1
|
Muñoz-Cazalla A, de Quinto I, Álvaro-Llorente L, Rodríguez-Beltrán J, Herencias C. The role of bacterial metabolism in human gut colonization. Int Microbiol 2024:10.1007/s10123-024-00550-6. [PMID: 38937311 DOI: 10.1007/s10123-024-00550-6] [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: 04/22/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024]
Abstract
Can we anticipate the emergence of the next pandemic antibiotic-resistant bacterial clone? Addressing such an ambitious question relies on our ability to comprehensively understand the ecological and epidemiological factors fostering the evolution of high-risk clones. Among these factors, the ability to persistently colonize and thrive in the human gut is crucial for most high-risk clones. Nonetheless, the causes and mechanisms facilitating successful gut colonization remain obscure. Here, we review recent evidence that suggests that bacterial metabolism plays a pivotal role in determining the ability of high-risk clones to colonize the human gut. Subsequently, we outline novel approaches that enable the exploration of microbial metabolism at an unprecedented scale and level of detail. A thorough understanding of the constraints and opportunities of bacterial metabolism in gut colonization will foster our ability to predict the emergence of high-risk clones and take appropriate containment strategies.
Collapse
Affiliation(s)
- Ada Muñoz-Cazalla
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Ignacio de Quinto
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Laura Álvaro-Llorente
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
| | - Cristina Herencias
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Hospital Universitario Ramón y Cajal, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
2
|
Uea-Anuwong T, Biggel M, Cernela N, Hung WW, Lugsomya K, Kiu LH, Gröhn YT, Boss S, Stephan R, Nüesch-Inderbinen M, Magouras I. Antimicrobial resistance and phylogenetic relatedness of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli in peridomestic rats (Rattus norvegicus and Rattus tanezumi) linked to city areas and animal farms in Hong Kong. ENVIRONMENTAL RESEARCH 2024; 251:118623. [PMID: 38462086 DOI: 10.1016/j.envres.2024.118623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/01/2024] [Accepted: 03/02/2024] [Indexed: 03/12/2024]
Abstract
Extended-spectrum β-lactamase-producing Escherichia (E.) coli (ESBL-EC) in the clinical setting have emerged as a major threat to public and animal health. Wildlife, including Rattus spp. may serve as reservoirs and spreaders of ESBL-EC in the environment. Peridomestic rats are well adapted to living in proximity to humans and animals in a variety of urban and agricultural environments and may serve as sentinels to identify variations of ESBL-EC within their different habitats. In this study, a set of 221 rats (Rattus norvegicus, R. tanezumi, R. andamanensis, and Niviventer huang) consisting of 104 rats from city areas, 44 from chicken farms, 52 from pig farms, and 21 from stables of horse-riding schools were screened for ESBL-EC. Overall, a total of 134 ESBL-EC were isolated from the caecal samples of 130 (59%) rats. The predominant blaESBL genes were blaCTX-M-14, blaCTX-M-15, blaCTX-M-55, and blaCTX-M-65. Phylogenetic analysis revealed a total of 62 sequence types (STs) and 17 SNP clusters. E. coli ST10 and ST155 were common to ESBL-EC from city areas and chicken farms, and ST44 were found among ESBL-EC from city areas and pig farms. Extra-intestinal pathogenic E. coli (ExPEC) ST69, ST131 and ST1193 were found exclusively among rats from city areas, and avian pathogenic E. coli (APEC) ST177 was restricted to ESBL-EC originating from chicken farms. Phylogenetic analysis showed that the populations of rodent ESBL-EC from city areas, chicken farms and pig farms were genetically different, suggesting a certain degree of partitioning between the human and animal locations. This study contributes to current understanding of ESBL-EC occurring in rats in ecologically diverse locations.
Collapse
Affiliation(s)
- Theethawat Uea-Anuwong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Michael Biggel
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - Wu Wai Hung
- Centre for Applied One Health Research and Policy Advice, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Kittitat Lugsomya
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Lam Hoi Kiu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| | - Yrjö Tapio Gröhn
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Sara Boss
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, 8057, Zurich, Switzerland
| | | | - Ioannis Magouras
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China; Centre for Applied One Health Research and Policy Advice, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region, China
| |
Collapse
|
3
|
Sokal A, Royer G, Esposito-Farese M, Clermont O, Condamine B, Laouénan C, Lefort A, Denamur E, de Lastours V. Clinical and Bacteriological Specificities of Escherichia coli Bloodstream Infections From Biliary Portal of Entries. J Infect Dis 2024; 229:1679-1687. [PMID: 38214565 DOI: 10.1093/infdis/jiad586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Escherichia coli is frequently responsible for bloodstream infections (BSIs). Among digestive BSIs, biliary infections appear to be less severe. Respective roles of host factors, bacterial determinants (phylogroups, virulence, and antibiotic resistance), and portal of entry on outcome are unknown. METHODS Clinical characteristics and prognosis of 770 episodes of E coli BSI were analyzed and isolates sequenced (Illumina technology) comparing phylogroups, multilocus sequence type, virulence, and resistance gene content. BSI isolates were compared with 362 commensal E coli from healthy subjects. RESULTS Among 770 episodes, 135 were biliary, 156 nonbiliary digestive, and 479 urinary. Compared to urinary infections, BSIs of digestive origin occurred significantly more in men, comorbid, and immunocompromised patients. Digestive portal of entry was significantly associated with septic shock and death. Among digestive infections, patients with biliary infections were less likely to die (P = .032), despite comparable initial severity. Biliary E coli resembled commensals (phylogroup distribution, sequence type, and few virulence-associated genes) whereas nonbiliary digestive and urinary strains carried many virulence-associated genes. CONCLUSIONS Escherichia coli strains responsible for biliary infections exhibit commensal characteristics and are associated with lower mortality rates, despite similar initial severity, than other digestive BSIs. Biliary drainage in addition to antibiotics in the management of biliary infections may explain improved outcome.
