1
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Molecular typification of Escherichia coli from community-acquired urinary tract infections in Mexico. Int J Antimicrob Agents 2022; 60:106667. [PMID: 36038094 DOI: 10.1016/j.ijantimicag.2022.106667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 08/11/2022] [Accepted: 08/21/2022] [Indexed: 11/20/2022]
Abstract
One hundred and five uropathogenic Escherichia coli (UPEC) strains from patients with community-acquired urinary tract infection were characterized according to their phylogenetic groups, virulence factors, serogroups, antibiotics resistance, and genotype. The pathogenic phylogenetic groups (B2, D, and F) were found in 71.4% of the tested strains. Among them, the main uropathogenic serogroups were O8, O25, and O75, in which 97.1% of the strains had a multidrug-resistant profile. Moreover, 16 virulence genes were analyzed using a combination of PCR assays, with the fimH, irp-2, iutA, aer, iucC, PAI, sat, iroN, usp, and cnf1 genes being mainly found in pathogenic phylogroups. The E. coli O25b-ST131 clone was identified in 32% of the strains assigned to the pathogenic phylogroup B2. Our findings demonstrate that virulence genes encoding adhesin components, iron acquisition systems, toxins, and pathogenicity-associated islands were highly prevalent among the pathogenic phylogroup of UPEC strains.
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2
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Bhat AH. Bacterial zoonoses transmitted by household pets and as reservoirs of antimicrobial resistant bacteria. Microb Pathog 2021; 155:104891. [PMID: 33878397 DOI: 10.1016/j.micpath.2021.104891] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 12/27/2022]
Abstract
Numerous individuals are committed to growing pet creatures like cats, dogs, and rats etc., pay care for them and as a result of this, there's a boost of their populace in advanced culture. The close interaction between family pets and individuals offers ideal conditions for bacterial transmission. Distinctive sorts of antimicrobial agents are exploited for animal husbandry and studies have revealed that many bacteria have attained confrontation against them viz., Staphylococcus intermedius, Escherichia coli, methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococci and multidrug-resistant Salmonella typhi etc. and a few of these are a prospective for zoonotic transmission. In the current review, the attention has been paid on how household pets, especially dogs disperse the antimicrobial resistance in contrast to that of food animals. A lot of evidences are accessible on food animals and nation-wide scrutiny programmes solely hub on food animals; therefore, for steerage antimicrobial use policy in small animal veterinary exercise as well as for gauging the chance of transmission of antimicrobial resistance to humans' statistics on pet animals are sincerely needed. Transmission of such organisms, especially pathogenic staphylococci, occurs between pets, owners, and veterinary staff, and pets can act as reservoirs of such bacteria; this may additionally have an impact on the use of antimicrobials in human medicine. There is a need to generate statistics concerning each the levels of carriage of such microorganism in pets and the risk factors associated with the switch of the microorganism to human beings who have contact with infected pets, as nicely as to improve hygiene measures in veterinary practice.
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Affiliation(s)
- Aashaq Hussain Bhat
- Department of Zoology, Government Degree College, Billawar, 184204, Kathua, Jammu and Kashmir, India.
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3
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Prevalence of fluoroquinolone-resistant and broad-spectrum cephalosporin-resistant community-acquired urinary tract infections in Rio de Janeiro: Impact of genotypes ST69 and ST131. INFECTION GENETICS AND EVOLUTION 2020; 85:104452. [DOI: 10.1016/j.meegid.2020.104452] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 12/11/2022]
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4
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La Combe B, Clermont O, Messika J, Eveillard M, Kouatchet A, Lasocki S, Corvec S, Lakhal K, Billard-Pomares T, Fernandes R, Armand-Lefevre L, Bourdon S, Reignier J, Fihman V, de Prost N, Bador J, Goret J, Wallet F, Denamur E, Ricard JD. Pneumonia-Specific Escherichia coli with Distinct Phylogenetic and Virulence Profiles, France, 2012-2014. Emerg Infect Dis 2019; 25:710-718. [PMID: 30882313 PMCID: PMC6433033 DOI: 10.3201/eid2504.180944] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In a prospective, nationwide study in France of Escherichia coli responsible for pneumonia in patients receiving mechanical ventilation, we determined E. coli antimicrobial susceptibility, phylotype, O-type, and virulence factor gene content. We compared 260 isolates with those of 2 published collections containing commensal and bacteremia isolates. The preponderant phylogenetic group was B2 (59.6%), and the predominant sequence type complex (STc) was STc73. STc127 and STc141 were overrepresented and STc95 underrepresented in pneumonia isolates compared with bacteremia isolates. Pneumonia isolates carried higher proportions of virulence genes sfa/foc, papGIII, hlyC, cnf1, and iroN compared with bacteremia isolates. Virulence factor gene content and antimicrobial drug resistance were higher in pneumonia than in commensal isolates. Genomic and phylogenetic characteristics of E. coli pneumonia isolates from critically ill patients indicate that they belong to the extraintestinal pathogenic E. coli pathovar but have distinguishable lung-specific traits.
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5
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) are important pathogens in humans and certain animals. Molecular epidemiological analyses of ExPEC are based on structured observations of E. coli strains as they occur in the wild. By assessing real-world phenomena as they occur in authentic contexts and hosts, they provide an important complement to experimental assessment. Fundamental to the success of molecular epidemiological studies are the careful selection of subjects and the use of appropriate typing methods and statistical analysis. To date, molecular epidemiological studies have yielded numerous important insights into putative virulence factors, host-pathogen relationships, phylogenetic background, reservoirs, antimicrobial-resistant strains, clinical diagnostics, and transmission pathways of ExPEC, and have delineated areas in which further study is needed. The rapid pace of discovery of new putative virulence factors and the increasing awareness of the importance of virulence factor regulation, expression, and molecular variation should stimulate many future molecular epidemiological investigations. The growing sophistication and availability of molecular typing methodologies, and of the new computational and statistical approaches that are being developed to address the huge amounts of data that whole genome sequencing generates, provide improved tools for such studies and allow new questions to be addressed.
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6
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Mostafavi SKS, Najar‐Peerayeh S, Mobarez AM, Parizi MK. Characterization of uropathogenic
E. coli
O25b‐B2‐ST131, O15:K52:H1, and CGA: Neutrophils apoptosis, serum bactericidal assay, biofilm formation, and virulence typing. J Cell Physiol 2019; 234:18272-18282. [DOI: 10.1002/jcp.28459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/05/2019] [Accepted: 02/14/2019] [Indexed: 12/18/2022]
Affiliation(s)
| | - Shahin Najar‐Peerayeh
- Department of Bacteriology Faculty of Medical Sciences, Tarbiat Modares University Tehran Iran
| | | | - Mehdi Kardoust Parizi
- Department of Urology Shariati Hospital, Tehran University of Medical Sciences Tehran Iran
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7
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Affiliation(s)
- Bente Olesen
- Department of Clinical Microbiology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
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8
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Messika J, Clermont O, Landraud L, Schmidt M, Aubry A, Sougakoff W, Fernandes R, Combes A, Denamur E, Ricard JD. Extra-corporeal membrane oxygenation-associated infections: implication of extra-intestinal pathogenic Escherichia coli clones. J Med Microbiol 2017; 66:1189-1195. [DOI: 10.1099/jmm.0.000554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Jonathan Messika
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700, Colombes, France
| | - Olivier Clermont
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Luce Landraud
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
- AP-HP, Hôpital Louis Mourier, Service de Microbiologie, F-92700, Colombes, France
| | - Matthieu Schmidt
- Medical Intensive Care Unit, iCAN, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié–Salpêtrière, Assistance Publique–Hôpitaux de Paris, Université Pierre-et-Marie-Curie, Paris 6, 75651 Paris Cedex 13, France
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
| | - Alexandra Aubry
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (NRC MyrMA), Bactériologie-Hygiène, Paris, France
| | - Wladimir Sougakoff
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (NRC MyrMA), Bactériologie-Hygiène, Paris, France
| | - Romain Fernandes
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Alain Combes
- Medical Intensive Care Unit, iCAN, Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié–Salpêtrière, Assistance Publique–Hôpitaux de Paris, Université Pierre-et-Marie-Curie, Paris 6, 75651 Paris Cedex 13, France
- Sorbonne Universités, UPMC Université Paris 06, CR7, INSERM, U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI, Team E13 (Bacteriology), Paris, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Génétique Moléculaire, F-75018, Paris, France
| | - Jean-Damien Ricard
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700, Colombes, France
- INSERM, IAME, UMR 1137, F-75018 Paris, France
- Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
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9
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Epidemic Emergence in the United States of Escherichia coli Sequence Type 131- H30 (ST131- H30), 2000 to 2009. Antimicrob Agents Chemother 2017; 61:AAC.00732-17. [PMID: 28533233 DOI: 10.1128/aac.00732-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/11/2017] [Indexed: 11/20/2022] Open
Abstract
The H30 subclone of Escherichia coli sequence type 131 (ST131-H30) has become the leading antimicrobial resistance E. coli lineage in the United States and often exhibits resistance to one or both of the two key antimicrobial classes for treating Gram-negative infections, extended-spectrum cephalosporins (ESCs) and fluoroquinolones (FQs). However, the timing of and reasons for its recent emergence are inadequately defined. Accordingly, from E. coli clinical isolates collected systematically across the United States by the SENTRY Antimicrobial Surveillance Program in 2000, 2003, 2006, and 2009, 234 isolates were selected randomly, stratified by year, within three resistance categories: (i) ESC-reduced susceptibility, regardless of FQ phenotype (ESC-RS); (ii) FQ resistance, ESC susceptible (FQ-R); and (iii) FQ susceptible, ESC susceptible (FQ-S). Susceptibility profiles, phylogroup, ST, ST131 subclone, and virulence genotypes were determined, and temporal trends and between-variable associations were assessed statistically. From 2000 to 2006, concurrently with the emergence of ESC-RS and FQ-R strains, the prevalence of (virulence-associated) phylogroup B2 among such strains also rose dramatically, due entirely to rapid emergence of ST131, especially H30. By 2009, H30 was the dominant E. coli lineage overall (22%), accounting for a median of 43% of all single-agent and multidrug resistance (68% for ciprofloxacin). H30's emergence increased the net virulence gene content of resistant (especially FQ-R) isolates, giving stable overall virulence gene scores despite an approximately 4-fold expansion of the historically less virulent resistant population. These findings define more precisely the timing and tempo of H30's emergence in the United States, identify possible reasons for it, and suggest potential consequences, including more frequent and/or aggressive antimicrobial-resistant infections.
