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Hammad AM, Gonzalez-Escalona N, El Tahan A, Abbas NH, Koenig SSK, Allué-Guardia A, Eppinger M, Hoffmann M. Pathogenome comparison and global phylogeny of Escherichia coli ST1485 strains. Sci Rep 2022; 12:18495. [PMID: 36323726 PMCID: PMC9630279 DOI: 10.1038/s41598-022-20342-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/12/2022] [Indexed: 01/06/2023] Open
Abstract
Escherichia coli ST1485 strains belong to the clinically important phylogroup F and have disseminated worldwide in humans, animals, and the environment. Here, we elucidated the pathogenome of a global collection of E. coli ST1485 isolates from diverse sources retrieved from public databases and a high-quality sequenced complete genome of colistin-resistant E. coli strain CFSAN061771 isolated from raw milk cheese which designated as a reference strain. CFSAN061771 belongs to O83:H42-ST1485 pathotype and carries a conjugative ColV plasmid, pCFSAN061771_01, combining extraintestinal virulence genes (ompt, sitA, iroN, etsC, traT, cvaC, hylF, iss, tsh, mchf, iucC, iutA) with a multidrug resistance island (blaTEM-1, aph(6)-Id, aph(3″)-Ib, sul2, dfrA14). Comparative genomic analysis revealed a high frequency of pCFSAN061771_01-like plasmids in E. coli ST1485. A notable evolutionary genetic event in E. coli ST1485 strains is the acquisition of a pCFSAN061771_02-like plasmid, which confers resistance to several antimicrobials, tellurium, and quaternary ammonium compounds. The identical virulence and antibiotic resistance profiles identified in some human and animal strains are worrisome. This is the first study to emphasize the significance of E. coli ST1485 as a global high-risk virulent and multidrug-resistant clone with zoonotic potential.
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Affiliation(s)
- Ahmed M Hammad
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt.
| | - Narjol Gonzalez-Escalona
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
| | - Amira El Tahan
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Nasser H Abbas
- Department of Environmental Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Sara S K Koenig
- Department of Molecular Microbiology and Immunology, South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Anna Allué-Guardia
- Department of Molecular Microbiology and Immunology, South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, USA
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2
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Neumann B, Lippmann N, Wendt S, Karlas T, Lübbert C, Werner G, Pfeifer Y, Schuster CF. Recurrent bacteremia with a hypermucoviscous Escherichia coli isolated from a patient with perihilar cholangiocarcinoma: insights from a comprehensive genome-based analysis. Ann Clin Microbiol Antimicrob 2022; 21:28. [PMID: 35751078 PMCID: PMC9233328 DOI: 10.1186/s12941-022-00521-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 02/07/2023] Open
Abstract
Background Escherichia coli (E. coli) is a common human pathogen, responsible for a broad spectrum of infections. Sites of infection can vary, but the hepato-biliary system is of particular concern due to the infection-associated formation of gallstones and the spread of pathogens from the bile ducts into the bloodstream. Case presentation The presented case is striking, as the detected isolate showed a positive string test. This hypermucoviscous phenotype is atypical for E. coli and a particular feature of hypervirulent Klebsiella pneumoniae (K. pneumoniae) variants. Objectives To provide new insights into the genomic background of an E. coli strain with an unusual hypermucoviscous phenotype using hybrid short- and long-read sequencing approaches. Results Complete hybrid assemblies of the E. coli genome and plasmids were done and used for genome based typing. Isolate 537–20 was assigned to the multilocus sequence type ST88 and serotype O8:H4. The strain showed a close relationship to avian pathogenic strains. Analysis of the chromosome and plasmids revealed the presence of several virulence factors, such as the Conserved Virulence Plasmidic (CVP) region on plasmid 537-20_1, including several iron acquisition genes (sitABCD, iroABCDEN, iucABCD, hbd) and the iutA gene encoding the receptor of the siderophore aerobactin. The hypermucoviscous phenotype could be caused by encapsulation of putative K. pneumoniae origin. Conclusions Hybrid sequencing enabled detailed genomic characterization of the hypermucoviscous E. coli strain, revealing virulence factors that have their putative origin in K. pneumoniae. Supplementary Information The online version contains supplementary material available at 10.1186/s12941-022-00521-7.
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Affiliation(s)
- Bernd Neumann
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany. .,Institute for Hospital Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Medical University, Nuremberg General Hospital, 90419, Nuremberg, Germany.
| | - Norman Lippmann
- Interdisciplinary Centre for Infectious Diseases, Leipzig University Hospital, 04103, Leipzig, Germany
| | - Sebastian Wendt
- Interdisciplinary Centre for Infectious Diseases, Leipzig University Hospital, 04103, Leipzig, Germany.,Division of Infectious Diseases and Tropical Medicine, Department of Medicine II, Leipzig University Hospital, 04103, Leipzig, Germany
| | - Thomas Karlas
- Division of Gastroenterology, Department of Medicine II, Leipzig University Medical Center, 04103, Leipzig, Germany
| | - Christoph Lübbert
- Interdisciplinary Centre for Infectious Diseases, Leipzig University Hospital, 04103, Leipzig, Germany.,Division of Infectious Diseases and Tropical Medicine, Department of Medicine II, Leipzig University Hospital, 04103, Leipzig, Germany
| | - Guido Werner
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany
| | - Yvonne Pfeifer
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany
| | - Christopher F Schuster
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany. .,Current Address: Center for Pandemic Vaccines and Therapeutics (ZEPAI), Paul-Ehrlich-Institute, 63225, Langen, Germany.
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3
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Reid CJ, Cummins ML, Börjesson S, Brouwer MSM, Hasman H, Hammerum AM, Roer L, Hess S, Berendonk T, Nešporová K, Haenni M, Madec JY, Bethe A, Michael GB, Schink AK, Schwarz S, Dolejska M, Djordjevic SP. A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58. Nat Commun 2022; 13:683. [PMID: 35115531 PMCID: PMC8813906 DOI: 10.1038/s41467-022-28342-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.
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Affiliation(s)
- Cameron J Reid
- iThree Institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Max L Cummins
- iThree Institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Stefan Börjesson
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), 75189, Uppsala, Sweden
- Department of Microbiology, Public Health Agency of Sweden, 17182, Solna, Sweden
| | | | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Anette M Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Louise Roer
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark
| | - Stefanie Hess
- Institute of Microbiology, Technische Universität Dresden, Dresden, Germany
| | - Thomas Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Kristina Nešporová
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Marisa Haenni
- Université de Lyon-ANSES, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Jean-Yves Madec
- Université de Lyon-ANSES, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163, Berlin, Germany
| | - Geovana B Michael
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163, Berlin, Germany
| | - Anne-Kathrin Schink
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163, Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163, Berlin, Germany
| | - Monika Dolejska
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Biomedical Center, Charles University, Charles, Czech Republic
| | - Steven P Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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4
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Starčič Erjavec M, Jeseničnik K, Elam LP, Kastrin A, Predojević L, Sysoeva TA. Complete sequence of classic F-type plasmid pRK100 shows unique conservation over time and geographic location. Plasmid 2022; 119-120:102618. [PMID: 35077724 PMCID: PMC8978152 DOI: 10.1016/j.plasmid.2022.102618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/05/2022]
Abstract
Plasmids exhibit great diversity of gene content and host ranges and are famous for quick adaptation to the genetic background of the bacterial host cell. In addition to observing ever evolving plasmids, some plasmids have conserved backbones: a stable core composition and arrangement of genes in addition to variable regions. There are a few reports of extremely conserved plasmids. Here we report the complete sequence of pRK100 plasmid - a large, well-characterized conjugative F-like plasmid found in an Escherichia coli strain isolated from a urinary tract infection patient in 1990. The sequence shows that the 142 kb-long pRK100 plasmid is nearly identical to plasmids circulating in distant geographical locations and found in different host E. coli strains between 2007 and 2017. We also performed additional functional characterization of pRK100. Our results showed that pRK100 does not have a strong pathogenicity phenotype in porcine primary bladder epithelial cell culture. Moreover, the conjugation of pRK100 seems to strongly depend on recipient characteristics. These observations and identification of the pRK100 plasmid in different strain genotypes leave the extreme sequence conservation and broad distribution of this plasmid unexplained.
