101
|
Vieira MA, Dos Santos LF, Dias RCB, Camargo CH, Pinheiro SRS, Gomes TAT, Hernandes RT. Atypical enteropathogenic Escherichia coli as aetiologic agents of sporadic and outbreak-associated diarrhoea in Brazil. J Med Microbiol 2016; 65:998-1006. [PMID: 27412254 DOI: 10.1099/jmm.0.000313] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) are important agents of diarrhoea in industrialized as well as developing countries, such as Brazil. The hallmark of EPEC pathogenesis is the establishment of attaching and effacing lesions in enterocytes, in which pedestal-like structures are formed underneath adherent bacteria. EPEC are divided into two subgroups, typical (tEPEC) and atypical (aEPEC), based on the presence of the EPEC adherence factor plasmid in tEPEC and its absence in aEPEC. This study was designed to characterize 82 aEPEC isolates obtained from stool samples of diarrhoeic patients during 2012 and 2013 in Brazil. The majority of the aEPEC were assigned to the phylo-group B1 (48.8 %), and intimin subtypes θ (20.7 %), β1 (9.7 %) and λ (9.7 %) were the most prevalent among the isolates. The nleB and nleE genes were concomitantly detected in 32.9 % of the isolates, demonstrating the occurrence of the pathogenicity island O122 among them. The O157-plasmid genes (ehxA and/or espP) were detected in 7.3 % of the isolates, suggesting that some aEPEC could be derived from Shiga-toxin-producing E. coli that lost the stx genes while trafficking in the host. PFGE of 14 aEPEC of serotypes O2 : H16, O33 : H34, O39 : H9, O108 : H- and ONT : H19 isolated from five distinct outbreaks showed serotype-specific PFGE clusters, indicating a high degree of similarity among the isolates from the same event, thus highlighting these serotypes as potential aetiologic agents of diarrhoeal outbreaks in Brazil.
Collapse
Affiliation(s)
- Melissa A Vieira
- Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual Paulista 'Júlio de Mesquita Filho' (UNESP), Botucatu, SP, Brazil
| | - Luís F Dos Santos
- Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), São Paulo, SP, Brazil
| | - Regiane C B Dias
- Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual Paulista 'Júlio de Mesquita Filho' (UNESP), Botucatu, SP, Brazil
| | - Carlos H Camargo
- Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), São Paulo, SP, Brazil
| | | | - Tânia A T Gomes
- Departamento de Microbiologia, Imunologia e Parasitologia da Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Rodrigo T Hernandes
- Departamento de Microbiologia e Imunologia, Instituto de Biociências, Universidade Estadual Paulista 'Júlio de Mesquita Filho' (UNESP), Botucatu, SP, Brazil
| |
Collapse
|
102
|
Dufour N, Clermont O, La Combe B, Messika J, Dion S, Khanna V, Denamur E, Ricard JD, Debarbieux L. Bacteriophage LM33_P1, a fast-acting weapon against the pandemic ST131-O25b:H4 Escherichia coli clonal complex. J Antimicrob Chemother 2016; 71:3072-3080. [PMID: 27387322 DOI: 10.1093/jac/dkw253] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/02/2016] [Accepted: 05/26/2016] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Amongst the highly diverse Escherichia coli population, the ST131-O25b:H4 clonal complex is particularly worrisome as it is associated with a high level of antibiotic resistance. The lack of new antibiotics, the worldwide continuous increase of infections caused by MDR bacteria and the need for narrow-spectrum antimicrobial agents have revived interest in phage therapy. In this article, we describe a virulent bacteriophage, LM33_P1, which specifically infects O25b strains, and provide data related to its therapeutic potential. METHODS A large panel of E. coli strains (n = 283) was used to assess both the specificity and the activity of bacteriophage LM33_P1. Immunology, biochemistry and genetics-based methods confirmed this specificity. Virology methods and sequencing were used to characterize this bacteriophage in vitro, while three relevant mouse models were employed to show its in vivo efficacy. RESULTS Bacteriophage LM33_P1 exclusively infects O25b E. coli strains with a 70% coverage on sequence types associated with high antibiotic resistance (ST131 and ST69). This specificity is due to an interaction with the LPS mediated by an original tail fibre. LM33_P1 also has exceptional intrinsic properties with a high adsorption constant and produces over 300 virions per cell in <10 min. Using animal pneumonia, septicaemia and urinary tract infection models, we showed the in vivo efficacy of LM33_P1 to reduce the bacterial load in several organs. CONCLUSIONS Bacteriophage LM33_P1 represents the first weapon that specifically and quickly kills O25b E. coli strains. Therapeutic approaches derived from this bacteriophage could be developed to stop or slow down the spread of the ST131-O25b:H4 drug-resistant clonal complex in humans.