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10
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Johnson JR, Porter S, Thuras P, Castanheira M. The Pandemic H30 Subclone of Sequence Type 131 (ST131) as the Leading Cause of Multidrug-Resistant Escherichia coli Infections in the United States (2011-2012). Open Forum Infect Dis 2017. [PMID: 28638846 DOI: 10.1093/ofid/ofx089] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Extraintestinal Escherichia coli infections are increasingly challenging due to emerging antimicrobial resistance, including resistance to extended-spectrum beta-lactams and fluoroquinolones. Sequence type 131 (ST131) is a leading contributor. METHODS Three hundred sixty E. coli clinical isolates from across the United States (2011-2012), selected randomly from the SENTRY collection within 3 resistance categories (extended-spectrum cephalosporin [ECS]-reduced susceptibility [RS]; fluoroquinolone-resistant, ESC-susceptible; and fluoroquinolone-susceptible, ESC-susceptible) were typed for phylogroup, sequence type complex (STc), subsets thereof, virulence genotype, O type, and beta-lactamase genes. Molecular results were compared with susceptibility profile, specimen type, age, and sex. RESULTS Phylogroup B2 accounted for most isolates, especially fluoroquinolone-resistant isolates (83%). Group B2-derived ST131 and its H30 subclone (divided between H30Rx and H30R1) predominated, especially among ESC-RS and fluoroquinolone-resistant isolates. In contrast, among fluoroquinolone-susceptible isolates, group B2-derived STc73 and STc95 predominated. Within each resistance category, ST131 isolates exhibited more extensive resistance and/or virulence profiles than non-ST131 isolates. ST131-H30 was distributed broadly by geographical region, age, and specimen type and exhibited distinctive beta-lactamase genes. Back-calculations indicated that within the source population ST131 accounted for 26.4% of isolates overall (vs 17% in 2007), including 19.8% ST131-H30, 13.2% ST131-H30R1, and 6.6% each ST131-H30Rx and non-H30 ST131. CONCLUSIONS ST131-H30, with its ESC resistance-associated H30Rx subset, caused most antimicrobial-resistant E. coli infections across the United States in 2011-2012 and, since 2007, increased in relative prevalence by >50%. Focused attention to this strain could help combat the current E. coli resistance epidemic.
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Affiliation(s)
- James R Johnson
- Minneapolis Veterans Affairs Healthcare System.,Departments of Medicine and Psychiatry, University of Minnesota, Minneapolis; and
| | - Stephen Porter
- Minneapolis Veterans Affairs Healthcare System.,Departments of Medicine and Psychiatry, University of Minnesota, Minneapolis; and
| | - Paul Thuras
- Minneapolis Veterans Affairs Healthcare System.,Departments of Medicine and Psychiatry, University of Minnesota, Minneapolis; and
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11
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Petit F, Clermont O, Delannoy S, Servais P, Gourmelon M, Fach P, Oberlé K, Fournier M, Denamur E, Berthe T. Change in the Structure of Escherichia coli Population and the Pattern of Virulence Genes along a Rural Aquatic Continuum. Front Microbiol 2017; 8:609. [PMID: 28458656 PMCID: PMC5394106 DOI: 10.3389/fmicb.2017.00609] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/24/2017] [Indexed: 12/15/2022] Open
Abstract
The aim of this study was to investigate the diversity of the Escherichia coli population, focusing on the occurrence of pathogenic E. coli, in surface water draining a rural catchment. Two sampling campaigns were carried out in similar hydrological conditions (wet period, low flow) along a river continuum, characterized by two opposite density gradients of animals (cattle and wild animals) and human populations. While the abundance of E. coli slightly increased along the river continuum, the abundance of both human and ruminant-associated Bacteroidales markers, as well as the number of E. coli multi-resistant to antibiotics, evidenced a fecal contamination originating from animals at upstream rural sites, and from humans at downstream urban sites. A strong spatial modification of the structure of the E. coli population was observed. At the upstream site close to a forest, a higher abundance of the B2 phylogroup and Escherichia clade strains were observed. At the pasture upstream site, a greater proportion of both E and B1 phylogroups was detected, therefore suggesting a fecal contamination of mainly bovine origin. Conversely, in downstream urban sites, A, D, and F phylogroups were more abundant. To assess the occurrence of intestinal pathogenic strains, virulence factors [afaD, stx1, stx2, eltB (LT), estA (ST), ipaH, bfpA, eae, aaiC and aatA] were screened among 651 E. coli isolates. Intestinal pathogenic strains STEC O174:H21 (stx2) and EHEC O26:H11 (eae, stx1) were isolated in water and sediments close to the pasture site. In contrast, in the downstream urban site aEPEC/EAEC and DAEC of human origin, as well as extra-intestinal pathogenic E. coli belonging to clonal group A of D phylogroup, were sampled. Even if the estimated input of STEC (Shiga toxin-producing E. coli) - released in water at the upstream pasture site - at the downstream site was low, we show that STEC could persist in sediment. These results show that, the run-off of small cattle farms contributed, as much as the wastewater effluent, in the dissemination of pathogenic E. coli in both water and sediments, even if the microbiological quality of the water was good or to average quality according to the French water index.
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Affiliation(s)
- Fabienne Petit
- Normandie Université, UniRouen, UniCaen, CNRS UMR M2CRouen, France.,Sorbonne Universités, UPMC, CNRS, EPHE, UMR 7619 METISParis, France
| | - Olivier Clermont
- INSERM UMR1137, IAME, Université Paris Diderot, Sorbonne Paris CitéParis, France
| | - Sabine Delannoy
- Université Paris-Est, Anses, Food Safety Laboratory, IdentyPath Platform, Maisons-AlfortFrance
| | - Pierre Servais
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la PlaineBruxelles, Belgium
| | - Michèle Gourmelon
- Institut Français de Recherche pour l'Exploitation de la Mer, RBE-SG2M-LSEMPlouzané, France
| | - Patrick Fach
- Université Paris-Est, Anses, Food Safety Laboratory, IdentyPath Platform, Maisons-AlfortFrance
| | - Kenny Oberlé
- Normandie Université, UniRouen, UniCaen, CNRS UMR M2CRouen, France
| | | | - Erick Denamur
- INSERM UMR1137, IAME, Université Paris Diderot, Sorbonne Paris CitéParis, France
| | - Thierry Berthe
- Normandie Université, UniRouen, UniCaen, CNRS UMR M2CRouen, France
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12
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Rapid and Specific Detection of the Escherichia coli Sequence Type 648 Complex within Phylogroup F. J Clin Microbiol 2017; 55:1116-1121. [PMID: 28100599 DOI: 10.1128/jcm.01949-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022] Open
Abstract
The Escherichia coli sequence type 648 complex (STc648) is an emerging lineage within phylogroup F-formerly included within phylogroup D-that is associated with multidrug resistance. Here, we designed and validated a novel multiplex PCR-based assay for STc648 that took advantage of (i) four distinctive single-nucleotide polymorphisms in icd allele 96 and gyrB allele 87, two of the multilocus sequence typing alleles that define ST648; and (ii) the typical absence within STc648 of uidA, an E. coli-specific gene encoding β-glucuronidase. Within a diverse 212-strain validation set that included 109 STs other than STc648, from phylogroups A, B1, B2, C, D, E, and F, the assay exhibited 100% sensitivity (95% confidence interval [CI], 82% to 100%) and specificity (95% CI, 98% to 100%). It functioned similarly well in two distant laboratories that used boiled lysates or DNAzol-purified DNA as the template DNA. Thus, this novel multiplex PCR-based assay should enable any laboratory equipped for diagnostic PCR to rapidly, accurately, and economically screen E. coli isolates for membership in STc648.