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Affiliation(s)
- Marjanca Starčič Erjavec
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Karmen Jeseničnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Lauren P Elam
- Department of Biological Sciences, The University of Alabama in Huntsville, 301 Sparkman Dr, Huntsville, AL 35899, USA
| | - Andrej Kastrin
- Institute for Biostatistics and Medical Informatics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Luka Predojević
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Tatyana A Sysoeva
- Department of Biological Sciences, The University of Alabama in Huntsville, 301 Sparkman Dr, Huntsville, AL 35899, USA.
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5
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Louge Uriarte EL, González Pasayo RA, Massó M, Carrera Paez L, Domínguez Moncla M, Donis N, Malena R, Méndez A, Morrell E, Giannitti F, Armendano JI, Faverin C, Centrón D, Parreño V, Odeón AC, Quiroga MP, Moreira AR. Molecular characterization of multidrug-resistant Escherichia coli of the phylogroups A and C in dairy calves with meningitis and septicemia. Microb Pathog 2022; 163:105378. [PMID: 34982979 DOI: 10.1016/j.micpath.2021.105378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/21/2021] [Accepted: 12/28/2021] [Indexed: 11/19/2022]
Abstract
Escherichia coli is an important cause of septicemia (SEPEC) and neonatal meningitis (NMEC) in dairy calves. However, the diversity of virulence profiles, phylogroups, antimicrobial resistance patterns, carriage of integron structures, and fluoroquinolone (FQ) resistance mechanisms have not been fully investigated. Also, there is a paucity of knowledge about the virulence profiles and frequency of potential SEPEC in feces from calves with or without diarrhea. This study aimed to characterize the virulence potential, phylogroups, antimicrobial susceptibility, integron content, and FQ-resistance mechanisms in Escherichia coli isolated from calves with meningitis and septicemia. Additionally, the virulence genes (VGs) and profiles of E. coli isolated from diarrheic and non-diarrheic calves were compared between them and together with NMEC and SEPEC in order to identify shared profiles. Tissue and fluid samples from eight dairy calves with septicemia, four of which had concurrent meningitis, were processed for bacteriology and histopathology. Typing of VGs was assessed in 166 isolates from diverse samples of each calf. Selected isolates were evaluated for antimicrobial susceptibility by the disk diffusion test. Phylogroups, integron gene cassettes cartography, and FQ-resistance determinants were analyzed by PCR, sequencing, and bioinformatic tools. Furthermore, 109 fecal samples and 700 fecal isolates from dairy calves with or without diarrhea were evaluated to detect 19 VGs by uniplex PCR. Highly diverse VG profiles were characterized among NMEC and SEPEC isolates, but iucD was the predominant virulence marker. Histologic lesions in all calves supported their pathogenicity. Selected isolates mainly belonged to phylogroups A and C and showed multidrug resistance. Classic (dfrA17 and arr3-dfrA27) and complex (dfrA17-aadA5::ISCR1::blaCTX-M-2) class 1 integrons were identified. Target-site mutations in GyrA (S83L and D87N) and ParC (S80I) encoding genes were associated with FQ resistance. The VGs detected more frequently in fecal samples included f17G (50%), papC (30%), iucD (20%), clpG (19%), eae (16%), and afaE-8 (13%). Fecal isolates displaying the profiles of f17 or potential SEPEC were found in 25% of calves with and without diarrhea. The frequency of E. coli VGs and profiles did not differ between both groups (p > 0.05) and were identical or similar to those found in NMEC and SEPEC. Overall, multidrug-resistant E. coli isolates with diverse VG profiles and belonging to phylogroups A and C can be implicated in natural cases of meningitis and septicemia. Their resistance phenotypes can be partially explained by class 1 integron gene cassettes and target-site mutations in gyrA and parC. These results highlight the value of antimicrobial resistance surveillance in pathogenic bacteria isolated from food-producing animals. Besides, calves frequently shed potential SEPEC in their feces as commensals ("Trojan horse"). Thus, these bacteria may be disseminated in the farm environment, causing septicemia and meningitis under predisposing factors.
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Affiliation(s)
- Enrique L Louge Uriarte
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina.
| | - Ramón A González Pasayo
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Mariana Massó
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Laura Carrera Paez
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Manuel Domínguez Moncla
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Nicolás Donis
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Rosana Malena
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Alejandra Méndez
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Eleonora Morrell
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Federico Giannitti
- Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 50 km 11, Estación Experimental La Estanzuela, Semillero, 70006, Colonia, Uruguay
| | - Joaquín I Armendano
- Departamento de Fisiopatología, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco s/n, Tandil, 7000, Argentina
| | - Claudia Faverin
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - Daniela Centrón
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina
| | - Viviana Parreño
- Incuinta, Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología e Innovaciones Tecnológicas, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IVIT, INTA-CONICET), Castelar, 1712, Buenos Aires, Argentina
| | - Anselmo C Odeón
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
| | - María Paula Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, C1121ABG, Argentina.
| | - Ana Rita Moreira
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible, INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (IPADS, INTA-CONICET), Ruta 226 km 73.5, Balcarce, 7620, Buenos Aires, Argentina
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6
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Mourand G, Paboeuf F, Grippon P, Lucas P, Bougeard S, Denamur E, Kempf I. Impact of Escherichia coli probiotic strains ED1a and Nissle 1917 on the excretion and gut carriage of extended-spectrum beta-lactamase-producing E. coli in pigs. Vet Anim Sci 2021; 14:100217. [PMID: 34825108 PMCID: PMC8604716 DOI: 10.1016/j.vas.2021.100217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 11/05/2022] Open
Abstract
The inoculated cefotaxime-resistant E. coli was a good pig gut colonizer. Probiotics could not reduce faecal excretion of resistant E. coli in inoculated pigs. Resistant E. coli titers were lower in digestive tracts of the probiotic-treated pigs. No transfer of the blaCTX−M-1 gene was detected.
We evaluated the impact of the administration of two Escherichia coli probiotic strains (ED1a and Nissle 1917) to pigs on the gut carriage or shedding of extended-spectrum beta-lactamase-producing E. coli. The probiotics were given to four sows from 12 days before farrowing to the weaning day, and to the 23 piglets (infected treated group (IPro)) from birth to the age of 49 days. Four other sows and their 24 piglets (infected non-treated group (INT)) did not receive the probiotics. IPro and INT piglets (n = 47) were orally inoculated with the strain E. coli 17–348F-RifR carrying the blaCTX−M-1 gene and resistant to rifampicin. Cefotaxime-resistant (CTXR) E. coli and rifampicin-resistant (RifR) E. coli were cultured and excretion of probiotics was studied using PCR on individual faecal and post-mortem samples, and from manure collected after the challenge with resistant E. coli. CTXR and RifRE.coli isolates were characterized to detect transfer of the blaCTX−M-1 to other strains.. Overall, there was no significant reduction in faecal excretion of CTXR and RifRE. coli in IPro pigs compared with INT pigs, although the CTXR and RifRE. coli titres were slightly, but significantly lower in the colon, caecum and rectum at post mortem. Excretion of the probiotics decreased with age, but Nissle 1917 was detected in most pigs at post-mortem. No transfer of the blaCTX−M-1 gene to probiotic and other E. coli strains was detected. In conclusion, in our experimental conditions, the used probiotics did not reduce shedding of the challenge strain.
