration of four chemical carcinogens was measured in a clonal assay. Human bronchial epithelial cells were obtained from outgrowths of explanted tissue pieces. Serum-free medium was used for both explant culture and clonal...

  16. The cacao pathogen Moniliophthora roreri (Marasmiaceae) possesses biallelic A and B mating loci but reproduces clonally.

    PubMed

    Díaz-Valderrama, J R; Aime, M C

    2016-06-01

    The cacao pathogen Moniliophthora roreri belongs to the mushroom-forming family Marasmiaceae, but it has never been observed to produce a fruiting body, which calls to question its capacity for sexual reproduction. In this study, we identified potential A (HD1 and HD2) and B (pheromone precursors and pheromone receptors) mating genes in M. roreri. A PCR-based method was subsequently devised to determine the mating type for a set of 47 isolates from across the geographic range of the fungus. We developed and generated an 11-marker microsatellite set and conducted association and linkage disequilibrium (standardized index of association, IA(s)) analyses. We also performed an ancestral reconstruction analysis to show that the ancestor of M. roreri is predicted to be heterothallic and tetrapolar, which together with sliding window analyses support that the A and B mating loci are likely unlinked and follow a tetrapolar organization within the genome. The A locus is composed of a pair of HD1 and HD2 genes, whereas the B locus consists of a paired pheromone precursor, Mr_Ph4, and receptor, STE3_Mr4. Two A and B alleles but only two mating types were identified. Association analyses divided isolates into two well-defined genetically distinct groups that correlate with their mating type; IA(s) values show high linkage disequilibrium as is expected in clonal reproduction. Interestingly, both mating types were found in South American isolates but only one mating type was found in Central American isolates, supporting a prior hypothesis of clonal dissemination throughout Central America after a single or very few introductions of the fungus from South America. PMID:26932308

  17. MDS-associated somatic mutations and clonal hematopoiesis are common in idiopathic cytopenias of undetermined significance

    PubMed Central

    Kwok, Brian; Hall, Jeff M.; Witte, John S.; Xu, Yin; Reddy, Prashanti; Lin, Keming; Flamholz, Rachel; Dabbas, Bashar; Yung, Aine; Al-Hafidh, Jenan; Balmert, Emily; Vaupel, Christine; El Hader, Carlos; McGinniss, Matthew J.; Nahas, Shareef A.; Kines, Julie

    2015-01-01

    Establishing a diagnosis in patients suspected of having a myelodysplastic syndrome (MDS) can be challenging and could be informed by the identification of somatic mutations. We performed a prospective study to examine the frequency and types of mutations encountered in 144 patients with unexplained cytopenias. Based on bone marrow findings, 17% were diagnosed with MDS, 15% with idiopathic cytopenias of undetermined significance (ICUS) and some evidence of dysplasia, and 69% with ICUS and no dysplasia. Bone marrow DNA was sequenced for mutations in 22 frequently mutated myeloid malignancy genes. Somatic mutations were identified in 71% of MDS patients, 62% of patients with ICUS and some dysplasia, and 20% of ICUS patients and no dysplasia. In total, 35% of ICUS patients carried a somatic mutation or chromosomal abnormality indicative of clonal hematopoiesis. We validated these results in a cohort of 91 lower-risk MDS and 249 ICUS cases identified over a 6-month interval. Mutations were found in 79% of those with MDS, in 45% of those with ICUS with dysplasia, and in 17% of those with ICUS without dysplasia. The spectrum of mutated genes was similar with the exception of SF3B1 which was rarely mutated in patients without dysplasia. Variant allele fractions were comparable between clonal ICUS (CCUS) and MDS as were mean age and blood counts. We demonstrate that CCUS is a more frequent diagnosis than MDS in cytopenic patients. Clinical and mutational features are similar in these groups and may have diagnostic utility once outcomes in CCUS patients are better understood. PMID:26429975

  18. SNP-based differentiation of Phytophthora infestans clonal lineages using locked nucleic acid probes and high resolution melt analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, exhibits a clonal reproductive lifestyle in North America. Phenotypes such as fungicide sensitivity and host preference are conserved among individuals within clonal lineages, while substantial phenotypic ...

  19. Pathogenic Escherichia coli.

    PubMed

    Kaper, James B; Nataro, James P; Mobley, Harry L

    2004-02-01

    Few microorganisms are as versatile as Escherichia coli. An important member of the normal intestinal microflora of humans and other mammals, E. coli has also been widely exploited as a cloning host in recombinant DNA technology. But E. coli is more than just a laboratory workhorse or harmless intestinal inhabitant; it can also be a highly versatile, and frequently deadly, pathogen. Several different E. coli strains cause diverse intestinal and extraintestinal diseases by means of virulence factors that affect a wide range of cellular processes. PMID:15040260

  20. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

    PubMed Central

    McGranahan, Nicholas; Furness, Andrew J. S.; Rosenthal, Rachel; Ramskov, Sofie; Lyngaa, Rikke; Saini, Sunil Kumar; Jamal-Hanjani, Mariam; Wilson, Gareth A.; Birkbak, Nicolai J.; Hiley, Crispin T.; Watkins, Thomas B. K.; Shafi, Seema; Murugaesu, Nirupa; Mitter, Richard; Akarca, Ayse U.; Linares, Joseph; Marafioti, Teresa; Henry, Jake Y.; Van Allen, Eliezer M.; Miao, Diana; Schilling, Bastian; Schadendorf, Dirk; Garraway, Levi A.; Makarov, Vladimir; Rizvi, Naiyer A.; Snyder, Alexandra; Hellmann, Matthew D.; Merghoub, Taha; Wolchok, Jedd D.; Shukla, Sachet A.; Wu, Catherine J.; Peggs, Karl S.; Chan, Timothy A.; Hadrup, Sine R.; Quezada, Sergio A.; Swanton, Charles

    2016-01-01

    As tumors grow, they acquire mutations, some of which create neoantigens that influence the response of patients to immune checkpoint inhibitors. We explored the impact of neoantigen intratumor heterogeneity (ITH) on antitumor immunity. Through integrated analysis of ITH and neoantigen burden, we demonstrate a relationship between clonal neoantigen burden and overall survival in primary lung adenocarcinomas. CD8+ tumor-infiltrating lymphocytes reactive to clonal neoantigens were identified in early-stage non–small cell lung cancer and expressed high levels of PD-1. Sensitivity to PD-1 and CTLA-4 blockade in patients with advanced NSCLC and melanoma was enhanced in tumors enriched for clonal neoantigens. T cells recognizing clonal neoantigens were detectable in patients with durable clinical benefit. Cytotoxic chemotherapy–induced subclonal neoantigens, contributing to an increased mutational load, were enriched in certain poor responders. These data suggest that neoantigen heterogeneity may influence immune surveillance and support therapeutic developments targeting clonal neoantigens. PMID:26940869

  1. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.

    PubMed

    McGranahan, Nicholas; Furness, Andrew J S; Rosenthal, Rachel; Ramskov, Sofie; Lyngaa, Rikke; Saini, Sunil Kumar; Jamal-Hanjani, Mariam; Wilson, Gareth A; Birkbak, Nicolai J; Hiley, Crispin T; Watkins, Thomas B K; Shafi, Seema; Murugaesu, Nirupa; Mitter, Richard; Akarca, Ayse U; Linares, Joseph; Marafioti, Teresa; Henry, Jake Y; Van Allen, Eliezer M; Miao, Diana; Schilling, Bastian; Schadendorf, Dirk; Garraway, Levi A; Makarov, Vladimir; Rizvi, Naiyer A; Snyder, Alexandra; Hellmann, Matthew D; Merghoub, Taha; Wolchok, Jedd D; Shukla, Sachet A; Wu, Catherine J; Peggs, Karl S; Chan, Timothy A; Hadrup, Sine R; Quezada, Sergio A; Swanton, Charles

    2016-03-25

    As tumors grow, they acquire mutations, some of which create neoantigens that influence the response of patients to immune checkpoint inhibitors. We explored the impact of neoantigen intratumor heterogeneity (ITH) on antitumor immunity. Through integrated analysis of ITH and neoantigen burden, we demonstrate a relationship between clonal neoantigen burden and overall survival in primary lung adenocarcinomas. CD8(+)tumor-infiltrating lymphocytes reactive to clonal neoantigens were identified in early-stage non-small cell lung cancer and expressed high levels of PD-1. Sensitivity to PD-1 and CTLA-4 blockade in patients with advanced NSCLC and melanoma was enhanced in tumors enriched for clonal neoantigens. T cells recognizing clonal neoantigens were detectable in patients with durable clinical benefit. Cytotoxic chemotherapy-induced subclonal neoantigens, contributing to an increased mutational load, were enriched in certain poor responders. These data suggest that neoantigen heterogeneity may influence immune surveillance and support therapeutic developments targeting clonal neoantigens. PMID:26940869

  2. Uncovering the Number and Clonal Dynamics of Mesp1 Progenitors during Heart Morphogenesis

    PubMed Central

    Chabab, Samira; Lescroart, Fabienne; Rulands, Steffen; Mathiah, Navrita; Simons, Benjamin D.; Blanpain, Cédric

    2015-01-01

    Summary The heart arises from distinct sources of cardiac progenitors that independently express Mesp1 during gastrulation. The precise number of Mesp1 progenitors that are specified during the early stage of gastrulation, and their clonal behavior during heart morphogenesis, is currently unknown. Here, we used clonal and mosaic tracing of Mesp1-expressing cells combined with quantitative biophysical analysis of the clonal data to define the number of cardiac progenitors and their mode of growth during heart development. Our data indicate that the myocardial layer of the heart derive from ∼250 Mesp1-expressing cardiac progenitors born during gastrulation. Despite arising at different time points and contributing to different heart regions, the temporally distinct cardiac progenitors present very similar clonal dynamics. These results provide insights into the number of cardiac progenitors and their mode of growth and open up avenues to decipher the clonal dynamics of progenitors in other organs and tissues. PMID:26725109

  3. Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.

    PubMed

    McPherson, Andrew; Roth, Andrew; Laks, Emma; Masud, Tehmina; Bashashati, Ali; Zhang, Allen W; Ha, Gavin; Biele, Justina; Yap, Damian; Wan, Adrian; Prentice, Leah M; Khattra, Jaswinder; Smith, Maia A; Nielsen, Cydney B; Mullaly, Sarah C; Kalloger, Steve; Karnezis, Anthony; Shumansky, Karey; Siu, Celia; Rosner, Jamie; Chan, Hector Li; Ho, Julie; Melnyk, Nataliya; Senz, Janine; Yang, Winnie; Moore, Richard; Mungall, Andrew J; Marra, Marco A; Bouchard-Côté, Alexandre; Gilks, C Blake; Huntsman, David G; McAlpine, Jessica N; Aparicio, Samuel; Shah, Sohrab P

    2016-07-01

    We performed phylogenetic analysis of high-grade serous ovarian cancers (68 samples from seven patients), identifying constituent clones and quantifying their relative abundances at multiple intraperitoneal sites. Through whole-genome and single-nucleus sequencing, we identified evolutionary features including mutation loss, convergence of the structural genome and temporal activation of mutational processes that patterned clonal progression. We then determined the precise clonal mixtures comprising each tumor sample. The majority of sites were clonally pure or composed of clones from a single phylogenetic clade. However, each patient contained at least one site composed of polyphyletic clones. Five patients exhibited monoclonal and unidirectional seeding from the ovary to intraperitoneal sites, and two patients demonstrated polyclonal spread and reseeding. Our findings indicate that at least two distinct modes of intraperitoneal spread operate in clonal dissemination and highlight the distribution of migratory potential over clonal populations comprising high-grade serous ovarian cancers. PMID:27182968

  4. Transplantation of Neural Stem Cells Clonally Derived from Embryonic Stem Cells Promotes Recovery After Murine Spinal Cord Injury

    PubMed Central

    Salewski, Ryan P.; Mitchell, Robert A.; Shen, Carl

    2015-01-01

    The pathology of spinal cord injury (SCI) makes it appropriate for cell-based therapies. Treatments using neural stem cells (NSCs) in animal models of SCI have shown positive outcomes, although uncertainty remains regarding the optimal cell source. Pluripotent cell sources such as embryonic stem cells (ESCs) provide a limitless supply of therapeutic cells. NSCs derived using embryoid bodies (EB) from ESCs have shown tumorigenic potential. Clonal neurosphere generation is an alternative method to generate safer and more clinically relevant NSCs without the use of an EB stage for use in cell-based therapies. We generated clonally derived definitive NSCs (dNSCs) from ESC. These cells were transplanted into a mouse thoracic SCI model. Embryonic stem cell-derived definitive neural stem cell (ES-dNSC)-transplanted mice were compared with controls using behavioral measures and histopathological analysis of tissue. In addition, the role of remyelination in injury recovery was investigated using transmission electron microscopy. The SCI group that received ES-dNSC transplantation showed significant improvements in locomotor function compared with controls in open field and gait analysis. The cell treatment group had a significant enhancement of spared neural tissue. Immunohistological assessments showed that dNSCs differentiated primarily to oligodendrocytes. These cells were shown to express myelin basic protein, associate with axons, and support nodal architecture as well as display proper compact, multilayer myelination in electron microscopic analysis. This study provides strong evidence that dNSCs clonally derived from pluripotent cells using the default pathway of neuralization improve motor function after SCI and enhance sparing of neural tissue, while remaining safe and clinically relevant. PMID:25119334

  5. Escherichia coli bacteriuria and contraceptive method.

    PubMed

    Hooton, T M; Hillier, S; Johnson, C; Roberts, P L; Stamm, W E

    1991-01-01

    We evaluated the effects of contraceptive method on the occurrence of bacteriuria and vaginal colonization with Escherichia coli in 104 women who were evaluated prior to having sexual intercourse, the morning after intercourse, and 24 hours later. After intercourse, the prevalence of E coli bacteriuria increased slightly in oral contraceptive users but dramatically in both foam and condom users and diaphragm-spermicide users. Twenty-four hours later, the prevalence of bacteriuria remained significantly elevated only in the latter two groups. Similarly, vaginal colonization with E coli was more dramatic and persistent in users of diaphragm-spermicide and foam and condoms. Vaginal colonization with Candida species, enterococci, and staphylococci also increased significantly in diaphragm-spermicide users after intercourse. We conclude that use of the diaphragm with spermicidal jelly or use of a spermicidal foam with a condom markedly alters normal vaginal flora and strongly predisposes users to the development of vaginal colonization and bacteriuria with E coli. PMID:1859519

  6. Detection of mcr-1 colistin resistance gene in polyclonal Escherichia coli isolates in Barcelona, Spain, 2012 to 2015.

    PubMed

    Prim, Núria; Rivera, Alba; Rodríguez-Navarro, Judith; Español, Montserrat; Turbau, Miquel; Coll, Pere; Mirelis, Beatriz

    2016-03-31

    Colistin resistance was detected in 53 of 10,011 Escherichia coli (0.5%) by prospective phenotypic testing of consecutive clinical isolates in a single hospital in Barcelona, Spain (2012-15). The mcr-1 gene was retrospectively identified by PCR and sequencing in 15 of 50 available isolates. Each isolate had a unique PFGE pattern except for two. This clonal diversity supports the hypothesis of horizontal dissemination of the mcr-1 gene in the local study population. PMID:27055477

  7. Scaling of processes shaping the clonal dynamics and genetic mosaic of seagrasses through temporal genetic monitoring.

    PubMed

    Becheler, R; Benkara, E; Moalic, Y; Hily, C; Arnaud-Haond, S

    2014-02-01

    Theoretically, the dynamics of clonal and genetic diversities of clonal plant populations are strongly influenced by the competition among clones and rate of seedling recruitment, but little empirical assessment has been made of such dynamics through temporal genetic surveys. We aimed to quantify 3 years of evolution in the clonal and genetic composition of Zostera marina meadows, comparing parameters describing clonal architecture and genetic diversity at nine microsatellite markers. Variations in clonal structure revealed a decrease in the evenness of ramet distribution among genets. This illustrates the increasing dominance of some clonal lineages (multilocus lineages, MLLs) in populations. Despite the persistence of these MLLs over time, genetic differentiation was much stronger in time than in space, at the local scale. Contrastingly with the short-term evolution of clonal architecture, the patterns of genetic structure and genetic diversity sensu stricto (that is, heterozygosity and allelic richness) were stable in time. These results suggest the coexistence of (i) a fine grained (at the scale of a 20 × 30 m quadrat) stable core of persistent genets originating from an initial seedling recruitment and developing spatial dominance through clonal elongation; and (ii) a local (at the scale of the meadow) pool of transient genets subjected to annual turnover. This simultaneous occurrence of initial and repeated recruitment strategies highlights the different spatial scales at which distinct evolutionary drivers and mating systems (clonal competition, clonal growth, propagule dispersal and so on) operate to shape the dynamics of populations and the evolution of polymorphism in space and time. PMID:24022498

  8. Demographic consequences of greater clonal than sexual reproduction in Dicentra canadensis.

    PubMed

    Lin, Chia-Hua; Miriti, Maria N; Goodell, Karen

    2016-06-01

    Clonality is a widespread life history trait in flowering plants that may be essential for population persistence, especially in environments where sexual reproduction is unpredictable. Frequent clonal reproduction, however, could hinder sexual reproduction by spatially aggregating ramets that compete with seedlings and reduce inter-genet pollination. Nevertheless, the role of clonality in relation to variable sexual reproduction in population dynamics is often overlooked. We combined population matrix models and pollination experiments to compare the demographic contributions of clonal and sexual reproduction in three Dicentra canadensis populations, one in a well-forested landscape and two in isolated forest remnants. We constructed stage-based transition matrices from 3 years of census data to evaluate annual population growth rates, λ. We used loop analysis to evaluate the relative contribution of different reproductive pathways to λ. Despite strong temporal and spatial variation in seed set, populations generally showed stable growth rates. Although we detected some pollen limitation of seed set, manipulative pollination treatments did not affect population growth rates. Clonal reproduction contributed significantly more than sexual reproduction to population growth in the forest remnants. Only at the well-forested site did sexual reproduction contribute as much as clonal reproduction to population growth. Flowering plants were more likely to transition to a smaller size class with reduced reproductive potential in the following year than similarly sized nonflowering plants, suggesting energy trade-offs between sexual and clonal reproduction at the individual level. Seed production had negligible effects on growth and tuber production of individual plants. Our results demonstrate that clonal reproduction is vital for population persistence in a system where sexual reproduction is unpredictable. The bias toward clonality may be driven by low fitness returns

  9. Scaling of processes shaping the clonal dynamics and genetic mosaic of seagrasses through temporal genetic monitoring

    PubMed Central

    Becheler, R; Benkara, E; Moalic, Y; Hily, C; Arnaud-Haond, S

    2014-01-01

    Theoretically, the dynamics of clonal and genetic diversities of clonal plant populations are strongly influenced by the competition among clones and rate of seedling recruitment, but little empirical assessment has been made of such dynamics through temporal genetic surveys. We aimed to quantify 3 years of evolution in the clonal and genetic composition of Zostera marina meadows, comparing parameters describing clonal architecture and genetic diversity at nine microsatellite markers. Variations in clonal structure revealed a decrease in the evenness of ramet distribution among genets. This illustrates the increasing dominance of some clonal lineages (multilocus lineages, MLLs) in populations. Despite the persistence of these MLLs over time, genetic differentiation was much stronger in time than in space, at the local scale. Contrastingly with the short-term evolution of clonal architecture, the patterns of genetic structure and genetic diversity sensu stricto (that is, heterozygosity and allelic richness) were stable in time. These results suggest the coexistence of (i) a fine grained (at the scale of a 20 × 30 m quadrat) stable core of persistent genets originating from an initial seedling recruitment and developing spatial dominance through clonal elongation; and (ii) a local (at the scale of the meadow) pool of transient genets subjected to annual turnover. This simultaneous occurrence of initial and repeated recruitment strategies highlights the different spatial scales at which distinct evolutionary drivers and mating systems (clonal competition, clonal growth, propagule dispersal and so on) operate to shape the dynamics of populations and the evolution of polymorphism in space and time. PMID:24022498

  10. Effects of clonality on the genetic variability of rare, insular species: the case of Ruta microcarpa from the Canary Islands

    PubMed Central

    Meloni, M; Reid, A; Caujapé-Castells, J; Marrero, Á; Fernández-Palacios, J M; Mesa-Coelo, R A; Conti, E

    2013-01-01

    Many plant species combine sexual and clonal reproduction. Clonal propagation has ecological costs mainly related to inbreeding depression and pollen discounting; at the same time, species able to reproduce clonally have ecological and evolutionary advantages being able to persist when conditions are not favorable for sexual reproduction. The presence of clonality has profound consequences on the genetic structure of populations, especially when it represents the predominant reproductive strategy in a population. Theoretical studies suggest that high rate of clonal propagation should increase the effective number of alleles and heterozygosity in a population, while an opposite effect is expected on genetic differentiation among populations and on genotypic diversity. In this study, we ask how clonal propagation affects the genetic diversity of rare insular species, which are often characterized by low levels of genetic diversity, hence at risk of extinction. We used eight polymorphic microsatellite markers to study the genetic structure of the critically endangered insular endemic Ruta microcarpa. We found that clonality appears to positively affect the genetic diversity of R. microcarpa by increasing allelic diversity, polymorphism, and heterozygosity. Moreover, clonal propagation seems to be a more successful reproductive strategy in small, isolated population subjected to environmental stress. Our results suggest that clonal propagation may benefit rare species. However, the advantage of clonal growth may be only short-lived for prolonged clonal growth could ultimately lead to monoclonal populations. Some degree of sexual reproduction may be needed in a predominantly clonal species to ensure long-term viability. PMID:23789068

  11. CTX-M-15-type extended-spectrum beta-lactamases-producing Escherichia coli from wild birds in Germany.

    PubMed

    Guenther, Sebastian; Grobbel, Mirjam; Beutlich, Janine; Bethe, Astrid; Friedrich, Nicole D; Goedecke, Andreas; Lübke-Becker, Antina; Guerra, Beatriz; Wieler, Lothar H; Ewers, Christa

    2010-10-01

    The isolation of Escherichia coli from wild birds in Germany revealed the occurrence of four CTX-M-15-producing strains from four different birds (2.3% of 172 isolates). CTX-M producers were recovered from two Eurasian Blackbirds, one Rock Pigeon and a Greater White-fronted Goose. All CTX-M-producing E. coli revealed a clonal relationship as determined by pulsed-field gel electrophoresis (PFGE) and were assigned to multilocus sequence type (ST) 648. Our findings suggest the emergence of a new clone with epidemiological importance and strengthen the role of wild bird species other than waterfowl as possible reservoirs of ESBL-producing Enterobacteriaceae. PMID:23766249

  12. Pathogenic Escherichia coli

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Escherichia coli, a member of the Enterobacteriaceae family, is a part of the normal flora of the intestinal tract of humans and a variety of animals. E. coli strains are classified on the basis of antigenic differences in two surface components (serotyping), the somatic antigen (O) of the lipopoly...