Collapse
Affiliation(s)
- Nicolas Dufour
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700 Colombes, France.,INSERM, IAME, UMR 1137, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.,Institut Pasteur, Department of Microbiology, Molecular Biology of Gene in Extremophiles, F-75015 Paris, France
| | - Olivier Clermont
- INSERM, IAME, UMR 1137, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Béatrice La Combe
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700 Colombes, France.,INSERM, IAME, UMR 1137, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Jonathan Messika
- AP-HP, Hôpital Louis Mourier, Service de Réanimation Médico-Chirurgicale, F-92700 Colombes, France.,INSERM, IAME, UMR 1137, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Sara Dion
- INSERM, IAME, UMR 1137, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Varun Khanna
- Institut Pasteur, Hub Bioinformatique et Biostatistique - C3BI, USR 3756 IP CNRS, F-75015 Paris, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, F-75018 Paris, France.,AP-HP, Hôpitaux Universitaires Paris Nord Val-de-Seine, Laboratoire de Génétique Moléculaire, Site Bichat, F-75018 Paris, France.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, 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.,Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Laurent Debarbieux
- Institut Pasteur, Department of Microbiology, Molecular Biology of Gene in Extremophiles, F-75015 Paris, France
| | | |
Collapse
|
103
|
Prevalence of CTX-M extended-spectrum beta-lactamases and sequence type 131 in Korean blood, urine, and rectal Escherichia coli isolates. INFECTION GENETICS AND EVOLUTION 2016; 41:292-295. [DOI: 10.1016/j.meegid.2016.04.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/15/2016] [Accepted: 04/16/2016] [Indexed: 11/18/2022]
|
104
|
Bromberg R, Grishin NV, Otwinowski Z. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer. PLoS Comput Biol 2016; 12:e1004985. [PMID: 27336403 PMCID: PMC4918981 DOI: 10.1371/journal.pcbi.1004985] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 05/10/2016] [Indexed: 01/20/2023] Open
Abstract
Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. Due to their lack of distinct morphological features, bacteria and archaea were extremely difficult to classify until technology was developed to obtain their DNA sequences; these sequences could then be compared to estimate evolutionary relationships. Now, due to technological advances, there is a flood of available sequences from a wide variety of organisms. These advances have spurred the development of algorithms which can estimate evolutionary relationships using whole genomes, in contrast to the more traditional methods which used single genes earlier and now typically use groups of conserved genes. However, there are many challenges when attempting to infer evolutionary relationships, in particular horizontal gene transfer, where DNA is transferred from one organism to another, resulting in an organism’s genome containing DNA that does not reflect its evolution by descent. We developed a new whole-genome method for estimating evolutionary distances which identifies and corrects for horizontal transfer. We found that for SlopeTree and all other whole-genome methods we applied, horizontal transfer causes some evolutionary distances to be grossly underestimated, and that our correction corrects for this.