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Affiliation(s)
| | - Frédéric Paboeuf
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Pauline Grippon
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Pierrick Lucas
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
| | | | - Erick Denamur
- Université de Paris, IAME, INSERM UMR 1137, Paris, France.,APHP, Hôpital Bichat Claude-Bernard, Laboratoire de Génétique Moléculaire, Paris, France
| | - Isabelle Kempf
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
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7
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Liu CW, Wang P, Cao GN, Zou QH. Complete genome sequence and virulence characterization of a neonatal meningitis Escherichia coli isolate. Microb Pathog 2021; 160:105199. [PMID: 34560248 DOI: 10.1016/j.micpath.2021.105199] [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: 08/31/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Neonatal bacterial meningitis is a life-threatening disease in newborns, and neonatal meningitis Escherichia coli (NMEC) is the second most frequent bacteria causing this disease worldwide. In order to further understand the characteristics of this pathogen, an E. coli isolate W224 N from newborns with meningitis was sequenced for detailed genetic characterization and the virulence was tested by a series of phenotypic experiments. W224 N has a circular chromosome and three plasmids. It belongs to ST95 and the serotype is O18:H7. Comparative genomic analysis showed that W224 N was closely related to E. coli neonatal meningitis isolates RS218 and NMEC O18. There are 11 genomic islands in W224 N and most of the GIs are specific to W224 N. W224 N has most of the virulence factors other neonatal meningitis isolates have. The virulence genes located both on the genome and plasmid. At the same time, we found a virulence factor cdiA only present in W224 N but absent in the other five genomes analyzed. In vitro experiment showed that W224 N has strong serum resistance ability, low biofilm formation ability and high flagellar motility. It also has a very strong toxicity to mice and amoeba. The whole genome as well as in vitro and in vivo experiments showed that W224 N is a high virulent strain. The results can help us better learn about the pathogenicity of neonatal meningitis E. coli.
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Affiliation(s)
- Cun-Wei Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ping Wang
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Guang-Na Cao
- Peking University Third Hospital, Beijing, 100191, China.
| | - Qing-Hua Zou
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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8
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Clermont O, Condamine B, Dion S, Gordon DM, Denamur E. The E phylogroup of Escherichia coli is highly diverse and mimics the whole E. coli species population structure. Environ Microbiol 2021; 23:7139-7151. [PMID: 34431197 DOI: 10.1111/1462-2920.15742] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/16/2021] [Accepted: 08/22/2021] [Indexed: 12/11/2022]
Abstract
To get a global picture of the population structure of the Escherichia coli phylogroup E, encompassing the O157:H7 EHEC lineage, we analysed the whole genome of 144 strains isolated from various continents, hosts and lifestyles and representative of the phylogroup diversity. The strains possess 4331 to 5440 genes with a core genome of 2771 genes and a pangenome of 33 722 genes. The distribution of these genes among the strains shows an asymmetric U-shaped distribution. E phylogenetic strains have the largest genomes of the species, partly explained by the presence of mobile genetic elements. Sixty-eight lineages were delineated, some of them exhibiting extra-intestinal virulence genes and being virulent in the mouse sepsis model. Except for the EHEC lineages and the reference EPEC, EIEC and ETEC strains, very few strains possess intestinal virulence genes. Most of the strains were devoid of acquired resistance genes, but eight strains possessed extended-spectrum beta-lactamase genes. Human strains belong to specific lineages, some of them being virulent and antibiotic-resistant [sequence type complexes (STcs) 350 and 2064]. The E phylogroup mimics all the features of the species as a whole, a phenomenon already observed at the STc level, arguing for a fractal population structure of E. coli.
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Affiliation(s)
- Olivier Clermont
- Université de Paris, IAME, UMR 1137, INSERM, Paris, F-75018, France
| | | | - Sara Dion
- Université de Paris, IAME, UMR 1137, INSERM, Paris, F-75018, France
| | - David M Gordon
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, Paris, F-75018, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat-Claude Bernard, Paris, F-75018, France
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9
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Johnson TJ. Role of Plasmids in the Ecology and Evolution of "High-Risk" Extraintestinal Pathogenic Escherichia coli Clones. EcoSal Plus 2021; 9:eESP-0013-2020. [PMID: 33634776 PMCID: PMC11163845 DOI: 10.1128/ecosalplus.esp-0013-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/12/2021] [Indexed: 11/20/2022]
Abstract
Bacterial plasmids have been linked to virulence in Escherichia coli and Salmonella since their initial discovery. Though the plasmid repertoire of these bacterial species is extremely diverse, virulence-associated attributes tend to be limited to a small subset of plasmid types. This is particularly true for extraintestinal pathogenic E. coli, or ExPEC, where a handful of plasmids have been recognized to confer virulence- and fitness-associated traits. The purpose of this review is to highlight the biological and genomic attributes of ExPEC virulence-associated plasmids, with an emphasis on high-risk dominant ExPEC clones. Two specific plasmid types are highlighted to illustrate the independently evolved commonalities of these clones relative to plasmid content. Furthermore, the dissemination of these plasmids within and between bacterial species is examined. These examples demonstrate the evolution of high-risk clones toward common goals, and they show that rare transfer events can shape the ecological landscape of dominant clones within a pathotype.
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Affiliation(s)
- Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108
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10
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A complex approach to a complex problem: the use of whole-genome sequencing in monitoring avian-pathogenic Escherichia coli – a review. ACTA VET BRNO 2020. [DOI: 10.2754/avb202089030273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Infections associated with Escherichia coli are responsible for immense losses in poultry production; moreover, poultry products may serve as a source of pathogenic and/or resistant strains for humans. As early as during the first hours of life, commercially hatched chickens are colonized with potentially pathogenic E. coli from the environment of hatcheries. The source of contamination has not been quite elucidated and the possibility of vertical spread of several avian pathogenic E. coli (APEC) lineages has been suggested, making the hatcheries an important node where cross-contamination of chicken of different origin can take place. The recent technological progress makes the method of whole-genome sequencing (WGS) widely accessible, allowing high-throughput analysis of a large amount of isolates. Whole-genome sequencing offers an opportunity to trace APEC and extended-spectrum/plasmid-encoded AmpC beta-lactamases-producing E. coli (ESBL/pAmpC-E.coli) along the poultry processing chain and to recognize the potential pathways of “epidemicˮ sequence types. Data from WGS may be used in monitoring antimicrobial resistance, comparative pathogenomic studies describing new virulence traits and their role in pathogenesis and, above all, epidemiologic monitoring of clonal outbreaks and description of different transmission routes and their significance. This review attempts to outline the complexity of poultry-associated E. coli issues and the possibility to employ WGS in elucidating them.
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11
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Abstract
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.