  13. PATHOGENIC ESCHERICHIA COLI

    EPA Science Inventory

    Escherichia coli is a bacterial species which inhabits the gastrointestinal tract of man and warm-blooded animals. Because of the ubiquity of this bacterium in the intestinal flora, it serves as an important indicator organism of fecal contamination. E. coli, aside from serving a...

  14. Molecular cloning and expression of Corynebacterium glutamicum genes for amino acid synthesis in Escherichia coli cells

    SciTech Connect

    Beskrovnaya, O.Yu.; Fonshtein, M.Yu.; Kolibaba, L.G.; Yankovskii, N.K.; Debabov, V.G.

    1989-01-01

    Molecular cloning of Corynebacterium glutamicum genes for threonine and lysine synthesis has been done in Escherichia coli cells. The clonal library of EcoRI fragments of chromosomal DNA of C. glutamicum was constructed on the plasmid vector /lambda/pSL5. The genes for threonine and lysine synthesis were identified by complementation of E. coli mutations in thrB and lysA genes, respectively. Recombinant plasmids, isolated from independent ThrB/sup +/ clone have a common 4.1-kb long EcoRI DNA fragment. Hybrid plasmids isolated from LysA/sup +/ transductants of E. coli have common 2.2 and 3.3 kb long EcoRI fragments of C. glutamicum DNA. The hybrid plasmids consistently transduced the markers thrB/sup +/ and lysA/sup +/. The Southern hybridization analysis showed that the cloned DNA fragments hybridized with the fragments of identical length in C. glutamicum chromosomes.

  15. Prevalence of Avian Pathogenic Escherichia coli (APEC) Clone Harboring sfa Gene in Brazil

    PubMed Central

    Knöbl, Terezinha; Micke Moreno, Andrea; Paixão, Renata; Gomes, Tânia Aparecida Tardelli; Vieira, Mônica Aparecida Midolli; da Silva Leite, Domingos; Blanco, Jesus E.; Ferreira, Antônio José Piantino

    2012-01-01

    Escherichia coli sfa+ strains isolated from poultry were serotyped and characterized by polymerase chain reaction (PCR) and amplified fragment length polymorphism (AFLP). Isolates collected from 12 Brazilian poultry farms mostly belonged to serogroup O6, followed by serogroups O2, O8, O21, O46, O78, O88, O106, O111, and O143. Virulence genes associated were: iuc 90%, fim 86% neuS 60%, hly 34%, tsh 28%, crl/csg 26%, iss 26%, pap 18%, and 14% cnf. Strains from the same farm presented more than one genotypic pattern belonging to different profiles in AFLP. AFLP showed a clonal relation between Escherichia coli sfa+ serogroup O6. The virulence genes found in these strains reveal some similarity with extraintestinal E. coli (ExPEC), thus alerting for potential zoonotic risk. PMID:22666122

  16. How Clonal Is Clonal? Genome Plasticity across Multicellular Segments of a “Candidatus Marithrix sp.” Filament from Sulfidic, Briny Seafloor Sediments in the Gulf of Mexico

    PubMed Central

    Salman-Carvalho, Verena; Fadeev, Eduard; Joye, Samantha B.; Teske, Andreas

    2016-01-01

    “Candidatus Marithrix” is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria). This genus of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 μm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, “Candidatus Marithrix” was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the “Candidatus Marithrix” genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98 and 100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes—the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs) between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or “intrasegmental sequence heterogeneity” (ISH) events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament. PMID

  17. Clonal Evolution of Stem Cells in the Gastrointestinal Tract.

    PubMed

    Fink, Juergen; Koo, Bon-Kyoung

    2016-01-01

    The field of gastrointestinal epithelial stem cells is a rapidly developing area of adult stem cell research. The discovery of Lgr5(+) intestinal stem cells has enabled us to study many hidden aspects of the biology of gastrointestinal adult stem cells. Marked by Lgr5 and Troy, several novel endodermal stem cells have been identified in the gastrointestinal tract. A precise working model of stem cell propagation, dynamics, and plasticity has been revealed by a genetic labeling method, termed lineage tracing. This chapter introduces the reidentification of crypt base columnar cells as Lgr5(+) stem cells in the intestine. Subsequently, it will discuss dynamic clonal evolution and cellular plasticity in the intestinal stem cell zone, as well as in stem cell zones of stomach glands. PMID:27573765

  18. A clonal selection algorithm model for daily rainfall data prediction.

    PubMed

    Noor Rodi, N S; Malek, M A; Ismail, Amelia Ritahani; Ting, Sie Chun; Tang, Chao-Wei

    2014-01-01

    This study applies the clonal selection algorithm (CSA) in an artificial immune system (AIS) as an alternative method to predicting future rainfall data. The stochastic and the artificial neural network techniques are commonly used in hydrology. However, in this study a novel technique for forecasting rainfall was established. Results from this study have proven that the theory of biological immune systems could be technically applied to time series data. Biological immune systems are nonlinear and chaotic in nature similar to the daily rainfall data. This study discovered that the proposed CSA was able to predict the daily rainfall data with an accuracy of 90% during the model training stage. In the testing stage, the results showed that an accuracy between the actual and the generated data was within the range of 75 to 92%. Thus, the CSA approach shows a new method in rainfall data prediction. PMID:25429452

  19. FTO influences adipogenesis by regulating mitotic clonal expansion

    PubMed Central

    Merkestein, Myrte; Laber, Samantha; McMurray, Fiona; Andrew, Daniel; Sachse, Gregor; Sanderson, Jeremy; Li, Mengdi; Usher, Samuel; Sellayah, Dyan; Ashcroft, Frances M.; Cox, Roger D.

    2015-01-01

    The fat mass and obesity-associated (FTO) gene plays a pivotal role in regulating body weight and fat mass; however, the underlying mechanisms are poorly understood. Here we show that primary adipocytes and mouse embryonic fibroblasts (MEFs) derived from FTO overexpression (FTO-4) mice exhibit increased potential for adipogenic differentiation, while MEFs derived from FTO knockout (FTO-KO) mice show reduced adipogenesis. As predicted from these findings, fat pads from FTO-4 mice fed a high-fat diet show more numerous adipocytes. FTO influences adipogenesis by regulating events early in adipogenesis, during the process of mitotic clonal expansion. The effect of FTO on adipogenesis appears to be mediated via enhanced expression of the pro-adipogenic short isoform of RUNX1T1, which enhanced adipocyte proliferation, and is increased in FTO-4 MEFs and reduced in FTO-KO MEFs. Our findings provide novel mechanistic insight into how upregulation of FTO leads to obesity. PMID:25881961

  20. Aging, Clonality, and Rejuvenation of Hematopoietic Stem Cells.

    PubMed

    Akunuru, Shailaja; Geiger, Hartmut

    2016-08-01

    Aging is associated with reduced organ function and increased disease incidence. Hematopoietic stem cell (HSC) aging driven by both cell intrinsic and extrinsic factors is linked to impaired HSC self-renewal and regeneration, aging-associated immune remodeling, and increased leukemia incidence. Compromised DNA damage responses and the increased production of reactive oxygen species (ROS) have been previously causatively attributed to HSC aging. However, recent paradigm-shifting concepts, such as global epigenetic and cytoskeletal polarity shifts, cellular senescence, as well as the clonal selection of HSCs upon aging, provide new insights into HSC aging mechanisms. Rejuvenating agents that can reprogram the epigenetic status of aged HSCs or senolytic drugs that selectively deplete senescent cells provide promising translational avenues for attenuating hematopoietic aging and, potentially, alleviating aging-associated immune remodeling and myeloid malignancies. PMID:27380967

  1. Clonal mixtures of Salix - a control measure for rust

    SciTech Connect

    McCracken, A.R.; Dawson, W.M.; Allen C.Y.

    1996-12-31

    Willow grown in short rotation coppice can be used as a renewable energy source. However, disease caused by Melampsora epitea var. epitea can be a severely limiting factor on its productivity. Populations of this pathogen in N. Ireland have been shown to be composed of at least fourteen pathotypes. Pathotype composition was influenced by time, age and clone. Fungicides were unacceptable to control disease, therefore the use of clonal mixtures was employed as an alternative strategy. When grown in mixtures the onset of disease was delayed, its build up slowed and final levels reduced. This was reflected in increased yield. Current work investigating the effect of planting density and increasing mixture diversity indicates that neither have a major impact on disease.

  2. [Molecular Mechanism and Malignant Clonal Evolution of Multiple Myeloma].

    PubMed

    Ding, Fei; Zhu, Ping; Wu, Xue-Qiang

    2015-10-01

    Almost all patients with multiple myeloma (MM) have chromosomal translocation which can result in genetic variation. There are mainly five types of chromosomal translocations, involving the IGH gene translocation to 11q13 (CCND1), 4p16 (FGFR/MMSET), 16q23 (MAF), 6p21 (CCND3) and 20q11 (MAFB). It is possible that all IGH translocations converge on a common cell cycle signal pathway. Some MM develops through a multistep transformation from monoclonal gammopathy of undetermined significance (MGUS) to smoldering MM (SMM) and eventually to MM and plasma cell leukemia (PCL). Similarly to what Darwin proposed in the mid-19th century-random genetic variation and natural selection in the context of limited resources, MM clonal evolution follow branching and nonlinear mode. The failure of MM treatment is usually related with the minimal subclone which is hardly found at newlydiagnosed. PMID:26524068

  3. Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors.

    PubMed

    Deshwar, Amit G; Vembu, Shankar; Morris, Quaid

    2015-01-01

    Statistical machine learning methods, especially nonparametric Bayesian methods, have become increasingly popular to infer clonal population structure of tumors. Here we describe the treeCRP, an extension of the Chinese restaurant process (CRP), a popular construction used in nonparametric mixture models, to infer the phylogeny and genotype of major subclonal lineages represented in the population of cancer cells. We also propose new split-merge updates tailored to the subclonal reconstruction problem that improve the mixing time of Markov chains. In comparisons with the tree-structured stick breaking prior used in PhyloSub, we demonstrate superior mixing and running time using the treeCRP with our new split-merge procedures. We also show that given the same number of samples, TSSB and treeCRP have similar ability to recover the subclonal structure of a tumor… PMID:25592565

  4. Environmental gradients structure Daphnia pulex × pulicaria clonal distribution.

    PubMed

    Pantel, J H; Juenger, T E; Leibold, M A

    2011-04-01

    The rarity of eukaryotic asexual reproduction is frequently attributed to the disadvantage of reduced genetic variation relative to sexual reproduction. However, parthenogenetic lineages that evolved repeatedly from sexual ancestors can generate regional pools of phenotypically diverse clones. Various theories to explain the maintenance of this genetic diversity as a result of environmental and spatial heterogeneity [frozen niche variation (FNV), general-purpose genotype] are conceptually similar to community ecological explanations for the maintenance of regional species diversity. We employed multivariate statistics common in community ecological research to study population genetic structure in the freshwater crustacean, Daphnia pulex × pulicaria. This parthenogenetic hybrid arose repeatedly from sexual ancestors. Daphnia pulex × pulicaria populations harboured substantial genetic variation among populations and the clonal composition at each pond corresponded to nutrient levels and invertebrate predator densities. The interclonal selection process described by the FNV hypothesis likely structured our D. pulex × pulicaria populations. PMID:21288271

  5. Genetic Structure in Aquatic Bladderworts: Clonal Propagation and Hybrid Perpetuation

    PubMed Central

    KAMEYAMA, YOSHIAKI; OHARA, MASASHI

    2006-01-01

    • Background and Aims The free-floating aquatic bladderwort Utricularia australis f. australis is a sterile F1 hybrid of U. australis f. tenuicaulis and U. macrorhiza. However, co-existence of the hybrids and parental species has not been observed. In the present study, the following questions are addressed. (a) Does the capacity of the two parental species to reproduce sexually contribute to higher genotypic diversity than that of sterile F1 hybrid? (b) Are there any populations where two parental species and their hybrid co-exist? (c) If not, where and how do hybrids originate? • Methods The presence and absence of Utricularia was thoroughly investigated in two regions in Japan. An amplified fragment length polymorphism (AFLP) analysis was conducted for 397 individuals collected from all populations (33 in total) where Utricularia was observed. • Key Results The mean number of genotypes per population (G) and genotypic diversity (D) were extremely low irrespective of the capacity to reproduce sexually: G was 1·1–1·2 and D was 0·02–0·04. The hybrid rarely co-existed with either parental species, and the co-existence of two parental species was not observed. Several AFLP bands observed in the hybrid are absent in both parental genotypes, and parent and hybrid genotypes in the same region do not show greater genetic similarity than those in distant regions. • Conclusions The capacity to reproduce sexually in parental species plays no role in increasing genotypic diversity within populations. The observed genotypes of the hybrid could not have originated from hybridization between the extant parental genotypes within the study regions. Considering the distribution ranges of three investigated taxa, it is clear that the hybrid originated in the past, and hybrid populations have been maintained exclusively by clonal propagation, which may be ensured by both hybrid vigor and long-distance dispersal of clonal offspring. PMID:16926229

  6. Genotypic richness predicts phenotypic variation in an endangered clonal plant.

    PubMed

    Evans, Suzanna M; Sinclair, Elizabeth A; Poore, Alistair G B; Bain, Keryn F; Vergés, Adriana

    2016-01-01

    Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen) was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of the species

  7. Genotypic richness predicts phenotypic variation in an endangered clonal plant

    PubMed Central

    Sinclair, Elizabeth A.; Poore, Alistair G.B.; Bain, Keryn F.; Vergés, Adriana

    2016-01-01

    Declines in genetic diversity within a species can affect the stability and functioning of populations. The conservation of genetic diversity is thus a priority, especially for threatened or endangered species. The importance of genetic variation, however, is dependent on the degree to which it translates into phenotypic variation for traits that affect individual performance and ecological processes. This is especially important for predominantly clonal species, as no single clone is likely to maximise all aspects of performance. Here we show that intraspecific genotypic diversity as measured using microsatellites is a strong predictor of phenotypic variation in morphological traits and shoot productivity of the threatened, predominantly clonal seagrass Posidonia australis, on the east coast of Australia. Biomass and surface area variation was most strongly predicted by genotypic richness, while variation in leaf chemistry (phenolics and nitrogen) was unrelated to genotypic richness. Genotypic richness did not predict tissue loss to herbivores or epiphyte load, however we did find that increased herbivore damage was positively correlated with allelic richness. Although there was no clear relationship between higher primary productivity and genotypic richness, variation in shoot productivity within a meadow was significantly greater in more genotypically diverse meadows. The proportion of phenotypic variation explained by environmental conditions varied among different genotypes, and there was generally no variation in phenotypic traits among genotypes present in the same meadows. Our results show that genotypic richness as measured through the use of presumably neutral DNA markers does covary with phenotypic variation in functionally relevant traits such as leaf morphology and shoot productivity. The remarkably long lifespan of individual Posidonia plants suggests that plasticity within genotypes has played an important role in the longevity of the species

  8. Highly Recombinant VGII Cryptococcus gattii Population Develops Clonal Outbreak Clusters through both Sexual Macroevolution and Asexual Microevolution

    PubMed Central

    Croll, Daniel; Li, Wenjun; Mieczkowski, Piotr; Carter, Dee A.; Cuomo, Christina A.; Kronstad, James W.

    2014-01-01

    ABSTRACT An outbreak of the fungal pathogen Cryptococcus gattii began in the Pacific Northwest (PNW) in the late 1990s. This outbreak consists of three clonal subpopulations: VGIIa/major, VGIIb/minor, and VGIIc/novel. Both VGIIa and VGIIc are unique to the PNW and exhibit increased virulence. In this study, we sequenced the genomes of isolates from these three groups, as well as global isolates, and analyzed a total of 53 isolates. We found that VGIIa/b/c populations show evidence of clonal expansion in the PNW. Whole-genome sequencing provided evidence that VGIIb originated in Australia, while VGIIa may have originated in South America, and these were likely independently introduced. Additionally, the VGIIa outbreak lineage may have arisen from a less virulent clade that contained a mutation in the MSH2 ortholog, but this appears to have reverted in the VGIIa outbreak strains, suggesting that a transient mutator phenotype may have contributed to adaptation and evolution of virulence in the PNW outbreak. PNW outbreak isolates share genomic islands, both between the clonal lineages and with global isolates, indicative of sexual recombination. This suggests that VGII C. gattii has undergone sexual reproduction, either bisexual or unisexual, in multiple locales contributing to the production of novel, virulent subtypes. We also found that the genomes of two basal VGII isolates from HIV+ patients contain an introgression tract spanning three genes. Introgression substantially contributed to intra-VGII polymorphism and likely occurred through sexual reproduction with VGI. More broadly, these findings illustrate how both microevolution and sexual reproduction play central roles in the development of infectious outbreaks from avirulent or less virulent progenitors. PMID:25073643

  9. Clonality as Expression of Distinctive Cell Kinetics Patterns in Nodular Hyperplasias and Adenomas of the Adrenal Cortex

    PubMed Central

    Díaz-Cano, Salvador J.; de Miguel, Manuel; Blanes, Alfredo; Tashjian, Robert; Galera, Hugo; Wolfe, Hubert J.

    2000-01-01

    Although histopathologic criteria for adrenal cortical nodular hyperplasias (ACNHs) and adenomas (ACAs) have been developed, their kinetics and clonality are virtually unknown. We studied 20 ACNHs and 25 ACAs (based on World Health Organization criteria) from 45 females. Representative samples were histologically evaluated, and the methylation pattern of the androgen receptor alleles was analyzed on microdissected samples. Consecutive sections were selected for slide cytometry, flow cytometry, and in situ end labeling (ISEL). Apoptosis was studied by flow cytometry (nuclear area/DNA content plotter analysis) and by ISEL. Appropriate tissue controls were run in every case. Polyclonal gel patterns were revealed in 14/18 informative ACNHs and in 3/22 informative ACAs, whereas monoclonal gel patterns were observed in 4/18 ACNHs and 19/22 ACAs. Overlapping proliferation rates (PRs) were observed in both clonal groups, and apoptosis was detected only in G0/G1 cells, especially in monoclonal ACNHs (3/4; 75%) and in polyclonal ACAs (2/3; 67%). Significantly higher PRs were observed in ACNHs with polyclonal patterns and G0/G1 apoptosis and in ACAs regardless of clonality pattern and presence of G0/G1 apoptosis. All except one ACNH (19/20; 95%) and 15/25 ACAs (60%) showed diploid DNA content, whereas the remaining cases were hyperdiploid. A direct correlation between PR and ISEL was observed in polyclonal lesions (PR = 29.32 ISEL − 1.93), whereas the correlation was inverse for monoclonal lesions (PR = −9.13 ISEL + 21.57). We concluded that only simultaneous down-regulated apoptosis and high proliferation result in selective kinetic advantage, dominant clone expansion, and unbalanced methylation patterns of androgen receptor alleles in ACNHs and ACAs. PMID:10623680

  10. Clonality as expression of distinctive cell kinetics patterns in nodular hyperplasias and adenomas of the adrenal cortex.

    PubMed

    Díaz-Cano, S J; de Miguel, M; Blanes, A; Tashjian, R; Galera, H; Wolfe, H J

    2000-01-01

    Although histopathologic criteria for adrenal cortical nodular hyperplasias (ACNHs) and adenomas (ACAs) have been developed, their kinetics and clonality are virtually unknown. We studied 20 ACNHs and 25 ACAs (based on World Health Organization criteria) from 45 females. Representative samples were histologically evaluated, and the methylation pattern of the androgen receptor alleles was analyzed on microdissected samples. Consecutive sections were selected for slide cytometry, flow cytometry, and in situ end labeling (ISEL). Apoptosis was studied by flow cytometry (nuclear area/DNA content plotter analysis) and by ISEL. Appropriate tissue controls were run in every case. Polyclonal gel patterns were revealed in 14/18 informative ACNHs and in 3/22 informative ACAs, whereas monoclonal gel patterns were observed in 4/18 ACNHs and 19/22 ACAs. Overlapping proliferation rates (PRs) were observed in both clonal groups, and apoptosis was detected only in G(0)/G(1) cells, especially in monoclonal ACNHs (3/4; 75%) and in polyclonal ACAs (2/3; 67%). Significantly higher PRs were observed in ACNHs with polyclonal patterns and G(0)/G(1) apoptosis and in ACAs regardless of clonality pattern and presence of G(0)/G(1) apoptosis. All except one ACNH (19/20; 95%) and 15/25 ACAs (60%) showed diploid DNA content, whereas the remaining cases were hyperdiploid. A direct correlation between PR and ISEL was observed in polyclonal lesions (PR = 29.32 ISEL - 1.93), whereas the correlation was inverse for monoclonal lesions (PR = -9.13 ISEL + 21.57). We concluded that only simultaneous down-regulated apoptosis and high proliferation result in selective kinetic advantage, dominant clone expansion, and unbalanced methylation patterns of androgen receptor alleles in ACNHs and ACAs. PMID:10623680

  11. Strong but diverging clonality - climate relationships of different plant clades explain weak overall pattern across China

    PubMed Central

    Ye, Duo; Liu, Guofang; Song, Yao-Bin; Cornwell, William K.; Dong, Ming; Cornelissen, Johannes H. C.