Collapse
Affiliation(s)
- Aurélien Sokal
- Service de Médecine Interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris (AP-HP) Clichy
| | - Guilhem Royer
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, Créteil
- Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Institut Pasteur, Unité mixte de recherche Centre National de la recherche Scientifique 6047, Université Paris Cité, Paris
| | | | - Olivier Clermont
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
| | - Bénédicte Condamine
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
| | - Cedric Laouénan
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
- Département d'épidémiologie, biostatistiques et recherche clinique
| | - Agnès Lefort
- Service de Médecine Interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris (AP-HP) Clichy
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
| | - Erick Denamur
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, Paris, France
| | - Victoire de Lastours
- Service de Médecine Interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris (AP-HP) Clichy
- Université Paris Cité, IAME (Infections, Antimicrobials, Modelling and Evolution), UMR 1137, INSERM, 75018 Paris, France
| |
Collapse
|
4
|
Zhang H, Tao S, Chen H, Fang Y, Xu Y, Chen L, Ma F, Liang W. The biological function of the type II toxin-antitoxin system ccdAB in recurrent urinary tract infections. Front Microbiol 2024; 15:1379625. [PMID: 38690370 PMCID: PMC11059956 DOI: 10.3389/fmicb.2024.1379625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Urinary tract infections (UTIs) represent a significant challenge in clinical practice, with recurrent forms (rUTIs) posing a continual threat to patient health. Escherichia coli (E. coli) is the primary culprit in a vast majority of UTIs, both community-acquired and hospital-acquired, underscoring its clinical importance. Among different mediators of pathogenesis, toxin-antitoxin (TA) systems are emerging as the most prominent. The type II TA system, prevalent in prokaryotes, emerges as a critical player in stress response, biofilm formation, and cell dormancy. ccdAB, the first identified type II TA module, is renowned for maintaining plasmid stability. This paper aims to unravel the physiological role of the ccdAB in rUTIs caused by E. coli, delving into bacterial characteristics crucial for understanding and managing this disease. We investigated UPEC-induced rUTIs, examining changes in type II TA distribution and number, phylogenetic distribution, and Multi-Locus Sequence Typing (MLST) using polymerase chain reaction (PCR). Furthermore, our findings revealed that the induction of ccdB expression in E. coli BL21 (DE3) inhibited bacterial growth, observed that the expression of both ccdAB and ccdB in E. coli BL21 (DE3) led to an increase in biofilm formation, and confirmed that ccdAB plays a role in the development of persistent bacteria in urinary tract infections. Our findings could pave the way for novel therapeutic approaches targeting these systems, potentially reducing the prevalence of rUTIs. Through this investigation, we hope to contribute significantly to the global effort to combat the persistent challenge of rUTIs.
Collapse
Affiliation(s)
- He Zhang
- Department of Medical Laboratory, Bengbu Medical University, Bengbu, China
| | - Shuan Tao
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Huimin Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yewei Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, China
| | - Luyan Chen
- Department of Blood Transfusion, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Fang Ma
- Department of Medical Laboratory, Bengbu Medical University, Bengbu, China
| | - Wei Liang
- Department of Clinical Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, China
| |
Collapse
|
5
|
Djordjevic SP, Jarocki VM, Seemann T, Cummins ML, Watt AE, Drigo B, Wyrsch ER, Reid CJ, Donner E, Howden BP. Genomic surveillance for antimicrobial resistance - a One Health perspective. Nat Rev Genet 2024; 25:142-157. [PMID: 37749210 DOI: 10.1038/s41576-023-00649-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Antimicrobial resistance (AMR) - the ability of microorganisms to adapt and survive under diverse chemical selection pressures - is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted 'One Health' approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.
Collapse
Affiliation(s)
- Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia.
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia.
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Torsten Seemann
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Anne E Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, South Australia, Australia
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Cameron J Reid
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
- Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia
| | - Benjamin P Howden
- Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| |
Collapse
|
6
|
Qiu L, Chirman D, Clark JR, Xing Y, Hernandez Santos H, Vaughan EE, Maresso AW. Vaccines against extraintestinal pathogenic Escherichia coli (ExPEC): progress and challenges. Gut Microbes 2024; 16:2359691. [PMID: 38825856 PMCID: PMC11152113 DOI: 10.1080/19490976.2024.2359691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/21/2024] [Indexed: 06/04/2024] Open
Abstract
The emergence of antimicrobial resistance (AMR) is a principal global health crisis projected to cause 10 million deaths annually worldwide by 2050. While the Gram-negative bacteria Escherichia coli is commonly found as a commensal microbe in the human gut, some strains are dangerously pathogenic, contributing to the highest AMR-associated mortality. Strains of E. coli that can translocate from the gastrointestinal tract to distal sites, called extraintestinal E. coli (ExPEC), are particularly problematic and predominantly afflict women, the elderly, and immunocompromised populations. Despite nearly 40 years of clinical trials, there is still no vaccine against ExPEC. One reason for this is the remarkable diversity in the ExPEC pangenome across pathotypes, clades, and strains, with hundreds of genes associated with pathogenesis including toxins, adhesins, and nutrient acquisition systems. Further, ExPEC is intimately associated with human mucosal surfaces and has evolved creative strategies to avoid the immune system. This review summarizes previous and ongoing preclinical and clinical ExPEC vaccine research efforts to help identify key gaps in knowledge and remaining challenges.