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Extended Phylogeny and Extraintestinal Virulence Potential of Commensal Escherichia coli from Piglets and Sows. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17010366. [PMID: 31935799 PMCID: PMC6981902 DOI: 10.3390/ijerph17010366] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022]
Abstract
Commensal Escherichia coli, naturally occurring in the intestinal tract, can be the origin of extraintestinal pathogenic E. coli (ExPEC) strains. ExPEC causes high mortality and significant economic losses in the swine industry in several countries and poses a serious threat to public health worldwide. The aim of this study was to analyze the extended phylogenetic structure and extraintestinal virulence potential in two groups of commensal E. coli isolates from post-weaning piglets and sows. The phylogenetic assignment to eight groups was determined using the revised Clermont phylogenetic typing method in quadruplex PCR. Identification of extraintestinal virulence genes (VGs) and adhesin operon genes was performed using multiplex or simplex PCR. The revised phylogenetic assignment allowed us to distinguish E. coli with significantly higher (groups C and F) or lower (group E) virulence potential in isolates from piglets. The majority of the tested VGs occurred more frequently in isolates from piglets than from sows, with statistically significant differences for seven genes: fimH, papAH, iutA, iroN, ompT, traT, and iss. Complete operons for type I and P fimbriae significantly prevailed among E. coli from piglets. This study provides insight into the extended phylogenetic structure of porcine commensal E. coli and showed that these strains, particularly from piglets, constitute a considerable reservoir of extraintestinal VGs and may increase the potential risk of extraintestinal infections.
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mcr-9, an Inducible Gene Encoding an Acquired Phosphoethanolamine Transferase in Escherichia coli, and Its Origin. Antimicrob Agents Chemother 2019; 63:AAC.00965-19. [PMID: 31209009 DOI: 10.1128/aac.00965-19] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/08/2019] [Indexed: 11/20/2022] Open
Abstract
The plasmid-located mcr-9 gene, encoding a putative phosphoethanolamine transferase, was identified in a colistin-resistant human fecal Escherichia coli strain belonging to a very rare phylogroup, the D-ST69-O15:H6 clone. This MCR-9 protein shares 33% to 65% identity with the other plasmid-encoded MCR-type enzymes identified (MCR-1 to -8) that have been found as sources of acquired resistance to polymyxins in Enterobacteriaceae Analysis of the lipopolysaccharide of the MCR-9-producing isolate revealed a function similar to that of MCR-1 by adding a phosphoethanolamine group to lipid A and subsequently modifying the structure of the lipopolysaccharide. However, a minor impact on susceptibility to polymyxins was noticed once the mcr-9 gene was cloned and produced in an E. coli K-12-derived strain. Nevertheless, we showed here that subinhibitory concentrations of colistin induced the expression of the mcr-9 gene, leading to increased MIC levels. This inducible expression was mediated by a two-component regulatory system encoded by the qseC and qseB genes located downstream of mcr-9 Genetic analysis showed that the mcr-9 gene was carried by an IncHI2 plasmid. In silico analysis revealed that the plasmid-encoded MCR-9 shared significant amino acid identity (ca. 80%) with the chromosomally encoded MCR-like proteins from Buttiauxella spp. In particular, Buttiauxella gaviniae was found to harbor a gene encoding MCR-BG, sharing 84% identity with MCR-9. That gene was neither expressed nor inducible in its original host, which was fully susceptible to polymyxins. This work showed that mcr genes may circulate silently and remain undetected unless induced by colistin.
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14
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Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) strains are responsible for a majority of human extraintestinal infections globally, resulting in enormous direct medical and social costs. ExPEC strains are comprised of many lineages, but only a subset is responsible for the vast majority of infections. Few systematic surveillance systems exist for ExPEC. To address this gap, we systematically reviewed and meta-analyzed 217 studies (1995 to 2018) that performed multilocus sequence typing or whole-genome sequencing to genotype E. coli recovered from extraintestinal infections or the gut. Twenty major ExPEC sequence types (STs) accounted for 85% of E. coli isolates from the included studies. ST131 was the most common ST from 2000 onwards, covering all geographic regions. Antimicrobial resistance-based isolate study inclusion criteria likely led to an overestimation and underestimation of some lineages. European and North American studies showed similar distributions of ExPEC STs, but Asian and African studies diverged. Epidemiology and population dynamics of ExPEC are complex; summary proportion for some STs varied over time (e.g., ST95), while other STs were constant (e.g., ST10). Persistence, adaptation, and predominance in the intestinal reservoir may drive ExPEC success. Systematic, unbiased tracking of predominant ExPEC lineages will direct research toward better treatment and prevention strategies for extraintestinal infections.
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Daga AP, Koga VL, Soncini JGM, de Matos CM, Perugini MRE, Pelisson M, Kobayashi RKT, Vespero EC. Escherichia coli Bloodstream Infections in Patients at a University Hospital: Virulence Factors and Clinical Characteristics. Front Cell Infect Microbiol 2019; 9:191. [PMID: 31245301 PMCID: PMC6563721 DOI: 10.3389/fcimb.2019.00191] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/20/2019] [Indexed: 01/24/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) isolates are responsible for many bloodstream infections. The aim of this study was to characterize E. coli isolated from the bloodstreams of patients (n = 48) at the University Hospital in Brazil. Epidemiological data were obtained through the analysis of medical records and laboratory tests. By PCR analysis, we investigated the presence of virulence factors (VFs), pathogenicity islands (PAIs), extended-spectrum β-lactamase (ESBL), phylogenetic classifications (A, B1, B2, C, D, E, and F) and molecular genotype by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). The mortality analysis showed that 33.3% of the deaths were associated with bacteraemia due to E. coli infections; in addition, an age between 60 and 75 years (p < 0.001; OR = 6.3[2.1–18.9]) and bacteraemia with an abdominal origin (p = 0.02; OR = 5[1.2–20.5]) were risk factors for the severity of the infection. Additionally, the presence of the afa gene was associated with mortality due to E. coli bacteraemia (p = 0.027; OR = 11.4[1.5–85.7]). Immunosuppression (27.1%), intestinal diseases (25.0%) and diabetes (18.8%), were prevalent among patients, and most of the bacteraemia cases were secondary to urinary tract infections (50.0%). The serum resistance gene traT was present in 77.1% of isolates, group capsular 2 (kpsMT II) was present in 45.8% and the K5 capsule was present in 20.8% of isolates. The isolates also showed a high prevalence for the siderophore yersiniabactina (fyuA) (70.8%) and PAI IV536 (77.1%). Phylogenetic analysis showed that group B2 (45.8%) was the most prevalent, and was the phylogroup that had a higher prevalence of VFs and PAIs. However, in this study, a considerable number of isolated bacteria were classified as group B1 (18.8%) and as group E (14.6%). Eight (16.7%) isolates were resistant to third and fourth generation cephalosporin and group CTX-M-1 (CTX-M-15) was the most prevalent ESBL type. The molecular genotyping showed two clonal lineages and several isolates that were not related to each other. This study provides additional information on the epidemiological and molecular characteristics of E. coli bloodstream infections in Brazil.
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Affiliation(s)
- Ana Paula Daga
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | - Vanessa Lumi Koga
- Laboratory of Microbiology, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | - João Gabriel Material Soncini
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | - Caroline Martins de Matos
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | - Marcia Regina Eches Perugini
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | - Marsileni Pelisson
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
| | | | - Eliana Carolina Vespero
- Laboratory of Clinical Microbiology, Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, State University of Londrina, Londrina, Brazil
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16
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Bok E, Mazurek J, Myc A, Stosik M, Wojciech M, Baldy-Chudzik K. Comparison of Commensal Escherichia coli Isolates from Adults and Young Children in Lubuskie Province, Poland: Virulence Potential, Phylogeny and Antimicrobial Resistance. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040617. [PMID: 29597292 PMCID: PMC5923659 DOI: 10.3390/ijerph15040617] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/14/2022]
Abstract
Commensal Escherichia coli population is a dynamic structure which may be important in the pathogenesis of extraintestinal infections. The aim of this study was the comparison of genetic diversity of commensal E. coli isolates from two age group—adults and young children. E. coli strains were isolated on MacConkey agar and identified by biochemical tests. Determination of four major phylogenetic groups, identification of virulence genes and antimicrobial resistance determinants were performed by using multiplex or simplex PCR. Phenotypic analysis of resistance was based on disc-diffusion method. The prevalence of virulence genes was significantly higher among isolates from adults than from young children. Phylogroup B2 predominated among E. coli from adults, whereas phylogroup A was the most common in isolates from young children. The analyses of antimicrobial resistance revealed that resistance to at least one antimicrobial agent and multidrug-resistance were detected significantly more frequent in the isolates from adults than from young children. This study documented that the commensal E. coli isolates from adults showed greater genetic diversity than from young children and constitutes a substantial reservoir of the virulence genes typical for extraintestinal pathogenic E. coli.