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13
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Two levels of specialization in bacteraemic Escherichia coli strains revealed by their comparison with commensal strains. Epidemiol Infect 2016; 145:872-882. [PMID: 28029088 DOI: 10.1017/s0950268816003010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Bacteraemia caused by Escherichia coli are particularly frequent and severe, contrasting with the commensal character of the strains found in the digestive tract. A better understanding of the relationships between strains of both origins is needed to unravel the pathogenesis of this disease. Two hundred and forty-three commensal strains were compared to 243 bacteraemic strains isolated from adult hosts matched in terms of gender and age, and from similar location and epoch. Phylogenetic grouping, O-type determination, virulence factor content and antibiotic resistance were compared. Compared to commensal strains, the bacteraemic strains were characterized by a higher proportion of B2, C and D phylogroups, and a lower proportion of A, E and F phylogroups. They also had a lower proportion of the B2 subgroup IV (STc141), a higher proportion of virulence factors, and a higher frequency of antibiotic resistance. These differences were more marked for the bacteraemic strains of urinary tract origin with the presence of specific clones, whereas the bacteraemic strains of digestive origin remained non-significantly different from the commensal strains, except for their antibiotic resistance. Thus, two levels of specialization from commensal strains were demonstrated in the bacteraemic strains: resistance to antibiotics in all cases, and virulence for those of urinary tract origin.
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14
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Manjarrez-Hernandez A, Molina-López J, Gavilanes-Parra S, Hernandez-Castro R. Escherichia coli clonal group A among uropathogenic infections in Mexico City. J Med Microbiol 2016; 65:1438-1444. [DOI: 10.1099/jmm.0.000389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Angel Manjarrez-Hernandez
- Dirección de Investigación, Hospital General Dr. Gea González, Tlalpan, Ciudad de México 14080, Mexico
- Departamento de Salud Pública, Facultad de Medicina, UNAM, Ciudad de México 04510, Mexico
| | - José Molina-López
- Departamento de Salud Pública, Facultad de Medicina, UNAM, Ciudad de México 04510, Mexico
- Laboratorio de Patogenicidad Bacteriana, Edificio de Investigación Hemato-Oncología 5to, Piso Hospital Infantil de México ‘Federico Gómez’, C.P. 06720 Ciudad de México, Mexico
| | - Sandra Gavilanes-Parra
- Departamento de Salud Pública, Facultad de Medicina, UNAM, Ciudad de México 04510, Mexico
- Dirección de Investigación, Hospital General Dr. Gea González, Tlalpan, Ciudad de México 14080, Mexico
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15
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Karami N, Wold AE, Adlerberth I. Antibiotic resistance is linked to carriage of papC and iutA virulence genes and phylogenetic group D background in commensal and uropathogenic Escherichia coli from infants and young children. Eur J Clin Microbiol Infect Dis 2016; 36:721-729. [PMID: 27924435 PMCID: PMC5366176 DOI: 10.1007/s10096-016-2854-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/22/2016] [Indexed: 01/07/2023]
Abstract
P fimbriae, enabling adherence to colonic and urinary epithelium, and aerobactin, an iron sequestering system, are both colonization factors in the human colon and virulence factors for urinary tract infection. The colonic microbiota is suggested to be a site suitable for the transfer of antibiotic resistance genes. We investigated whether phenotypic resistance to antibiotics in commensal and uropathogenic Escherichia coli from infants and young children is associated with carriage of virulence genes and to phylogenetic group origin and, in the case of fecal strains, to persistence in the gut and fecal population levels. The commensal strains (n = 272) were derived from a birth cohort study, while the urinary isolates (n = 205) were derived from outpatient clinics. Each strain was assessed for phenotypic antibiotic resistance and for carriage of virulence genes (fimA, papC, sfaD/E, hlyA, iutA, kfiC, and neuB), phylogenetic group (A, B1, B2, or D), and markers of particular virulent clones (CGA-D-ST69, O15:H1-D-ST393, and O25b:H4-B2-ST131). Resistance to ampicillin, tetracycline, and trimethoprim was most prevalent. Multivariate analysis showed that resistance to any antibiotic was significantly associated with carriage of genes encoding P fimbriae (papC) and aerobactin (iutA), and a phylogenetic group D origin. Neither fecal population numbers nor the capacity for long-term persistence in the gut were related to antibiotic resistance among fecal strains. Our study confirms the importance of phylogenetic group D origin for antibiotic resistance in E. coli and identifies the virulence genes papC and iutA as determinants of antibiotic resistance. The reason for the latter association is currently unclear.
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Affiliation(s)
- N Karami
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. .,Department of Clinical Microbiology, University of Gothenburg, Guldhedsgatan 10A, 413 46, Göteborg, Sweden.
| | - A E Wold
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - I Adlerberth
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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16
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Escherichia coli Sequence Type 131 H30 Is the Main Driver of Emerging Extended-Spectrum-β-Lactamase-Producing E. coli at a Tertiary Care Center. mSphere 2016; 1:mSphere00314-16. [PMID: 27904884 PMCID: PMC5120173 DOI: 10.1128/msphere.00314-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/04/2016] [Indexed: 11/20/2022] Open
Abstract
The ever-rising prevalence of resistance to first-line antibiotics among clinical Escherichia coli isolates leads to worse clinical outcomes and higher health care costs, thereby creating a need to discover its basis so that effective interventions can be developed. We found that the H30 subset within E. coli sequence type 131 (ST131-H30) is currently, and has been since at least 2004, the main E. coli lineage contributing to key resistance phenotypes—including extended-spectrum-beta-lactamase (ESBL) production, fluoroquinolone resistance, multidrug resistance, and dual ESBL production-plus-fluoroquinolone resistance—at a United States tertiary care center with a rising prevalence of ESBL-producing E. coli isolates. This identifies ST131-H30 as a target for diagnostic tests and preventive measures designed to curb the emergence of multidrug-resistant E. coli isolates and/or to blunt its clinical impact. The H30 strain of Escherichia coli sequence type 131 (ST131-H30) is a recently emerged, globally disseminated lineage associated with fluoroquinolone resistance and, via its H30Rx subclone, the CTX-M-15 extended-spectrum beta-lactamase (ESBL). Here, we studied the clonal background and resistance characteristics of 109 consecutive recent E. coli clinical isolates (2015) and 41 historical ESBL-producing E. coli blood isolates (2004 to 2011) from a public tertiary care center in California with a rising prevalence of ESBL-producing E. coli isolates. Among the 2015 isolates, ST131, which was represented mainly by ST131-H30, was the most common clonal lineage (23% overall). ST131-H30 accounted for 47% (8/17) of ESBL-producing, 47% (14/30) of fluoroquinolone-resistant, and 33% (11/33) of multidrug-resistant isolates. ST131-H30 also accounted for 53% (8/14) of dually fluoroquinolone-resistant, ESBL-producing isolates, with the remaining 47% comprised of diverse clonal groups that contributed a single isolate each. ST131-H30Rx, with CTX-M-15, was the major ESBL producer (6/8) among ST131-H30 isolates. ST131-H30 and H30Rx also dominated (46% and 37%, respectively) among the historical ESBL-producing isolates (2004 to 2011), without significant temporal shifts in relative prevalence. Thus, this medical center’s recently emerging ESBL-producing E. coli strains, although multiclonal, are dominated by ST131-H30 and H30Rx, which are the only clonally expanded fluoroquinolone-resistant, ESBL-producing lineages. Measures to rapidly and effectively detect, treat, and control these highly successful lineages are needed. IMPORTANCE The ever-rising prevalence of resistance to first-line antibiotics among clinical Escherichia coli isolates leads to worse clinical outcomes and higher health care costs, thereby creating a need to discover its basis so that effective interventions can be developed. We found that the H30 subset within E. coli sequence type 131 (ST131-H30) is currently, and has been since at least 2004, the main E. coli lineage contributing to key resistance phenotypes—including extended-spectrum-beta-lactamase (ESBL) production, fluoroquinolone resistance, multidrug resistance, and dual ESBL production-plus-fluoroquinolone resistance—at a United States tertiary care center with a rising prevalence of ESBL-producing E. coli isolates. This identifies ST131-H30 as a target for diagnostic tests and preventive measures designed to curb the emergence of multidrug-resistant E. coli isolates and/or to blunt its clinical impact.