Collapse
Affiliation(s)
- Ling Qiu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Dylan Chirman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Justin R. Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
| | - Yikun Xing
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Haroldo Hernandez Santos
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
| | - Ellen E. Vaughan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Anthony W. Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research (TAILΦR), Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
7
|
Hernández-Chiñas U, Ahumada-Cota RE, Navarro-Ocaña A, Chávez-Berrocal ME, Molina-López J, Rocha-Ramírez LM, Navarro-Cid del Prado A, Eslava CA. Phenotypic and genotypic characteristics of Escherichia coli strains isolated during a longitudinal follow-up study of chronic urinary tract infections. Front Public Health 2023; 11:1240392. [PMID: 38074750 PMCID: PMC10702777 DOI: 10.3389/fpubh.2023.1240392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
Worldwide, Urinary Tract Infections (UTIs) are an important health problem with many cases reported annually, women being the most affected. UTIs are relevant because they can become a recurrent condition, associated with different factors that contribute to the chronicity of the disease (cUTI). cUTI can be classified as persistent (peUTI) when the causative agent is the same each time the infection occurs or as reinfection (reUTI) when the associated microorganism is different. The purpose of this work was to characterize Escherichia coli isolates obtained in two prospective studies of patients with cUTI, to define which of them corresponded to peUTI and which to reUTI. A total of 394 isolates of E. coli were analyzed by agglutination with specific sera, antimicrobial susceptibility by diffusion disc test, and the phylogroups and presence of genes associated with virulence by PCR assays. Additionally, in some characterized strains adherence, invasiveness, and biofilm formation were analyzed by in vitro assays. The results showed that the peUTI strains belonged mainly to the classical UPEC serogroups (O25, O75, O6), were included in the B2 phylogroup, carried a great number of virulence genes, and were adherent, invasive, and biofilm-forming. Meanwhile, reUTI strains showed great diversity of serogroups, belonged mainly in the A phylogroup, and carried fewer virulence genes. Both peUTI and reUTI strains showed extensively drug-resistant (XDR) and multidrug-resistant (MDR) profiles in the antimicrobial susceptibility test. In conclusion, it appears that peUTIs are caused principally by classical UPEC strains, while reUTIs are caused by strains that appear to be a part of the common E. coli intestinal biota. Moreover, although both peUTI and reUTI strains presented different serotypes and phylogroups, their antimicrobial resistance profile (XDR and MDR) was similar, confirming the importance of regulating prophylactic treatments and seeking alternatives for the treatment and control of cUTI. Finally, it was possible to establish the features of the E. coli strains responsible for peUTI and reUTI which could be helpful to develop a fast diagnostic methodology.
Collapse
Affiliation(s)
- Ulises Hernández-Chiñas
- Research Division, Public Health Department, Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Faculty of Medicine, UNAM, Mexico City, Mexico
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - Ricardo E. Ahumada-Cota
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - Armando Navarro-Ocaña
- Bacteriology Laboratory, Public Health Department, Faculty of Medicine, UNAM, Mexico City, Mexico
| | - María E. Chávez-Berrocal
- Research Division, Public Health Department, Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Faculty of Medicine, UNAM, Mexico City, Mexico
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - José Molina-López
- Research Division, Public Health Department, Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Faculty of Medicine, UNAM, Mexico City, Mexico
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| | - Luz M. Rocha-Ramírez
- Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico City, Mexico
| | | | - Carlos A. Eslava
- Research Division, Public Health Department, Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Faculty of Medicine, UNAM, Mexico City, Mexico
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Mexico City, Mexico
| |
Collapse
|
8
|
Jacquier H, Assao B, Chau F, Guindo O, Condamine B, Magnan M, Bridier-Nahmias A, Sayingoza-Makombe N, Moumouni A, Page AL, Langendorf C, Coldiron ME, Denamur E, de Lastours V. Faecal carriage of extended-spectrum β-lactamase-producing Escherichia coli in a remote region of Niger. J Infect 2023; 87:199-209. [PMID: 37369264 DOI: 10.1016/j.jinf.2023.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 06/29/2023]
Abstract
OBJECTIVE Whole genome sequencing (WGS) of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) in developing countries is lacking. Here we describe the population structure and molecular characteristics of ESBL-E. coli faecal isolates in rural Southern Niger. METHODS Stools of 383 healthy participants were collected among which 92.4% were ESBL-Enterobacterales carriers. A subset of 90 ESBL-E. coli containing stools (109 ESBL-E. coli isolates) were further analysed by WGS, using short- and long-reads. RESULTS Most isolates belonged to the commensalism-adapted phylogroup A (83.5%), with high clonal diversity. The blaCTX-M-15 gene was the major ESBL determinant (98.1%), chromosome-integrated in approximately 50% of cases, in multiple integration sites. When plasmid-borne, blaCTX-M-15 was found in IncF (57.4%) and IncY plasmids (26.2%). Closely related plasmids were found in different genetic backgrounds. Genomic environment analysis of blaCTX-M-15 in closely related strains argued for mobilisation between plasmids or from plasmid to chromosome. CONCLUSIONS Massive prevalence of community faecal carriage of CTX-M-15-producing E. coli was observed in a rural region of Niger due to the spread of highly diverse A phylogroup commensalism-adapted clones, with frequent chromosomal integration of blaCTX-M-15. Plasmid spread was also observed. These data suggest a risk of sustainable implementation of ESBL in community faecal carriage.