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Affiliation(s)
- Ewa Bok
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra, 65-561 Zielona Góra, Poland.
| | - Justyna Mazurek
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra, 65-561 Zielona Góra, Poland.
| | - Andrzej Myc
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra, 65-561 Zielona Góra, Poland.
- Laboratory of Virology, Department of Immunology of Infectious Diseases, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland.
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI 48109-5648, USA.
| | - Michał Stosik
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra, 65-561 Zielona Góra, Poland.
| | - Magdalena Wojciech
- Department of Mathematical Statistics and Econometrics, Faculty of Mathematics, Computer Science and Econometrics, University of Zielona Góra, 65-516 Zielona Góra, Poland.
| | - Katarzyna Baldy-Chudzik
- Department of Microbiology and Genetics, Faculty of Biological Sciences, University of Zielona Góra, 65-561 Zielona Góra, Poland.
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17
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de Campos ACLP, Puño-Sarmiento JJ, Medeiros LP, Gazal LES, Maluta RP, Navarro A, Kobayashi RKT, Fagan EP, Nakazato G. Virulence Genes and Antimicrobial Resistance in Escherichia coli from Cheese Made from Unpasteurized Milk in Brazil. Foodborne Pathog Dis 2017; 15:94-100. [PMID: 29215297 DOI: 10.1089/fpd.2017.2345] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Cow raw milk cheese is widely eaten in Brazil. These products may be contaminated with pathogenic bacteria. In this work, we investigated the presence of Escherichia coli in raw milk cheese from different States in Brazil. From 147 "Minas" cheese samples, 28 cheeses were positive for E. coli. Among 39 E. coli isolates of the cheeses, one was positive for eae and negative for bpfA and efa1/lifA using PCR, and so was classified as atypical Enteropathogenic E. coli (aEPEC). Two other isolates were positive for extraintestinal pathogenic E. coli (ExPEC) genes. The aEPEC isolate belongs to serogroup O127 and was classified in A phylogenetic group, and ExPEC isolates were found in O73:H12 (EC-2 strain) and O64474:H8 (EC-9 strain) serotype. This ExPEC belongs to A and C phylogenetic group, respectively. Most of E. coli strains belonged to Clermont phylogenetic groups A (28.2%), C, and E (23.1%). Six strains (15.4%) of E. coli were positive for group B1 and two (5.1%) for B2. E. coli isolates presented an aggregative (46.0%) and diffuse (12.6%) adherence pattern to HeLa cells, and the other isolates did not show adhesion (41.4%). Four E. coli isolates (10.3%) were shown to produce moderate biofilm. The antimicrobial resistance rate was tetracycline (25.6%), followed by ampicillin (17.9%), cefoxitin (7.7%), nalidixic acid (5.1%), and amoxicillin-clavulanic acid (2.6%). One strain was resistant to three antimicrobials (tetracycline, ampicillin, and nalidixic acid). The presence of these microorganisms, the O127 strain, and a new serogroup in Brazil is a potential risk for public health.
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Affiliation(s)
- Anna C L P de Campos
- 1 Departamento de Microbiologia, Universidade Estadual de Londrina , Paraná, Brazil
| | | | - Leonardo P Medeiros
- 1 Departamento de Microbiologia, Universidade Estadual de Londrina , Paraná, Brazil
| | - Luís E S Gazal
- 1 Departamento de Microbiologia, Universidade Estadual de Londrina , Paraná, Brazil
| | - Renato Pariz Maluta
- 1 Departamento de Microbiologia, Universidade Estadual de Londrina , Paraná, Brazil
| | - Armando Navarro
- 2 Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autônoma de México , Ciudad Universitaria, Mexico City, Mexico
| | - Renata K T Kobayashi
- 1 Departamento de Microbiologia, Universidade Estadual de Londrina , Paraná, Brazil
| | - Eder P Fagan
- 3 Setor de Veterinária e Produção Animal, Universidade Estadual do Norte do Paraná , Paraná, Brazil
| | - Gerson Nakazato
- 1 Departamento de Microbiologia, Universidade Estadual de Londrina , Paraná, Brazil
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18
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Moran RA, Hall RM. Evolution of Regions Containing Antibiotic Resistance Genes in FII-2-FIB-1 ColV-Colla Virulence Plasmids. Microb Drug Resist 2017; 24:411-421. [PMID: 28922058 DOI: 10.1089/mdr.2017.0177] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Three ColV virulence plasmids carrying antibiotic resistance genes were assembled from draft genome sequences of commensal ST95, ST131, and ST2705 Escherichia coli isolates from healthy Australians. Plasmids pCERC4, pCERC5, and pCERC9 include almost identical backbones containing FII-2 and FIB-1 replicons and the conserved ColV virulence region with an additional ColIa determinant. Only pCERC5 includes a complete, uninterrupted F-like transfer region and was able to conjugate. pCERC5 and pCERC9 contain Tn1721, carrying the tet(A) tetracycline resistance determinant in the same location, with Tn2 (blaTEM; ampicillin resistance) interrupting the Tn1721 in pCERC5. pCERC4 has a Tn1721/Tn21 hybrid transposon carrying dfrA5 (trimethoprim resistance) and sul1 (sulfamethoxazole resistance) in a class 1 integron. Four FII-2:FIB-1 ColV-ColIa plasmids in the GenBank nucleotide database have a related transposon in the same position, but an IS26 has reshaped the resistance gene region, deleting 2,069 bp of the integron 3'-CS, including sul1, and serving as a target for IS26 translocatable units containing blaTEM, sul2 and strAB (streptomycin resistance), or aphA1 (kanamycin/neomycin resistance). Another ColV-ColIa plasmid containing a related resistance gene region has lost the FII replicon and acquired a unique transfer region via recombination within the resistance region and at oriT. Eighteen further complete ColV plasmid sequences in GenBank contained FIB-1, but the FII replicons were of three types, FII-24, FII-18, and a variant of FII-36.