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Schaumburg F, Onwugamba FC, Akulenko R, Peters G, Mellmann A, Köck R, Becker K. A geospatial analysis of flies and the spread of antimicrobial resistant bacteria. Int J Med Microbiol 2016; 306:566-571. [DOI: 10.1016/j.ijmm.2016.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/30/2016] [Accepted: 06/12/2016] [Indexed: 02/06/2023] Open
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Massot M, Daubié AS, Clermont O, Jauréguy F, Couffignal C, Dahbi G, Mora A, Blanco J, Branger C, Mentré F, Eddi A, Picard B, Denamur E. Phylogenetic, virulence and antibiotic resistance characteristics of commensal strain populations of Escherichia coli from community subjects in the Paris area in 2010 and evolution over 30 years. MICROBIOLOGY-SGM 2016; 162:642-650. [PMID: 26822436 DOI: 10.1099/mic.0.000242] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
It is important to study commensal populations of Escherichia coli because they appear to be the reservoir of both extra-intestinal pathogenic E. coli and antibiotic resistant strains of E. coli. We studied 279 dominant faecal strains of E. coli from 243 adults living in the community in the Paris area in 2010. The phylogenetic group and subgroup [sequence type complex (STc)] of the isolates and the presence of 20 virulence genes were determined by PCR assays. The O-types and resistance to 18 antibiotics were assessed phenotypically. The B2 group was the most frequently recovered (34.0 %), followed by the A group (28.7 %), and other groups were more rare. The most prevalent B2 subgroups were II (STc73), IV (STc141), IX (STc95) and I (STc131), with 22.1, 21.1, 16.8 and 13.7 %, respectively, of the B2 group strains. Virulence factors (VFs) were more common in B2 group than other strains. One or more resistances were found in 125 strains (44.8 % of the collection) but only six (2.2 % of the collection) were multiresistant; no extended-spectrum beta-lactamase-producing strain was isolated. The C phylogroup and clonal group A strains were the most resistant. No trade-off between virulence and resistance was evidenced. We compared these strains with collections of strains gathered under the same conditions 30 and 10 years ago. There has been a parallel and linked increase in the frequency of B2 group strains (from 9.4 % in 1980, to 22.7 % in 2000 and 34.0 % in 2010) and of VFs. Antibiotic resistance also increased, from 22.6 % of strains resistant to at least one antibiotic in 1980, to 31.8 % in 2000 and 44.8 % in 2010; resistance to streptomycin, however, remained stable. Commensal human E. coli populations have clearly evolved substantially over time, presumably reflecting changes in human practices, and particularly increasing antibiotic use.
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Affiliation(s)
- Méril Massot
- INSERM, IAME, UMR1137, Paris, France
- Univ Paris Diderot, IAME, UMR1137, Sorbonne Paris Cité, Paris, France
| | - Anne-Sophie Daubié
- Univ Paris Nord, IAME, UMR1137, Sorbonne Paris Cité, Bobigny, France
- APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Site Avicenne, Bobigny, France
- INSERM, IAME, UMR1137, Paris, France
| | - Olivier Clermont
- INSERM, IAME, UMR1137, Paris, France
- Univ Paris Diderot, IAME, UMR1137, Sorbonne Paris Cité, Paris, France
| | - Françoise Jauréguy
- INSERM, IAME, UMR1137, Paris, France
- APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Site Avicenne, Bobigny, France
- Univ Paris Nord, IAME, UMR1137, Sorbonne Paris Cité, Bobigny, France
| | - Camille Couffignal
- INSERM, IAME, UMR1137, Paris, France
- Univ Paris Diderot, IAME, UMR1137, Sorbonne Paris Cité, Paris, France
| | - Ghizlane Dahbi
- Laboratorio de Referencia de E. coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de E. coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de E. coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Catherine Branger
- INSERM, IAME, UMR1137, Paris, France
- Univ Paris Diderot, IAME, UMR1137, Sorbonne Paris Cité, Paris, France
| | - France Mentré
- INSERM, IAME, UMR1137, Paris, France
- Univ Paris Diderot, IAME, UMR1137, Sorbonne Paris Cité, Paris, France
| | - Alain Eddi
- Département de Médecine Générale, Univ Paris Diderot, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Bertrand Picard
- INSERM, IAME, UMR1137, Paris, France
- APHP, Hôpitaux Universitaires Paris Seine Saint-Denis, Site Avicenne, Bobigny, France
- Univ Paris Nord, IAME, UMR1137, Sorbonne Paris Cité, Bobigny, France
| | - Erick Denamur
- INSERM, IAME, UMR1137, Paris, France
- Univ Paris Diderot, IAME, UMR1137, Sorbonne Paris Cité, Paris, France
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Insight into neonatal septicaemic Escherichia coli from India with respect to phylogroups, serotypes, virulence, extended-spectrum-β-lactamases and association of ST131 clonal group. Epidemiol Infect 2015; 143:3266-76. [PMID: 25858453 DOI: 10.1017/s0950268815000539] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
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.
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Clermont O, Gordon D, Denamur E. Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes. MICROBIOLOGY-SGM 2015; 161:980-988. [PMID: 25714816 DOI: 10.1099/mic.0.000063] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/19/2015] [Indexed: 02/02/2023]
Abstract
Numerous tools allowing the rapid and universal identification of the clones/clonal complexes/phylogroups of Escherichia coli have been developed, as it is a commensal of the vertebrate gut, a major pathogen in veterinary and human medicine, and a bacterial indicator of faecal contamination. The ability to identify clones/clonal complexes/phylogroups is crucial, as a strain's ecological niche, lifestyle and propensity to cause disease vary with its phylogenetic origins. There are currently three multi-locus sequence typing (MLST) schemes for E. coli, as well as several PCR-based assays for determining a strain's phylogroup or clonal complex. In this work, we present data that will enable investigators to determine the correspondence between the PCR-based assays and the three MLST schemes, and provide the means for assigning a sequence type (ST) to a phylogroup when no other data on the strain phylogroup membership are available. Such information will help the scientific community to accurately identify the E. coli clones reported in various publications. Although whole-genome sequencing will replace classical MLST and most alternative PCR-based methods, the ST nomenclature of the MLST scheme hosted at the University of Warwick will largely persist.
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Affiliation(s)
- Olivier Clermont
- Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.,INSERM, IAME, UMR 1137, F-75018 Paris, France
| | - David Gordon
- Division of Evolution, Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200 Australia
| | - Erick Denamur
- Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.,INSERM, IAME, UMR 1137, F-75018 Paris, France
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Bajaj P, Singh NS, Kanaujia PK, Virdi JS. Distribution and molecular characterization of genes encoding CTX-M and AmpC β-lactamases in Escherichia coli isolated from an Indian urban aquatic environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 505:350-6. [PMID: 25461036 DOI: 10.1016/j.scitotenv.2014.09.084] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/14/2014] [Accepted: 09/25/2014] [Indexed: 05/21/2023]
Abstract
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.
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Affiliation(s)
- Priyanka Bajaj
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Nambram Somendro Singh
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Pawan Kumar Kanaujia
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Jugsharan Singh Virdi
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
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Surgers L, Bleibtreu A, Burdet C, Clermont O, Laouénan C, Lefort A, Mentré F, Carbonne B, Bingen E, Meynard JL, Denamur E, on behalf of the COLIBAFI Group. Escherichia coli bacteraemia in pregnant women is life-threatening for foetuses. Clin Microbiol Infect 2014; 20:O1035-41. [DOI: 10.1111/1469-0691.12742] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/14/2014] [Accepted: 06/25/2014] [Indexed: 12/22/2022]
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Within-population distribution of trimethoprim resistance in Escherichia coli before and after a community-wide intervention on trimethoprim use. Antimicrob Agents Chemother 2014; 58:7492-500. [PMID: 25288078 DOI: 10.1128/aac.03228-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 2-year prospective intervention on the prescription of trimethoprim reduced the use by 85% in a health care region with 178,000 inhabitants. Here, we performed before-and-after analyses of the within-population distribution of trimethoprim resistance in Escherichia coli. Phylogenetic and population genetic methods were applied to multilocus sequence typing data of 548 consecutively collected E. coli isolates from clinical urinary specimens. Results were analyzed in relation to antibiotic susceptibility and the presence and genomic location of different trimethoprim resistance gene classes. A total of 163 E. coli sequence types (STs) were identified, of which 68 were previously undescribed. The isolates fell into one of three distinct genetic clusters designated BAPS 1 (E. coli phylogroup B2), BAPS 2 (phylogroup A and B1), and BAPS 3 (phylogroup D), each with a similar frequency before and after the intervention. BAPS 2 and BAPS 3 were positively and BAPS 1 was negatively associated with trimethoprim resistance (odds ratios of 1.97, 3.17, and 0.26, respectively). In before-and-after analyses, trimethoprim resistance frequency increased in BAPS 1 and decreased in BAPS 2. Resistance to antibiotics other than trimethoprim increased in BAPS 2. Analysis of the genomic location of different trimethoprim resistance genes in isolates of ST69, ST58, and ST73 identified multiple independent acquisition events in isolates of the same ST. The results show that despite a stable overall resistance frequency in E. coli before and after the intervention, marked within-population changes occurred. A decrease of resistance in one major genetic cluster was masked by a reciprocal increase in another major cluster.
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The rpoS gene is predominantly inactivated during laboratory storage and undergoes source-sink evolution in Escherichia coli species. J Bacteriol 2014; 196:4276-84. [PMID: 25266386 DOI: 10.1128/jb.01972-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The rpoS gene codes for an alternative RNA polymerase sigma factor, which acts as a general regulator of the stress response. Inactivating alleles of rpoS in collections of natural Escherichia coli isolates have been observed at very variable frequencies, from less than 1% to more than 70% of strains. rpoS is easily inactivated in nutrient-deprived environments such as stab storage, which makes it difficult to determine the true frequency of rpoS inactivation in nature. We studied the evolutionary history of rpoS and compared it to the phylogenetic history of bacteria in two collections of 82 human commensal and extraintestinal E. coli strains. These strains were representative of the phylogenetic diversity of the species and differed only by their storage conditions. In both collections, the phylogenetic histories of rpoS and of the strains were congruent, indicating that horizontal gene transfer had not occurred at the rpoS locus, and rpoS was under strong purifying selection, with a ratio of the nonsynonymous mutation rate (Ka) to the synonymous substitution rate (Ks) substantially smaller than 1. Stab storage was associated with a high frequency of inactivating alleles, whereas almost no amino acid sequence variation was observed in RpoS in the collection studied directly after isolation of the strains from the host. Furthermore, the accumulation of variations in rpoS was typical of source-sink dynamics. In conclusion, rpoS is rarely inactivated in natural E. coli isolates within their mammalian hosts, probably because such strains rapidly become evolutionary dead ends. Our data should encourage bacteriologists to freeze isolates immediately and to avoid the use of stab storage.