Collapse
Affiliation(s)
- Hervé Jacquier
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France; Assistance Publique - Hôpitaux de Paris, Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, 94000 Créteil, France.
| | - Bachir Assao
- Epicentre, Médecins Sans Frontières, Maradi, Niger
| | - Françoise Chau
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France
| | | | | | - Mélanie Magnan
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France
| | | | | | | | | | | | | | - Erick Denamur
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France; Assistance Publique - Hôpitaux de Paris, Laboratoire de Génétique Moléculaire, Hôpital Universitaire Bichat, 75018 Paris, France
| | - Victoire de Lastours
- Université Paris Cité, IAME UMR 1137, INSERM, 75018 Paris, France; Assistance Publique - Hôpitaux de Paris, Service de Médecine Interne, Hôpital Universitaire Beaujon, 92110 Clichy, France
| |
Collapse
|
9
|
El-Shenawy FA, El-Sherbeny EME, Kassem S. Efficacy of zinc oxide and copper oxide nanoparticles on virulence genes of avian pathogenic E. coli (APEC) in broilers. BMC Vet Res 2023; 19:108. [PMID: 37542317 PMCID: PMC10401765 DOI: 10.1186/s12917-023-03643-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 07/12/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND Colibacillosis is one of the broilers' most dominant bacterial diseases, either as a primary or a secondary infection. As E. coli antimicrobial drug resistance is rising; there is a need to develop new approaches to its control. In light of this, a comparative study of the in-vitro antibacterial activity of Arabic gum stabilized zinc and copper nanoparticles (AG-ZnNPs and AG-CuNPs) against PCR-identified field avian pathogenic E. coli (APEC) strains and virulence genes (ibeA, hlyA, iss, pap C and ompA) was applied to study the therapeutic effect of zinc and copper nanoparticles to be used as an antibiotic alternative (Nanobiotic). Furthermore, the in-vivo effects of CuNPs were evaluated. Additionally, the CuNPs liver and muscle residues with or without infection were examined. The eighty broilers were divided into four groups; G1: negative control, G2: infected control with E. coli O17, G3: non-infected treated (AG-CuNPs 50 mg/kg body weight), and G4: infected treated (AG-CuNPs 50 mg/kg body weight). AG-CuNPs treatment was given to broilers for five days in drinking water. RESULTS E. coli was isolated from diseased broilers at an average incidence rate of 20% from intestinal and liver samples. All identified serotypes (O17, O78, O91, O121, and O159) were resistant to AG-ZnNPs and sensitive to AG-CuNPs. AG-CuNPs minimal inhibitory and bactericidal concentrations (MIC and MBC) for O17 were 7.5 and 60 mg/ml, respectively. Conventional uniplex PCR results showed that strain O17 contained virulence genes (ibeA, hlyA, iss, and papC), where AG-CuNPs significantly reduced the expression of all target genes when examined by Real-time quantitative PCR. Additionally, the bactericidal activity of AG-CuNPs on O17 was 100% at 20 minutes and 40 mg/ml and confirmed by transmission electron microscopy. Furthermore, no mortality was recorded in treated groups compared to G2. Subsequently, no E. coli was re-isolated from the liver in the G4 after treatment. The total protein, albumin, globulin, and lysozyme activity were significantly increased in G4 compared to G2, while the activities of liver enzymes (alanine aminotransferase (ALT), Gamma-glutamyl transferase (GGT), and alkaline phosphatase (ALP)) were markedly decreased in G4 compared to G2. Additionally, uric acid, creatinine, and C-reactive protein levels were decreased in G4 compared to G2. However, the liver enzymes, kidney functions, C-reactive protein levels, and Cu residues were non-significantly changed in G4 compared to G1. CONCLUSION Green synthesized AG-CuNPs are recommended as an effective antimicrobial alternative against APEC strains.