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Affiliation(s)
- Robert A Moran
- School of Life and Environmental Sciences, The University of Sydney , Sydney, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney , Sydney, Australia
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19
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In silico analysis and recombinant expression of BamA protein as a universal vaccine against Escherichia coli in mice. Appl Microbiol Biotechnol 2016; 100:5089-98. [DOI: 10.1007/s00253-016-7467-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/07/2016] [Accepted: 03/10/2016] [Indexed: 02/05/2023]
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20
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Jost C, Bidet P, Carrère T, Mariani-Kurkdjian P, Bonacorsi S. Susceptibility of enterohaemorrhagicEscherichia colito azithromycin in France and analysis of resistance mechanisms. J Antimicrob Chemother 2016; 71:1183-7. [DOI: 10.1093/jac/dkv477] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/14/2015] [Indexed: 11/14/2022] Open
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21
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Nicholson BA, West AC, Mangiamele P, Barbieri N, Wannemuehler Y, Nolan LK, Logue CM, Li G. Genetic Characterization of ExPEC-Like Virulence Plasmids among a Subset of NMEC. PLoS One 2016; 11:e0147757. [PMID: 26800268 PMCID: PMC4723317 DOI: 10.1371/journal.pone.0147757] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/07/2016] [Indexed: 12/29/2022] Open
Abstract
Neonatal Meningitis Escherichia coli (NMEC) is one of the most common causes of neonatal bacterial meningitis in the US and elsewhere resulting in mortality or neurologic deficits in survivors. Large plasmids have been shown experimentally to increase the virulence of NMEC in the rat model of neonatal meningitis. Here, 9 ExPEC-like plasmids were isolated from NMEC and sequenced to identify the core and accessory plasmid genes of ExPEC-like virulence plasmids in NMEC and create an expanded plasmid phylogeny. Results showed sequenced virulence plasmids carry a strongly conserved core of genes with predicted functions in five distinct categories including: virulence, metabolism, plasmid stability, mobile elements, and unknown genes. The major functions of virulence-associated and plasmid core genes serve to increase in vivo fitness by adding multiple iron uptake systems to the genetic repertoire to facilitate NMEC’s survival in the host’s low iron environment, and systems to enhance bacterial resistance to host innate immunity. Phylogenetic analysis based on these core plasmid genes showed that at least two lineages of ExPEC-like plasmids could be discerned. Further, virulence plasmids from Avian Pathogenic E. coli and NMEC plasmids could not be differentiated based solely on the genes of the core plasmid genome.
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Affiliation(s)
- Bryon A. Nicholson
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Aaron C. West
- Department of Chemistry, College of Liberal Arts and Sciences, Iowa State University, Ames, Iowa, United States of America
| | - Paul Mangiamele
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Nicolle Barbieri
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Yvonne Wannemuehler
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Lisa K. Nolan
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Catherine M. Logue
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, 1802 University Blvd, Iowa State University, Ames, Iowa, 50011, United States of America
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, P. R. China
- * E-mail:
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22
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Gallois C, Hauw-Berlemont C, Richaud C, Bonacorsi S, Diehl JL, Mainardi JL. Fatal necrotizing fasciitis due to necrotic toxin-producing Escherichia coli strain. New Microbes New Infect 2015; 8:109-12. [PMID: 26693024 PMCID: PMC4652023 DOI: 10.1016/j.nmni.2015.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 05/29/2015] [Accepted: 06/08/2015] [Indexed: 01/23/2023] Open
Abstract
We report a fatal case of necrotizing soft tissues infection caused by an Escherichia coli strain belonging to phylogenetic group C and harbouring numerous virulence factors reported to be part of a pathogenicity island (PAI) such as PAI IIJ96 and conserved virulence plasmidic region.
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Affiliation(s)
- C Gallois
- Medical Intensive Care Unit, Paris, France
| | | | - C Richaud
- Department of Microbiology, European Georges Pompidou Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Descartes, Paris, France
| | - S Bonacorsi
- IAME, UMR 1137, INSERM, Paris, France ; IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France ; AP-HP, Hôpital Robert-Debré, Service de Microbiologie, Centre National de Référence associé Escherichia coli , Paris, France
| | - J-L Diehl
- Medical Intensive Care Unit, Paris, France
| | - J-L Mainardi
- Department of Microbiology, European Georges Pompidou Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Descartes, Paris, France
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Koga VL, Rodrigues GR, Scandorieiro S, Vespero EC, Oba A, de Brito BG, de Brito KCT, Nakazato G, Kobayashi RKT. Evaluation of the Antibiotic Resistance and Virulence of Escherichia coli Strains Isolated from Chicken Carcasses in 2007 and 2013 from Paraná, Brazil. Foodborne Pathog Dis 2015; 12:479-85. [PMID: 25974222 DOI: 10.1089/fpd.2014.1888] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The frequent use of antimicrobials in commercial poultry production has raised concerns regarding the potential impact of antimicrobials on human health due to selection for resistant bacteria. Several studies have reported similarities between extraintestinal pathogenic Escherichia coli (ExPEC) strains isolated from birds and humans, indicating that these contaminant bacteria in poultry may be linked to human disease. The aim of our study was to analyze the frequency of antimicrobial resistance and virulence factors among E. coli strains isolated from commercial chicken carcasses in Paraná, Brazil, in 2007 and 2013. A total of 84 E. coli strains were isolated from chicken carcasses in 2007, and 121 E. coli strains were isolated in 2013. Polymerase chain reaction was used to detect virulence genes (hlyF, iss, ompT, iron, and iutA) and to determine phylogenetic classification. Antimicrobial susceptibility testing was performed using 15 antimicrobials. The strains were also confirmed as extended-spectrum β-lactamase (ESBL)-producing E. coli with phenotypic and genotypic tests. The results indicated that our strains harbored virulence genes characteristic of ExPEC, with the iutA gene being the most prevalent. The phylogenetic groups D and B1 were the most prevalent among the strains isolated in 2007 and 2013, respectively. There was an increase in the frequency of resistance to a majority of antimicrobials tested. An important finding in this study was the large number of ESBL-producing E. coli strains isolated from chicken carcasses in 2013, primarily for the group 2 cefotaximase (CTX-M) enzyme. ESBL production confers broad-spectrum resistance and is a health risk because ESBL genes are transferable from food-producing animals to humans via poultry meat. These findings suggest that our strains harbored virulence and resistance genes, which are often associated with plasmids that can facilitate their transmission between bacteria derived from different hosts, suggesting zoonotic risks.
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Affiliation(s)
- Vanessa L Koga
- 1 Departamento de Microbiologia, Centro de Ciências Biológicas, Campus Universitário, Universidade Estadual de Londrina , Paraná, Brasil
| | - Gabriela R Rodrigues
- 1 Departamento de Microbiologia, Centro de Ciências Biológicas, Campus Universitário, Universidade Estadual de Londrina , Paraná, Brasil
| | - Sara Scandorieiro
- 1 Departamento de Microbiologia, Centro de Ciências Biológicas, Campus Universitário, Universidade Estadual de Londrina , Paraná, Brasil
| | - Eliana C Vespero
- 2 Departamento de Patologia e Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Hospital Universitário, Universidade Estadual de Londrina , Paraná, Brasil
| | - Alexandre Oba
- 3 Departamento de Zootecnia, Centro de Ciências Agrárias, Campus Universitário, Universidade Estadual de Londrina , Paraná, Brasil
| | - Benito G de Brito
- 4 Laboratório de Saúde das Aves, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF)-Fepagro Saúde Animal , Rio Grande do Sul, Brasil
| | - Kelly C T de Brito
- 4 Laboratório de Saúde das Aves, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF)-Fepagro Saúde Animal , Rio Grande do Sul, Brasil
| | - Gerson Nakazato
- 1 Departamento de Microbiologia, Centro de Ciências Biológicas, Campus Universitário, Universidade Estadual de Londrina , Paraná, Brasil
| | - Renata K T Kobayashi
- 1 Departamento de Microbiologia, Centro de Ciências Biológicas, Campus Universitário, Universidade Estadual de Londrina , Paraná, Brasil
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24
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Basmaci R, Bonacorsi S, Bidet P, Biran V, Aujard Y, Bingen E, Béchet S, Cohen R, Levy C. Escherichia Coli Meningitis Features in 325 Children From 2001 to 2013 in France. Clin Infect Dis 2015; 61:779-86. [PMID: 25944342 DOI: 10.1093/cid/civ367] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/24/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND We aimed to describe features of Escherichia coli meningitis in a large population of children and the molecular characteristics of the involved strains to determine factors associated with severe disease or death. METHODS Between 2001 and 2013, a prospective national survey collected data for 325 children hospitalized with E. coli meningitis. The national reference center genetically characterized 141 isolates. RESULTS Among the 325 cases, 65.2% were term, 22.4% late preterm, and 12.5% very/extremely preterm infants. Escherichia coli meningitis was 7-fold more frequent in preterm than term infants. Median age at diagnosis was 14 days; 71.1% of infants were neonates, with 2 peaks of infection at age 0-3 days (mostly preterm neonates) and 11-15 days (mostly term neonates); 8.9% were >89 days old. In total, 51.1% patients were considered to have severe disease, and 9.2% died. B2.1 phylogenetic subgroup (56%) and O1 serogroup (27.7%) were the most frequently identified. On multivariate analysis, death was associated with preterm birth (odds ratio [OR], 3.3 [95% confidence interval {CI}, 1.3-8.4], P = .015 for late preterm infants; OR, 7.3 [95% CI, 2.7-20.9], P < .001 for very/extremely preterm infants) and cerebrospinal fluid (CSF) to blood glucose ratio <0.10 (OR, 15.3 [95% CI, 1.8-128.3], P = .012). Death was associated with uncommon O serogroup strains (P = .014) and severe disease with O7 serogroup (P = .034) and PapGII adhesin (OR, 2.3 [95% CI, 1.2-4.5], P = .015). CONCLUSIONS In this large study of 325 cases of E. coli meningitis, risk factors of severe disease or death were preterm birth, severe hypoglycorrhachia, CSF/blood glucose ratio <0.10, and molecular characteristics of strains, which should help optimize therapeutic management.