Collapse
Affiliation(s)
- Raquel Bromberg
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Zbyszek Otwinowski
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- * E-mail:
| |
Collapse
|
105
|
Birgy A, Levy C, Bidet P, Thollot F, Derkx V, Béchet S, Mariani-Kurkdjian P, Cohen R, Bonacorsi S. ESBL-producingEscherichia coliST131 versus non-ST131: evolution and risk factors of carriage among French children in the community between 2010 and 2015. J Antimicrob Chemother 2016; 71:2949-56. [DOI: 10.1093/jac/dkw219] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/11/2016] [Indexed: 01/27/2023] Open
|
106
|
Mainda G, Lupolova N, Sikakwa L, Bessell PR, Muma JB, Hoyle DV, McAteer SP, Gibbs K, Williams NJ, Sheppard SK, La Ragione RM, Cordoni G, Argyle SA, Wagner S, Chase-Topping ME, Dallman TJ, Stevens MP, Bronsvoort BMD, Gally DL. Phylogenomic approaches to determine the zoonotic potential of Shiga toxin-producing Escherichia coli (STEC) isolated from Zambian dairy cattle. Sci Rep 2016; 6:26589. [PMID: 27220895 PMCID: PMC4879551 DOI: 10.1038/srep26589] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/27/2016] [Indexed: 11/17/2022] Open
Abstract
This study assessed the prevalence and zoonotic potential of Shiga toxin-producing Escherichia coli (STEC) sampled from 104 dairy units in the central region of Zambia and compared these with isolates from patients presenting with diarrhoea in the same region. A subset of 297 E. coli strains were sequenced allowing in silico analyses of phylo- and sero-groups. The majority of the bovine strains clustered in the B1 ‘commensal’ phylogroup (67%) and included a diverse array of serogroups. 11% (41/371) of the isolates from Zambian dairy cattle contained Shiga toxin genes (stx) while none (0/73) of the human isolates were positive. While the toxicity of a subset of these isolates was demonstrated, none of the randomly selected STEC belonged to key serogroups associated with human disease and none encoded a type 3 secretion system synonymous with typical enterohaemorrhagic strains. Positive selection for E. coli O157:H7 across the farms identified only one positive isolate again indicating this serotype is rare in these animals. In summary, while Stx-encoding E. coli strains are common in this dairy population, the majority of these strains are unlikely to cause disease in humans. However, the threat remains of the emergence of strains virulent to humans from this reservoir.
Collapse
Affiliation(s)
- Geoffrey Mainda
- Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK.,Ministry Livestock and Fisheries, Kabwe, Zambia
| | - Nadejda Lupolova
- Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | | | - Paul R Bessell
- Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | | | - Deborah V Hoyle
- Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - Sean P McAteer
- Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | | | | | | | | | | | - Sally A Argyle
- Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | - Sam Wagner
- Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | | | | | - Mark P Stevens
- Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| | | | - David L Gally
- Roslin Institute and Royal (Dick) School of Veterinary Studies, Edinburgh, UK
| |
Collapse
|
107
|
Ortega A, Sáez D, Bautista V, Fernández-Romero S, Lara N, Aracil B, Pérez-Vázquez M, Campos J, Oteo J. Carbapenemase-producing Escherichia coli is becoming more prevalent in Spain mainly because of the polyclonal dissemination of OXA-48. J Antimicrob Chemother 2016; 71:2131-8. [PMID: 27147304 DOI: 10.1093/jac/dkw148] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/30/2016] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES The objective of this study was to analyse the microbiological traits and the population structure of carbapenemase-producing (CP) Escherichia coli isolates collected in Spain between 2012 and 2014. METHODS Two-hundred-and-thirty-nine E. coli isolates non-susceptible to carbapenems were studied. The carbapenemase genes and the phylogenetic groups were characterized using PCR. MLST was carried out using the typing schemes of the University of Warwick and the Institut Pasteur. The diversity of the population structure was estimated by calculating a simple diversity index (SDI). RESULTS One-hundred-and-twenty-one isolates (50.6%) produced carbapenemases, of which 87 (71.9%) were OXA-48, 27 (22.3%) were VIM-1, 4 (3.3%) were KPC-2, 2 (1.7%) were NDM and 1 (0.8%) was IMP-22; 4 isolates were collected in 2012, 40 in 2013 and 77 in 2014. Ertapenem was more sensitive than imipenem or meropenem for screening for OXA-48-producing E. coli. Using the Warwick typing scheme, 59 different STs were identified, the most prevalent being ST131 (16.5%). The population diversity was higher among VIM-1-producing isolates (SDI = 81.5%) than among OXA-48-producing isolates (SDI = 44.8%). The Pasteur scheme had a higher discrimination capability (SDI = 55.4%) than the Warwick scheme (SDI = 48.8%). CONCLUSIONS A progressive increase in the prevalence of CP E. coli was observed, mainly due to the dissemination of OXA-48 producers. The most sensitive method for detecting decreased susceptibility of CP E. coli to carbapenems was disc diffusion with ertapenem using the EUCAST screening cut-offs. The spread of CP E. coli was due to a polyclonal population. The Pasteur scheme showed the highest discrimination power. Surveillance is crucial for the early detection of CP E. coli.