Collapse
Affiliation(s)
- Fawzia A El-Shenawy
- Bacteriology unit, Tanta lab. (AHRI), Animal Health Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Eman M El El-Sherbeny
- Pharmacology unit, Tanta lab. (AHRI), Animal Health Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Samr Kassem
- Nanomaterials research and Synthesis unit, Animal Health Research Institute (AHRI), Agricultural Research Center (ARC), Giza, Egypt.
| |
Collapse
|
10
|
Li D, Elankumaran P, Kudinha T, Kidsley AK, Trott DJ, Jarocki VM, Djordjevic SP. Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids. Microb Genom 2023; 9:mgen001068. [PMID: 37471138 PMCID: PMC10438821 DOI: 10.1099/mgen.0.001068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/20/2023] [Indexed: 07/21/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) are the most frequent cause of urinary tract infections (UTIs) globally. Most studies of clinical E. coli isolates are selected based on their antimicrobial resistance (AMR) phenotypes; however, this selection bias may not provide an accurate portrayal of which sequence types (STs) cause the most disease. Here, whole genome sequencing (WGS) was performed on 320 E. coli isolates from urine samples sourced from a regional hospital in Australia in 2006. Most isolates (91%) were sourced from patients with UTIs and were not selected based on any AMR phenotypes. No significant differences were observed in AMR and virulence genes profiles across age sex, and uro-clinical syndromes. While 88 STs were identified, ST73, ST95, ST127 and ST131 dominated. F virulence plasmids carrying senB-cjrABC (126/231; 55%) virulence genes were a feature of this collection. These senB-cjrABC+ plasmids were split into two categories: pUTI89-like (F29:A-:B10 and/or >95 % identity to pUTI89) (n=73) and non-pUTI89-like (n=53). Compared to all other plasmid replicons, isolates with pUTI89-like plasmids carried fewer antibiotic resistance genes (ARGs), whilst isolates with senB-cjrABC+/non-pUTI89 plasmids had a significantly higher load of ARGs and class 1 integrons. F plasmids were not detected in 89 genomes, predominantly ST73. Our phylogenomic analyses identified closely related isolates from the same patient associated with different pathologies and evidence of strain-sharing events involving isolates sourced from companion and wild animals.
Collapse
Affiliation(s)
- Dmitriy Li
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia
| | - Paarthiphan Elankumaran
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia
| | - Timothy Kudinha
- Central West Pathology Laboratory, Charles Sturt University, Orange, NSW, Australia
| | - Amanda K. Kidsley
- School of Animal and Veterinary Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - Darren J. Trott
- School of Animal and Veterinary Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - Veronica Maria Jarocki
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia
| | - Steven Philip Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, NSW, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia
| |
Collapse
|
11
|
Gu X, Ma X, Wu Q, Tao Q, Chai Y, Zhou X, Han M, Li J, Huang X, Wu T, Zhang X, Zhong F, Cao Y, Zhang L. Isolation, identification, molecular typing, and drug resistance of Escherichia coli from infected cattle and sheep in Xinjiang, China. Vet Med Sci 2023; 9:1359-1368. [PMID: 36977209 DOI: 10.1002/vms3.1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Escherichia coli infections are common in Xinjiang, a major region of cattle and sheep breeding in China. Therefore, strategies are required to control E. coli. The aim of this study was to investigate the phylogenetic groups, virulence genes, and antibiotic resistance characteristics of E. coli isolates. METHODS In this study, 116 tissue samples were collected from the organs of cattle and sheep that were suspected of having E. coli infections between 2015 and 2019. Bacteria in the samples were identified using a biochemical identification system and amplification of 16S rRNA, and the phylogenetic groupings of E. coli isolates were determined by multiplex polymerase chain reactions. In addition, PCR detection and analysis of virulence factors, antibiotic resistance genes, and drug-resistant phenotypes of E. coli isolates were performed. RESULTS A total of 116 pathogenic E. coli strains belonging to seven phylogenetic groups were isolated, with the majority of isolates in groups A and B1. Among the virulence genes, curli-encoding crl had the highest detection rate of 97.4%, followed by hemolysin-encoding hlyE with the detection rate of 94.82%. Antimicrobial susceptibility test results indicated that the isolates had the highest rates of resistance against streptomycin (81.9%). CONCLUSION These characteristics complicate the prevention and treatment of E. coli-related diseases in Xinjiang.
Collapse
Affiliation(s)
- Xiaoxiao Gu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xue Ma
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Qin Wu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Qiaoxiaoci Tao
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yingjin Chai
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xia Zhou
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Mengli Han
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Jie Li
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xin Huang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Tongzhong Wu
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xingxing Zhang
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Fagang Zhong
- State Key Laboratory for Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Yiheng Cao
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Liyuan Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| |
Collapse
|
12
|
Virulence Profile, Antibiotic Resistance, and Phylogenetic Relationships among Escherichia coli Strains Isolated from the Feces and Urine of Hospitalized Patients. Pathogens 2022; 11:pathogens11121528. [PMID: 36558862 PMCID: PMC9782660 DOI: 10.3390/pathogens11121528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) may inhabit the human gut microbiota without causing disease. However, if they reach extra-intestinal sites, common cystitis to bloodstream infections may occur, putting patients at risk. To examine the human gut as a source of endogenous infections, we evaluated the E. coli clonal diversity of 18 inpatients' guts and their relationship with strains isolated from urinary tract infection (UTI) in the same hospital. Random amplified polymorphic DNA evaluated the clonal diversity, and the antimicrobial susceptibility was determined by disk diffusion. One isolate of each clone detected was sequenced, and their virulome and resistome were determined. Overall, 177 isolates were screened, among which 32 clones were identified (mean of two clones per patient), with ExPEC strains found in over 75% of the inpatients' guts. Endogenous infection was confirmed in 75% of the cases. ST10, ST59, ST69, ST131, and ST1193 clones and critical mobile drug-resistance encoding genes (blaCTX-M-15, blaOXA-1, blaDHA-1, aac(6')-lb-cr, mcr-1.26, qnrB4, and qnrB19) were identified in the gut of inpatients. The genomic analysis highlighted the diversity of the fecal strains, colonization by lactose-negative E. coli, the high frequency of ExPEC in the gut of inpatients without infections, and the presence of β-lactamase producing E. coli in the gut of inpatients regardless of the previous antibiotics' usage. Considering that we found more than one ExPEC clone in the gut of several inpatients, surveillance of inpatients' fecal pathogens may prevent UTI caused by E. coli in the hospital and dissemination of risk clones.