    2016-01-01

    The clonal strategy should be relatively important in stressful environments (i.e. of low resource availability or harsh climate), e.g. in cold habitats. However, our understanding of the distribution pattern of clonality along environmental gradients is still far from universal. The weakness and inconsistency of overall clonality-climate relationships across taxa, as reported in previous studies, may be due to different phylogenetic lineages having fundamental differences in functional traits other than clonality determining their climate response. Thus, in this study we compared the clonality-climate relationships along a latitudinal gradient within and between different lineages at several taxonomic levels, including four major angiosperm lineages (Magnoliidae, Monocotyledoneae, Superrosidae and Superasteridae), orders and families. To this aim we used a species clonality dataset for 4015 vascular plant species in 545 terrestrial communities across China. Our results revealed clear predictive patterns of clonality proportion in relation to environmental gradients for the predominant representatives of each of the taxonomic levels above, but the relationships differed in shape and strength between the 4 major angiosperm lineages, between the 12 orders and between the 12 families. These different relationships canceled out one another when all lineages at a certain taxonomic level were pooled. Our findings highlight the importance of explicitly accounting for the functional or taxonomic scale for studying variation in plant ecological strategy across environmental gradients. PMID:27246203

  12. Clonal reproduction shapes evolution in the lizard malaria parasite Plasmodium floridense.

    PubMed

    Falk, Bryan G; Glor, Richard E; Perkins, Susan L

    2015-06-01

    The preponderant clonal evolution hypothesis (PCE) predicts that frequent clonal reproduction (sex between two clones) in many pathogens capable of sexual recombination results in strong linkage disequilibrium and the presence of discrete genetic subdivisions characterized by occasional gene flow. We expand on the PCE and predict that higher rates of clonal reproduction will result in: (1) morphologically cryptic species that exhibit (2) low within-species variation and (3) recent between-species divergence. We tested these predictions in the Caribbean lizard malaria parasite Plasmodium floridense using 63 single-infection samples in lizards collected from across the parasite's range, and sequenced them at two mitochondrial, one apicoplast, and five nuclear genes. We identified 11 provisionally cryptic species within P. floridense, each of which exhibits low intraspecific variation and recent divergence times between species (some diverged approximately 110,000 years ago). Our results are consistent with the hypothesis that clonal reproduction can profoundly affect diversification of species capable of sexual recombination, and suggest that clonal reproduction may have led to a large number of unrecognized pathogen species. The factors that may influence the rates of clonal reproduction among pathogens are unclear, and we discuss how prevalence and virulence may relate to clonal reproduction. PMID:25959003

  13. Strong but diverging clonality - climate relationships of different plant clades explain weak overall pattern across China.

    PubMed

    Ye, Duo; Liu, Guofang; Song, Yao-Bin; Cornwell, William K; Dong, Ming; Cornelissen, Johannes H C

    2016-01-01

    The clonal strategy should be relatively important in stressful environments (i.e. of low resource availability or harsh climate), e.g. in cold habitats. However, our understanding of the distribution pattern of clonality along environmental gradients is still far from universal. The weakness and inconsistency of overall clonality-climate relationships across taxa, as reported in previous studies, may be due to different phylogenetic lineages having fundamental differences in functional traits other than clonality determining their climate response. Thus, in this study we compared the clonality-climate relationships along a latitudinal gradient within and between different lineages at several taxonomic levels, including four major angiosperm lineages (Magnoliidae, Monocotyledoneae, Superrosidae and Superasteridae), orders and families. To this aim we used a species clonality dataset for 4015 vascular plant species in 545 terrestrial communities across China. Our results revealed clear predictive patterns of clonality proportion in relation to environmental gradients for the predominant representatives of each of the taxonomic levels above, but the relationships differed in shape and strength between the 4 major angiosperm lineages, between the 12 orders and between the 12 families. These different relationships canceled out one another when all lineages at a certain taxonomic level were pooled. Our findings highlight the importance of explicitly accounting for the functional or taxonomic scale for studying variation in plant ecological strategy across environmental gradients. PMID:27246203

  14. Strong but diverging clonality - climate relationships of different plant clades explain weak overall pattern across China

    NASA Astrophysics Data System (ADS)

    Ye, Duo; Liu, Guofang; Song, Yao-Bin; Cornwell, William K.; Dong, Ming; Cornelissen, Johannes H. C.

    2016-06-01

    The clonal strategy should be relatively important in stressful environments (i.e. of low resource availability or harsh climate), e.g. in cold habitats. However, our understanding of the distribution pattern of clonality along environmental gradients is still far from universal. The weakness and inconsistency of overall clonality-climate relationships across taxa, as reported in previous studies, may be due to different phylogenetic lineages having fundamental differences in functional traits other than clonality determining their climate response. Thus, in this study we compared the clonality-climate relationships along a latitudinal gradient within and between different lineages at several taxonomic levels, including four major angiosperm lineages (Magnoliidae, Monocotyledoneae, Superrosidae and Superasteridae), orders and families. To this aim we used a species clonality dataset for 4015 vascular plant species in 545 terrestrial communities across China. Our results revealed clear predictive patterns of clonality proportion in relation to environmental gradients for the predominant representatives of each of the taxonomic levels above, but the relationships differed in shape and strength between the 4 major angiosperm lineages, between the 12 orders and between the 12 families. These different relationships canceled out one another when all lineages at a certain taxonomic level were pooled. Our findings highlight the importance of explicitly accounting for the functional or taxonomic scale for studying variation in plant ecological strategy across environmental gradients.

  15. Clonally related uterine leiomyomas are common and display branched tumor evolution.

    PubMed

    Mehine, Miika; Heinonen, Hanna-Riikka; Sarvilinna, Nanna; Pitkänen, Esa; Mäkinen, Netta; Katainen, Riku; Tuupanen, Sari; Bützow, Ralf; Sjöberg, Jari; Aaltonen, Lauri A

    2015-08-01

    Uterine leiomyomas are extremely frequent benign smooth muscle tumors often presenting as multiple concurrent lesions and causing symptoms such as abnormal menstrual bleeding, abdominal pain and infertility. While most leiomyomas are believed to arise independently, a few studies have encountered separate lesions harboring identical genetic changes, suggesting a common clonal origin. To investigate the frequency of clonally related leiomyomas, genome-wide tools need to be utilized, and thus little is known about this phenomenon. Using MED12 sequencing and SNP arrays, we searched for clonally related uterine leiomyomas in a set of 103 tumors from 14 consecutive patients who entered hysterectomy owing to symptomatic lesions. Whole-genome sequencing was also utilized to study the genomic architecture of clonally related tumors. This revealed four patients to have two or more tumors that were clonally related, all of which lacked MED12 mutations. Furthermore, some tumors were composed of genetically distinct subclones, indicating a nonlinear, branched model of tumor evolution. DEPDC5 was discovered as a novel tumor suppressor gene playing a role in the progression of uterine leiomyomas. Perhaps counterintuitively—considering Knudson's two-hit hypothesis—a large shared deletion was followed by different truncating DEPDC5 mutations in four clonally related leiomyomas. This study provides insight into the intratumor heterogeneity of these tumors and suggests that a shared clonal origin is a common feature of leiomyomas that do not carry an MED12 mutation. These observations also offer one explanation to the common occurrence of multiple concurrent lesions. PMID:25964426

  16. Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata)

    PubMed Central

    2013-01-01

    Background Clonal propagation is a particular reproductive system found in both the plant and animal kingdoms, from human parasites to clonally propagated crops. Clonal diversity provides information about plant and animal evolutionary history, i.e. how clones spread, or the age of a particular clone. In plants, this could provide valuable information about agrobiodiversity dynamics and more broadly about the evolutionary history of a particular crop. We studied the evolutionary history of yam, Dioscorea rotundata. In Africa, Yam is cultivated by tuber clonal propagation. Results We used 12 microsatellite markers to identify intra-clonal diversity in yam varieties. We then used this diversity to assess the relative ages of clones. Using simulations, we assessed how Approximate Bayesian Computation could use clonal diversity to estimate the age of a clone depending on the size of the sample, the number of independent samples and the number of markers. We then applied this approach to our particular dataset and showed that the relative ages of varieties could be estimated, and that each variety could be ranked by age. Conclusions We give a first estimation of clone age in an approximate Bayesian framework. However the precise estimation of clone age depends on the precision of the mutation rate. We provide useful information on agrobiodiversity dynamics and suggest recurrent creation of varietal diversity in a clonally propagated crop. PMID:24219837

  17. Evidence for clonal origin of neoplastic neuronal and glial cells in gangliogliomas.

    PubMed Central

    Zhu, J. J.; Leon, S. P.; Folkerth, R. D.; Guo, S. Z.; Wu, J. K.; Black, P. M.

    1997-01-01

    Gangliogliomas are rare tumors of the central nervous system that account for approximately 1% of all brain tumors. Histologically, gangliogliomas are composed of intimately admixed glial and neuronal components, the pathological origins of which remain to be characterized. Clonal analysis through examination of the pattern of the X chromosome inactivation allows one to distinguish monoclonal differentiation of a genetically abnormal progenitor cell from parallel, but independent, clonal expansion of two different cell types during tumorigenesis in biphasic neoplasms, such as gangliogliomas. In the present study, we investigated the clonality of eight gangliogliomas from female patients using both methylation- and transcription-based clonality assays at the androgen receptor locus (HUMARA) on the X chromosome. Among tumors from seven patients who were heterozygous at the HUMARA locus, five were identified as monoclonal with the methylation-based clonality assay, and the results were confirmed by the transcription-based method, whereas two were shown to be polyclonal by the methylation-based clonality assay but monoclonal by transcription-based clonality analysis. We conclude that the predominant cell types in most gangliogliomas are monoclonal in origin and derive from a common precursor cell that subsequently differentiates to form neoplastic glial and neuronal elements. Images Figure 2 Figure 3 PMID:9250169

  18. Molecular serotyping of Escherichia coli: A verification and reclassification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Serotyping of E. coli, based on the O- (polysaccharide side chain) and H- (flagellar) antigens using antisera is a common practice for diagnostics, outbreak investigations, and epidemiological surveillance. The full set of E. coli serogroups comprises O-groups O1 to O181, with several O...

  19. Clonal Plasticity of Aquatic Plant Species Submitted to Mechanical Stress: Escape versus Resistance Strategy

    PubMed Central

    Puijalon, Sara; Bouma, Tjeerd J.; Van Groenendael, Jan; Bornette, Gudrun

    2008-01-01

    Background and Aims The plastic alterations of clonal architecture are likely to have functional consequences, as they affect the spatial distribution of ramets over patchy environments. However, little is known about the effect of mechanical stresses on the clonal growth. The aim of the present study was to investigate the clonal plasticity induced by mechanical stress consisting of continuous water current encountered by aquatic plants. More particularly, the aim was to test the capacity of the plants to escape this stress through clonal plastic responses. Methods The transplantation of ramets of the same clone in two contrasting flow velocity conditions was carried out for two species (Potamogeton coloratus and Mentha aquatica) which have contrasting clonal growth forms. Relative allocation to clonal growth, to creeping stems in the clonal biomass, number and total length of creeping stems, spacer length and main creeping stem direction were measured. Key Results For P. coloratus, plants exposed to water current displayed increased total length of creeping stems, increased relative allocation to creeping stems within the clonal dry mass and increased spacer length. For M. aquatica, plants exposed to current displayed increased number and total length of creeping stems. Exposure to current induced for both species a significant increase of the proportion of creeping stems in the downstream direction to the detriment of creeping stems perpendicular to flow. Conclusions This study demonstrates that mechanical stress from current flow induced plastic variation in clonal traits for both species. The responses of P. coloratus could lead to an escape strategy, with low benefits with respect to sheltering and anchorage. The responses of M. aquatica that may result in a denser canopy and enhancement of anchorage efficiency could lead to a resistance strategy. PMID:18854376

  20. Variation in resistance traits, phylogenetic backgrounds, and virulence genotypes among Escherichia coli clinical isolates from adjacent hospital campuses serving distinct patient populations.

    PubMed

    Drawz, Sarah M; Porter, Stephen; Kuskowski, Michael A; Johnston, Brian; Clabots, Connie; Kline, Susan; Ferrieri, Patricia; Johnson, James R

    2015-09-01

    Escherichia coli sequence type 13 (ST131), an emergent cause of multidrug-resistant extraintestinal infections, has important phylogenetic subsets, notably the H30 and H30Rx subclones, with distinctive resistance profiles and, possibly, clinical associations. To clarify the local prevalence of these ST131 subclones and their associations with antimicrobial resistance, ecological source, and virulence traits, we extensively characterized 233 consecutive E. coli clinical isolates (July and August 2013) from the University of Minnesota Medical Center-Fairview Infectious Diseases and Diagnostic Laboratory, Minneapolis, MN, which serves three adjacent facilities (a children's hospital and low- and high-acuity adult facilities). ST131 accounted for 26% of the study isolates (more than any other clonal group), was distributed similarly by facility, and was closely associated with ciprofloxacin resistance and extended-spectrum β-lactamase (ESBL) production. The H30 and H30Rx subclones accounted for most ST131 isolates and for the association of ST131 with fluoroquinolone resistance and ESBL production. Unlike ST131 per se, these subclones were distributed differentially by hospital, being most prevalent at the high-acuity adult facility and were absent from the children's hospital. The virulence gene profiles of ST131 and its subclones were distinctive and more extensive than those of other fluoroquinolone-resistant or ESBL-producing isolates. Within ST131, bla CTX-M-15 was confined to H30Rx isolates and other bla CTX-M variants to non-Rx H30 isolates. Pulsed-field gel electrophoresis documented a predominance of globally distributed pulsotypes and no local outbreak pattern. These findings help clarify the epidemiology, ecology, and bacterial correlates of the H30 and H30Rx ST131 subclones by documenting a high overall prevalence but significant segregation by facility, strong associations with fluoroquinolone resistance and specific ESBL variants, and distinctive

  1. Multiple ESBL-Producing Escherichia coli Sequence Types Carrying Quinolone and Aminoglycoside Resistance Genes Circulating in Companion and Domestic Farm Animals in Mwanza, Tanzania, Harbor Commonly Occurring Plasmids.

    PubMed

    Seni, Jeremiah; Falgenhauer, Linda; Simeo, Nabina; Mirambo, Mariam M; Imirzalioglu, Can; Matee, Mecky; Rweyemamu, Mark; Chakraborty, Trinad; Mshana, Stephen E

    2016-01-01

    The increased presence of extended-spectrum beta-lactamase (ESBL)-producing bacteria in humans, animals, and their surrounding environments is of global concern. Currently there is limited information on ESBL presence in rural farming communities worldwide. We performed a cross-sectional study in Mwanza, Tanzania, involving 600 companion and domestic farm animals between August/September 2014. Rectal swab/cloaca specimens were processed to identify ESBL-producing Enterobacteriaceae. We detected 130 (21.7%) animals carrying ESBL-producing bacteria, the highest carriage being among dogs and pigs [39.2% (51/130) and 33.1% (43/130), respectively]. The majority of isolates were Escherichia coli [93.3% (125/134)] and exotic breed type [OR (95%CI) = 2.372 (1.460-3.854), p-value < 0.001] was found to be a predictor of ESBL carriage among animals. Whole-genome sequences of 25 ESBL-producing E. coli were analyzed for phylogenetic relationships using multi-locus sequence typing (MLST) and core genome comparisons. Fourteen different sequence types were detected of which ST617 (7/25), ST2852 (3/25), ST1303 (3/25) were the most abundant. All isolates harbored the bla CTX-M-15 allele, 22/25 carried strA and strB, 12/25 aac(6')-lb-cr, and 11/25 qnrS1. Antibiotic resistance was associated with IncF, IncY, as well as non-typable plasmids. Eleven isolates carried pPGRT46-related plasmids, previously reported from isolates in Nigeria. Five isolates had plasmids exhibiting 85-99% homology to pCA28, previously detected in isolates from the US. Our findings indicate a pan-species distribution of ESBL-producing E. coli clonal groups in farming communities and provide evidence for plasmids harboring antibiotic resistances of regional and international impact. PMID:26904015

  2. Multiple ESBL-Producing Escherichia coli Sequence Types Carrying Quinolone and Aminoglycoside Resistance Genes Circulating in Companion and Domestic Farm Animals in Mwanza, Tanzania, Harbor Commonly Occurring Plasmids

    PubMed Central

    Seni, Jeremiah; Falgenhauer, Linda; Simeo, Nabina; Mirambo, Mariam M.; Imirzalioglu, Can; Matee, Mecky; Rweyemamu, Mark; Chakraborty, Trinad; Mshana, Stephen E.

    2016-01-01

    The increased presence of extended-spectrum beta-lactamase (ESBL)-producing bacteria in humans, animals, and their surrounding environments is of global concern. Currently there is limited information on ESBL presence in rural farming communities worldwide. We performed a cross-sectional study in Mwanza, Tanzania, involving 600 companion and domestic farm animals between August/September 2014. Rectal swab/cloaca specimens were processed to identify ESBL-producing Enterobacteriaceae. We detected 130 (21.7%) animals carrying ESBL-producing bacteria, the highest carriage being among dogs and pigs [39.2% (51/130) and 33.1% (43/130), respectively]. The majority of isolates were Escherichia coli [93.3% (125/134)] and exotic breed type [OR (95%CI) = 2.372 (1.460–3.854), p-value < 0.001] was found to be a predictor of ESBL carriage among animals. Whole-genome sequences of 25 ESBL-producing E. coli were analyzed for phylogenetic relationships using multi-locus sequence typing (MLST) and core genome comparisons. Fourteen different sequence types were detected of which ST617 (7/25), ST2852 (3/25), ST1303 (3/25) were the most abundant. All isolates harbored the blaCTX-M-15 allele, 22/25 carried strA and strB, 12/25 aac(6′)-lb-cr, and 11/25 qnrS1. Antibiotic resistance was associated with IncF, IncY, as well as non-typable plasmids. Eleven isolates carried pPGRT46-related plasmids, previously reported from isolates in Nigeria. Five isolates had plasmids exhibiting 85–99% homology to pCA28, previously detected in isolates from the US. Our findings indicate a pan-species distribution of ESBL-producing E. coli clonal groups in farming communities and provide evidence for plasmids harboring antibiotic resistances of regional and international impact. PMID:26904015

  3. Variation in Resistance Traits, Phylogenetic Backgrounds, and Virulence Genotypes among Escherichia coli Clinical Isolates from Adjacent Hospital Campuses Serving Distinct Patient Populations

    PubMed Central

    Porter, Stephen; Kuskowski, Michael A.; Johnston, Brian; Clabots, Connie; Kline, Susan; Ferrieri, Patricia; Johnson, James R.

    2015-01-01

    Escherichia coli sequence type 13 (ST131), an emergent cause of multidrug-resistant extraintestinal infections, has important phylogenetic subsets, notably the H30 and H30Rx subclones, with distinctive resistance profiles and, possibly, clinical associations. To clarify the local prevalence of these ST131 subclones and their associations with antimicrobial resistance, ecological source, and virulence traits, we extensively characterized 233 consecutive E. coli clinical isolates (July and August 2013) from the University of Minnesota Medical Center-Fairview Infectious Diseases and Diagnostic Laboratory, Minneapolis, MN, which serves three adjacent facilities (a children's hospital and low- and high-acuity adult facilities). ST131 accounted for 26% of the study isolates (more than any other clonal group), was distributed similarly by facility, and was closely associated with ciprofloxacin resistance and extended-spectrum β-lactamase (ESBL) production. The H30 and H30Rx subclones accounted for most ST131 isolates and for the association of ST131 with fluoroquinolone resistance and ESBL production. Unlike ST131 per se, these subclones were distributed differentially by hospital, being most prevalent at the high-acuity adult facility and were absent from the children's hospital. The virulence gene profiles of ST131 and its subclones were distinctive and more extensive than those of other fluoroquinolone-resistant or ESBL-producing isolates. Within ST131, blaCTX-M-15 was confined to H30Rx isolates and other blaCTX-M variants to non-Rx H30 isolates. Pulsed-field gel electrophoresis documented a predominance of globally distributed pulsotypes and no local outbreak pattern. These findings help clarify the epidemiology, ecology, and bacterial correlates of the H30 and H30Rx ST131 subclones by documenting a high overall prevalence but significant segregation by facility, strong associations with fluoroquinolone resistance and specific ESBL variants, and distinctive virulence

  4. War Wound Treatment Complications Due to Transfer of an IncN Plasmid Harboring blaOXA-181 from Morganella morganii to CTX-M-27-Producing Sequence Type 131 Escherichia coli

    PubMed Central

    Snesrud, Erik; Ong, Ana C.; Appalla, Lakshmi; Koren, Michael; Kwak, Yoon I.; Waterman, Paige E.; Lesho, Emil P.