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Affiliation(s)
- Romain Basmaci
- Infection, Antimicrobials, Modelling, Evolution (IAME), Unité Mixte de Recherche (UMR) 1137, Institut National de la Santé Et de la Recherche Médicale IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité Assistance Publique - Hôpitaux de Paris (AP-HP), Laboratoire de Microbiologie, Centre National de Référence associé Escherichia coli AP-HP, Service de Pédiatrie Générale
| | - Stéphane Bonacorsi
- Infection, Antimicrobials, Modelling, Evolution (IAME), Unité Mixte de Recherche (UMR) 1137, Institut National de la Santé Et de la Recherche Médicale IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité Assistance Publique - Hôpitaux de Paris (AP-HP), Laboratoire de Microbiologie, Centre National de Référence associé Escherichia coli
| | - Philippe Bidet
- Infection, Antimicrobials, Modelling, Evolution (IAME), Unité Mixte de Recherche (UMR) 1137, Institut National de la Santé Et de la Recherche Médicale IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité Assistance Publique - Hôpitaux de Paris (AP-HP), Laboratoire de Microbiologie, Centre National de Référence associé Escherichia coli
| | - Valérie Biran
- AP-HP, Service de Réanimation et Pédiatrie Néonatales, Hôpital Robert-Debré, Paris
| | - Yannick Aujard
- AP-HP, Service de Réanimation et Pédiatrie Néonatales, Hôpital Robert-Debré, Paris
| | - Edouard Bingen
- Assistance Publique - Hôpitaux de Paris (AP-HP), Laboratoire de Microbiologie, Centre National de Référence associé Escherichia coli
| | - Stéphane Béchet
- Association Clinique Thérapeutique Infantile du Val de Marne, Saint Maur des Fossés
| | - Robert Cohen
- Association Clinique Thérapeutique Infantile du Val de Marne, Saint Maur des Fossés Groupe de Pathologie Infectieuse Pédiatrique, Paris Unité Court Séjour, Petits Nourrisson, Service de Néonatologie Centre de Recherche Clinique, Centre Hospitalier Intercommunal de Créteil, France
| | - Corinne Levy
- Association Clinique Thérapeutique Infantile du Val de Marne, Saint Maur des Fossés Groupe de Pathologie Infectieuse Pédiatrique, Paris Centre de Recherche Clinique, Centre Hospitalier Intercommunal de Créteil, France
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25
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Goldstone RJ, Popat R, Schuberth HJ, Sandra O, Sheldon IM, Smith DGE. Genomic characterisation of an endometrial pathogenic Escherichia coli strain reveals the acquisition of genetic elements associated with extra-intestinal pathogenicity. BMC Genomics 2014; 15:1075. [PMID: 25481482 PMCID: PMC4298941 DOI: 10.1186/1471-2164-15-1075] [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: 07/07/2014] [Accepted: 11/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Strains of Escherichia coli cause a wide variety of intestinal and extra-intestinal diseases in both humans and animals, and are also often found in healthy individuals or the environment. Broadly, a strong phylogenetic relationship exists that distinguishes most E. coli causing intestinal disease from those that cause extra-intestinal disease, however, isolates within a recently described subclass of Extra-Intestinal Pathogenic E. coli (ExPEC), termed endometrial pathogenic E. coli, tend to be phylogenetically distant from the vast majority of characterised ExPECs, and more closely related to human intestinal pathogens. In this work, we investigate the genetic basis for ExPEC infection in the prototypic endometrial pathogenic E. coli strain MS499. RESULTS By investigating the genome of MS499 in comparison with a range of other E. coli sequences, we have discovered that this bacterium has acquired substantial lengths of DNA which encode factors more usually associated with ExPECs and less frequently found in the phylogroup relatives of MS499. Many of these acquired factors, including several iron acquisition systems and a virulence plasmid similar to that found in several ExPECs such as APEC O1 and the neonatal meningitis E. coli S88, play characterised roles in a variety of typical ExPEC infections and appear to have been acquired recently by the evolutionary lineage leading to MS499. CONCLUSIONS Taking advantage of the phylogenetic relationship we describe between MS499 and several other closely related E. coli isolates from across the globe, we propose a step-wise evolution of a novel clade of sequence type 453 ExPECs within phylogroup B1, involving the recruitment of ExPEC virulence factors into the genome of an ancestrally non-extraintestinal E. coli, which has repurposed this lineage with the capacity to cause extraintestinal disease. These data reveal the genetic components which may be involved in this phenotype switching, and argue that horizontal gene exchange may be a key factor in the emergence of novel lineages of ExPECs.
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Affiliation(s)
| | | | | | | | | | - David G E Smith
- Institute for Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
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Abstract
ABSTRACT
Plasmids confer genetic information that benefits the bacterial cells containing them. In pathogenic bacteria, plasmids often harbor virulence determinants that enhance the pathogenicity of the bacterium. The ability to acquire iron in environments where it is limited, for instance the eukaryotic host, is a critical factor for bacterial growth. To acquire iron, bacteria have evolved specific iron uptake mechanisms. These systems are often chromosomally encoded, while those that are plasmid-encoded are rare. Two main plasmid types, ColV and pJM1, have been shown to harbor determinants that increase virulence by providing the cell with essential iron for growth. It is clear that these two plasmid groups evolved independently from each other since they do not share similarities either in the plasmid backbones or in the iron uptake systems they harbor. The siderophores aerobactin and salmochelin that are found on ColV plasmids fall in the hydroxamate and catechol group, respectively, whereas both functional groups are present in the anguibactin siderophore, the only iron uptake system found on pJM1-type plasmids. Besides siderophore-mediated iron uptake, ColV plasmids carry additional genes involved in iron metabolism. These systems include ABC transporters, hemolysins, and a hemoglobin protease. ColV- and pJM1-like plasmids have been shown to confer virulence to their bacterial host, and this trait can be completely ascribed to their encoded iron uptake systems.