Collapse
Affiliation(s)
- Adriana Ortega
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Majadahonda, Madrid, Spain Red Española de Investigación en Patología Infecciosa (REIPI), Spain
| | - David Sáez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Majadahonda, Madrid, Spain
| | - Verónica Bautista
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Majadahonda, Madrid, Spain Red Española de Investigación en Patología Infecciosa (REIPI), Spain
| | - Sara Fernández-Romero
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Majadahonda, Madrid, Spain Red Española de Investigación en Patología Infecciosa (REIPI), Spain
| | - Noelia Lara
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Majadahonda, Madrid, Spain Red Española de Investigación en Patología Infecciosa (REIPI), Spain
| | - Belén Aracil
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Majadahonda, Madrid, Spain Red Española de Investigación en Patología Infecciosa (REIPI), Spain
| | - María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Majadahonda, Madrid, Spain Red Española de Investigación en Patología Infecciosa (REIPI), Spain
| | - José Campos
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Majadahonda, Madrid, Spain Red Española de Investigación en Patología Infecciosa (REIPI), Spain Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jesús Oteo
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Majadahonda, Madrid, Spain Red Española de Investigación en Patología Infecciosa (REIPI), Spain
| | | |
Collapse
|
108
|
Wang J, Vermerris W. Antimicrobial Nanomaterials Derived from Natural Products-A Review. MATERIALS (BASEL, SWITZERLAND) 2016; 9:E255. [PMID: 28773379 PMCID: PMC5502919 DOI: 10.3390/ma9040255] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 03/18/2016] [Accepted: 03/23/2016] [Indexed: 01/21/2023]
Abstract
Modern medicine has relied heavily on the availability of effective antibiotics to manage infections and enable invasive surgery. With the emergence of antibiotic-resistant bacteria, novel approaches are necessary to prevent the formation of biofilms on sensitive surfaces such as medical implants. Advances in nanotechnology have resulted in novel materials and the ability to create novel surface topographies. This review article provides an overview of advances in the fabrication of antimicrobial nanomaterials that are derived from biological polymers or that rely on the incorporation of natural compounds with antimicrobial activity in nanofibers made from synthetic materials. The availability of these novel materials will contribute to ensuring that the current level of medical care can be maintained as more bacteria are expected to develop resistance against existing antibiotics.
Collapse
Affiliation(s)
- Ji Wang
- Department of Microbiology & Cell Science, IFAS, University of Florida, Cancer/Genetics Research Complex 302, 2033 Mowry Road, Gainesville, FL 32610, USA.
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science, IFAS, University of Florida, Cancer/Genetics Research Complex 302, 2033 Mowry Road, Gainesville, FL 32610, USA.
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
| |
Collapse
|
109
|
Evaluation of two multi-locus sequence typing schemes for commensal Escherichia coli from dairy cattle in Washington State. J Microbiol Methods 2016; 124:57-61. [PMID: 27001705 DOI: 10.1016/j.mimet.2016.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 11/24/2022]
Abstract
Multi-locus sequence typing (MLST) is a useful system for phylogenetic and epidemiological studies of multidrug-resistant Escherichiacoli. Most studies utilize a seven-locus MLST, but an alternate two-locus typing method (fumC and fimH; CH typing) has been proposed that may offer a similar degree of discrimination at lower cost. Herein, we compare CH typing to the standard seven-locus method for typing commensal E. coli isolates from dairy cattle. In addition, we evaluated alternative combinations of eight loci to identify combinations that maximize discrimination and congruence with standard seven-locus MLST among commensal E. coli while minimizing the cost. We also compared both methods when used for typing uropathogenic E. coli (UPEC). CH typing was less discriminatory for commensal E. coli than the standard seven-locus method (Simpson's Index of Diversity=0.933 [0.902-0.964] and 0.97 [0.96-0.979], respectively). Combining fimH with housekeeping gene loci improved discriminatory power for commensal E. coli from cattle but resulted in poor congruence with MLST. We found that a four-locus typing method including the housekeeping genes adk, purA, gyrB and recA could be used to minimize cost without sacrificing discriminatory power or congruence with Achtman seven-locus MLST when typing commensal E. coli.