    2015-01-01

    A 22-year-old male developed a recurrent sacral abscess associated with embedded shrapnel following a blast injury. Cultures grew extended-spectrum β-lactamase (ESBL)-producing, carbapenem-susceptible Escherichia coli. Ertapenem was administered, but the infection recurred after each course of antibiotics. Initial surgical interventions were unsuccessful, and subsequent cultures yielded E. coli and Morganella morganii, both nonsusceptible to carbapenems. The isolates were Carba NP test negative, gave ambiguous results with the modified Hodge test, and amplified the blaOXA48-like gene by real-time PCR. All E. coli isolates were sequence type 131 (ST131), carried nine resistance genes (including blaCTX-M-27) on an IncF plasmid, and were identical by genome sequencing, except for 150 kb of plasmid DNA in carbapenem-nonsusceptible isolates only. Sixty kilobases of this was shared by M. morganii and represented an IncN plasmid harboring blaOXA-181. In M. morganii, the gene was flanked by IS3000 and ISKpn19, but in all but one of the E. coli isolates containing blaOXA-181, a second copy of ISKpn19 had inserted adjacent to IS3000. To the best of our knowledge, this is the first report of blaOXA-181 in the virulent ST131 clonal group and carried by the promiscuous IncN family of plasmids. The tendency of M. morganii to have high MICs of imipenem, a blaOXA-181 substrate profile that includes penicillins but not extended-spectrum cephalosporins, and weak carbapenemase activity almost resulted in the presence of blaOXA-181 being overlooked. We highlight the importance of surveillance for carbapenem resistance in all species, even those with intrinsic resistances, and the value of advanced molecular techniques in detecting subtle genetic changes. PMID:25870058

  5. Enterohemorrhagic Escherichia coli Adhesins.

    PubMed

    McWilliams, Brian D; Torres, Alfredo G

    2014-06-01

    Adhesins are a group of proteins in enterohemorrhagic Escherichia coli (EHEC) that are involved in the attachment or colonization of this pathogen to abiotic (plastic or steel) and biological surfaces, such as those found in bovine and human intestines. This review provides the most up-to-date information on these essential adhesion factors, summarizing important historical discoveries and analyzing the current and future state of this research. In doing so, the proteins intimin and Tir are discussed in depth, especially regarding their role in the development of attaching and effacing lesions and in EHEC virulence. Further, a series of fimbrial proteins (Lpf1, Lpf2, curli, ECP, F9, ELF, Sfp, HCP, and type 1 fimbria) are also described, emphasizing their various contributions to adherence and colonization of different surfaces and their potential use as genetic markers in detection and classification of different EHEC serotypes. This review also discusses the role of several autotransporter proteins (EhaA-D, EspP, Saa and Sab, and Cah), as well as other proteins associated with adherence, such as flagella, EibG, Iha, and OmpA. While these proteins have all been studied to varying degrees, all of the adhesins summarized in this article have been linked to different stages of the EHEC life cycle, making them good targets for the development of more effective diagnostics and therapeutics. PMID:26103974

  6. Cytomegalovirus infection associated with clonal proliferation of T-cell large granular lymphocytes: causal or casual?

    PubMed

    Wong, K F; Yip, S F; So, C C; Lau, G T C; Yeung, Y M

    2003-04-01

    Clonal proliferation of T-cell large granular lymphocytes (LGL) is an indolent disorder characterized by splenomegaly, lymphocytosis and frequent manifestations of immune disturbances. The LGL are CD3(+) CD4(-) CD8(+) CD56(-). The clonality of the tumor cell population is often only demonstrable by T-cell receptor (TCR) gene rearrangement study because chromosomal abnormality is distinctly rare. We describe a case of T-cell LGL leukemia that presented initially as cytomegalovirus infection. The leukemic LGL are shown to be clonal by both TCR gene rearrangement and chromosomal studies. They persist after subsidence of the cytomegalovirus infection. PMID:12660039

  7. The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

    PubMed Central

    Lourenço, Marta; Bergman, Marie-Louise; Sobral, Daniel; Demengeot, Jocelyne; Xavier, Karina B.; Gordo, Isabel

    2014-01-01

    The accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal interference - the competition of clones carrying different beneficial mutations - which leads to the loss of many small effect mutations and fixation of large effect ones. If interference is abundant, then mechanisms for horizontal transfer of genes, which allow the immediate combination of beneficial alleles in a single background, are expected to evolve. However, the relevance of interference in natural complex environments, such as the gut, is poorly known. To address this issue, we have developed an experimental system which allows to uncover the nature of the adaptive process as Escherichia coli adapts to the mouse gut. This system shows the invasion of beneficial mutations in the bacterial populations and demonstrates the pervasiveness of clonal interference. The observed dynamics of change in frequency of beneficial mutations are consistent with soft sweeps, where different adaptive mutations with similar phenotypes, arise repeatedly on different haplotypes without reaching fixation. Despite the complexity of this ecosystem, the genetic basis of the adaptive mutations revealed a striking parallelism in independently evolving populations. This was mainly characterized by the insertion of transposable elements in both coding and regulatory regions of a few genes. Interestingly, in most populations we observed a complete phenotypic sweep without loss of genetic variation. The intense clonal interference during adaptation to the gut environment, here demonstrated, may be important for our understanding of the levels of strain diversity of E. coli inhabiting the human gut microbiota and of its recombination rate. PMID:24603313

  8. Genetic diversity and antimicrobial resistance of Escherichia coli from human and animal sources uncovers multiple resistances from human sources.

    PubMed

    Ibekwe, A Mark; Murinda, Shelton E; Graves, Alexandria K

    2011-01-01

    Escherichia coli are widely used as indicators of fecal contamination, and in some cases to identify host sources of fecal contamination in surface water. Prevalence, genetic diversity and antimicrobial susceptibility were determined for 600 generic E. coli isolates obtained from surface water and sediment from creeks and channels along the middle Santa Ana River (MSAR) watershed of southern California, USA, after a 12 month study. Evaluation of E. coli populations along the creeks and channels showed that E. coli were more prevalent in sediment compared to surface water. E. coli populations were not significantly different (P = 0.05) between urban runoff sources and agricultural sources, however, E. coli genotypes determined by pulsed-field gel electrophoresis (PFGE) were less diverse in the agricultural sources than in urban runoff sources. PFGE also showed that E. coli populations in surface water were more diverse than in the sediment, suggesting isolates in sediment may be dominated by clonal populations.Twenty four percent (144 isolates) of the 600 isolates exhibited resistance to more than one antimicrobial agent. Most multiple resistances were associated with inputs from urban runoff and involved the antimicrobials rifampicin, tetracycline, and erythromycin. The occurrence of a greater number of E. coli with multiple antibiotic resistances from urban runoff sources than agricultural sources in this watershed provides useful evidence in planning strategies for water quality management and public health protection. PMID:21687635

  9. Sequence Type 4821 Clonal Complex Serogroup B Neisseria meningitidis in China, 1978–2013

    PubMed Central

    Zhu, Bingqing; Xu, Zheng; Du, Pengcheng; Xu, Li; Sun, Xiaofang; Gao, Yuan

    2015-01-01

    Serogroup B Neisseria meningitidis strains belonging to sequence type 4821 clonal complex (CC4821), a hyperinvasive lineage first identified for serogroup C in 2003, have been increasingly isolated in China. We characterized the outer membrane protein genes of 48 serogroup B and 214 serogroup C strains belonging to CC4821 and analyzed the genomic sequences of 22 strains. Four serogroup B strains had porin A (i.e., PorA), PorB, and ferric enterobactin transport (i.e., FetA) genotypes identical to those for serogroup C. Phylogenetic analysis of the genomic sequences showed that the 22 CC4821 strains from patients and healthy carriers were unevenly clustered into 2 closely related groups; each group contained serogroup B and C strains. Serogroup B strains appeared variable at the capsule locus, and several recombination events had occurred at uncertain breakpoints. These findings suggest that CC4821 serogroup C N. meningitidis is the probable origin of highly pathogenic CC4821 serogroup B strains. PMID:25989189

  10. Modelling the epidemiology of Escherichia coli ST131 and the impact of interventions on the community and healthcare centres.

    PubMed

    Talaminos, A; López-Cerero, L; Calvillo, J; Pascual, A; Roa, L M; Rodríguez-Baño, J

    2016-07-01

    ST131 Escherichia coli is an emergent clonal group that has achieved successful worldwide spread through a combination of virulence and antimicrobial resistance. Our aim was to develop a mathematical model, based on current knowledge of the epidemiology of ESBL-producing and non-ESBL-producing ST131 E. coli, to provide a framework enabling a better understanding of its spread within the community, in hospitals and long-term care facilities, and the potential impact of specific interventions on the rates of infection. A model belonging to the SEIS (Susceptible-Exposed-Infected-Susceptible) class of compartmental models, with specific modifications, was developed. Quantification of the model is based on the law of mass preservation, which helps determine the relationships between flows of individuals and different compartments. Quantification is deterministic or probabilistic depending on subpopulation size. The assumptions for the model are based on several developed epidemiological studies. Based on the assumptions of the model, an intervention capable of sustaining a 25% reduction in person-to-person transmission shows a significant reduction in the rate of infections caused by ST131; the impact is higher for non-ESBL-producing ST131 isolates than for ESBL producers. On the other hand, an isolated intervention reducing exposure to antimicrobial agents has much more limited impact on the rate of ST131 infection. Our results suggest that interventions achieving a continuous reduction in the transmission of ST131 in households, nursing homes and hospitals offer the best chance of reducing the burden of the infections caused by these isolates. PMID:26838136

  11. Relationship between indole production and differentiation of Klebsiella species: indole-positive and -negative isolates of Klebsiella determined to be clonal.

    PubMed Central

    Maslow, J N; Brecher, S M; Adams, K S; Durbin, A; Loring, S; Arbeit, R D

    1993-01-01

    Klebsiellae are an important cause of nosocomial infections. The two clinically relevant species, Klebsiella pneumoniae and Klebsiella oxytoca, are differentiated by the ability to produce indole from tryptophan, K. oxytoca being indole positive. We report here the detailed biochemical and molecular analysis of two isolates of Klebsiella, cultured from the same urine specimen, that differed only in their ability to produce indole. The two isolates were identical as determined by ribotyping and pulsed-field gel electrophoresis, and they differed from 10 epidemiologically unrelated strains. Probing with the Escherichia coli tryptophanase operon, tna, revealed seven restriction fragment length polymorphisms (RFLP) among the 12 strains. The two index strains had identical RFLP; no single RFLP could account for all of the indole-positive or -negative strains. Thus, the identification of epidemiologically related strains of Klebsiella differing only in indole production may warrant further examination to determine whether the strains are clonal. Images PMID:8370726

  12. E. Coli Infections

    MedlinePlus

    ... You can also get the infection by swallowing water in a swimming pool contaminated with human waste. Most cases of E. coli infection get better without treatment in 5 to 10 days. NIH: National Institute ...

  13. [Enterohemorrhagic E. coli (EHEC)].

    PubMed

    Goto, Tetsushi; Shirano, Michinori

    2012-08-01

    Escherichia coli (E. coli) is a bacterium that is commonly found in the gut of humans and warm-blooded animals. Most strains of E. coli are harmless. Some strains however, such as enterohemorrhagic E. coli (EHEC), can cause severe foodborne disease. It is transmitted to humans primarily through consumption of contaminated foods, such as raw meal. EHEC produces toxins, known as verotoxins. EHEC that induces bloody diarrhea leads to HUS in 10% of cases. The clinical manifestations of post-diarrheal HUS include acute renal failure, microangiopathic hemolytic anemia, and thrombocytopenia. The verocytotoxin can directly damage renal and endothelial cells. Thrombocytopenia occurs as platelets are consumed by clotting. Hemolytic anemia results from intravascular fibrin deposition, increased fragility of red blood cells, and fragmentation. PMID:22894069

  14. Dexamethazone protects against Escherichia coli induced sickness behavior in rats.

    PubMed

    Hanaa-Mansour, A; Hassan, Wedad A; Georgy, Gehan S

    2016-01-01

    Systemic bacterial infection results in systemic inflammatory response syndrome due to the release of lipopolysaccharide (LPS) in blood that can lead to multiple organ failure, shock, and potentially death. Other impact, LPS exposure produces robust increase in anxiety-like behavior, suppression of locomotor, exploratory activity, and reduced social behavior. The therapeutic use of glucocorticoids in septic shock remains one of the first-aid approaches for their anti-inflammatory properties. The aim of this study was to evaluate the possible protective effect of dexamethazone (DEX), the most commonly used corticosteroid, against Escherichia coli (E. coli) immunohistochemical changes and neurobehavioral dysfunction. To this end, male Sprague-Dawley rats were divided into four groups; (1) Control group (2) E. coli infected group, where animals received 0.2 ml of 24 h growth of E. coli suspension in nutrient broth containing approximately 1.8×10(8) cfu/ml i.p for once, 48 h before sacrificing (3) DEX (20 mg/kg, i.p, 3 days) treated group (4) DEX and E. coli treated group. The results revealed that DEX significantly protected animals against most E. coli-induced behavioral deficits, reduced signs of cognitive impairment. DEX also reduced the LPS-evoked rise in C-reactive protein (CRP), Interferon gamma (IFγ), as well as, expression of Caspase-3. In conclusion, DEX provides neuroprotection against E. coli-associated neurobehavioral and immunological changes via its anti-inflammatory and immunomodulatory effects. PMID:26541583

  15. Escherichia coli Serotype O15:K52:H1 as a Uropathogenic Clone

    PubMed Central

    Prats, Guillem; Navarro, Ferran; Mirelis, Beatriz; Dalmau, David; Margall, Nuria; Coll, Pere; Stell, Adam; Johnson, James R.

    2000-01-01

    To clarify the clinical and bacteriological correlates of urinary-tract infection (UTI) due to Escherichia coli O15:K52:H1, during a 1-year surveillance period we prospectively screened all 1,871 significant E. coli urine isolates at the Hospital de la Santa Creu i Sant Pau, Barcelona, Spain, for this serotype and assessed the epidemiological features of community-acquired UTI due to E. coli O15:K52:H1 versus other E. coli serotypes. We also compared the 25 O15:K52:H1 UTI isolates from the present study with 22 O15:K52:H1 isolates from other, diverse geographic locales and with 23 standard control strains (8 strains from the ECOR reference collection and 15 strains of nonpathogenic O:K:H serotypes) with respect to multiple phenotypic and genotypic traits. Although E. coli O15:K52:H1 caused only 1.4% of community-acquired E. coli UTIs during the surveillance period, these UTIs were more likely to present as pyelonephritis and to occur in younger hosts, with similar risk factors, than were UTIs due to other E. coli serotypes. Irrespective of geographic origin, E. coli O15:K52:H1 strains exhibited a comparatively restricted repertoire of distinctive virulence factor profiles (typically, they were positive for papG allele II, papA allele F16, and aer and negative for sfa, afa, hly, and cnf1), biotypes, ribotypes, and amplotypes, consistent with a common clonal origin. In contrast, their antimicrobial resistance profiles were more extensive and more diverse than those of control strains. These findings indicate that E. coli O15:K52:H1 constitutes a broadly distributed and clinically significant uropathogenic clone with fluid antimicrobial resistance capabilities. PMID:10618088

  16. Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer

    PubMed Central

    Murtaza, Muhammed; Dawson, Sarah-Jane; Pogrebniak, Katherine; Rueda, Oscar M.; Provenzano, Elena; Grant, John; Chin, Suet-Feung; Tsui, Dana W. Y.; Marass, Francesco; Gale, Davina; Ali, H. Raza; Shah, Pankti; Contente-Cuomo, Tania; Farahani, Hossein; Shumansky, Karey; Kingsbury, Zoya; Humphray, Sean; Bentley, David; Shah, Sohrab P.; Wallis, Matthew; Rosenfeld, Nitzan; Caldas, Carlos

    2015-01-01

    Circulating tumour DNA analysis can be used to track tumour burden and analyse cancer genomes non-invasively but the extent to which it represents metastatic heterogeneity is unknown. Here we follow a patient with metastatic ER-positive and HER2-positive breast cancer receiving two lines of targeted therapy over 3 years. We characterize genomic architecture and infer clonal evolution in eight tumour biopsies and nine plasma samples collected over 1,193 days of clinical follow-up using exome and targeted amplicon sequencing. Mutation levels in the plasma samples reflect the clonal hierarchy inferred from sequencing of tumour biopsies. Serial changes in circulating levels of sub-clonal private mutations correlate with different treatment responses between metastatic sites. This comparison of biopsy and plasma samples in a single patient with metastatic breast cancer shows that circulating tumour DNA can allow real-time sampling of multifocal clonal evolution. PMID:26530965

  17. Clonality in myeloproliferative disorders: Analysis by means of polymerase chain reaction

    SciTech Connect

    Gilliland, D.G.; Blanchard, K.L.; Levy, J.; Perrin, S.; Bunn, H.F. )

    1991-08-01

    The myeloproliferative syndromes are acquired disorders of hematopoiesis that provide insights into the transition from somatic cell mutation to neoplasia. The clonal origin of specific blood cells can be assessed in patients with X chromosome-linked polymorphisms, taking advantage of random inactivation of the X chromosome. The authors have adapted the PCR for determination of clonality on as few as 100 cells, including individual colonies grown in culture. Amplifying a polymorphic portion of the X chromosome-linked phosphoglycerate kinase (PGK) gene after selective digestion of the active X chromosome with a methylation-sensitive restriction enzyme gave results fully concordant with standard Southern blotting of DNA samples form normal (polyclonal) polymorphonuclear cells (PMN) as well as clonal PMN from patients with myelodysplastic syndrome and polycythemia vera (PCV). They have used this technique to demonstrate heterogeneity of lineage involvement in patients with PCV. The same clinical phenotype may arise from clonal proliferation of different hematopoietic progenitors.

  18. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

    PubMed Central

    Kamvar, Zhian N.; Brooks, Jonah C.; Grünwald, Niklaus J.

    2015-01-01

    To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytical tools. With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before. We previously contributed the R package poppr specifically addressing issues with analysis of clonal populations. In this paper we provide several significant extensions to poppr with a focus on large, genome-wide SNP data. Specifically, we provide several new functionalities including the new function mlg.filter to define clone boundaries allowing for inspection and definition of what is a clonal lineage, minimum spanning networks with reticulation, a sliding-window analysis of the index of association, modular bootstrapping of any genetic distance, and analyses across any level of hierarchies. PMID:26113860

  19. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality.

    PubMed

    Kamvar, Zhian N; Brooks, Jonah C; Grünwald, Niklaus J

    2015-01-01

    To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytical tools. With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before. We previously contributed the R package poppr specifically addressing issues with analysis of clonal populations. In this paper we provide several significant extensions to poppr with a focus on large, genome-wide SNP data. Specifically, we provide several new functionalities including the new function mlg.filter to define clone boundaries allowing for inspection and definition of what is a clonal lineage, minimum spanning networks with reticulation, a sliding-window analysis of the index of association, modular bootstrapping of any genetic distance, and analyses across any level of hierarchies. PMID:26113860

  20. Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer.

    PubMed

    Murtaza, Muhammed; Dawson, Sarah-Jane; Pogrebniak, Katherine; Rueda, Oscar M; Provenzano, Elena; Grant, John; Chin, Suet-Feung; Tsui, Dana W Y; Marass, Francesco; Gale, Davina; Ali, H Raza; Shah, Pankti; Contente-Cuomo, Tania; Farahani, Hossein; Shumansky, Karey; Kingsbury, Zoya; Humphray, Sean; Bentley, David; Shah, Sohrab P; Wallis, Matthew; Rosenfeld, Nitzan; Caldas, Carlos

    2015-01-01

    Circulating tumour DNA analysis can be used to track tumour burden and analyse cancer genomes non-invasively but the extent to which it represents metastatic heterogeneity is unknown. Here we follow a patient with metastatic ER-positive and HER2-positive breast cancer receiving two lines of targeted therapy over 3 years. We characterize genomic architecture and infer clonal evolution in eight tumour biopsies and nine plasma samples collected over 1,193 days of clinical follow-up using exome and targeted amplicon sequencing. Mutation levels in the plasma samples reflect the clonal hierarchy inferred from sequencing of tumour biopsies. Serial changes in circulating levels of sub-clonal private mutations correlate with different treatment responses between metastatic sites. This comparison of biopsy and plasma samples in a single patient with metastatic breast cancer shows that circulating tumour DNA can allow real-time sampling of multifocal clonal evolution. PMID:26530965

  1. Clonal B cells in Waldenström's macroglobulinemia exhibit functional features of chronic active B-cell receptor signaling

    PubMed Central

    Argyropoulos, K V; Vogel, R; Ziegler, C; Altan-Bonnet, G; Velardi, E; Calafiore, M; Dogan, A; Arcila, M; Patel, M; Knapp, K; Mallek, C; Hunter, Z R; Treon, S P; van den Brink, M R M; Palomba, M L

    2016-01-01

    Waldenström's macroglobulinemia (WM) is a B-cell non-Hodgkin's lymphoma (B-NHL) characterized by immunoglobulin M (IgM) monoclonal gammopathy and the medullary expansion of clonal lymphoplasmacytic cells. Neoplastic transformation has been partially attributed to hyperactive MYD88 signaling, secondary to the MYD88 L265P mutation, occurring in the majority of WM patients. Nevertheless, the presence of chronic active B-cell receptor (BCR) signaling, a feature of multiple IgM+ B-NHL, remains a subject of speculation in WM. Here, we interrogated the BCR signaling capacity of primary WM cells by utilizing multiparametric phosphoflow cytometry and found heightened basal phosphorylation of BCR-related signaling proteins, and augmented phosphoresponses on surface IgM (sIgM) crosslinking, compared with normal B cells. In support of those findings we observed high sIgM expression and loss of phosphatase activity in WM cells, which could both lead to signaling potentiation in clonal cells. Finally, led by the high-signaling heterogeneity among WM samples, we generated patient-specific phosphosignatures, which subclassified patients into a ‘high' and a ‘healthy-like' signaling group, with the second corresponding to patients with a more indolent clinical phenotype. These findings support the presence of chronic active BCR signaling in WM while providing a link between differential BCR signaling utilization and distinct clinical WM subgroups. PMID:26867669

  2. [Spatial distribution paittern of Populus euphratica and P. pruinosa1 clonal ramets in Ta.rim River Basin, China].