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27
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Group A Escherichia coli-related purpura fulminans: an unusual manifestation due to an unusual strain? J Clin Microbiol 2014; 52:4404-6. [PMID: 25232165 DOI: 10.1128/jcm.01362-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe an exceptional case of life-threatening group A Escherichia coli-induced purpura fulminans. Genotyping of common polymorphisms in genes involved in innate immunity or coagulation did not reveal known susceptibility to such a manifestation. Genetic analysis of the strain revealed an unusual conserved virulence plasmidic region, pointing out its potential virulence.
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28
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Turrientes MC, González-Alba JM, del Campo R, Baquero MR, Cantón R, Baquero F, Galán JC. Recombination blurs phylogenetic groups routine assignment in Escherichia coli: setting the record straight. PLoS One 2014; 9:e105395. [PMID: 25137251 PMCID: PMC4138120 DOI: 10.1371/journal.pone.0105395] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 07/24/2014] [Indexed: 01/24/2023] Open
Abstract
The characterization of population structures plays a main role for understanding outbreaks and the dynamics of bacterial spreading. In Escherichia coli, the widely used combination of multiplex-PCR scheme together with goeBURST has some limitations. The purpose of this study is to show that the combination of different phylogenetic approaches based on concatenated sequences of MLST genes results in a more precise assignment of E. coli phylogenetic groups, complete understanding of population structure and reconstruction of ancestral clones. A collection of 80 Escherichia coli strains of different origins was analyzed following the Clermont and Doumith's multiplex-PCR schemes. Doumith's multiplex-PCR showed only 1.7% of misassignment, whereas Clermont's-2000 protocol reached 14.0%, although the discrepancies reached 30% and 38.7% respectively when recombinant C, F and E phylogroups were considered. Therefore, correct phylogroup attribution is highly variable and depends on the clonal composition of the sample. As far as population structure of these E. coli strains, including 48 E. coli genomes from GenBank, goeBURST provides a quite dispersed population structure; whereas NeighborNet approach reveals a complex population structure. MLST-based eBURST can infer different founder genotypes, for instance ST23/ST88 could be detected as the founder genotypes for STC23; however, phylogenetic reconstructions might suggest ST410 as the ancestor clone and several evolutionary trajectories with different founders. To improve our routine understanding of E. coli molecular epidemiology, we propose a strategy based on three successive steps; first, to discriminate three main groups A/B1/C, D/F/E and B2 following Doumith's protocol; second, visualization of population structure based on MLST genes according to goeBURST, using NeighborNet to establish more complex relationships among STs; and third, to perform, a cost-free characterization of evolutionary trajectories in variants emerging along the clonal expansion using parsimony methods of phylogenetic analysis.
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Affiliation(s)
- María-Carmen Turrientes
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - José-María González-Alba
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Rosa del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española para la Investigación en Enfermedades Infecciosas (REIPI), Madrid, Spain
| | | | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española para la Investigación en Enfermedades Infecciosas (REIPI), Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- * E-mail: (FB); (JCG)
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- * E-mail: (FB); (JCG)
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29
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First identification of a chromosomally located penicillinase gene in Kingella kingae species isolated in continental Europe. Antimicrob Agents Chemother 2014; 58:6258-9. [PMID: 25049250 DOI: 10.1128/aac.03562-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Kingella kingae is the major pathogen causing osteoarticular infections (OAI) in young children in numerous countries. Plasmid-borne TEM-1 penicillinase production has been sporadically detected in a few countries but not in continental Europe, despite a high prevalence of K. kingae infections. We describe here for the first time a K. kingae β-lactamase-producing strain in continental Europe and demonstrate the novel chromosomal location of the blaTEM-1 gene in K. kingae species.
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30
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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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31
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Mariani-Kurkdjian P, Lemaître C, Bidet P, Perez D, Boggini L, Kwon T, Bonacorsi S. Haemolytic-uraemic syndrome with bacteraemia caused by a new hybrid Escherichia coli pathotype. New Microbes New Infect 2014; 2:127-31. [PMID: 25356358 PMCID: PMC4184582 DOI: 10.1002/nmi2.49] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/18/2014] [Accepted: 04/24/2014] [Indexed: 12/21/2022] Open
Abstract
We describe a new atypical Shiga-toxin-producing Escherichia coli (STEC) responsible for a severe episode of haemolytic–uraemic syndrome in an adult with a relapse associated with bacteraemia. This STECs train of serotype O80:H2 harboured stx2c and stx2d gene subtypes, the rare eae ξ variant and a ColV plasmid with a conserved virulence plasmidic region involved in virulence of human and avian extraintestinal pathogenic E. coli. This atypical hybrid pathotype, which represents a new threat, is a further demonstration that STEC may be a recipient for extraintestinal virulence factors and raises again the question of antibiotic therapy during STEC infection.
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Affiliation(s)
- P Mariani-Kurkdjian
- Centre National de Référence associé Escherichia coli, Hôpital Robert-Debré, AP-HP Paris, France
| | - C Lemaître
- Centre National de Référence associé Escherichia coli, Hôpital Robert-Debré, AP-HP Paris, France
| | - P Bidet
- Centre National de Référence associé Escherichia coli, Hôpital Robert-Debré, AP-HP Paris, France ; IAME, UMR 1137, INSERM Paris, France ; IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité Paris, France
| | - D Perez
- Service de Réanimation, Centre hospitalier de Lons-le-Saunier Lons-le-Saunier, France
| | - L Boggini
- Service de Microbiologie, Centre hospitalier de Lons-le-Saunier Lons-le-Saunier, France
| | - T Kwon
- Service de Néphrologie, Hôpital Robert-Debré, AP-HP Paris, France
| | - S Bonacorsi
- Centre National de Référence associé Escherichia coli, Hôpital Robert-Debré, AP-HP Paris, France ; IAME, UMR 1137, INSERM Paris, France ; IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité Paris, France
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32
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Koga VL, Tomazetto G, Cyoia PS, Neves MS, Vidotto MC, Nakazato G, Kobayashi RKT. Molecular screening of virulence genes in extraintestinal pathogenic Escherichia coli isolated from human blood culture in Brazil. BIOMED RESEARCH INTERNATIONAL 2014; 2014:465054. [PMID: 24822211 PMCID: PMC4009324 DOI: 10.1155/2014/465054] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 03/13/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is one of the main etiological agents of bloodstream infections caused by Gram-negative bacilli. In the present study, 20 E. coli isolates from human hemocultures were characterized to identify genetic features associated with virulence (pathogenicity islands markers, phylogenetic group, virulence genes, plasmid profiles, and conjugative plasmids) and these results were compared with commensal isolates. The most prevalent pathogenicity island, in strains from hemoculture, were PAI IV536, described by many researchers as a stable island in enterobacteria. Among virulence genes, iutA gene was found more frequently and this gene enconding the aerobactin siderophore receptor. According to the phylogenetic classification, group B2 was the most commonly found. Additionally, through plasmid analysis, 14 isolates showed plasmids and 3 of these were shown to be conjugative. Although in stool samples of healthy people the presence of commensal strains is common, human intestinal tract may serve as a reservoir for ExPEC.
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Affiliation(s)
- Vanessa L. Koga
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, 86051-980 Londrina, PR, Brazil
| | - Geizecler Tomazetto
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, 86051-980 Londrina, PR, Brazil
| | - Paula S. Cyoia
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, 86051-980 Londrina, PR, Brazil
| | - Meiriele S. Neves
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, 86051-980 Londrina, PR, Brazil
| | - Marilda C. Vidotto
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, 86051-980 Londrina, PR, Brazil
| | - Gerson Nakazato
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, 86051-980 Londrina, PR, Brazil
| | - Renata K. T. Kobayashi
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, 86051-980 Londrina, PR, Brazil
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