Collapse
|
110
|
Garcia BG, Ooka T, Gotoh Y, Vieira MAM, Yamamoto D, Ogura Y, Girão DM, Sampaio SCF, Melo AB, Irino K, Hayashi T, Gomes TAT. Genetic relatedness and virulence properties of enteropathogenic Escherichia coli strains of serotype O119:H6 expressing localized adherence or localized and aggregative adherence-like patterns on HeLa cells. Int J Med Microbiol 2016; 306:152-64. [PMID: 27083266 DOI: 10.1016/j.ijmm.2016.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 02/01/2016] [Accepted: 02/25/2016] [Indexed: 10/22/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) induce attaching and effacing (A/E) lesions in enterocytes and produce the bundle-forming pilus (BFP) contributing to the localized adherence (LA) pattern formation on HeLa cells. Enteroaggregative E. coli (EAEC) produce aggregative adherence (AA) on HeLa cells and form prominent biofilms. The ability to produce LA or AA is an important hallmark to classify fecal E. coli isolates as EPEC or EAEC, respectively. E. coli strains of serotype O119:H6 exhibit an LA+ phenotype and have been considered as comprising a clonal group of EPEC strains. However, we have recently identified O119:H6 EPEC strains that produce LA and an AA-like pattern concurrently (LA/AA-like+). In this study, we evaluated the relatedness of three LA/AA-like+ and three LA+ O119:H6 strains by comparing their virulence and genotypic properties. We first found that the LA/AA-like+ strains induced actin accumulation in HeLa cells (indicative of A/E lesions formation) and formed biofilms on abiotic surfaces more efficiently than the LA+ strains. MLST analysis showed that the six strains all belong to the ST28 complex. All strains carried multiple plasmids, but as plasmid profiles were highly variable, this cannot be used to differentiate LA/AA-like+ and LA+ strains. We further obtained their draft genome sequences and the complete sequences of four plasmids harbored by one LA/AA-like+ strain. Analysis of these sequences and comparison with 37 fully sequenced E. coli genomes revealed that both O119:H6 groups belong to the E. coli phylogroup B2 and are very closely related with only 58-67 SNPs found between LA/AA-like+ and LA+ strains. Search of the draft sequences of the six strains for adhesion-related genes known in EAEC and other E. coli pathotypes detected no genes specifically present in LA/AA-like+ strains. Unexpectedly however, we found that a large plasmid distinct from pEAF is responsible for the AA-like phenotype of the LA/AA-like+ strains. Although we have not identified any plasmid genes specifically present in all LA/AA-like+ strains and absent in the LA+ strains, these results suggest the presence of an unknown mechanism to promote the AA-like pattern production and biofilm formation by the LA/AA-like+ strains. Because their ability to produce A/E lesions and biofilm concomitantly could exacerbate the clinical condition of the patient and lead to persistent diarrhea, the mechanism underlying the enhanced biofilm formation by the LA/AA-like+ O119:H6 strains and their spread and involvement in severe diarrheal diseases should be more intensively investigated.
Collapse
Affiliation(s)
- Bruna G Garcia
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo-Escola Paulista de Medicina, São Paulo, Brazil.
| | - Tadasuke Ooka
- Department of Microbiology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - Yasuhiro Gotoh
- Department of Infectious Diseases, Division of Microbiology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
| | - Mônica A M Vieira
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo-Escola Paulista de Medicina, São Paulo, Brazil.
| | - Denise Yamamoto
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo-Escola Paulista de Medicina, São Paulo, Brazil.
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Dennys M Girão
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Prof. Paulo de Góes, Centro de Ciências da Saúde-Ilha do Fundão, Rio de Janeiro, Brazil.
| | - Suely C F Sampaio
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo-Escola Paulista de Medicina, São Paulo, Brazil.
| | - Alexis Bonfim Melo
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo-Escola Paulista de Medicina, São Paulo, Brazil.
| | - Kinue Irino
- Seção de Bacteriologia, Instituto Adolfo Lutz, Secretaria de Estado da Saúde, São Paulo, Brazil.
| | - Tetsuya Hayashi
- Department of Infectious Diseases, Division of Microbiology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
| | - Tânia A T Gomes
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo-Escola Paulista de Medicina, São Paulo, Brazil.
| |
Collapse
|
111
|
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.