    PubMed

    Zhao, Zheng-shuai; Zheng, Ya-qiong; Liang, Ji-ye; Han, Zhan-jiang; Li, Zhi-jun

    2016-02-01

    Spatial distribution pattern of Populus euphratica and P. pruinosa clonal ramets at three sites was studied, including natural mixed forest of P. euphratica and P. pruinosa in Awati County located in the downstream of Yarkant River, natural P. pruinosa forest in Group 16 of Nongyishi in the Tarim River upstream area, and natural P. euphratica forest in Luntai County located in the middle reach of the Tarim River. The clonal ramets of the three sites showed a cluster distribution pattern at eight sampling scales, i.e., 5 mx5 m, 5 mx10 m, 5 mx15 m, 10 mx10 m, 10 mx15 m, 15 mx15 m, 15 mx20 m, and 20 mX20 m. This pattern revealed that the cluster distribution was a basic property in the spatial distribution pattern of P. euphratica and P. pruinosa populations. At 5 mx5 m scale, negative binomial parameter was minimum, while Cassie index, patchiness inex and aggregation strength were maximum for the two ramet populations at the three sites. PMID:27396111

  3. 'Clonal pluralization of the self': a new form of delusional misidentification syndrome.

    PubMed

    Vörös, Viktor; Tényi, Tamás; Simon, Mária; Trixler, Mátyás

    2003-01-01

    The authors present a patient with paranoid schizophrenia, who has the delusion that he exists in plural numbers. The patient declares these doubles to be both psychologically and physically completely identical to him, and he believes 'them' to be in fact women. In connection with the case, the authors discuss the phenomena of reduplicative paramnesia and clonal pluralization, and they suggest introducing the psychopathological term 'clonal pluralization of the self' for the reported phenomenon. PMID:12679592

  4. Differential Influence of Clonal Integration on Morphological and Growth Responses to Light in Two Invasive Herbs

    PubMed Central

    Xu, Cheng-Yuan; Schooler, Shon S.; Van Klinken, Rieks D.

    2012-01-01

    Background and aims In contrast to seeds, high sensitivity of vegetative fragments to unfavourable environments may limit the expansion of clonal invasive plants. However, clonal integration promotes the establishment of propagules in less suitable habitats and may facilitate the expansion of clonal invaders into intact native communities. Here, we examine the influence of clonal integration on the morphology and growth of ramets in two invasive plants, Alternanthera philoxeroides and Phyla canescens, under varying light conditions. Methods In a greenhouse experiment, branches, connected ramets and severed ramets of the same mother plant were exposed under full sun and 85% shade and their morphological and growth responses were assessed. Key results The influence of clonal integration on the light reaction norm (connection×light interaction) of daughter ramets was species-specific. For A. philoxeroides, clonal integration evened out the light response (total biomass, leaf mass per area, and stem number, diameter and length) displayed in severed ramets, but these connection×light interactions were largely absent for P. canescens. Nevertheless, for both species, clonal integration overwhelmed light effect in promoting the growth of juvenile ramets during early development. Also, vertical growth, as an apparent shade acclimation response, was more prevalent in severed ramets than in connected ramets. Finally, unrooted branches displayed smaller organ size and slower growth than connected ramets, but the pattern of light reaction was similar, suggesting mother plants invest in daughter ramets prior to their own branches. Conclusions Clonal integration modifies light reaction norms of morphological and growth traits in a species-specific manner for A. philoxeroides and P. canescens, but it improves the establishment of juvenile ramets of both species in light-limiting environments by promoting their growth during early development. This factor may be partially

  5. Longevity of clonal plants: why it matters and how to measure it

    PubMed Central

    de Witte, Lucienne C.; Stöcklin, Jürg

    2010-01-01

    Background Species' life-history and population dynamics are strongly shaped by the longevity of individuals, but life span is one of the least accessible demographic traits, particularly in clonal plants. Continuous vegetative reproduction of genets enables persistence despite low or no sexual reproduction, affecting genet turnover rates and population stability. Therefore, the longevity of clonal plants is of considerable biological interest, but remains relatively poorly known. Scope Here, we critically review the present knowledge on the longevity of clonal plants and discuss its importance for population persistence. Direct life-span measurements such as growth-ring analysis in woody plants are relatively easy to take, although, for many clonal plants, these methods are not adequate due to the variable growth pattern of ramets and difficult genet identification. Recently, indirect methods have been introduced in which genet size and annual shoot increments are used to estimate genet age. These methods, often based on molecular techniques, allow the investigation of genet size and age structure of whole populations, a crucial issue for understanding their viability and persistence. However, indirect estimates of clonal longevity are impeded because the process of ageing in clonal plants is still poorly understood and because their size and age are not always well correlated. Alternative estimators for genet life span such as somatic mutations have recently been suggested. Conclusions Empirical knowledge on the longevity of clonal species has increased considerably in the last few years. Maximum age estimates are an indicator of population persistence, but are not sufficient to evaluate turnover rates and the ability of long-lived clonal plants to enhance community stability and ecosystem resilience. In order to understand the dynamics of populations it will be necessary to measure genet size and age structure, not only life spans of single individuals, and to

  6. Phenotypic bistability in Escherichia coli's central carbon metabolism

    PubMed Central

    Kotte, Oliver; Volkmer, Benjamin; Radzikowski, Jakub L; Heinemann, Matthias

    2014-01-01

    Fluctuations in intracellular molecule abundance can lead to distinct, coexisting phenotypes in isogenic populations. Although metabolism continuously adapts to unpredictable environmental changes, and although bistability was found in certain substrate-uptake pathways, central carbon metabolism is thought to operate deterministically. Here, we combine experiment and theory to demonstrate that a clonal Escherichia coli population splits into two stochastically generated phenotypic subpopulations after glucose-gluconeogenic substrate shifts. Most cells refrain from growth, entering a dormant persister state that manifests as a lag phase in the population growth curve. The subpopulation-generating mechanism resides at the metabolic core, overarches the metabolic and transcriptional networks, and only allows the growth of cells initially achieving sufficiently high gluconeogenic flux. Thus, central metabolism does not ensure the gluconeogenic growth of individual cells, but uses a population-level adaptation resulting in responsive diversification upon nutrient changes. PMID:24987115

  7. Plant Clonal Integration Mediates the Horizontal Redistribution of Soil Resources, Benefiting Neighboring Plants

    PubMed Central

    Ye, Xue-Hua; Zhang, Ya-Lin; Liu, Zhi-Lan; Gao, Shu-Qin; Song, Yao-Bin; Liu, Feng-Hong; Dong, Ming

    2016-01-01

    Resources such as water taken up by plants can be released into soils through hydraulic redistribution and can also be translocated by clonal integration within a plant clonal network. We hypothesized that the resources from one (donor) microsite could be translocated within a clonal network, released into different (recipient) microsites and subsequently used by neighbor plants in the recipient microsite. To test these hypotheses, we conducted two experiments in which connected and disconnected ramet pairs of Potentilla anserina were grown under both homogeneous and heterogeneous water regimes, with seedlings of Artemisia ordosica as neighbors. The isotopes [15N] and deuterium were used to trace the translocation of nitrogen and water, respectively, within the clonal network. The water and nitrogen taken up by P. anserina ramets in the donor microsite were translocated into the connected ramets in the recipient microsites. Most notably, portions of the translocated water and nitrogen were released into the recipient microsite and were used by the neighboring A. ordosica, which increased growth of the neighboring A. ordosica significantly. Therefore, our hypotheses were supported, and plant clonal integration mediated the horizontal hydraulic redistribution of resources, thus benefiting neighboring plants. Such a plant clonal integration-mediated resource redistribution in horizontal space may have substantial effects on the interspecific relations and composition of the community and consequently on ecosystem processes. PMID:26904051

  8. Chromosome aberrations of clonal origin are present in astronauts' blood lymphocytes

    NASA Technical Reports Server (NTRS)

    George, K.; Durante, M.; Willingham, V.; Cucinotta, F. A.

    2004-01-01

    Radiation-induced chromosome translocations remain in peripheral blood cells over many years, and can potentially be used to measure retrospective doses or prolonged low-dose rate exposures. However, several recent studies have indicated that some individuals possess clones of cells with balanced chromosome abnormalities, which can result in an overestimation of damage and, therefore, influence the accuracy of dose calculations. We carefully examined the patterns of chromosome damage found in the blood lymphocytes of twelve astronauts, and also applied statistical methods to screen for the presence of potential clones. Cells with clonal aberrations were identified in three of the twelve individuals. These clonal cells were present in samples collected both before and after space flight, and yields are higher than previously reported for healthy individuals in this age range (40-52 years of age). The frequency of clonal damage appears to be even greater in chromosomes prematurely condensed in interphase, when compared with equivalent analysis in metaphase cells. The individuals with clonal aberrations were followed-up over several months and the yields of all clones decreased during this period. Since clonal aberrations may be associated with increased risk of tumorigenesis, it is important to accurately identify cells containing clonal rearrangements for risk assessment as well as biodosimetry. Copyright 2003 S. Karger AG, Basel.

  9. Clonal hematopoiesis of indeterminate potential and its distinction from myelodysplastic syndromes

    PubMed Central

    Bejar, Rafael; Jaiswal, Siddhartha; Lindsley, R. Coleman; Sekeres, Mikkael A.; Hasserjian, Robert P.; Ebert, Benjamin L.

    2015-01-01

    Recent genetic analyses of large populations have revealed that somatic mutations in hematopoietic cells leading to clonal expansion are commonly acquired during human aging. Clonally restricted hematopoiesis is associated with an increased risk of subsequent diagnosis of myeloid or lymphoid neoplasia and increased all-cause mortality. Although myelodysplastic syndromes (MDS) are defined by cytopenias, dysplastic morphology of blood and marrow cells, and clonal hematopoiesis, most individuals who acquire clonal hematopoiesis during aging will never develop MDS. Therefore, acquisition of somatic mutations that drive clonal expansion in the absence of cytopenias and dysplastic hematopoiesis can be considered clonal hematopoiesis of indeterminate potential (CHIP), analogous to monoclonal gammopathy of undetermined significance and monoclonal B-cell lymphocytosis, which are precursor states for hematologic neoplasms but are usually benign and do not progress. Because mutations are frequently observed in healthy older persons, detection of an MDS-associated somatic mutation in a cytopenic patient without other evidence of MDS may cause diagnostic uncertainty. Here we discuss the nature and prevalence of CHIP, distinction of this state from MDS, and current areas of uncertainty regarding diagnostic criteria for myeloid malignancies. PMID:25931582

  10. [Fitness analysis of seed- and vegetative reproduction of clonal tree Symplocos laurina].

    PubMed

    Zhang, Yunchun; Du, Xiaojun; Zhang, Qiaoying; Gao, Xianming; Su, Zhixian

    2005-09-01

    There are two ways in Symplocos laurina propagation, clonal and sexual reproduction. The study showed that under different habitat conditions, Symplocos laurina could adopt different ways to propagate and occupy space. In conditions with abundant water and nutrient resources, such as in evergreen broad-leaved forests or bamboo forests, the survival rate and space-occupying ability of both ramets and sexual seedlings were relatively high, with clonal ramets took advantage in terms of number and space, suggesting that clonal propagation was the dominant way in such environments. Oppositely, in habitats lack of sufficient nutrition, the survival rate and space-occupying ability of seedlings were low, and grown-up plantlets would preempt in number and space occupation. Bottleneck in sexual propagation appeared in the stage from seed to seedling, while clonal propagation appeared during the period from seedling to ramet. The way of Symplocos laurina invasion was to settle a plantlet, and then occupied the space rapidly by clonal growth, with clonal seedlings dominated in initial stage and lost the advantage after 15 ages. PMID:16355784

  11. Clonal cell populations unresponsive to radiosensitization induced by telomerase inhibition

    SciTech Connect

    Ju, Yeun-Jin; Shin, Hyun-Jin; Park, Jeong-Eun; Juhn, Kyoung-Mi; Woo, Seon Rang; Kim, Hee-Young; Han, Young-Hoon; Hwang, Sang-Gu; Hong, Sung-Hee; Kang, Chang-Mo; Yoo, Young-Do; Park, Won-Bong; Cho, Myung-Haing; Park, Gil Hong; Lee, Kee-Ho

    2010-11-12

    Research highlights: {yields} In our present manuscript, we have clearly showed an interesting but problematic obstacle of a radiosensitization strategy based on telomerase inhibition by showing that: Clonal population unresponsive to this radiosensitization occasionally arise. {yields} The telomere length of unsensitized clones was reduced, as was that of most sensitized clones. {yields} The unsensitized clones did not show chromosome end fusion which was noted in all sensitized clones. {yields} P53 status is not associated with the occurrence of unsensitized clone. {yields} Telomere end capping in unsensitized clone is operative even under telomerase deficiency. -- Abstract: A combination of a radiotherapeutic regimen with telomerase inhibition is valuable when tumor cells are to be sensitized to radiation. Here, we describe cell clones unresponsive to radiosensitization after telomere shortening. After extensive division of individual transformed clones of mTERC{sup -/-} cells, about 22% of clones were unresponsive to radiosensitization even though telomerase action was inhibited. The telomere lengths of unsensitized mTERC{sup -/-} clones were reduced, as were those of most sensitized clones. However, the unsensitized clones did not exhibit chromosomal end-to-end fusion to the extent noted in all sensitized clones. Thus, a defense mechanism preventing telomere erosion is operative even when telomeres become shorter under conditions of telomerase deficiency, and results in unresponsiveness to the radiosensitization generally mediated by telomere shortening.

  12. Clonal selection drives genetic divergence of metastatic medulloblastoma.

    PubMed

    Wu, Xiaochong; Northcott, Paul A; Dubuc, Adrian; Dupuy, Adam J; Shih, David J H; Witt, Hendrik; Croul, Sidney; Bouffet, Eric; Fults, Daniel W; Eberhart, Charles G; Garzia, Livia; Van Meter, Timothy; Zagzag, David; Jabado, Nada; Schwartzentruber, Jeremy; Majewski, Jacek; Scheetz, Todd E; Pfister, Stefan M; Korshunov, Andrey; Li, Xiao-Nan; Scherer, Stephen W; Cho, Yoon-Jae; Akagi, Keiko; MacDonald, Tobey J; Koster, Jan; McCabe, Martin G; Sarver, Aaron L; Collins, V Peter; Weiss, William A; Largaespada, David A; Collier, Lara S; Taylor, Michael D

    2012-02-23

    Medulloblastoma, the most common malignant paediatric brain tumour, arises in the cerebellum and disseminates through the cerebrospinal fluid in the leptomeningeal space to coat the brain and spinal cord. Dissemination, a marker of poor prognosis, is found in up to 40% of children at diagnosis and in most children at the time of recurrence. Affected children therefore are treated with radiation to the entire developing brain and spinal cord, followed by high-dose chemotherapy, with the ensuing deleterious effects on the developing nervous system. The mechanisms of dissemination through the cerebrospinal fluid are poorly studied, and medulloblastoma metastases have been assumed to be biologically similar to the primary tumour. Here we show that in both mouse and human medulloblastoma, the metastases from an individual are extremely similar to each other but are divergent from the matched primary tumour. Clonal genetic events in the metastases can be demonstrated in a restricted subclone of the primary tumour, suggesting that only rare cells within the primary tumour have the ability to metastasize. Failure to account for the bicompartmental nature of metastatic medulloblastoma could be a major barrier to the development of effective targeted therapies. PMID:22343890

  13. Global evolution of multidrug-resistant Acinetobacter baumannii clonal lineages.

    PubMed

    Zarrilli, Raffaele; Pournaras, Spyros; Giannouli, Maria; Tsakris, Athanassios

    2013-01-01

    The rapid expansion of Acinetobacter baumannii clinical isolates exhibiting resistance to carbapenems and most or all available antibiotics during the last decade is a worrying evolution. The apparent predominance of a few successful multidrug-resistant lineages worldwide underlines the importance of elucidating the mode of spread and the epidemiology of A. baumannii isolates in single hospitals, at a country-wide level and on a global scale. The evolutionary advantage of the dominant clonal lineages relies on the capability of the A. baumannii pangenome to incorporate resistance determinants. In particular, the simultaneous presence of divergent strains of the international clone II and their increasing prevalence in international hospitals further support the ongoing adaptation of this lineage to the hospital environment. Indeed, genomic and genetic studies have elucidated the role of mobile genetic elements in the transfer of antibiotic resistance genes and substantiate the rate of genetic alterations associated with acquisition in A. baumannii of various resistance genes, including OXA- and metallo-β-lactamase-type carbapenemase genes. The significance of single nucleotide polymorphisms and transposon mutagenesis in the evolution of A. baumannii has been also documented. Establishment of a network of reference laboratories in different countries would generate a more complete picture and a fuller understanding of the importance of high-risk A. baumannii clones in the international dissemination of antibiotic resistance. PMID:23127486

  14. Emerging sporotrichosis is driven by clonal and recombinant Sporothrix species.

    PubMed

    Rodrigues, Anderson Messias; de Hoog, GSybren; Zhang, Yu; de Camargo, Zoilo Pires

    2014-05-01

    Sporotrichosis, caused by agents of the fungal genus Sporothrix, occurs worldwide, but the infectious species are not evenly distributed. Sporothrix propagules usually gain entry into the warm-blooded host through minor trauma to the skin from contaminated plant debris or through scratches or bites from felines carrying the disease, generally in the form of outbreaks. Over the last decade, sporotrichosis has changed from a relatively obscure endemic infection to an epidemic zoonotic health problem. We evaluated the impact of the feline host on the epidemiology, spatial distribution, prevalence and genetic diversity of human sporotrichosis. Nuclear and mitochondrial markers revealed large structural genetic differences between S. brasiliensis and S. schenckii populations, suggesting that the interplay of host, pathogen and environment has a structuring effect on the diversity, frequency and distribution of Sporothrix species. Phylogenetic data support a recent habitat shift within S. brasiliensis from plant to cat that seems to have occurred in southeastern Brazil and is responsible for its emergence. A clonal structure was found in the early expansionary phase of the cat-human epidemic. However, the prevalent recombination structure in the plant-associated pathogen S. schenckii generates a diversity of genotypes that did not show any significant increase in frequency as etiological agents of human infection over time. These results suggest that closely related pathogens can follow different strategies in epidemics. Thus, species-specific types of transmission may require distinct public health strategies for disease control. PMID:26038739

  15. Clonal dominance among T-lymphocyte infiltrates in arthritis

    SciTech Connect

    Stamenkovic, I.; Stegagno, M.; Wright, K.A.; Krane, S.M.; Amento, E.P.; Colvin, R.B.; Duquesnoy, R.J.; Kurnick, J.T.

    1988-02-01

    Synovial membranes in patients with rheumatoid arthritis as well as other types of chronic destructive inflammatory arthritis contain infiltrates of activated T lymphocytes that probably contribute to the pathogenesis of the disease. In an effort to elucidate the nature of these infiltrates, interleukin 2 (IL-2)-responsive T lymphocytes were grown out of synovial fragments from 14 patients undergoing surgery for advanced destructive inflammatory joint disease. Eleven of the samples examined were from patients with classical rheumatoid arthritis, while three others were obtained from individuals with clinical osteoarthritis. Southern blot analysis of T-cell receptor (TCR) ..beta..-chain genes in 13 of 14 cultures showed distinct rearrangements, indicating that each culture was characterized by the predominance of a limited number of clones. T-cell populations from peripheral blood stimulated with a variety of activators and expanded with IL-2 did not demonstrate evidence of similar clonality in long-term culture. These results suggest that a limited number of activated T-cell clones predominate at the site of tissue injury in rheumatoid synovial membranes as well as in other types of destructive inflammatory joint disease. Further characterization of these T-cell clones may aid our understanding of the pathogenesis of these rheumatic disorders.

  16. Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution

    PubMed Central

    Bozic, Ivana; Gerold, Jeffrey M.; Nowak, Martin A.