Collapse
|
13
|
Xia F, Cheng J, Jiang M, Wang Z, Wen Z, Wang M, Ren J, Zhuge X. Genomics Analysis to Identify Multiple Genetic Determinants That Drive the Global Transmission of the Pandemic ST95 Lineage of Extraintestinal Pathogenic Escherichia coli (ExPEC). Pathogens 2022; 11:pathogens11121489. [PMID: 36558824 PMCID: PMC9781279 DOI: 10.3390/pathogens11121489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is a pathogen that causes host extraintestinal diseases. The ST95 E. coli lineage is one of the dominant ExPEC lineages in humans and poultry. In this study, we took advantage of extensive E. coli genomes available through public open-access databases to construct a detailed understanding of the phylogeny and evolution of ST95. We used a high variability of accessory genomes to highlight the diversity and dynamic traits of ST95. Isolates from diverse hosts and geographic sources were randomly located on the phylogenetic tree, which suggested that there is no host specificity for ST95. The time-scaled phylogeny showed that ST95 is an ancient and long-lasting lineage. The virulence genes, resistance genes, and pathogenicity islands (PAIs) were characterized in ST95 pan-genomes to provide novel insights into the pathogenicity and multidrug resistance (MDR) genotypes. We found that a pool of large plasmids drives virulence and MDR. Based on the unique genes in the ST95 pan-genome, we designed a novel multiplex PCR reaction to rapidly detect ST95. Overall, our study addressed a gap in the current understanding of ST95 ExPEC genomes, with significant implications for recognizing the success and spread of ST95.
Collapse
Affiliation(s)
- Fufang Xia
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
| | - Jinlong Cheng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
| | - Min Jiang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
| | - Zhongxing Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
| | - Zhe Wen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Min Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
| | - Jianluan Ren
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (J.R.); (X.Z.)
| | - Xiangkai Zhuge
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong 226019, China
- Correspondence: (J.R.); (X.Z.)
| |
Collapse
|
14
|
Aguirre-Sánchez JR, Valdez-Torres JB, Del Campo NC, Martínez-Urtaza J, Del Campo NC, Lee BG, Quiñones B, Chaidez-Quiroz C. Phylogenetic group and virulence profile classification in Escherichia coli from distinct isolation sources in Mexico. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 106:105380. [PMID: 36283634 DOI: 10.1016/j.meegid.2022.105380] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022]
Abstract
Escherichia coli is a leading cause of human enteric diseases worldwide. The rapid and accurate causal agent identification to a particular source represents a crucial step in the establishment of safety and health measures in the affected human populations and would thus provide insights into the relationship of traits that may contribute for pathogen persistence in a particular reservoir. The objective of the present study was to characterize over two hundred E. coli strains from different isolation sources in Mexico by conducting a correspondence analysis to explore associations with the detected phylogenetic groups. The results indicated that E. coli strains, recovered from distinct sources in Mexico, were classified into phylogroups B1 (35.8%), A (27.8%), and D (12.3%) and were clustered to particular clades according to the predicted phylogroups. The results from correspondence analysis showed that E. coli populations from distinct sources in Mexico, belonging to different phylogroups, were not dispersed randomly and were associated with a particular isolation source. Phylogroup A was strongly associated with human sources, and the phylogroup B1 showed a significant relationship with food sources. Additionally, phylogroup D was also related to human sources. Phylogroup B2 was associated with herbivorous and omnivorous mammals. Moreover, common virulence genes in the examined E. coli strains, assigned to all phylogroups, were identified as essential markers for survival and invasion in the host. Although virulence profiles varied among the detected phylogroups, E. coli strains belonging to phylogroup D, associated with humans, were found to contain the largest virulence gene repertoire conferring for persistence and survival in the host. In summary, these findings provide fundamental information for a better characterization of pathogenic E. coli, recovered from distinct isolation sources in Mexico and would assist in the development of better tools for identifying potential transmission routes of contamination.
Collapse
Affiliation(s)
- José R Aguirre-Sánchez
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico
| | - José B Valdez-Torres
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico
| | - Nohemí Castro Del Campo
- Facultad de Medicina Veterinaria y Zootecnia de la Universidad Autónoma de Sinaloa, 80260 Culiacán, Sinaloa, Mexico
| | - Jaime Martínez-Urtaza
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Nohelia Castro Del Campo
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico
| | - Bertram G Lee
- U.S. Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA 94710, United States
| | - Beatriz Quiñones
- U.S. Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA 94710, United States
| | - Cristóbal Chaidez-Quiroz
- Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, 80110 Culiacán, Sinaloa, Mexico.