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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. Antimicrob Agents Chemother 2014; 58:6886-95. [PMID: 25199783 DOI: 10.1128/aac.03679-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
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.
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Burdet C, Clermont O, Bonacorsi S, Laouénan C, Bingen E, Aujard Y, Mentré F, Lefort A, Denamur E. Escherichia coli bacteremia in children: age and portal of entry are the main predictors of severity. Pediatr Infect Dis J 2014; 33:872-9. [PMID: 25222308 DOI: 10.1097/inf.0000000000000309] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Escherichia coli bacteremia is a major cause of severe sepsis in children. Little is known about predictors of severity. METHODS We analyzed 84 children ≤ 18 years of age with E. coli bacteremia from the prospective COLIBAFI study performed during 2005-2007. The severity of bacteremia was defined as occurrence of death or transfer to intensive care unit. Studied characteristics included age, gender, birth weight, history of prematurity, immunodepression, nosocomial infection, portal of entry, phylogenetic group and subgroup belonging, O-type, virulence gene content and antimicrobial susceptibility. We compared bacterial characteristics in urinary- versus digestive-source bacteremia, in children ≤ 3 versus >3 month of age, and in children versus adults. We also searched for risk factors of severity. RESULTS Median age was 2.4 months, 57% males. Most frequent portals of entry were urinary (66.2%) and digestive (19.5%) tracts. Most isolates (63.1%) belonged to B2 phylogroup. Strains in children ≤ 3 months of age exhibited more virulence genes, especially neuC and fyuA/irp2, and were less resistant to antibiotics than in children >3 months of age. Comparing community-acquired urinary-source bacteremia between children and adults, we found that bacteremia were less severe in children, whose strains exhibited a specific virulence gene repertoire and had a higher resistance score than in adults. Seventeen children (20.2%) had a severe bacteremia and 8 died. Non-urinary portal of entry and age ≤ 3 months of age were the only risk factors associated with severity. CONCLUSIONS E. coli strains responsible for bacteremia exhibit specific characteristics according to age of children. However, host characteristics and portal of entry are the main determinants of severity of E. coli bacteremia in children, as observed in adults.
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Affiliation(s)
- Charles Burdet
- From the *AP-HP, Hôpital Bichat, Service de Biostatistiques; †IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité; ‡EA 3105, Univ Paris Diderot, Sorbonne Paris Cité; §AP-HP, Hôpital Robert-Debré, Laboratoire de Microbiologie; ¶AP-HP, Hôpital Robert Debré, Service de Néonatologie, Paris; and ‖AP-HP, Hôpital Beaujon, Service de Médecine Interne, Clichy, France
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Morgand M, Vimont S, Bleibtreu A, Boyd A, Thien HV, Zahar JR, Denamur E, Arlet G. Extended-spectrum beta-lactamase-producing Escherichia coli infections in children: are community-acquired strains different from nosocomial strains? Int J Med Microbiol 2014; 304:970-6. [PMID: 25023074 DOI: 10.1016/j.ijmm.2014.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/04/2014] [Accepted: 06/11/2014] [Indexed: 11/29/2022] Open
Abstract
Infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are an important cause of morbidity and mortality, especially in children. We compared 58 epidemiologically unrelated ESBL-producing E. coli strains that caused infections. They were isolated between 2008 and 2012 in two Parisian pediatric hospitals and grouped according to their origin into either community-acquired (CA) (n=37) or nosocomially acquired (NA) (n=21) strains. Molecular characteristics of the ESBLs, phylogenetic traits of the strains including their belonging to clone O25b-ST131, prevalence of associated virulence genes, growth capacities in different media, metabolic phenotype and biofilm formation abilities were studied. ESBL type, associated resistance and distribution of phylogenetic groups were similar in the CA and NA groups. More than 60% of the B2 phylogroup strains in both groups belonged to the ST131 clone. Interestingly, CA strains possessed more genes encoding virulence factors and the distribution of these genes differed significantly between the two groups: fyuA, hlyC, papC and papGII were more frequent in the CA group, whereas iroN was more frequent in the NA group. CA strains also showed enhanced growth capacities in Luria Bertani rich medium. They tended to produce more biofilm but the difference was not significant. This study confirms the wide spread of clone ST131 among infected children, regardless of whether their infections were community- or nosocomially acquired. It highlights genotypic and phenotypic differences according to the origin of the strains that could indicate adaptability of these multi-resistant bacteria to specific environmental and host factors.
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Affiliation(s)
- Marjolaine Morgand
- Université Pierre et Marie Curie, Faculté de Médecine, Département de Bactériologie, F-75012 Paris, France
| | - Sophie Vimont
- Université Pierre et Marie Curie, Faculté de Médecine, Département de Bactériologie, F-75012 Paris, France; Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaire de l'Est Parisien, Département de Bactériologie, F-75012 Paris, France
| | - Alexandre Bleibtreu
- IAME, UMR 1137, INSERM, F-75018 Paris, France; IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France
| | | | - Hoang Vu Thien
- Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaire de l'Est Parisien, Département de Bactériologie, F-75012 Paris, France
| | - Jean-Ralph Zahar
- Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Unité d'hygiène et de lutte contre les infections nosocomiales, F-75015 Paris, France
| | - Erick Denamur
- IAME, UMR 1137, INSERM, F-75018 Paris, France; IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France
| | - Guillaume Arlet
- Université Pierre et Marie Curie, Faculté de Médecine, Département de Bactériologie, F-75012 Paris, France; Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaire de l'Est Parisien, Département de Bactériologie, F-75012 Paris, France.
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Strand L, Jenkins A, Henriksen IH, Allum AG, Grude N, Kristiansen BE. High levels of multiresistance in quinolone resistant urinary tract isolates of Escherichia coli from Norway; a non clonal phenomen? BMC Res Notes 2014; 7:376. [PMID: 24941949 PMCID: PMC4077835 DOI: 10.1186/1756-0500-7-376] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 05/28/2014] [Indexed: 11/10/2022] Open
Abstract
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 SOS response. The spread of clones seems to be less important than previously reported in regard to emergence of quinolone resistance and multiresistance as both are associated primarily with singleton isolates.
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Diverse high-risk B2 and D Escherichia coli clones depicted by Fourier Transform Infrared Spectroscopy. Sci Rep 2013; 3:3278. [PMID: 24252832 PMCID: PMC3834554 DOI: 10.1038/srep03278] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 11/01/2013] [Indexed: 12/28/2022] Open
Abstract
We aimed to develop a reliable method based on Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR) to discriminate Escherichia coli clones from B2(n = 9) and D(n = 13) phylogenetic groups. Eighty-eight E. coli isolates belonging to phylogenetic groups B2(n = 39) and D(n = 49), including particularly widespread high risk clones or clonal complexes (HiRCC) ST131, ST69, ST393 and ST405 were studied. Spectra were analysed by unsupervised (hierarchical cluster analysis-HCA) and supervised methods (soft independent modelling of class analogy-SIMCA and partial least square discriminant analysis-PLSDA). B2-ST131 isolates were discriminated from B2 non-ST131 and D phylogroup isolates (ST69, ST393, ST405) by HCA, SIMCA and PLSDA. D-ST69, D-ST393 and D-ST405 isolates were also distinguished from each other and from other STs from phylogroup D by the three methods. We demonstrate that FTIR-ATR coupled with chemometrics is a reliable and alternative method to accurately discriminate particular E. coli clones. Its validation towards an application at a routine basis could revolutionize high-throughput bacterial typing.
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Prevalence and characteristics of the epidemic multiresistant Escherichia coli ST131 clonal group among extended-spectrum beta-lactamase-producing E. coli isolates in Copenhagen, Denmark. J Clin Microbiol 2013; 51:1779-85. [PMID: 23554186 DOI: 10.1128/jcm.00346-13] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.