    2016-01-01

    The vast majority of mutations in the exome of cancer cells are passengers, which do not affect the reproductive rate of the cell. Passengers can provide important information about the evolutionary history of an individual cancer, and serve as a molecular clock. Passengers can also become targets for immunotherapy or confer resistance to treatment. We study the stochastic expansion of a population of cancer cells describing the growth of primary tumors or metastatic lesions. We first analyze the process by looking forward in time and calculate the fixation probabilities and frequencies of successive passenger mutations ordered by their time of appearance. We compute the likelihood of specific evolutionary trees, thereby informing the phylogenetic reconstruction of cancer evolution in individual patients. Next, we derive results looking backward in time: for a given subclonal mutation we estimate the number of cancer cells that were present at the time when that mutation arose. We derive exact formulas for the expected numbers of subclonal mutations of any frequency. Fitting this formula to cancer sequencing data leads to an estimate for the ratio of birth and death rates of cancer cells during the early stages of clonal expansion. PMID:26828429

  17. Genetic variegation of clonal architecture and propagating cells in leukaemia.

    PubMed

    Anderson, Kristina; Lutz, Christoph; van Delft, Frederik W; Bateman, Caroline M; Guo, Yanping; Colman, Susan M; Kempski, Helena; Moorman, Anthony V; Titley, Ian; Swansbury, John; Kearney, Lyndal; Enver, Tariq; Greaves, Mel

    2011-01-20

    Little is known of the genetic architecture of cancer at the subclonal and single-cell level or in the cells responsible for cancer clone maintenance and propagation. Here we have examined this issue in childhood acute lymphoblastic leukaemia in which the ETV6-RUNX1 gene fusion is an early or initiating genetic lesion followed by a modest number of recurrent or 'driver' copy number alterations. By multiplexing fluorescence in situ hybridization probes for these mutations, up to eight genetic abnormalities can be detected in single cells, a genetic signature of subclones identified and a composite picture of subclonal architecture and putative ancestral trees assembled. Subclones in acute lymphoblastic leukaemia have variegated genetics and complex, nonlinear or branching evolutionary histories. Copy number alterations are independently and reiteratively acquired in subclones of individual patients, and in no preferential order. Clonal architecture is dynamic and is subject to change in the lead-up to a diagnosis and in relapse. Leukaemia propagating cells, assayed by serial transplantation in NOD/SCID IL2Rγ(null) mice, are also genetically variegated, mirroring subclonal patterns, and vary in competitive regenerative capacity in vivo. These data have implications for cancer genomics and for the targeted therapy of cancer. PMID:21160474

  18. Clonal propagation of Cyclamen persicum via somatic embryogenesis.

    PubMed

    Winkelmann, Traud

    2010-01-01

    Cyclamen (Cyclamen persicum) is an economically important ornamental pot plant with local use as cut flower as well. Traditionally, it is propagated via seeds, but interest is given in vegetative propagation of parental lines as well as superior single plants. Somatic embryogenesis is an efficient in vitro propagation method for many cyclamen cultivars. Starting from ovules of unpollinated flowers, callus is induced and propagated in a medium containing 2,4-dichlorophenoxyacetic acid (2,4-D) and 6-(gamma,gamma-dimethylallylamino)purine (2iP). Transfer to hormone-free medium results in the differentiation of somatic embryos, which afterwards germinate on the same medium. These first culture stages take about 6-7 months and are carried out in complete darkness. Two to four months after the transfer to light, plantlets develop which can be acclimatized in the greenhouse. The regenerated plants are characterized by low percentages of somaclonal variation. This protocol has proven useful not only for clonal propagation, but also for artificial seed preparation, cryopreservation, genetic transformation and protoplast regeneration. PMID:20099110

  19. Adapting populations in space: clonal interference and genetic diversity

    NASA Astrophysics Data System (ADS)

    Weissman, Daniel; Barton, Nick

    Most species inhabit ranges much larger than the scales over which individuals interact. How does this spatial structure interact with adaptive evolution? We consider a simple model of a spatially-extended, adapting population and show that, while clonal interference severely limits the adaptation of purely asexual populations, even rare recombination is enough to allow adaptation at rates approaching those of well-mixed populations. We also find that the genetic hitchhiking produced by the adaptive alleles sweeping through the population has strange effects on the patterns of genetic diversity. In large spatial ranges, even low rates of adaptation cause all individuals in the population to rapidly trace their ancestry back to individuals living in a small region in the center of the range. The probability of fixation of an allele is thus strongly dependent on the allele's spatial location, with alleles from the center favored. Surprisingly, these effects are seen genome-wide (instead of being localized to the regions of the genome undergoing the sweeps). The spatial concentration of ancestry produces a power-law dependence of relatedness on distance, so that even individuals sampled far apart are likely to be fairly closely related, masking the underlying spatial structure.

  20. Is cancer really a 'local' cellular clonal disease?

    PubMed

    Bronchud, M H

    2002-11-01

    Cancer is not simply the result of specific genetic alterations in key regulatory genes, but rather a complex multistep process involving selection of a clonal population of cells. To accumulate three, or often as many as seven, specific mutations in a single cell without incurring a significant number of additional mutations that might lead to cell lethality requires a large number of target cells, some mutagenic activity acting on those target cells for a variable period of time, and efficient selection strategies, which may be to some extent tissue-specific. A number of 'protective' intracellular regulatory circuits might be present in proliferating cells deliberately to protect against carcinogenesis. If it does require some seven sequential carcinogenic 'genetic hits' in a single cellular clone for a malignant tumor to develop, it is mathematically more likely to occur in a tissue with a high background of genetic alterations in neighboring cellular clones, than in a tissue with a low background of such alterations, or with no detectable carcinogenic mutations at all. In this context, the old 'field cancerization' theory by Slaughter and the more recent 'multistep carcinogenesis' model by Fearon and Vogelstein can come together in a single model: 'multistep field cancerization'. This simple conclusion, and our ability to measure 'background carcinogenesis' in different parts of the body, might allow early detection of cancer risk, and eventually help us to develop suitable therapeutic strategies to delay or suppress the carcinogenic process. Molecular technologies are just beginning to be sufficiently sensitive to start testing the hypothesis. PMID:12376079

  1. Detectable clonal mosaicism and its relationship to aging and cancer

    PubMed Central

    Jacobs, Kevin B; Yeager, Meredith; Zhou, Weiyin; Wacholder, Sholom; Wang, Zhaoming; Rodriguez-Santiago, Benjamin; Hutchinson, Amy; Deng, Xiang; Liu, Chenwei; Horner, Marie-Josephe; Cullen, Michael; Epstein, Caroline G; Burdett, Laurie; Dean, Michael C; Chatterjee, Nilanjan; Sampson, Joshua; Chung, Charles C; Kovaks, Joseph; Gapstur, Susan M; Stevens, Victoria L; Teras, Lauren T; Gaudet, Mia M; Albanes, Demetrius; Weinstein, Stephanie J; Virtamo, Jarmo; Taylor, Philip R; Freedman, Neal D; Abnet, Christian C; Goldstein, Alisa M; Hu, Nan; Yu, Kai; Yuan, Jian-Min; Liao, Linda; Ding, Ti; Qiao, You-Lin; Gao, Yu-Tang; Koh, Woon-Puay; Xiang, Yong-Bing; Tang, Ze-Zhong; Fan, Jin-Hu; Aldrich, Melinda C; Amos, Christopher; Blot, William J; Bock, Cathryn H; Gillanders, Elizabeth M; Harris, Curtis C; Haiman, Christopher A; Henderson, Brian E; Kolonel, Laurence N; Le Marchand, Loic; McNeill, Lorna H; Rybicki, Benjamin A; Schwartz, Ann G; Signorello, Lisa B; Spitz, Margaret R; Wiencke, John K; Wrensch, Margaret; Wu, Xifeng; Zanetti, Krista A; Ziegler, Regina G; Figueroa, Jonine D; Garcia-Closas, Montserrat; Malats, Nuria; Marenne, Gaelle; Prokunina-Olsson, Ludmila; Baris, Dalsu; Schwenn, Molly; Johnson, Alison; Landi, Maria Teresa; Goldin, Lynn; Consonni, Dario; Bertazzi, Pier Alberto; Rotunno, Melissa; Rajaraman, Preetha; Andersson, Ulrika; Freeman, Laura E Beane; Berg, Christine D; Buring, Julie E; Butler, Mary A; Carreon, Tania; Feychting, Maria; Ahlbom, Anders; Gaziano, J Michael; Giles, Graham G; Hallmans, Goran; Hankinson, Susan E; Hartge, Patricia; Henriksson, Roger; Inskip, Peter D; Johansen, Christoffer; Landgren, Annelie; McKean-Cowdin, Roberta; Michaud, Dominique S; Melin, Beatrice S; Peters, Ulrike; Ruder, Avima M; Sesso, Howard D; Severi, Gianluca; Shu, Xiao-Ou; Visvanathan, Kala; White, Emily; Wolk, Alicja; Zeleniuch-Jacquotte, Anne; Zheng, Wei; Silverman, Debra T; Kogevinas, Manolis; Gonzalez, Juan R; Villa, Olaya; Li, Donghui; Duell, Eric J; Risch, Harvey A; Olson, Sara H; Kooperberg, Charles; Wolpin, Brian M; Jiao, Li; Hassan, Manal; Wheeler, William; Arslan, Alan A; Bas Bueno-de-Mesquita, H; Fuchs, Charles S; Gallinger, Steven; Gross, Myron D; Holly, Elizabeth A; Klein, Alison P; LaCroix, Andrea; Mandelson, Margaret T; Petersen, Gloria; Boutron-Ruault, Marie-Christine; Bracci, Paige M; Canzian, Federico; Chang, Kenneth; Cotterchio, Michelle; Giovannucci, Edward L; Goggins, Michael; Bolton, Judith A Hoffman; Jenab, Mazda; Khaw, Kay-Tee; Krogh, Vittorio; Kurtz, Robert C; McWilliams, Robert R; Mendelsohn, Julie B; Rabe, Kari G; Riboli, Elio; Tjønneland, Anne; Tobias, Geoffrey S; Trichopoulos, Dimitrios; Elena, Joanne W; Yu, Herbert; Amundadottir, Laufey; Stolzenberg-Solomon, Rachael Z; Kraft, Peter; Schumacher, Fredrick; Stram, Daniel; Savage, Sharon A; Mirabello, Lisa; Andrulis, Irene L; Wunder, Jay S; García, Ana Patiño; Sierrasesúmaga, Luis; Barkauskas, Donald A; Gorlick, Richard G; Purdue, Mark; Chow, Wong-Ho; Moore, Lee E; Schwartz, Kendra L; Davis, Faith G; Hsing, Ann W; Berndt, Sonja I; Black, Amanda; Wentzensen, Nicolas; Brinton, Louise A; Lissowska, Jolanta; Peplonska, Beata; McGlynn, Katherine A; Cook, Michael B; Graubard, Barry I; Kratz, Christian P; Greene, Mark H; Erickson, Ralph L; Hunter, David J; Thomas, Gilles; Hoover, Robert N; Real, Francisco X; Fraumeni, Joseph F; Caporaso, Neil E; Tucker, Margaret; Rothman, Nathaniel; Pérez-Jurado, Luis A; Chanock, Stephen J

    2012-01-01

    In an analysis of 31,717 cancer cases and 26,136 cancer-free controls drawn from 13 genome-wide association studies (GWAS), we observed large chromosomal abnormalities in a subset of clones from DNA obtained from blood or buccal samples. Mosaic chromosomal abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of size >2 Mb were observed in autosomes of 517 individuals (0.89%) with abnormal cell proportions between 7% and 95%. In cancer-free individuals, the frequency increased with age; 0.23% under 50 and 1.91% between 75 and 79 (p=4.8×10−8). Mosaic abnormalities were more frequent in individuals with solid-tumors (0.97% versus 0.74% in cancer-free individuals, OR=1.25, p=0.016), with a stronger association for cases who had DNA collected prior to diagnosis or treatment (OR=1.45, p=0.0005). Detectable clonal mosaicism was common in individuals for whom DNA was collected at least one year prior to diagnosis of leukemia compared to cancer-free individuals (OR=35.4, p=3.8×10−11). These findings underscore the importance of the role and time-dependent nature of somatic events in the etiology of cancer and other late-onset diseases. PMID:22561519

  2. Timing of induced resistance in a clonal plant network.

    PubMed

    Gómez, Sara; van Dijk, William; Stuefer, Josef F

    2010-05-01

    After local herbivory, plants can activate defense traits both at the damaged site and in undamaged plant parts such as in connected ramets of clonal plants. Since defense induction has costs, a mismatch in time and space between defense activation and herbivore feeding might result in negative consequences for plant fitness. A short time lag between attack and defense activation is important to ensure efficient protection of the plant. Additionally, the duration of induced defense production once the attack has stopped is also relevant in assessing the cost-benefit balance of inducible defenses, which will depend on the absence or presence of subsequent attacks. In this study we quantified the timing of induced responses in ramet networks of the stoloniferous herb Trifolium repens after local damage by Mamestra brassicae larvae. We studied the activation time of systemic defense induction in undamaged ramets and the decay time of the response after local attack. Undamaged ramets became defense-induced 38-51 h after the initial attack. Defense induction was measured as a reduction in leaf palatability. Defense induction lasted at least 28 days, and there was strong genotypic variation in the duration of this response. Ramets formed after the initial attack were also defense-induced, implying that induced defense can extend to new ramet generations, thereby contributing to protection of plant tissue that is both very vulnerable to herbivores and most valuable in terms of future plant growth and fitness. PMID:20522188

  3. Emerging sporotrichosis is driven by clonal and recombinant Sporothrix species

    PubMed Central

    Rodrigues, Anderson Messias; de Hoog, GSybren; Zhang, Yu; de Camargo, Zoilo Pires

    2014-01-01

    Sporotrichosis, caused by agents of the fungal genus Sporothrix, occurs worldwide, but the infectious species are not evenly distributed. Sporothrix propagules usually gain entry into the warm-blooded host through minor trauma to the skin from contaminated plant debris or through scratches or bites from felines carrying the disease, generally in the form of outbreaks. Over the last decade, sporotrichosis has changed from a relatively obscure endemic infection to an epidemic zoonotic health problem. We evaluated the impact of the feline host on the epidemiology, spatial distribution, prevalence and genetic diversity of human sporotrichosis. Nuclear and mitochondrial markers revealed large structural genetic differences between S. brasiliensis and S. schenckii populations, suggesting that the interplay of host, pathogen and environment has a structuring effect on the diversity, frequency and distribution of Sporothrix species. Phylogenetic data support a recent habitat shift within S. brasiliensis from plant to cat that seems to have occurred in southeastern Brazil and is responsible for its emergence. A clonal structure was found in the early expansionary phase of the cat–human epidemic. However, the prevalent recombination structure in the plant-associated pathogen S. schenckii generates a diversity of genotypes that did not show any significant increase in frequency as etiological agents of human infection over time. These results suggest that closely related pathogens can follow different strategies in epidemics. Thus, species-specific types of transmission may require distinct public health strategies for disease control. PMID:26038739

  4. Clonal competition with alternating dominance in multiple myeloma

    PubMed Central

    Keats, Jonathan J.; Chesi, Marta; Egan, Jan B.; Garbitt, Victoria M.; Palmer, Stephen E.; Braggio, Esteban; Van Wier, Scott; Blackburn, Patrick R.; Baker, Angela S.; Dispenzieri, Angela; Kumar, Shaji; Rajkumar, S. Vincent; Carpten, John D.; Barrett, Michael; Fonseca, Rafael; Stewart, A. Keith

    2012-01-01

    Emerging evidence indicates that tumors can follow several evolutionary paths over a patient's disease course. With the use of serial genomic analysis of samples collected at different points during the disease course of 28 patients with multiple myeloma, we found that the genomes of standard-risk patients show few changes over time, whereas those of cytogenetically high-risk patients show significantly more changes over time. The results indicate the existence of 3 temporal tumor types, which can either be genetically stable, linearly evolving, or heterogeneous clonal mixtures with shifting predominant clones. A detailed analysis of one high-risk patient sampled at 7 time points over the entire disease course identified 2 competing subclones that alternate in a back and forth manner for dominance with therapy until one clone underwent a dramatic linear evolution. With the use of the Vk*MYC genetically engineered mouse model of myeloma we modeled this competition between subclones for predominance occurring spontaneously and with therapeutic selection. PMID:22498740

  5. Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution.

    PubMed

    Zhao, Boyang; Sedlak, Joseph C; Srinivas, Raja; Creixell, Pau; Pritchard, Justin R; Tidor, Bruce; Lauffenburger, Douglas A; Hemann, Michael T

    2016-03-24

    The prevailing approach to addressing secondary drug resistance in cancer focuses on treating the resistance mechanisms at relapse. However, the dynamic nature of clonal evolution, along with potential fitness costs and cost compensations, may present exploitable vulnerabilities-a notion that we term "temporal collateral sensitivity." Using a combined pharmacological screen and drug resistance selection approach in a murine model of Ph(+) acute lymphoblastic leukemia, we indeed find that temporal and/or persistent collateral sensitivity to non-classical BCR-ABL1 drugs arises in emergent tumor subpopulations during the evolution of resistance toward initial treatment with BCR-ABL1-targeted inhibitors. We determined the sensitization mechanism via genotypic, phenotypic, signaling, and binding measurements in combination with computational models and demonstrated significant overall survival extension in mice. Additional stochastic mathematical models and small-molecule screens extended our insights, indicating the value of focusing on evolutionary trajectories and pharmacological profiles to identify new strategies to treat dynamic tumor vulnerabilities. PMID:26924578

  6. Decoding astrocyte heterogeneity: New tools for clonal analysis.

    PubMed

    Bribián, A; Figueres-Oñate, M; Martín-López, E; López-Mascaraque, L

    2016-05-26

    The importance of astrocyte heterogeneity came out as a hot topic in neurosciences especially over the last decades, when the development of new methodologies allowed demonstrating the existence of big differences in morphological, neurochemical and physiological features between astrocytes. However, although the knowledge about the biology of astrocytes is increasing rapidly, an important characteristic that remained unexplored, until the last years, has been the relationship between astrocyte lineages and cell heterogeneity. To fill this gap, a new method called StarTrack was recently developed, a powerful genetic tool that allows tracking astrocyte lineages forming cell clones. Using StarTrack, a single astrocyte progenitor and its progeny can be specifically labeled from its generation, during embryonic development, to its final fate in the adult brain. Because of this specific labeling, astrocyte clones, exhibiting heterogeneous morphologies and features, can be easily analyzed in relation to their ontogenetic origin. This review summarizes how astrocyte heterogeneity can be decoded studying the embryonic development of astrocyte lineages and their clonal relationship. Finally, we discuss about some of the challenges and opportunities emerging in this exciting area of investigation. PMID:25917835

  7. Affected chromosome homeostasis and genomic instability of clonal yeast cultures.

    PubMed

    Adamczyk, Jagoda; Deregowska, Anna; Panek, Anita; Golec, Ewelina; Lewinska, Anna; Wnuk, Maciej

    2016-05-01

    Yeast cells originating from one single colony are considered genotypically and phenotypically identical. However, taking into account the cellular heterogeneity, it seems also important to monitor cell-to-cell variations within a clone population. In the present study, a comprehensive yeast karyotype screening was conducted using single chromosome comet assay. Chromosome-dependent and mutation-dependent changes in DNA (DNA with breaks or with abnormal replication intermediates) were studied using both single-gene deletion haploid mutants (bub1, bub2, mad1, tel1, rad1 and tor1) and diploid cells lacking one active gene of interest, namely BUB1/bub1, BUB2/bub2, MAD1/mad1, TEL1/tel1, RAD1/rad1 and TOR1/tor1 involved in the control of cell cycle progression, DNA repair and the regulation of longevity. Increased chromosome fragility and replication stress-mediated chromosome abnormalities were correlated with elevated incidence of genomic instability, namely aneuploid events-disomies, monosomies and to a lesser extent trisomies as judged by in situ comparative genomic hybridization (CGH). The tor1 longevity mutant with relatively balanced chromosome homeostasis was found the most genomically stable among analyzed mutants. During clonal yeast culture, spontaneously formed abnormal chromosome structures may stimulate changes in the ploidy state and, in turn, promote genomic heterogeneity. These alterations may be more accented in selected mutated genetic backgrounds, namely in yeast cells deficient in proper cell cycle regulation and DNA repair. PMID:26581629

  8. Phenotypes and Virulence among Staphylococcus aureus USA100, USA200, USA300, USA400, and USA600 Clonal Lineages

    PubMed Central

    King, Jessica M.; Kulhankova, Katarina; Stach, Christopher S.; Vu, Bao G.