| |
Collapse
|
15
|
Pérez-Etayo L, González D, Vitas AI. Clonal Complexes 23, 10, 131 and 38 as Genetic Markers of the Environmental Spread of Extended-Spectrum β-Lactamase (ESBL)-Producing E. coli. Antibiotics (Basel) 2022; 11:1465. [PMID: 36358120 PMCID: PMC9686695 DOI: 10.3390/antibiotics11111465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 07/30/2023] Open
Abstract
In accordance with the global action plan on antimicrobial resistance adopted by the World Health Assembly in 2015, there is a need to develop surveillance programs for antimicrobial resistant bacteria. In this context, we have analyzed the clonal diversity of Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) isolated from aquatic environments and human and food samples in Spain, with the aim of determining possible clonal complexes (CCs) that act as markers of the potential risk of transmission of these resistant bacteria. The phylogenetic groups, sequence types (STs) and CCs were determined by different Polymerase Chain Reaction (PCR) and Multilocus Sequence Typing (MLST) techniques. Phylogroup A was prevalent and was mainly present in food and water strains, while human strains were mostly associated with phylogroup B2. According to the observed prevalence in the different niches, CC23 and CC10 are proposed as markers of phylogroups A and C, related with the spread of blaCTX-M1 and blaCTX-M15 genes. Similarly, CC131 and CC38 could be associated to the dissemination of pathogenic strains (phylogroups B2 and D) carrying mainly blaCTX-M14 and blaCTX-M15 genes. Some strains isolated from wastewater treatment plants (WWTPs) showed identical profiles to those isolated from other environments, highlighting the importance that water acquires in the dissemination of bacterial resistance. In conclusion, the detection of these genetic markers in different environments could be considered as an alert in the spread of ESBL.
Collapse
Affiliation(s)
- Lara Pérez-Etayo
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - David González
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Ana Isabel Vitas
- Department of Microbiology and Parasitology, University of Navarra, 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| |
Collapse
|
16
|
The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France. Appl Environ Microbiol 2022; 88:e0066422. [PMID: 35862685 PMCID: PMC9361829 DOI: 10.1128/aem.00664-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Escherichia coli is a commensal species of the lower intestine but is also a major pathogen causing intestinal and extraintestinal infections that is increasingly prevalent and resistant to antibiotics. Most studies on genomic evolution of E. coli used isolates from infections. Here, instead, we whole-genome sequenced a collection of 403 commensal E. coli isolates from fecal samples of healthy adult volunteers in France (1980 to 2010). These isolates were distributed mainly in phylogroups A and B2 (30% each) and belonged to 152 sequence types (STs), the five most frequent being ST10 (phylogroup A; 16.3%), ST73 and ST95 (phylogroup B2; 6.3 and 5.0%, respectively), ST69 (phylogroup D; 4.2%), and ST59 (phylogroup F; 3.9%), and 224 O:H serotypes. ST and serotype diversity increased over time. The O1, O2, O6, and O25 groups used in bioconjugate O-antigen vaccine against extraintestinal infections were found in 23% of the strains of our collection. The increase in frequency of virulence-associated genes and antibiotic resistance was driven by two evolutionary mechanisms. Evolution of virulence gene frequency was driven by both clonal expansion of STs with more virulence genes ("ST-driven") and increases in gene frequency within STs independent of changes in ST frequencies ("gene-driven"). In contrast, the evolution of resistance was dominated by increases in frequency within STs ("gene-driven"). This study provides a unique picture of the phylogenomic evolution of E. coli in its human commensal habitat over 30 years and will have implications for the development of preventive strategies. IMPORTANCE Escherichia coli is an opportunistic pathogen with the greatest burden of antibiotic resistance, one of the main causes of bacterial infections and an increasing concern in an aging population. Deciphering the evolutionary dynamics of virulence and antibiotic resistance in commensal E. coli is important to understand adaptation and anticipate future changes. The gut of vertebrates is the primary habitat of E. coli and probably where selection for virulence and resistance takes place. Unfortunately, most whole-genome-sequenced strains are isolated from pathogenic conditions. Here, we whole-genome sequenced 403 E. coli commensals isolated from healthy French subjects over a 30-year period. Virulence genes increased in frequency by both clonal expansion of clones carrying them and increases in frequency within clones, whereas resistance genes increased by within-clone increased frequency. Prospective studies of E. coli commensals should be performed worldwide to have a broader picture of evolution and adaptation of this species.