Collapse
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
| |
Collapse
|
112
|
Skurnik D, Clermont O, Guillard T, Launay A, Danilchanka O, Pons S, Diancourt L, Lebreton F, Kadlec K, Roux D, Jiang D, Dion S, Aschard H, Denamur M, Cywes-Bentley C, Schwarz S, Tenaillon O, Andremont A, Picard B, Mekalanos J, Brisse S, Denamur E. Emergence of Antimicrobial-Resistant Escherichia coli of Animal Origin Spreading in Humans. Mol Biol Evol 2015; 33:898-914. [PMID: 26613786 DOI: 10.1093/molbev/msv280] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In the context of the great concern about the impact of human activities on the environment, we studied 403 commensal Escherichia coli/Escherichia clade strains isolated from several animal and human populations that have variable contacts to one another. Multilocus sequence typing (MLST) showed a decrease of diversity 1) in strains isolated from animals that had an increasing contact with humans and 2) in all strains that had increased antimicrobial resistance. A specific B1 phylogroup clonal complex (CC87, Institut Pasteur schema nomenclature) of animal origin was identified and characterized as being responsible for the increased antimicrobial resistance prevalence observed in strains from the environments with a high human-mediated antimicrobial pressure. CC87 strains have a high capacity of acquiring and disseminating resistance genes with specific metabolic and genetic determinants as demonstrated by high-throughput sequencing and phenotyping. They are good mouse gut colonizers but are not virulent. Our data confirm the predominant role of human activities in the emergence of antimicrobial resistance in the environmental bacterial strains and unveil a particular E. coli clonal complex of animal origin capable of spreading antimicrobial resistance to other members of microbial communities.
Collapse
Affiliation(s)
- David Skurnik
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA INSERM, IAME, UMR 1137, Paris, France Univ Paris Diderot, IAME, Sorbonne Paris Cité, UMR 1137, Faculté De Médecine, Site Xavier Bichat, Paris, France French National Reference Center for Bacterial Resistance in Commensal Flora, Laboratory of Bacteriology, Bichat-Claude Bernard Hospital, Assistance Publique-Hôpitaux De Paris, Paris, France
| | - Olivier Clermont
- INSERM, IAME, UMR 1137, Paris, France Univ Paris Diderot, IAME, Sorbonne Paris Cité, UMR 1137, Faculté De Médecine, Site Xavier Bichat, Paris, France
| | - Thomas Guillard
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Adrien Launay
- INSERM, IAME, UMR 1137, Paris, France Univ Paris Diderot, IAME, Sorbonne Paris Cité, UMR 1137, Faculté De Médecine, Site Xavier Bichat, Paris, France
| | | | - Stéphanie Pons
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Laure Diancourt
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | | | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Damien Roux
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA INSERM, IAME, UMR 1137, Paris, France Univ Paris Diderot, IAME, Sorbonne Paris Cité, UMR 1137, Faculté De Médecine, Site Xavier Bichat, Paris, France
| | - Deming Jiang
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Sara Dion
- INSERM, IAME, UMR 1137, Paris, France Univ Paris Diderot, IAME, Sorbonne Paris Cité, UMR 1137, Faculté De Médecine, Site Xavier Bichat, Paris, France
| | | | - Maurice Denamur
- INSERM, IAME, UMR 1137, Paris, France Univ Paris Diderot, IAME, Sorbonne Paris Cité, UMR 1137, Faculté De Médecine, Site Xavier Bichat, Paris, France
| | - Colette Cywes-Bentley
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Olivier Tenaillon
- INSERM, IAME, UMR 1137, Paris, France Univ Paris Diderot, IAME, Sorbonne Paris Cité, UMR 1137, Faculté De Médecine, Site Xavier Bichat, Paris, France
| | - Antoine Andremont
- INSERM, IAME, UMR 1137, Paris, France Univ Paris Diderot, IAME, Sorbonne Paris Cité, UMR 1137, Faculté De Médecine, Site Xavier Bichat, Paris, France French National Reference Center for Bacterial Resistance in Commensal Flora, Laboratory of Bacteriology, Bichat-Claude Bernard Hospital, Assistance Publique-Hôpitaux De Paris, Paris, France
| | - Bertrand Picard
- INSERM, IAME, UMR 1137, Paris, France Univ Paris Nord, Sorbonne Paris Cité, UMR 1137, Faculté De Médecine, Site Xavier Bichat, Paris, France
| | | | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | - Erick Denamur
- INSERM, IAME, UMR 1137, Paris, France Univ Paris Diderot, IAME, Sorbonne Paris Cité, UMR 1137, Faculté De Médecine, Site Xavier Bichat, Paris, France
| |
Collapse
|
113
|
Plasmid-Mediated OqxAB Is an Important Mechanism for Nitrofurantoin Resistance in Escherichia coli. Antimicrob Agents Chemother 2015; 60:537-43. [PMID: 26552976 DOI: 10.1128/aac.02156-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/03/2015] [Indexed: 11/20/2022] Open