    2016-01-01

    ABSTRACT Staphylococcus aureus diseases affect ~500,000 individuals per year in the United States. Worldwide, the USA100, USA200, USA400, and USA600 lineages cause many of the life-threatening S. aureus infections, such as bacteremia, infective endocarditis, pneumonia, toxic shock syndrome, and surgical site infections. However, the virulence mechanisms associated with these clonal lineages, in particular the USA100 and USA600 isolates, have been severely understudied. We investigated the virulence of these strains, in addition to strains in the USA200, USA300, and USA400 types, in well-established in vitro assays and in vivo in the rabbit model of infective endocarditis and sepsis. We show in the infective endocarditis and sepsis model that strains in the USA100 and USA600 lineages cause high lethality and are proficient in causing native valve infective endocarditis. Strains with high cytolytic activity or producing toxic shock syndrome toxin 1 (TSST-1) or staphylococcal enterotoxin C (SEC) caused lethal sepsis, even with low cytolytic activity. Strains in the USA100, USA200, USA400, and USA600 lineages consistently contained genes that encode for the enterotoxin gene cluster proteins, SEC, or TSST-1 and were proficient at causing infective endocarditis, while the USA300 strains lacked these toxins and were deficient in promoting vegetation growth. The USA100, USA200, and USA400 strains in our collection formed strong biofilms in vitro, whereas the USA200 and USA600 strains exhibited increased blood survival. Hence, infective endocarditis and lethal sepsis are multifactorial and not intrinsic to any one individual clonal group, further highlighting the importance of expanding our knowledge of S. aureus pathogenesis to clonal lineages causative of invasive disease. IMPORTANCE S. aureus is the leading cause of infective endocarditis in the developed world, affecting ~40,000 individuals each year in the United States, and the second leading cause of bacteremia (D

  9. Phenotypes and Virulence among Staphylococcus aureus USA100, USA200, USA300, USA400, and USA600 Clonal Lineages.

    PubMed

    King, Jessica M; Kulhankova, Katarina; Stach, Christopher S; Vu, Bao G; Salgado-Pabón, Wilmara

    2016-01-01

    Staphylococcus aureus diseases affect ~500,000 individuals per year in the United States. Worldwide, the USA100, USA200, USA400, and USA600 lineages cause many of the life-threatening S. aureus infections, such as bacteremia, infective endocarditis, pneumonia, toxic shock syndrome, and surgical site infections. However, the virulence mechanisms associated with these clonal lineages, in particular the USA100 and USA600 isolates, have been severely understudied. We investigated the virulence of these strains, in addition to strains in the USA200, USA300, and USA400 types, in well-established in vitro assays and in vivo in the rabbit model of infective endocarditis and sepsis. We show in the infective endocarditis and sepsis model that strains in the USA100 and USA600 lineages cause high lethality and are proficient in causing native valve infective endocarditis. Strains with high cytolytic activity or producing toxic shock syndrome toxin 1 (TSST-1) or staphylococcal enterotoxin C (SEC) caused lethal sepsis, even with low cytolytic activity. Strains in the USA100, USA200, USA400, and USA600 lineages consistently contained genes that encode for the enterotoxin gene cluster proteins, SEC, or TSST-1 and were proficient at causing infective endocarditis, while the USA300 strains lacked these toxins and were deficient in promoting vegetation growth. The USA100, USA200, and USA400 strains in our collection formed strong biofilms in vitro, whereas the USA200 and USA600 strains exhibited increased blood survival. Hence, infective endocarditis and lethal sepsis are multifactorial and not intrinsic to any one individual clonal group, further highlighting the importance of expanding our knowledge of S. aureus pathogenesis to clonal lineages causative of invasive disease. IMPORTANCE S. aureus is the leading cause of infective endocarditis in the developed world, affecting ~40,000 individuals each year in the United States, and the second leading cause of bacteremia (D. R

  10. Genetic Features of MCR-1-Producing Colistin-Resistant Escherichia coli Isolates in South Africa.

    PubMed

    Poirel, Laurent; Kieffer, Nicolas; Brink, Adrian; Coetze, Jennifer; Jayol, Aurélie; Nordmann, Patrice

    2016-07-01

    A series of colistin-resistant Escherichia coli clinical isolates was recovered from hospitalized and community patients in South Africa. Seven clonally unrelated isolates harbored the mcr-1 gene located on different plasmid backbones. Two distinct plasmids were fully sequenced, and identical 2,600-bp-long DNA sequences defining a mcr-1 cassette were identified. Promoter sequences responsible for the expression of mcr-1, deduced from the precise identification of the +1 transcription start site for mcr-1, were characterized. PMID:27161623

  11. Genomic Comparative Study of Bovine Mastitis Escherichia coli

    PubMed Central

    Kempf, Florent; Slugocki, Cindy; Blum, Shlomo E.; Leitner, Gabriel; Germon, Pierre

    2016-01-01

    Escherichia coli, one of the main causative agents of bovine mastitis, is responsible for significant losses on dairy farms. In order to better understand the pathogenicity of E. coli mastitis, an accurate characterization of E. coli strains isolated from mastitis cases is required. By using phylogenetic analyses and whole genome comparison of 5 currently available mastitis E. coli genome sequences, we searched for genotypic traits specific for mastitis isolates. Our data confirm that there is a bias in the distribution of mastitis isolates in the different phylogenetic groups of the E. coli species, with the majority of strains belonging to phylogenetic groups A and B1. An interesting feature is that clustering of strains based on their accessory genome is very similar to that obtained using the core genome. This finding illustrates the fact that phenotypic properties of strains from different phylogroups are likely to be different. As a consequence, it is possible that different strategies could be used by mastitis isolates of different phylogroups to trigger mastitis. Our results indicate that mastitis E. coli isolates analyzed in this study carry very few of the virulence genes described in other pathogenic E. coli strains. A more detailed analysis of the presence/absence of genes involved in LPS synthesis, iron acquisition and type 6 secretion systems did not uncover specific properties of mastitis isolates. Altogether, these results indicate that mastitis E. coli isolates are rather characterized by a lack of bona fide currently described virulence genes. PMID:26809117

  12. Clonal-Level Responses of Functionally Distinct Hematopoietic Stem Cells to Trophic Factors

    PubMed Central

    Mallaney, Cates; Kothari, Alok; Martens, Andrew; Challen, Grant A.

    2014-01-01

    Recent findings from several groups have identified distinct classes of hematopoietic stem cells (HSCs) in the bone marrow, each with inherent functional biases in terms of their differentiation, self-renewal, proliferation and lifespan. It has previously been demonstrated that myeloid- and lymphoid-biased HSCs can be prospectively enriched based on their degree of Hoechst dye efflux. In the present study, we used differential Hoechst efflux to enrich lineage-biased HSC subtypes and analyzed their functional potentials. Despite similar outputs in vitro, bone marrow transplantation assays revealed contrasting lineage differentiation in vivo. To stratify the molecular differences underlying these contrasting functional potentials at the clonal level, single-cell gene expression analysis was performed using the Fluidigm Biomark system and revealed dynamic expression of genes including Meis1, CEBP/α, Sfpi1 and Dnmt3a. Finally, single-cell gene expression analysis was used to unravel the opposing proliferative responses of lineage-biased HSCs to the growth factor TGFβ1, revealing a potential role for the cell cycle inhibitor Cdkn1c as molecular mediator. This work lends further credence to the concept of HSC heterogeneity and presents unprecedented molecular resolution of the HSC response to trophic factors using single-cell gene expression analysis. PMID:24373928

  13. Clonal-level responses of functionally distinct hematopoietic stem cells to trophic factors.

    PubMed

    Mallaney, Cates; Kothari, Alok; Martens, Andrew; Challen, Grant A

    2014-04-01

    Recent findings from several groups have identified distinct classes of hematopoietic stem cells (HSCs) in the bone marrow, each with inherent functional biases in terms of their differentiation, self-renewal, proliferation, and lifespan. It has previously been demonstrated that myeloid- and lymphoid-biased HSCs can be prospectively enriched based on their degree of Hoechst dye efflux. In the present study, we used differential Hoechst efflux to enrich lineage-biased HSC subtypes and analyzed their functional potentials. Despite similar outputs in vitro, bone marrow transplantation assays revealed contrasting lineage differentiation in vivo. To stratify the molecular differences underlying these contrasting functional potentials at the clonal level, single-cell gene expression analysis was performed using the Fluidigm BioMark system and revealed dynamic expression of genes including Meis1, CEBP/α, Sfpi1, and Dnmt3a. Finally, single-cell gene expression analysis was used to unravel the opposing proliferative responses of lineage-biased HSCs to the growth factor TGF-β1, revealing a potential role for the cell cycle inhibitor Cdkn1c as molecular mediator. This work lends further credence to the concept of HSC heterogeneity, and it presents unprecedented molecular resolution of the HSC response to trophic factors using single-cell gene expression analysis. PMID:24373928

  14. Comparing regression methods for the two-stage clonal expansion model of carcinogenesis.

    PubMed

    Kaiser, J C; Heidenreich, W F

    2004-11-15

    In the statistical analysis of cohort data with risk estimation models, both Poisson and individual likelihood regressions are widely used methods of parameter estimation. In this paper, their performance has been tested with the biologically motivated two-stage clonal expansion (TSCE) model of carcinogenesis. To exclude inevitable uncertainties of existing data, cohorts with simple individual exposure history have been created by Monte Carlo simulation. To generate some similar properties of atomic bomb survivors and radon-exposed mine workers, both acute and protracted exposure patterns have been generated. Then the capacity of the two regression methods has been compared to retrieve a priori known model parameters from the simulated cohort data. For simple models with smooth hazard functions, the parameter estimates from both methods come close to their true values. However, for models with strongly discontinuous functions which are generated by the cell mutation process of transformation, the Poisson regression method fails to produce reliable estimates. This behaviour is explained by the construction of class averages during data stratification. Thereby, some indispensable information on the individual exposure history was destroyed. It could not be repaired by countermeasures such as the refinement of Poisson classes or a more adequate choice of Poisson groups. Although this choice might still exist we were unable to discover it. In contrast to this, the individual likelihood regression technique was found to work reliably for all considered versions of the TSCE model. PMID:15490436

  15. Age-associated changes in CD8+ and CD16+ cell reactivity: clonal analysis.

    PubMed Central

    Mariani, E; Roda, P; Mariani, A R; Vitale, M; Degrassi, A; Papa, S; Facchini, A

    1990-01-01

    A cloning technique was used to estimate the frequency of proliferating T cell precursors, the growth capacity of clone-forming cells and the functional activity of clones established in vitro from peripheral blood lymphocytes of young and old people. The mean frequency of proliferating precursors was lower in the elderly as was the proliferative capacity of CD8+ clones. In contrast, CD4+ and CD16+ clones showed a proliferation similar to that obtained from young subjects. When the clones were examined for their functional activity, CD4+ clones from both groups failed to show any cytolytic activity, while CD8+ clones exerted cytolysis against K562 and in antibody-dependent cell-mediated cytotoxicity but this function was reduced in clones derived from old subjects. Similarly, CD16+ clones from the elderly showed a decreased activity at some effector-to-target cell ratios. We conclude that the impaired functional activity (T or NK-dependent) found in the peripheral blood of aged subjects persists after in vitro selection when these cells are analysed at clonal level. PMID:2144486

  16. Major clonal lineages in impetigo Staphylococcus aureus strains isolated in Czech and Slovak maternity hospitals.

    PubMed

    Růžičková, Vladislava; Pantůček, Roman; Petráš, Petr; Machová, Ivana; Kostýlková, Karla; Doškař, Jiří

    2012-11-01

    One hundred and twenty-seven exfoliative toxin-producing (ET-positive) strains of Staphylococcus aureus collected in 23 Czech and one Slovak maternity hospitals from 1998 to 2011 were genotypically characterized by multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) profiling, spa gene polymorphism analysis, and ETA-converting prophage carriage, which resulted in the identification of 21 genotypes grouped into 4 clonal complexes (CC). Ninety-one isolates carried the eta gene alone whilst 12 isolates harboured only the etb gene. Two new, to date not defined, spa types (t6644 and t6645) and 2 novel sequence types (ST2194 and ST2195) were identified in the set of strains under study. The predominant CC121 occurred in 13 Czech hospitals. CC15, CC9, and ST88 (CC88) exclusively included eta gene-positive strains while the strains belonging to ST121 harboured the eta and/or etb genes. This study highlights not only significant genomic diversity among impetigo strains and the distribution of major genotypes disseminated in the Czech and Slovak maternity hospitals, but also reveals their impact in epidermolytic infections. PMID:22664376

  17. Characterisation of free and glycosidically bound odourant compounds of Aragonez clonal musts by GC-O.

    PubMed

    Botelho, Goreti; Mendes-Faia, Arlete; Clímaco, Maria Cristina

    2010-01-11

    To evaluate the potential aroma of Aragonez clonal red musts, several free and glycosidically bound odourant compounds were extracted. Then, the gas chromatography-olfactometry (GC-O) posterior intensity method was used to evaluate their odour intensity and the compounds were identified by gas chromatography-mass spectrometry (GC-MS). A group of eight sniffers evaluated free and bound fractions of Aragonez musts and perceived forty-three and twenty-two odourant peaks respectively. Furaneol (burnt sugar, candy-cotton) and vanillin (vanilla, sweet) were identified in both free and bound fractions of Aragonez musts, indicating their grape-derived origin. Principal component analysis (PCA) was applied to the posterior intensity method data and a relationship between the different odourant compound variables and the free fractions was established. Two principal components (PCs) were found which together explained 100% of the total variance. A large number of potentially important but yet unknown odourants was detected by the GC-O analysis. PMID:20005332

  18. Dissemination of clonally related multidrug-resistant Klebsiella pneumoniae in Ireland.

    PubMed

    Morris, D; O'Connor, M; Izdebski, R; Corcoran, M; Ludden, C E; McGrath, E; Buckley, V; Cryan, B; Gniadkowski, M; Cormican, M

    2016-01-01

    In October 2012, an outbreak of gentamicin-resistant, ciprofloxacin non-susceptible extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae occurred in a neonatal intensive care unit in Ireland. In order to determine whether the outbreak strain was more widely dispersed in the country, 137 isolates of K. pneumoniae with this resistance phenotype collected from 17 hospitals throughout Ireland between January 2011 and July 2013 were examined. ESBL production was confirmed phenotypically and all isolates were screened for susceptibility to 19 antimicrobial agents and for the presence of genes encoding bla TEM, bla SHV, bla OXA, and bla CTX-M; 22 isolates were also screened for bla KPC, bla NDM, bla VIM, bla IMP and bla OXA-48 genes. All isolates harboured bla SHV and bla CTX-M and were resistant to ciprofloxacin, gentamicin, nalidixic acid, amoxicillin-clavulanate, and cefpodoxime; 15 were resistant to ertapenem, seven to meropenem and five isolates were confirmed as carbapenemase producers. Pulsed-field gel electrophoresis of all isolates identified 16 major clusters, with two clusters comprising 61% of the entire collection. Multilocus sequence typing of a subset of these isolates identified a novel type, ST1236, a single locus variant of ST48. Data suggest that two major clonal groups, ST1236/ST48 (CG43) and ST15/ST14 (CG15) have been circulating in Ireland since at least January 2011. PMID:26113052

  19. Genomic diversity of "deep ecotype" Alteromonas macleodii isolates: evidence for Pan-Mediterranean clonal frames.

    PubMed

    López-Pérez, Mario; Gonzaga, Aitor; Rodriguez-Valera, Francisco

    2013-01-01

    We have compared genomes of Alteromonas macleodii "deep ecotype" isolates from two deep Mediterranean sites and two surface samples from the Aegean and the English Channel. A total of nine different genomes were analyzed. They belong to five clonal frames (CFs) that differ among them by approximately 30,000 single-nucleotide polymorphisms (SNPs) over their core genomes. Two of the CFs contain three strains each with nearly identical genomes (~100 SNPs over the core genome). One of the CFs had representatives that were isolated from samples taken more than 1,000 km away, 2,500 m deeper, and 5 years apart. These data mark the longest proven persistence of a CF in nature (outside of clinical settings). We have found evidence for frequent recombination events between or within CFs and even with the distantly related A. macleodii surface ecotype. The different CFs had different flexible genomic islands. They can be classified into two groups; one type is additive, that is, containing different numbers of gene cassettes, and is very variable in short time periods (they often varied even within a single CF). The other type was more stable and produced the complete replacement of a genomic fragment by another with different genes. Although this type was more conserved within each CF, we found examples of recombination among distantly related CFs including English Channel and Mediterranean isolates. PMID:23729633

  20. EcoR phylogenetic analysis and virulence genotyping of avian pathogenic Escherichia coli strains and Escherichia coli isolates from commercial chicken carcasses in southern Brazil.

    PubMed

    Kobayashi, Renata K T; Aquino, Ivani; Ferreira, Ana Lívia da S; Vidotto, Marilda C

    2011-05-01

    Escherichia coli strains designated as avian pathogenic E. coli (APEC) are responsible for avian colibacillosis, an acute and largely systemic disease that promotes significant economic losses in poultry industry worldwide because of mortality increase, medication costs, and condemnation of carcasses. APEC is a subgroup of extraintestinal pathogenic E. coli pathotype, which includes uropathogenic E. coli, neonatal meningitis E. coli, and septicemic E. coli. We isolated E. coli from commercial chicken carcasses in a Brazilian community and compared by polymerase chain reaction-defined phylogenetic group (A, B1, B2, or D) with APEC strains isolated from sick chickens from different poultry farms. A substantial number of strains assigned to phylogenetic E. coli reference collection group B2, which is known to harbor potent extraintestinal human and animal E. coli pathogens, were identified as APEC (26.0%) in both commercial chicken carcasses and retail poultry meat (retail poultry E. coli [RPEC]) (21.25%). The majority of RPEC were classified as group A (35%), whereas the majority of APEC were groups B1 (30.8) and A (27.6%). APEC and RPEC presented the genes pentaplex, iutA, hly, iron, ompT, and iss, but with different virulence profiles. The similarity between APEC and RPEC indicates RPEC as potentially pathogenic strains and supports a possible zoonotic risk for humans. PMID:21254888

  1. Single cell genotyping of exome sequencing-identified mutations to characterize the clonal composition and evolution of inv(16) AML in a CBL mutated clonal hematopoiesis.

    PubMed

    Niemöller, Christoph; Renz, Nathalie; Bleul, Sabine; Blagitko-Dorfs, Nadja; Greil, Christine; Yoshida, Kenichi; Pfeifer, Dietmar; Follo, Marie; Duyster, Justus; Claus, Rainer; Ogawa, Seishi; Lübbert, Michael; Becker, Heiko

    2016-08-01

    We recently described the development of an inv(16) acute myeloid leukemia (AML) in a CBL mutated clonal hematopoiesis. Here, we further characterized the clonal composition and evolution of the AML based on the genetic information from the bulk specimen and analyses of individual bone marrow cells for mutations in CAND1, PTPRT, and DOCK6. To control for allele dropout, heterozygous polymorphisms located close to the respective mutation loci were assessed in parallel. The clonal composition concluded from exome sequencing suggested a proliferation advantage associated with the acquisition of mutations in CAND1, PTPRT, and DOCK6. Out of 102 single cell sequencing reactions on these mutations and the respective polymorphisms, analyses yielded conclusive results for at least 2 mutation sites in 12 cells. The single cell genotyping not only confirmed the co-occurrence of the PTPRT, CAND1 and DOCK6 mutations in the same AML clone but also revealed a clonal hierarchy, as the PTPRT mutation was likely acquired after the CAND1 and DOCK6 mutations. This insight had not been possible based solely on the exome sequencing data and suggests that the mutation in PTPRT, which encodes a STAT3-inhibiting protein tyrosine phosphatase, contributed to the AML development at a later stage by enhancing proliferation. PMID:27244256

  2. Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

    PubMed Central

    Garcillán-Barcia, M. Pilar; Mora, Azucena; Blanco, Jorge; Coque, Teresa M.; de la Cruz, Fernando

    2014-01-01

    Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ–proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages. PMID:25522143

  3. Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences.

    PubMed

    Lanza, Val F; de Toro, María; Garcillán-Barcia, M Pilar; Mora, Azucena; Blanco, Jorge; Coque, Teresa M; de la Cruz, Fernando

    2014-12-01

    Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ-proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages. PMID:25522143

  4. Phylogenetic Meta-Analysis of the Functional Traits of Clonal Plants Foraging in Changing Environments

    PubMed Central

    Xie, Xiu-Fang; Song, Yao-Bin; Zhang, Ya-Lin; Pan, Xu; Dong, Ming

    2014-01-01

    Foraging behavior, one of the adaptive strategies of clonal plants, has stimulated a tremendous amount of research. However, it is a matter of debate whether there is any general pattern in the foraging traits (functional traits related to foraging behavior) of clonal plants in response to diverse environments. We collected data from 97 published papers concerning the relationships between foraging traits (e.g., spacer length, specific spacer length, branch intensity and branch angle) of clonal plants and essential resources (e.g., light, nutrients and water) for plant growth and reproduction. We incorporated the phylogenetic information of 85 plant species to examine the universality of foraging hypotheses using phylogenetic meta-analysis. The trends toward forming longer spacers and fewer branches in shaded environments were detected in clonal plants, but no evidence for a relation between foraging traits and nutrient availability was detected, except that there was a positive correlation between branch intensity and nutrient availability in stoloniferous plants. The response of the foraging traits of clonal plants to water availability was also not obvious. Additionally, our results indicated that the foraging traits of stoloniferous plants were more sensitive to resource availability than those of rhizomatous plants. In consideration of plant phylogeny, these results implied that the foraging traits of clonal plants (notably stoloniferous plants) only responded to light intensity in a general pattern but did not respond to nutrient or water availability. In conclusion, our findings on the effects of the environment on the foraging traits of clonal plants avoided the confounding effects of phylogeny because we incorporated phylogeny into the meta-analysis. PMID:25216101

  5. Clonal Patch Size and Ramet Position of Leymus chinensis Affected Reproductive Allocation

    PubMed Central

    Zhang, Zhuo; Yang, Yunfei

    2015-01-01

    Reproductive allocation is critically important for population maintenance and usually varies with not only environmental factors but also biotic ones. As a typical rhizome clonal plant in China's northern grasslands, Leymus chinensis usually dominates the steppe communities and grows in clonal patches. In order to clarify the sexual reproductive allocation of L. chinensis in the process of the growth and expansion, we selected L. chinensis clonal patches of a range of sizes to examine the reproductive allocation and allometric growth of the plants. Moreover, the effects of position of L. chinensis ramets within the patch on their reproductive allocation were also examined. Clonal patch size and position both significantly affected spike biomass, reproductive tiller biomass and SPIKE/TILLER biomass ratio. From the central to the marginal zone, both the spike biomass and reproductive tiller biomass displayed an increasing trend in all the five patch size categories except for reproductive tiller biomass in 15–40m2 category. L. chinensis had significantly larger SPIKE/TILLER biomass ratio in marginal zone than in central zone of clonal patches that are larger than 15 m2 in area. Regression analysis showed that the spike biomass and SPIKE/TILLER biomass ratio were negatively correlated with clonal patch size while patch size showed significantly positive effect on SEED/SPIKE biomass ratio, but the reproductive tiller biomass and SEED/TILLER biomass ratio were not dependent on clonal patch size. The relationships between biomass of spike and reproductive tiller, between mature seed biomass and spike biomass and between mature seed biomass and reproductive tiller biomass were significant allometric for all or some of patch size categories, respectively. The slopes of all these allometric relationships were significantly different from 1. The allometric growth of L. chinensis is patch size-dependent. This finding will be helpful for developing appropriate practices for

  6. Revealing hidden clonal complexity in Mycobacterium tuberculosis infection by qualitative and quantitative improvement of sampling.