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Matsumura Y, Yamamoto M, Nagao M, Hotta G, Matsushima A, Ito Y, Takakura S, Ichiyama S. Emergence and spread of B2-ST131-O25b, B2-ST131-O16 and D-ST405 clonal groups among extended-spectrum-β-lactamase-producing Escherichia coli in Japan. J Antimicrob Chemother 2012; 67:2612-20. [PMID: 22843833 DOI: 10.1093/jac/dks278] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The increasing prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has been associated with the emergence of the CTX-M-producing sequence type 131 (ST131) pandemic clonal group, a member of the O25b serogroup and the B2 phylogenetic group. To assess the clonal spread of ESBL-producing E. coli in Japan, a regional surveillance programme was conducted. METHODS A total of 581 ESBL-producing clinical specimen E. coli isolates were collected between 2001 and 2010. Clonal groups, including ST131, D-ST405, D-ST393 and D-ST69, were determined using the PCR O type, phylogenetic grouping by triplex PCR, allele-specific PCR and multilocus sequence typing (MLST). A subset of clonal groups underwent PFGE. RESULTS Among clonal strains, 215 isolates (37%) were identified as belonging to the ST131 group, 185 as B2-ST131-O25b (32%), 26 as B2-ST131-O16 (4%), 3 as B1-ST131-O25b (0.5%) and 1 as B2-ST131-O-non-typeable (0.1%). Forty-one isolates (7%) were identified as belonging to the D-ST405 clonal group, seven (1%) as D-ST69 and two (0.3%) as D-ST393. The B2-ST131-O16 clonal group was characterized by CTX-M-14 and a significantly lower ciprofloxacin resistance rate than the B2-ST131-O25b clonal group. The B2-ST131-O16 and B2-ST131-O25b clonal groups each made up a single PFGE cluster, with 65% similarity. The rate of ESBL-producing E. coli increased over the years (0.2% in 2001 to 9.7% in 2010) and corresponded to increases in the numbers of the B2-ST131-O25b, B2-ST131-O16 and D-ST405 clonal groups. CONCLUSIONS The B2-ST131-O25b, B2-ST131-O16 and D-ST405 clonal groups have contributed to the spread of ESBL-producing E. coli in Japan.
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Affiliation(s)
- Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto, Japan.
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Blanco J, Mora A, Mamani R, Lopez C, Blanco M, Dahbi G, Herrera A, Blanco JE, Alonso MP, Garcia-Garrote F, Chaves F, Orellana MA, Martinez-Martinez L, Calvo J, Prats G, Larrosa MN, Gonzalez-Lopez JJ, Lopez-Cerero L, Rodriguez-Bano J, Pascual A. National survey of Escherichia coli causing extraintestinal infections reveals the spread of drug-resistant clonal groups O25b:H4-B2-ST131, O15:H1-D-ST393 and CGA-D-ST69 with high virulence gene content in Spain. J Antimicrob Chemother 2011; 66:2011-21. [DOI: 10.1093/jac/dkr235] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Molecular Typing Methods for Analysis of Extraintestinal Pathogenic
Escherichia coli. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Strand L, Jenkins A, Grude N, Allum AG, Mykland HC, Nowrouzian FL, Kristiansen BE. Emergence of fluoroquinolone-resistant clonal group A: clonal analysis of Norwegian and Russian E. coli isolates. APMIS 2010; 118:571-7. [PMID: 20666738 DOI: 10.1111/j.1600-0463.2010.02623.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We describe a study of urinary tract and intestinal isolates of Escherichia coli from Norway and Russia using automated ribotyping, single nucleotide polymorphism analysis for clonal group A (CgA) supplemented with phylogrouping, virulence gene profiling and resistance profiling. CgA comprised 19% of the Norwegian UTI isolates from 2001. Two highly multiresistant fluoroquinolone-resistant CgA isolates were found. Ribotypes clustered into four major and six minor groups (ribogroups). Fluoroquinolone-resistant isolates and phylogroups A and B1 were associated with ribogroup (R)A. Ribogroup (R)B predominated among Russian UTI isolates and was predominantly phylogroup A and depleted in P-fimbriae. Ribogroup (R)C predominated among Norwegian UTI isolates and was rich in virulence factors (S-fimbriae, haemagglutinin and haemolysin) and predominantly phylogroup B2 and D. Ribogroup (R)G was associated with CgA and predominantly phylogroup D. Ribogroups (R)D, (R)E and (R)F had too few members for statistical analysis. The correlation between ribotype and phylogenetic group was not as strong as reported in other studies.
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Platell JL, Cobbold RN, Johnson JR, Trott DJ. Clonal group distribution of fluoroquinolone-resistant Escherichia coli among humans and companion animals in Australia. J Antimicrob Chemother 2010; 65:1936-8. [DOI: 10.1093/jac/dkq236] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hilbert DW, Paulish TE, Mordechai E, Adelson ME, Gygax SE, Trama JP. Antimicrobial non-susceptibility of cervico-vaginal and rectal Escherichia coli isolates is associated with phylogeny and plasmid carriage. Eur J Clin Microbiol Infect Dis 2009; 28:1399-403. [DOI: 10.1007/s10096-009-0788-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 07/12/2009] [Indexed: 10/20/2022]
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Epidemic clonal groups of Escherichia coli as a cause of antimicrobial-resistant urinary tract infections in Canada, 2002 to 2004. Antimicrob Agents Chemother 2009; 53:2733-9. [PMID: 19398649 DOI: 10.1128/aac.00297-09] [Citation(s) in RCA: 228] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The extent to which clonal spread contributes to emerging antimicrobial resistance in Escherichia coli is incompletely defined. To address this question within a recent, nationally representative strain collection, three established drug-resistant E. coli clonal groups (i.e., clonal group A, E. coli O15:K52:H1, and sequence type 131 [ST131]) were sought among 199 E. coli urine isolates recovered from across Canada from 2002 to 2004, with stratification by resistance to trimethoprim-sulfamethoxazole (TS) and fluoroquinolones (FQs). The isolates' clonal backgrounds, virulence genotypes, and macrorestriction profiles were assessed. The three clonal groups were found to account for 37.2% of isolates overall, but accounted for 0% of TS-susceptible (TS-S) and FQ-susceptible (FQ-S) isolates, 20% of TS-resistant (TS-R) and FQ-S isolates, 60% of TS-S and FQ-R isolates, and 68% of TS-R and FQ-R isolates (P < 0.001). E. coli ST131, the most prevalent clonal group, accounted for 23.1% of isolates overall and for 44% of the FQ-R isolates. Nearly all ST131 isolates were FQ-R (96%) but, notably, cephalosporin susceptible (98%). Although the distinctive virulence profiles of the FQ-R clonal group isolates were less extensive than those of the susceptible isolates, they were significantly more extensive than those of the other FQ-R isolates. These findings indicate that among the E. coli urine isolates studied, resistance to TS and FQs has a prominent clonal component, with the O15:K52:H1 clonal group and especially E. coli ST131 being the major contributors. These clonal groups appear to be more virulent than comparably resistant isolates, possibly contributing to their success as emerging multi-drug-resistant pathogens.
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Wallace-Gadsden F, Johnson JR, Wain J, Okeke IN. Enteroaggregative Escherichia coli related to uropathogenic clonal group A. Emerg Infect Dis 2008; 13:757-60. [PMID: 17553259 PMCID: PMC2738470 DOI: 10.3201/eid1305.061057] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) are heterogeneous, diarrheagenic E. coli. Of EAEC strains from Nigeria, 10 independent antimicrobial-resistant isolates belonged to the multilocus sequence type 69 clonal complex, to which uropathogenic E. coli clonal group A belongs. This finding suggests a recent common ancestor for these distinct groups of pathogenic E. coli.
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Affiliation(s)
- Faith Wallace-Gadsden
- Haverford College, Haverford, Pennsylvania, USA
- Current affiliation: Tufts University School of Medicine, Boston, Massachusetts, USA
| | - James R. Johnson
- Minneapolis Veterans Administration Medical Center, Minneapolis, Minnesota, USA
- University of Minnesota, Minneapolis, Minnesota, USA; and
| | - John Wain
- Wellcome Trust Sanger Institute, Cambridgeshire, United Kingdom
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Risk factors for trimethoprim-sulfamethoxazole resistance in patients with acute uncomplicated cystitis. Antimicrob Agents Chemother 2007; 52:846-51. [PMID: 18086847 DOI: 10.1128/aac.01200-07] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Emerging antimicrobial resistance among uropathogens makes the management of acute uncomplicated cystitis increasingly challenging. Few prospective data are available on the risk factors for resistance to trimethoprim-sulfamethoxazole (TMP-SMX), the drug of choice in most settings. In order to evaluate this, we prospectively enrolled women 18 to 50 years of age presenting to an urban primary care practice with symptoms of cystitis. Potentially eligible women provided a urine sample for culture and completed a questionnaire regarding putative risk factors for TMP-SMX resistance. Escherichia coli isolates were tested for clonal group A (CGA) membership by a fumC-specific PCR. Of 165 women with cystitis symptoms, 103 had a positive urine culture and were eligible for participation. E. coli was the predominant uropathogen (86%). Fifteen (14.6%) women had a TMP-SMX-resistant (TMP-SMX r) organism (all of which were E. coli). Compared with the women who had a TMP-SMX-susceptible organism, women in the TMP-SMX r group were more likely to have traveled (odds ratio [OR], 15.4; 95% confidence interval [CI], 4.4 to 54.3; P < 0.001) and to be Asian (OR, 6.1; 95% CI, 1.0 to 36.4; P = 0.048). CGA was also independently associated with TMP-SMX resistance (OR, 105; 95% CI, 6.3 to 1,777.6; P = 0.001). No association with TMP-SMX resistance was demonstrated for the use of either TMP-SMX or another antibiotic in the past 3 months or with having a child in day care. Among these women with acute uncomplicated cystitis, Asian race and recent travel were independently associated with TMP-SMX resistance. TMP-SMX r isolates were more likely to belong to CGA. Knowledge of these risk factors for TMP-SMX resistance could facilitate the accurate selection of empirical therapy.