Abstract
Increasing consumption of nitrofurantoin (NIT) for treatment of acute uncomplicated urinary tract infections (UTI) highlights the need to monitor emerging NIT resistance mechanisms. This study investigated the molecular epidemiology of the multidrug-resistant efflux gene oqxAB and its contribution to nitrofurantoin resistance by using Escherichia coli isolates originating from patients with UTI (n = 205; collected in 2004 to 2013) and food-producing animals (n = 136; collected in 2012 to 2013) in Hong Kong. The oqxAB gene was highly prevalent among NIT-intermediate (11.5% to 45.5%) and -resistant (39.2% to 65.5%) isolates but rare (0% to 1.7%) among NIT-susceptible (NIT-S) isolates. In our isolates, the oqxAB gene was associated with IS26 and was carried by plasmids of diverse replicon types. Multilocus sequence typing revealed that the clones of oqxAB-positive E. coli were diverse. The combination of oqxAB and nfsA mutations was found to be sufficient for high-level NIT resistance. Curing of oqxAB-carrying plasmids from 20 NIT-intermediate/resistant UTI isolates markedly reduced the geometric mean MIC of NIT from 168.9 μg/ml to 34.3 μg/ml. In the plasmid-cured variants, 20% (1/5) of isolates with nfsA mutations were NIT-S, while 80% (12/15) of isolates without nfsA mutations were NIT-S (P = 0.015). The presence of plasmid-based oqxAB increased the mutation prevention concentration of NIT from 128 μg/ml to 256 μg/ml and facilitated the development of clinically important levels of nitrofurantoin resistance. In conclusion, plasmid-mediated oqxAB is an important nitrofurantoin resistance mechanism. There is a great need to monitor the dissemination of this transferable multidrug-resistant efflux pump.
Collapse
|
114
|
Dale AP, Woodford N. Extra-intestinal pathogenic Escherichia coli (ExPEC): Disease, carriage and clones. J Infect 2015; 71:615-26. [PMID: 26409905 DOI: 10.1016/j.jinf.2015.09.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/16/2015] [Indexed: 10/23/2022]
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) have a complex phylogeny, broad virulence factor (VF) armament and significant genomic plasticity, and are associated with a spectrum of host infective syndromes ranging from simple urinary tract infection to life-threatening bacteraemia. Their importance as pathogens has come to the fore in recent years, particularly in the context of the global emergence of hyper-virulent and antibiotic resistant strains. Despite this, the mechanisms underlying ExPEC transmission dynamics and clonal selection remain poorly understood. Large-scale epidemiological and clinical studies are urgently required to ascertain the mechanisms underlying these processes to enable the development of novel evidence-based preventative and therapeutic strategies. In the current review, we provide a concise summary of the methods utilised for ExPEC phylogenetic delineation before exploring in detail the associations between ExPEC VFs and site-specific disease. We then consider the role of ExPEC as an intestinal colonist and outline known associations between ExPEC clonal variation, specific disease syndromes and antibiotic resistance.
Collapse
Affiliation(s)
- Adam P Dale
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, South Academic Block, Tremona Road, Southampton SO16 6YD, UK.
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Reference Microbiology Services, Public Health England, London NW9 5EQ, UK; The NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0HS, UK
| |
Collapse
|
115
|
Phylogenetic Group Determination of Escherichia coli Isolated from Animals Samples. ScientificWorldJournal 2015; 2015:258424. [PMID: 26421310 PMCID: PMC4572460 DOI: 10.1155/2015/258424] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/26/2015] [Indexed: 11/18/2022] Open
Abstract
This study analyzes the occurrence and distribution of phylogenetic groups of 391 strains of Escherichia coli isolated from poultry, cattle, and water buffalo. The frequency of the phylogroups was A = 19%, B1 = 57%, B2 = 2.3%, C = 4.6%, D = 2.8%, E = 11%, and F = 3.3%. Phylogroups A (P < 0.001) and F (P = 0.018) were associated with E. coli strains isolated from poultry, phylogroups B1 (P < 0.001) and E (P = 0.002) were associated with E. coli isolated from cattle, and phylogroups B2 (P = 0.003) and D (P = 0.017) were associated with E. coli isolated from water buffalo. This report demonstrated that some phylogroups are associated with the host analyzed and the results provide knowledge of the phylogenetic composition of E. coli from domestic animals.
Collapse
|