    PubMed

    Pérez-Lago, L; Palacios, J J; Herranz, M; Ruiz Serrano, M J; Bouza, E; García-de-Viedma, D

    2015-02-01

    The analysis of microevolution events, its functional relevance and impact on molecular epidemiology strategies, constitutes one of the most challenging aspects of the study of clonal complexity in infection by Mycobacterium tuberculosis. In this study, we retrospectively evaluated whether two improved sampling schemes could provide access to the clonal complexity that is undetected by the current standards (analysis of one isolate from one sputum). We evaluated in 48 patients the analysis by mycobacterial interspersed repetitive unit-variable number tandem repeat of M. tuberculosis isolates cultured from bronchial aspirate (BAS) or bronchoalveolar lavage (BAL) and, in another 16 cases, the analysis of a higher number of isolates from independent sputum samples. Analysis of the isolates from BAS/BAL specimens revealed clonal complexity in a very high proportion of cases (5/48); in most of these cases, complexity was not detected when the isolates from sputum samples were analysed. Systematic analysis of isolates from multiple sputum samples also improved the detection of clonal complexity. We found coexisting clonal variants in two of 16 cases that would have gone undetected in the analysis of the isolate from a single sputum specimen. Our results suggest that analysis of isolates from BAS/BAL specimens is highly efficient for recording the true clonal composition of M. tuberculosis in the lungs. When these samples are not available, we recommend increasing the number of isolates from independent sputum specimens, because they might not harbour the same pool of bacteria. Our data suggest that the degree of clonal complexity in tuberculosis has been underestimated because of the deficiencies inherent in a simplified procedure. PMID:25658553

  7. Molecular characterization of diarrheagenic Escherichia coli from Libya.

    PubMed

    Ali, Mostafa Mohamed M; Mohamed, Zienat Kamel; Klena, John D; Ahmed, Salwa Fouad; Moussa, Tarek A A; Ghenghesh, Khalifa Sifaw

    2012-05-01

    Diarrheagenic Escherichia coli (DEC) are important enteric pathogens that cause a wide variety of gastrointestinal diseases, particularly in children. Escherichia coli isolates cultured from 243 diarrheal stool samples obtained from Libyan children and 50 water samples were screened by polymerase chain reaction (PCR) for genes characteristic of enteroaggregative E. coli (EAEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enterohemorrhagic E. coli (EHEC), and enteroinvasive E. coli (EIEC). The DEC were detected in 21 (8.6%) children with diarrhea; 10 (4.1%) cases were identified as EAEC, 3 (1.2%) as EPEC, and 8 (3.3%) were ETEC; EHEC, and EIEC were not detected. All DEC were grouped phylogenetically by PCR with the majority (> 70%) identified as phylogenetic groups A and B1. The EAEC isolates were also tested for eight genes associated with virulence using PCR. Multi-virulence (≥ 3 virulence factors) was found in 50% of EAEC isolates. Isolated EAEC possessed different virulence traits and belonged to different phylogenetic groups indicating their heterogeneity. PMID:22556089

  8. Molecular Characterization of Diarrheagenic Escherichia coli from Libya

    PubMed Central

    Ali, Mostafa Mohamed M.; Mohamed, Zienat Kamel; Klena, John D.; Ahmed, Salwa Fouad; Moussa, Tarek A. A.; Ghenghesh, Khalifa Sifaw

    2012-01-01

    Diarrheagenic Escherichia coli (DEC) are important enteric pathogens that cause a wide variety of gastrointestinal diseases, particularly in children. Escherichia coli isolates cultured from 243 diarrheal stool samples obtained from Libyan children and 50 water samples were screened by polymerase chain reaction (PCR) for genes characteristic of enteroaggregative E. coli (EAEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enterohemorrhagic E. coli (EHEC), and enteroinvasive E. coli (EIEC). The DEC were detected in 21 (8.6%) children with diarrhea; 10 (4.1%) cases were identified as EAEC, 3 (1.2%) as EPEC, and 8 (3.3%) were ETEC; EHEC, and EIEC were not detected. All DEC were grouped phylogenetically by PCR with the majority (> 70%) identified as phylogenetic groups A and B1. The EAEC isolates were also tested for eight genes associated with virulence using PCR. Multi-virulence (≥ 3 virulence factors) was found in 50% of EAEC isolates. Isolated EAEC possessed different virulence traits and belonged to different phylogenetic groups indicating their heterogeneity. PMID:22556089

  9. Characterization of the extra-intestinal pathogenic Escherichia coli ST131 clone among isolates recovered from urinary and bloodstream infections in the United Kingdom.

    PubMed

    Ciesielczuk, H; Doumith, M; Hope, R; Woodford, N; Wareham, D W

    2015-12-01

    The multidrug-resistant ST131-O25b clone of Escherichia coli is well established as a significant cause of extra-intestinal infections worldwide. However, there have been only two small regional studies comparing ST131 isolates from the UK. Therefore, we characterized 143 ST131 E. coli (38 urinary, 105 bloodstream) collected between January 2011 and March 2012 from 38 centres located across the UK and Republic of Ireland. Phenotypic and genotypic characterization of clonal isolates revealed high rates of resistance to amoxicillin-clavulanate (56 %), cefotaxime (32 %), ciprofloxacin (79 %), temocillin (69 %, bloodstream isolates only), gentamicin (67 %) and trimethoprim-sulfamethoxazole (59 %). The most frequently detected extended-spectrum beta-lactamase was CTX-M-15 (87 %), predominantly encoded on IncF plasmids, although it was also associated with IncU plasmids in two isolates. The majority of UK ST131 clonal isolates possessed the O25b antigen (97 %) and the H30 fimH allele (92 %), but three serogroups (O19a, O136 and O153) novel to ST131 were identified among our strains. Contrary to previous reports, UK ST131-O16 isolates were typically susceptible to ciprofloxacin and lacked beta-lactamase genes (n = 12/12). In summary, ST131 strains of E. coli circulating in the UK possess characteristic clonal features, but are becoming more diverse than other international ST131 populations. PMID:26445772

  10. Diagnostic Utility of a Clonality Test for Lymphoproliferative Diseases in Koreans Using the BIOMED-2 PCR Assay

    PubMed Central

    Kim, Young; Choi, Yoo Duk; Choi, Chan

    2013-01-01

    Background A clonality test for immunoglobulin (IG) and T cell receptor (TCR) is a useful adjunctive method for the diagnosis of lymphoproliferative diseases (LPDs). Recently, the BIOMED-2 multiplex polymerase chain reaction (PCR) assay has been established as a standard method for assessing the clonality of LPDs. We tested clonality in LPDs in Koreans using the BIOMED-2 multiplex PCR and compared the results with those obtained in European, Taiwanese, and Thai participants. We also evaluated the usefulness of the test as an ancillary method for diagnosing LPDs. Methods Two hundred and nineteen specimens embedded in paraffin, including 78 B cell lymphomas, 80 T cell lymphomas and 61 cases of reactive lymphadenitis, were used for the clonality test. Results Mature B cell malignancies showed 95.7% clonality for IG, 2.9% co-existing clonality, and 4.3% polyclonality. Mature T cell malignancies exhibited 83.8% clonality for TCR, 8.1% co-existing clonality, and 16.2% polyclonality. Reactive lymphadenitis showed 93.4% polyclonality for IG and TCR. The majority of our results were similar to those obtained in Europeans. However, the clonality for IGK of B cell malignancies and TCRG of T cell malignancies was lower in Koreans than Europeans. Conclusions The BIOMED-2 multiplex PCR assay was a useful adjunctive method for diagnosing LPDs. PMID:24255634

  11. Traceable clonal culture and chemodrug assay of heterogeneous prostate carcinoma PC3 cells in microfluidic single cell array chips

    PubMed Central

    Chung, Jaehoon; Ingram, Patrick N.; Bersano-Begey, Tom; Yoon, Euisik

    2014-01-01

    Cancer heterogeneity has received considerable attention for its role in tumor initiation and progression, and its implication for diagnostics and therapeutics in the clinic. To facilitate a cellular heterogeneity study in a low cost and highly efficient manner, we present a microfluidic platform that allows traceable clonal culture and characterization. The platform captures single cells into a microwell array and cultures them for clonal expansion, subsequently allowing on-chip characterization of clonal phenotype and response against drug treatments. Using a heterogeneous prostate cancer model, the PC3 cell line, we verified our prototype, identifying three different sub-phenotypes and correlating their clonal drug responsiveness to cell phenotype. PMID:25553180

  12. Phenotypic profile of expanded NK cells in chronic lymphoproliferative disorders: a surrogate marker for NK-cell clonality

    PubMed Central

    Bárcena, Paloma; Jara-Acevedo, María; Tabernero, María Dolores; López, Antonio; Sánchez, María Luz; García-Montero, Andrés C.; Muñoz-García, Noemí; Vidriales, María Belén; Paiva, Artur; Lecrevisse, Quentin; Lima, Margarida; Langerak, Anton W.; Böttcher, Sebastian; van Dongen, Jacques J.M.

    2015-01-01

    Currently, the lack of a universal and specific marker of clonality hampers the diagnosis and classification of chronic expansions of natural killer (NK) cells. Here we investigated the utility of flow cytometric detection of aberrant/altered NK-cell phenotypes as a surrogate marker for clonality, in the diagnostic work-up of chronic lymphoproliferative disorders of NK cells (CLPD-NK). For this purpose, a large panel of markers was evaluated by multiparametric flow cytometry on peripheral blood (PB) CD56low NK cells from 60 patients, including 23 subjects with predefined clonal (n = 9) and polyclonal (n = 14) CD56low NK-cell expansions, and 37 with CLPD-NK of undetermined clonality; also, PB samples from 10 healthy adults were included. Clonality was established using the human androgen receptor (HUMARA) assay. Clonal NK cells were found to show decreased expression of CD7, CD11b and CD38, and higher CD2, CD94 and HLADR levels vs. normal NK cells, together with a restricted repertoire of expression of the CD158a, CD158b and CD161 killer-associated receptors. In turn, NK cells from both clonal and polyclonal CLPD-NK showed similar/overlapping phenotypic profiles, except for high and more homogeneous expression of CD94 and HLADR, which was restricted to clonal CLPD-NK. We conclude that the CD94hi/HLADR+ phenotypic profile proved to be a useful surrogate marker for NK-cell clonality. PMID:26556869

  13. Prevalence, characterization and clonal analysis of Escherichia coli O157 non-H7 serotypes that carry eae alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We characterized nineteen O157 non-H7 strains that were isolated from food, water, and both symptomatic and asymptomatic patients in various countries. All the isolates were serologically and genetically confirmed to be O157 non-H7 strains, but could not be H serotyped. None of the strains had tra...

  14. Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors

    PubMed Central

    Schwab, Richard; Harismendy, Olivier; Pu, Minya; Crain, Brian; Yost, Shawn; Frazer, Kelly A.; Rana, Brinda; Hasteh, Farnaz; Wallace, Anne; Parker, Barbara A.

    2015-01-01

    Background Synchronous tumors can be independent primary tumors or a primary-metastatic (clonal) pair, which may have clinical implications. Mutational profiling of tumor DNA is increasingly common in the clinic. We investigated whether mutational profiling can distinguish independent from clonal tumors in breast and other cancers, using a carefully defined test based on the Clonal Likelihood Score (CLS = 100 x # shared high confidence (HC) mutations/ # total HC mutations). Methods Statistical properties of a formal test using the CLS were investigated. A high CLS is evidence in favor of clonality; the test is implemented as a one-sided binomial test of proportions. Test parameters were empirically determined using 16,422 independent breast tumor pairs and 15 primary-metastatic tumor pairs from 10 cancer types using The Cancer Genome Atlas. Results We validated performance of the test with its established parameters, using five published data sets comprising 15,758 known independent tumor pairs (maximum CLS = 4.1%, minimum p-value = 0.48) and 283 known tumor clonal pairs (minimum CLS 13%, maximum p-value <0.01), across renal cell, testicular, and colorectal cancer. The CLS test correctly classified all validation samples but one, which it appears may have been incorrectly classified in the published data. As proof-of-concept we then applied the CLS test to two new cases of invasive synchronous bilateral breast cancer at our institution, each with one hormone receptor positive (ER+/PR+/HER2-) lobular and one triple negative ductal carcinoma. High confidence mutations were identified by exome sequencing and results were validated using deep targeted sequencing. The first tumor pair had CLS of 81% (p-value < 10–15), supporting clonality. In the second pair, no common mutations of 184 variants were validated (p-value >0.99), supporting independence. A plausible molecular mechanism for the shift from hormone receptor positive to triple negative was identified in the

  15. Increased prevalence of carbapenem resistant Enterobacteriaceae in hospital setting due to cross-species transmission of the bla NDM-1 element and clonal spread of progenitor resistant strains.

    PubMed

    Wang, Xuan; Chen, Gongxiang; Wu, Xiaoyan; Wang, Liangping; Cai, Jiachang; Chan, Edward W; Chen, Sheng; Zhang, Rong

    2015-01-01

    This study investigated the transmission characteristics of carbapenem-resistant Enterobacteriaceae (CRE) strains collected from a hospital setting in China, in which consistent emergence of CRE strains were observable during the period of May 2013 to February 2014. Among the 45 CRE isolates tested, 21 (47%) strains were found to harbor the bla NDM-1 element, and the rest of 24 CRE strains were all positive for bla KPC-2. The 21 bla NDM-1-borne strains were found to comprise multiple Enterobacteriaceae species including nine Enterobacter cloacae, three Escherichia coli, three Citrobacter freundii, two Klebsiella pneumoniae, two Klebsiella oxytoca, and two Morganella morganii strains, indicating that cross-species transmission of bla NDM-1 is a common event. Genetic analyses by PFGE and MLST showed that, with the exception of E. coli and E. cloacae, strains belonging to the same species were often genetically unrelated. In addition to bla NDM-1, several CRE strains were also found to harbor the bla KPC-2, bla VIM-1, and bla IMP-4 elements. Conjugations experiments confirmed that the majority of carbapenem resistance determinants were transferable. Taken together, our findings suggest that transmission of mobile resistance elements among members of Enterobacteriaceae and clonal spread of CRE strains may contribute synergistically to a rapid increase in the population of CRE in clinical settings, prompting a need to implement more rigorous infection control measures to arrest such vicious transmission cycle in CRE-prevalent areas. PMID:26136735

  16. Clonal haematopoiesis harbouring AML-associated mutations is ubiquitous in healthy adults.

    PubMed

    Young, Andrew L; Challen, Grant A; Birmann, Brenda M; Druley, Todd E

    2016-01-01

    Clonal haematopoiesis is thought to be a rare condition that increases in frequency with age and predisposes individuals to haematological malignancy. Recent studies, utilizing next-generation sequencing (NGS), observed haematopoietic clones in 10% of 70-year olds and rarely in younger individuals. However, these studies could only detect common haematopoietic clones->0.02 variant allele fraction (VAF)-due to the error rate of NGS. To identify and characterize clonal mutations below this threshold, here we develop methods for targeted error-corrected sequencing, which enable the accurate detection of clonal mutations as rare as 0.0003 VAF. We apply these methods to study serially banked peripheral blood samples from healthy 50-60-year-old participants in the Nurses' Health Study. We observe clonal haematopoiesis, frequently harbouring mutations in DNMT3A and TET2, in 95% of individuals studied. These clonal mutations are often stable longitudinally and present in multiple haematopoietic compartments, suggesting a long-lived haematopoietic stem and progenitor cell of origin. PMID:27546487

  17. Clonal haematopoiesis harbouring AML-associated mutations is ubiquitous in healthy adults

    PubMed Central

    Young, Andrew L.; Challen, Grant A.; Birmann, Brenda M.; Druley, Todd E.

    2016-01-01

    Clonal haematopoiesis is thought to be a rare condition that increases in frequency with age and predisposes individuals to haematological malignancy. Recent studies, utilizing next-generation sequencing (NGS), observed haematopoietic clones in 10% of 70-year olds and rarely in younger individuals. However, these studies could only detect common haematopoietic clones—>0.02 variant allele fraction (VAF)—due to the error rate of NGS. To identify and characterize clonal mutations below this threshold, here we develop methods for targeted error-corrected sequencing, which enable the accurate detection of clonal mutations as rare as 0.0003 VAF. We apply these methods to study serially banked peripheral blood samples from healthy 50–60-year-old participants in the Nurses' Health Study. We observe clonal haematopoiesis, frequently harbouring mutations in DNMT3A and TET2, in 95% of individuals studied. These clonal mutations are often stable longitudinally and present in multiple haematopoietic compartments, suggesting a long-lived haematopoietic stem and progenitor cell of origin. PMID:27546487

  18. Phenotypic, transcriptomic, and genomic features of clonal plasma cells in light-chain amyloidosis.

    PubMed

    Paiva, Bruno; Martinez-Lopez, Joaquin; Corchete, Luis A; Sanchez-Vega, Beatriz; Rapado, Inmaculada; Puig, Noemi; Barrio, Santiago; Sanchez, Maria-Luz; Alignani, Diego; Lasa, Marta; García de Coca, Alfonso; Pardal, Emilia; Oriol, Alberto; Garcia, Maria-Esther Gonzalez; Escalante, Fernando; González-López, Tomás J; Palomera, Luis; Alonso, José; Prosper, Felipe; Orfao, Alberto; Vidriales, Maria-Belen; Mateos, María-Victoria; Lahuerta, Juan-Jose; Gutierrez, Norma C; San Miguel, Jesús F

    2016-06-16

    Immunoglobulin light-chain amyloidosis (AL) and multiple myeloma (MM) are 2 distinct monoclonal gammopathies that involve the same cellular compartment: clonal plasma cells (PCs). Despite the fact that knowledge about MM PC biology has significantly increased in the last decade, the same does not apply for AL. Here, we used an integrative phenotypic, molecular, and genomic approach to study clonal PCs from 24 newly diagnosed patients with AL. Through principal-component-analysis, we demonstrated highly overlapping phenotypic profiles between AL and both monoclonal gammopathy of undetermined significance and MM PCs. However, in contrast to MM, highly purified fluorescence-activated cell-sorted clonal PCs from AL (n = 9) showed almost normal transcriptome, with only 38 deregulated genes vs normal PCs; these included a few tumor-suppressor (CDH1, RCAN) and proapoptotic (GLIPR1, FAS) genes. Notwithstanding, clonal PCs in AL (n = 11) were genomically unstable, with a median of 9 copy number alterations (CNAs) per case, many of such CNAs being similar to those found in MM. Whole-exome sequencing (WES) performed in 5 AL patients revealed a median of 15 nonrecurrent mutations per case. Altogether, our results show that in the absence of a unifying mutation by WES, clonal PCs in AL display phenotypic and CNA profiles similar to MM, but their transcriptome is remarkably similar to that of normal PCs. PMID:27069257

  19. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing.

    PubMed

    Ding, Li; Ley, Timothy J; Larson, David E; Miller, Christopher A; Koboldt, Daniel C; Welch, John S; Ritchey, Julie K; Young, Margaret A; Lamprecht, Tamara; McLellan, Michael D; McMichael, Joshua F; Wallis, John W; Lu, Charles; Shen, Dong; Harris, Christopher C; Dooling, David J; Fulton, Robert S; Fulton, Lucinda L; Chen, Ken; Schmidt, Heather; Kalicki-Veizer, Joelle; Magrini, Vincent J; Cook, Lisa; McGrath, Sean D; Vickery, Tammi L; Wendl, Michael C; Heath, Sharon; Watson, Mark A; Link, Daniel C; Tomasson, Michael H; Shannon, William D; Payton, Jacqueline E; Kulkarni, Shashikant; Westervelt, Peter; Walter, Matthew J; Graubert, Timothy A; Mardis, Elaine R; Wilson, Richard K; DiPersio, John F

    2012-01-26

    Most patients with acute myeloid leukaemia (AML) die from progressive disease after relapse, which is associated with clonal evolution at the cytogenetic level. To determine the mutational spectrum associated with relapse, we sequenced the primary tumour and relapse genomes from eight AML patients, and validated hundreds of somatic mutations using deep sequencing; this allowed us to define clonality and clonal evolution patterns precisely at relapse. In addition to discovering novel, recurrently mutated genes (for example, WAC, SMC3, DIS3, DDX41 and DAXX) in AML, we also found two major clonal evolution patterns during AML relapse: (1) the founding clone in the primary tumour gained mutations and evolved into the relapse clone, or (2) a subclone of the founding clone survived initial therapy, gained additional mutations and expanded at relapse. In all cases, chemotherapy failed to eradicate the founding clone. The comparison of relapse-specific versus primary tumour mutations in all eight cases revealed an increase in transversions, probably due to DNA damage caused by cytotoxic chemotherapy. These data demonstrate that AML relapse is associated with the addition of new mutations and clonal evolution, which is shaped, in part, by the chemotherapy that the patients receive to establish and maintain remissions. PMID:22237025

  20. Clonal diversity of Acinetobacter baumannii clinical isolates revealed by a snapshot study

    PubMed Central

    2013-01-01

    Background Acinetobacter baumannii is a notorious opportunistic pathogen mainly associated with hospital-acquired infections. Studies on the clonal relatedness of isolates could lay the foundation for effective infection control. A snapshot study was performed to investigate the clonal relatedness of A. baumannii clinical isolates in our local sett