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Boczek LA, Rice EW, Johnston B, Johnson JR. Occurrence of antibiotic-resistant uropathogenic Escherichia coli clonal group A in wastewater effluents. Appl Environ Microbiol 2007; 73:4180-4. [PMID: 17483270 PMCID: PMC1932775 DOI: 10.1128/aem.02225-06] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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. All 15 CGA isolates (1% of the 1,484 isolates analyzed) exhibited resistance to trimethoprim-sulfamethoxazole (TMP-SMZ), accounting for 19.5% of the 77 TMP-SMZ-resistant isolates. Antimicrobial resistance patterns, virulence traits, O:H serotypes, and phylogenetic groupings were compared for CGA and selected non-CGA isolates. The CGA isolates exhibited a wider diversity of resistance profiles and somatic antigens than that found in most previous characterizations of this clonal group. This is the first report of recovery from outside a human host of E. coli CGA isolates with virulence factor and antibiotic resistance profiles typical of CGA isolates from a human source. The occurrence of "human-type" CGA in wastewater effluents demonstrates a potential mode for the dissemination of this clonal group in the environment, with possible secondary transmission to new human or animal hosts.
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Moritz RL, Welch RA. The Escherichia coli argW-dsdCXA genetic island is highly variable, and E. coli K1 strains commonly possess two copies of dsdCXA. J Clin Microbiol 2006; 44:4038-48. [PMID: 17088369 PMCID: PMC1698345 DOI: 10.1128/jcm.01172-06] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The genome sequences of Escherichia coli pathotypes reveal extensive genetic variability in the argW-dsdCXA island. Interestingly, the archetype E. coli K1 neonatal meningitis strain, strain RS218, has two copies of the dsdCXA genes for d-serine utilization at the argW and leuX islands. Because the human brain contains d-serine, an epidemiological study emphasizing K1 isolates surveyed the dsdCXA copy number and function. Forty of 41 (97.5%) independent E. coli K1 isolates could utilize d-serine. Southern blot hybridization revealed physical variability within the argW-dsdC region, even among 22 E. coli O18:K1:H7 isolates. In addition, 30 of 41 K1 strains, including 21 of 22 O18:K1:H7 isolates, had two dsdCXA loci. Mutational analysis indicated that each of the dsdA genes is functional in a rifampin-resistant mutant of RS218, mutant E44. The high percentage of K1 strains that can use d-serine is in striking contrast to our previous observation that only 4 of 74 (5%) isolates in the diarrheagenic E. coli (DEC) collection have this activity. The genome sequence of diarrheagenic E. coli isolates indicates that the csrRAKB genes for sucrose utilization are often substituted for dsdC and a portion of dsdX present at the argW-dsdCXA island of extraintestinal isolates. Among DEC isolates there is a reciprocal pattern of sucrose fermentation versus d-serine utilization. The ability to use d-serine is a trait strongly selected for among E. coli K1 strains, which have the ability to infect a wide range of extraintestinal sites. Conversely, diarrheagenic E. coli pathotypes appear to have substituted sucrose for d-serine as a potential nutrient.
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Affiliation(s)
- Rebecca L Moritz
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Solberg OD, Ajiboye RM, Riley LW. Origin of class 1 and 2 integrons and gene cassettes in a population-based sample of uropathogenic Escherichia coli. J Clin Microbiol 2006; 44:1347-51. [PMID: 16597861 PMCID: PMC1448660 DOI: 10.1128/jcm.44.4.1347-1351.2006] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The prevalence of urinary tract infections (UTI) caused by trimethoprim-sulfamethoxazole (TMP-SMX)-resistant Escherichia coli is increasing and varies geographically in the United States. Recent community-based UTI studies have demonstrated geographic clustering of an Escherichia coli clonal group, suggesting occurrence of a community outbreak of UTI. A large proportion of this clonal group (designated CgA) isolated from women in a California college community was found to be resistant to TMP-SMX. We wished to determine if the acquisition of TMP-SMX resistance by CgA occurred before or after the CgA strains were introduced into this community. Between October 1999 and January 2000 and between October 2000 and January 2001, 482 E. coli isolates were consecutively collected from the urine samples of women with UTI at a student health clinic and analyzed for determinants of TMP-SMX resistance. In particular, the distribution of integrons harboring resistance cassettes for TMP-SMX (dfr) was examined. Among 95 TMP-SMX-resistant isolates, 68 and 27 isolates carried class 1 and class 2 integrons, respectively. A class 1 integron was found in 25 (93%) of 27 TMP-SMX-resistant CgA isolates but in only 43 (63%) of 68 TMP-SMX-resistant non-CgA isolates (P < 0.001) and in none of 44 TMP-SMX-susceptible E. coli isolates (P < 0.0001). CgA strains carried only a single arrangement of class 1 gene cassettes (dfrA17-aadA5), while the non-clonal group strains carried nine different cassette arrangements. These results support the idea that CgA strains acquired their resistance at a common site prior to their spread to the college community.
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Affiliation(s)
- Owen D Solberg
- Divisions of Epidemiology and Infectious Diseases, School of Public Health, University of California-Berkeley, 140 Warren Hall, Berkeley CA 94720, USA.
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Hart WS, Heuzenroeder MW, Barton MD. A Study of the Transfer of Tetracycline Resistance Genes Between Escherichia coli in the Intestinal Tract of a Mouse and a Chicken Model. ACTA ACUST UNITED AC 2006; 53:333-40. [PMID: 16930278 DOI: 10.1111/j.1439-0450.2006.00967.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Experiments to demonstrate the transfer of genes within a natural environment are technically difficult because of the unknown numbers and strains of bacteria present, as well as difficulties designing adequate control experiments. The results of such studies should be viewed within the limits of the experimental design. Most experiments to date have been based on artificial models, which only give approximations of the real-life situation. The current study uses more natural models and provides information about tetracycline resistance as it occurs in wild-type bacteria within the environment of the normal intestinal tract of an animal. Tetracycline sensitive, nalidixic acid resistant Escherichia coli isolates of human origin were administered to mice and chicken animal models. They were monitored for acquisition of tetracycline resistance from indigenous or administered donor E. coli. Five sets of in vivo experiments demonstrated unequivocal transfer of tetracycline resistance to tetracycline sensitive recipients. The addition of tetracycline in the drinking water of the animals increased the probability of transfer between E. coli strains originating from the same animal species. The co-transfer of unselected antibiotic resistance in animal models was also demonstrated.
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Affiliation(s)
- W S Hart
- Sansom Institute, School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA 5000, Australia
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Johnson JR, Owens KL, Clabots CR, Weissman SJ, Cannon SB. Phylogenetic relationships among clonal groups of extraintestinal pathogenic Escherichia coli as assessed by multi-locus sequence analysis. Microbes Infect 2006; 8:1702-13. [PMID: 16820314 DOI: 10.1016/j.micinf.2006.02.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Revised: 01/26/2006] [Accepted: 02/01/2006] [Indexed: 11/24/2022]
Abstract
The evolutionary origins of extraintestinal pathogenic Escherichia coli (ExPEC) remain uncertain despite these organisms' relevance to human disease. A valid understanding of ExPEC phylogeny is needed as a framework against which the observed distribution of virulence factors and clinical associations can be analyzed. Accordingly, phylogenetic relationships were defined by multi-locus sequence analysis among 44 representatives of selected ExPEC clonal groups and the E. coli Reference (ECOR) collection. Recombination, which significantly obscured the phylogenetic signal for several strains, was dealt with by excluding strains or specific sequences. Conflicting overall phylogenies, and internal phylogenies for virulence-associated phylogenetic group B2, were inferred depending on the specific dataset (i.e., how extensively purged of recombination), outgroup (Salmonella enterica and/or Escherichia fergusonii), and analysis method (neighbor joining, maximum parsimony, maximum likelihood, or Bayesian likelihood). Nonetheless, the major E. coli phylogenetic groups A, B1, and B2 were consistently well resolved, as was a major sub-component of group D and an ECOR 37-O157:H7 clade. Moreover, nine important ExPEC clonal groups within groups B2 and D, characterized by serotypes O6:K2:H1, O18:K1:H7, O6:H31, and O4:K+:H+ (from group B2), and O1:K1:H-, O7:K1:H-, O157:K+:H (non-7), O15:K52:H1, and O11/17/77:K52:H18 ("clonal group A") (from group D), were consistently well resolved, regardless of clinical background (cystitis, pyelonephritis, neonatal meningitis, sepsis, or fecal), host group, geographical origin, and virulence profile. Among the group B2-derived clonal groups the O6:K2:H1 clade appeared basal. Within group D, "clonal group A" and the O15:K52:H1 clonal group were consistently placed with ECOR 47 and ECOR 44, respectively, as nearest neighbors. These findings clarify phylogenetic relationships among key ExPEC clonal groups but also emphasize that recombination appears to obscure the oldest evolutionary relationships, despite extensive targeted sequencing and use of a wide range of analysis techniques.
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Affiliation(s)
- James R Johnson
- Mucosal and Vaccine Research Center, Minneapolis VA Medical Center, Infectious Diseases (111F), Minneapolis, MN 55417, USA.
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Snyder JA, Lloyd AL, Lockatell CV, Johnson DE, Mobley HLT. Role of phase variation of type 1 fimbriae in a uropathogenic Escherichia coli cystitis isolate during urinary tract infection. Infect Immun 2006; 74:1387-93. [PMID: 16428790 PMCID: PMC1360342 DOI: 10.1128/iai.74.2.1387-1393.2006] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Type 1 fimbrial phase-locked mutants of uropathogenic Escherichia coli cystitis isolate F11 were used to assess the role of the invertible element during urinary tract infection. Compared to the wild type, the phase-locked off mutant was attenuated, and constitutive production of type 1 fimbriae by the phase-locked on mutant did not provide a competitive advantage.
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Tartof SY, Solberg OD, Manges AR, Riley LW. Analysis of a uropathogenic Escherichia coli clonal group by multilocus sequence typing. J Clin Microbiol 2006; 43:5860-4. [PMID: 16333067 PMCID: PMC1317175 DOI: 10.1128/jcm.43.12.5860-5864.2005] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although many strain typing methods exist for pathogenic Escherichia coli, most have drawbacks in terms of resolving power, interpretability, or scalability. For this reason, multilocus sequence typing (MLST) is an appealing alternative. However, its applicability to different pathogens in specific epidemiologic contexts is not well understood. Here, we applied a previously established MLST method based on housekeeping genes to a well-characterized collection of uropathogenic E. coli isolates to compare the discriminatory ability of this procedure with that of enterobacterial repeat intergenic consensus (ERIC2) PCR, serogrouping, and pulsed-field gel electrophoresis (PFGE). Among 45 E. coli isolates studied, 17 different multilocus sequence types (ST) were identified. One MLST group (designated ST69 complex) was comprised of 22 isolates, all belonging to uropathogenic and bacteremic E. coli strains previously defined as clonal group A (CgA) by ERIC2 PCR. The ST69 strains contained five different serogroups and 14 PFGE types. ERIC2 PCR CgA strains belonging to different MLST groups were also identified. Interestingly, one cow E. coli isolate, previously shown by PFGE to be closely related to a human uropathogenic CgA strain, was found to cluster with the ST69 strains. All of the other animal and environmental CgA isolates had different MLST profiles. The discriminatory power of this MLST method based on housekeeping genes appears to be higher than that of ERIC2 PCR but lower than that of PFGE for epidemiologic study of uropathogenic E. coli.
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Affiliation(s)
- Sara Y Tartof
- Divisions of Epidemiology and Infectious Diseases and Immunity, 140 Warren Hall, School of Public Health, University of California at Berkeley, Berkeley, CA 94720, USA
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Pitout JDD, Laupland KB, Church DL, Menard ML, Johnson JR. Virulence factors of Escherichia coli isolates that produce CTX-M-type extended-spectrum beta-lactamases. Antimicrob Agents Chemother 2006; 49:4667-70. [PMID: 16251310 PMCID: PMC1280161 DOI: 10.1128/aac.49.11.4667-4670.2005] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study determined the phylogenetic groups and virulence factors of 37 Escherichia coli isolates producing types of CTX-M compared with those of 19 isolates producing different types of extended-spectrum beta-lactamases (ESBLs) in a well-defined North American population. Most CTX-M-14 producers (97%) were from phylogenic group D; 67% of the CTX-M-15 producers were from group B2. A single CTX-M-14-producing strain belonged to clonal group A. There were significant prevalence differences for individual virulence factors among CTX-M producers and nonproducers; however, aggregate virulence factor scores were similar. CTX-M producers more commonly caused repeat urinary tract infections. Our results indicate that CTX-M type predicts phylogenetic background, and the virulence potential of ESBL-producing E. coli isolates is a complex issue, requiring further study and ongoing surveillance.
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Affiliation(s)
- Johann D D Pitout
- Department of Pathology and Laboratory Medicine, University of Calgary, Alberta, Canada.
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Moreno E, Prats G, Sabaté M, Pérez T, Johnson JR, Andreu A. Quinolone, fluoroquinolone and trimethoprim/sulfamethoxazole resistance in relation to virulence determinants and phylogenetic background among uropathogenic Escherichia coli. J Antimicrob Chemother 2006; 57:204-11. [PMID: 16390858 DOI: 10.1093/jac/dki468] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
INTRODUCTION The goal of this study was to assess how resistance to quinolones, fluoroquinolones and trimethoprim/sulfamethoxazole relates to the virulence potential and phylogenetic background of clinical Escherichia coli isolates. METHODS Among 150 uropathogens (21% resistant to quinolones, 12% resistant to fluoroquinolones and 29.3% resistant to trimethoprim/sulfamethoxazole), E. coli phylogenetic group, 15 virulence-associated genes and 7 O antigens were analysed. Clonal group A (CGA) and genomic PCR profiles were studied among trimethoprim/sulfamethoxazole-resistant isolates. RESULTS Isolates susceptible to the three antimicrobial agents were significantly associated with phylogenetic group B2, whereas resistant isolates exhibited shifts to non-B2 groups (quinolone and fluoroquinolone-resistant isolates to group A; trimethoprim/sulfamethoxazole-resistant isolates to group D). Diverse virulence traits, including UTI-associated O antigens, were significantly less frequent among resistant isolates, particularly those resistant to fluoroquinolones (median score, 3.9 virulence factors/strain) and also to quinolones (5.2) or trimethoprim/sulfamethoxazole (6.4), as compared with the corresponding drug-susceptible isolates (median scores of 7.9, 8.6 and 7.9, respectively). Among 44 trimethoprim/sulfamethoxazole-resistant isolates, 3 (6.8%) belonged to CGA. All these 3 CGA strains caused pyelonephritis (P=0.02) and exhibited the consensus virulence profile of previously described CGA strains from abroad. CONCLUSIONS E. coli isolates resistant to quinolones, trimethoprim/sulfamethoxazole and especially fluoroquinolones were associated with reductions in virulence traits and shifts to non-B2 phylogenetic groups. Moreover, fluoroquinolone resistance usually occurred in low-virulence E. coli group A isolates rather than in isolates from groups B2 and D which had lost virulence traits. CGA accounted for 23% of trimethoprim/sulfamethoxazole-resistant E. coli producing pyelonephritis.
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Affiliation(s)
- Eva Moreno
- Microbiology Department, Hospital Vall d'Hebron, Universitat Autonoma de Barcelona, Barcelona, Spain
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Johnson JR, Clabots C, Rosen H. Effect of inactivation of the global oxidative stress regulator oxyR on the colonization ability of Escherichia coli O1:K1:H7 in a mouse model of ascending urinary tract infection. Infect Immun 2006; 74:461-8. [PMID: 16369002 PMCID: PMC1346679 DOI: 10.1128/iai.74.1.461-468.2006] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2004] [Revised: 11/09/2004] [Accepted: 10/12/2005] [Indexed: 11/20/2022] Open
Abstract
To survive within the host urinary tract, Escherichia coli strains that cause urinary tract infection (UTI) presumably must overcome powerful oxidant stresses, including the oxygen-dependent killing mechanisms of neutrophils. Accordingly, we assessed the global oxygen stress regulator OxyR of Escherichia coli as a possible virulence factor in UTI by determining the impact of oxyR inactivation on experimental urovirulence in CBA/J and C57BL (both wild-type and p47(phox-/-)) mice. The oxyR and oxyS genes of wild-type E. coli strain Ec1a (O1:K1:H7) were replaced with a kanamycin resistance cassette to produce an oxyRS mutant. During in vitro growth in broth or human urine, the oxyRS mutant exhibited the same log-phase growth rate (broth) and plateau density (broth and urine) as Ec1a, despite its prolonged lag phase (broth) or initial decrease in concentration (urine). The mutant, and oxyRS mutants of other wild-type ExPEC strains, exhibited significantly increased in vitro susceptibility to inhibition by H(2)O(2), which, like the altered growth kinetics observed with oxyRS inactivation, were reversed by restoration of oxyR on a multiple-copy-number plasmid. In CBA/J mice, Ec1a significantly outcompeted its oxyRS mutant (by >1 log(10)) in urine, bladder, and kidney cultures harvested 48 h after perurethral inoculation of mice, whereas an oxyR-complemented mutant exhibited equal or greater colonizing ability than that of the parent. Although C57BL mice were less susceptible to experimental UTI than CBA/J mice, wild-type and p47(phox-/-) C57BL mice were similarly susceptible, and the oxyR mutant of Ec1a was similarly attenuated in C57BL mice, regardless of the p47(phox) genotype, as in CBA/J mice. Within the E. coli Reference collection, 94% of strains were positive for oxyR. These findings fulfill the second and third of Koch's molecular postulates for oxyR as a candidate virulence-facilitating factor in E. coli and indicate that oxyR is a broadly prevalent potential target for future preventive interventions against UTI due to E. coli. They also suggest that neutrophil phagocyte oxidase is not critical for defense against E. coli UTI and that the major oxidative stresses against which OxyR protects E. coli within the host milieu are not phagocyte derived.
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Affiliation(s)
- James R Johnson
- University of Minnesota Department of Medicine, Infectious Diseases (111F), Minneapolis VA Medical Center, 1 Veterans Drive, Minneapolis, MN 55417, USA.
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