Collapse
|
17
|
Bidet P, Birgy A, Ouldali N, Béchet S, Levy C, Madhi F, Sobral E, Cohen R, Bonacorsi S. Comparative genomic analysis of ESBL-producing Escherichia coli from faecal carriage and febrile urinary tract infection in children: a prospective multicentre study. JAC Antimicrob Resist 2022; 4:dlac056. [PMID: 35611261 PMCID: PMC9123598 DOI: 10.1093/jacamr/dlac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/02/2022] [Indexed: 11/26/2022] Open
Abstract
Background The reliability of ESBL-producing Escherichia coli (ESBL-Ec) faecal carriage monitoring to guide probabilistic treatment of febrile urinary tract infection (FUTI) in children remains unclear. Objectives To compare the genomic characteristics of ESBL-Ec isolates from faecal carriage and FUTI to assess their correlation and identify a FUTI-associated virulence profile. Methods We conducted a prospective multicentre hospital and ambulatory-based study. We analysed the genotypes and virulence factors of both faecal and FUTI ESBL-Ec by whole genome sequencing. Correlations were assessed by non-parametric Spearman coefficient and virulence factors were assessed by chi-squared tests with Bonferroni correction. Results We included 218 ESBL-Ec causing FUTI and 154 ESBL-Ec faecal carriage isolates. The most frequent ST was ST131 (44%) in both collections. We found high correlation between carriage and ESBL-Ec FUTI regarding genes/alleles (rho = 0.88, P < 0.0001) and combinations of virulence genes, MLST and serotypes (rho = 0.90, P < 0.0001, rho = 0.99, P = 0.0003, rho = 0.97, P = 0.005 respectively). Beside this strong correlation, we found five genes that were significantly associated with FUTI (papC, papGII, hlyC, hek and traJ). The strongest association with FUTI was found with adhesin gene allele papGII (54% in FUTI versus 16% in carriage) and for papGII and gene traJ alone or in combination (63% versus 24%). Conclusions The genomic profile of ESBL-Ec causing FUTI in children strongly correlates with faecal carriage isolates except for a few genes. The presence of papGII and/or traJ in a previously identified carriage strain could be used as a marker of uropathogenicity and may guide the empirical antimicrobial choice in subsequent FUTI.
Collapse
Affiliation(s)
- Philippe Bidet
- Université Paris Cité, IAME, INSERM, F-75018 Paris, France
- Service de Microbiologie, Centre National de Référence associé pour Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - André Birgy
- Université Paris Cité, IAME, INSERM, F-75018 Paris, France
- Service de Microbiologie, Centre National de Référence associé pour Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - Naim Ouldali
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
- Service de Pédiatrie Générale, Hôpital Robert-Debré, AP-HP, Paris, France
| | - Stéphane Béchet
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
| | - Corinne Levy
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
- Université Paris Est, IMRB-GRC GEMINI, Créteil, France
- GPIP (Groupe de Pathologie Infectieuse Pédiatrique) de la SFP (Société Française de Pédiatrie), Paris, France
| | - Fouad Madhi
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
- Université Paris Est, IMRB-GRC GEMINI, Créteil, France
- GPIP (Groupe de Pathologie Infectieuse Pédiatrique) de la SFP (Société Française de Pédiatrie), Paris, France
- Service de Pédiatrie Générale, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Elsa Sobral
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
| | - Robert Cohen
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Créteil, France
- Université Paris Est, IMRB-GRC GEMINI, Créteil, France
- GPIP (Groupe de Pathologie Infectieuse Pédiatrique) de la SFP (Société Française de Pédiatrie), Paris, France
| | - Stéphane Bonacorsi
- Université Paris Cité, IAME, INSERM, F-75018 Paris, France
- Service de Microbiologie, Centre National de Référence associé pour Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| |
Collapse
|
18
|
Urban Wildlife Crisis: Australian Silver Gull Is a Bystander Host to Widespread Clinical Antibiotic Resistance. mSystems 2022; 7:e0015822. [PMID: 35469421 PMCID: PMC9238384 DOI: 10.1128/msystems.00158-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Australian silver gull is an urban-adapted species that frequents anthropogenic waste sites. The enterobacterial flora of synanthropic birds often carries antibiotic resistance genes. Whole-genome sequence analyses of 425 Escherichia coli isolates from cloacal swabs of chicks inhabiting three coastal sites in New South Wales, Australia, cultured on media supplemented with meropenem, cefotaxime, or ciprofloxacin are reported. Phylogenetically, over 170 antibiotic-resistant lineages from 96 sequence types (STs) representing all major phylogroups were identified. Remarkably, 25 STs hosted the carbapenemase gene blaIMP-4, sourced only from Five Islands. Class 1 integrons carrying blaIMP and blaOXA alongside blaCTX-M and qnrS were notable. Multiple plasmid types mobilized blaIMP-4 and blaOXA-1, and 121 isolates (28%) carried either a ColV-like (18%) or a pUTI89-like (10%) F virulence plasmid. Phylogenetic comparisons to human isolates provided evidence of interspecies transmission. Our study underscores the importance of bystander species in the transmission of antibiotic-resistant and pathogenic E. coli. IMPORTANCE By compiling various genomic and phenotypic data sets, we have provided one of the most comprehensive genomic studies of Escherichia coli isolates from the Australian silver gull, on media containing clinically relevant antibiotics. The analysis of genetic structures capturing antimicrobial resistance genes across three gull breeding colonies in New South Wales, Australia, and comparisons to clinical data have revealed a range of trackable genetic signatures that highlight the broad distribution of clinical antimicrobial resistance in more than 170 different lineages of E. coli. Conserved truncation sizes of the class 1 integrase gene, a key component of multiple-drug resistance structures in the Enterobacteriaceae, represent unique deletion events that are helping to link seemingly disparate isolates and highlight epidemiologically relevant data between wildlife and clinical sources. Notably, only the most anthropogenically affected of the three sites (Five Islands) was observed to host carbapenem resistance, indicating a potential reservoir among the sites sampled.
Collapse
|
19
|
Giannattasio-Ferraz S, Ene A, Gomes VJ, Queiroz CO, Maskeri L, Oliveira AP, Putonti C, Barbosa-Stancioli EF. Escherichia coli and Pseudomonas aeruginosa Isolated From Urine of Healthy Bovine Have Potential as Emerging Human and Bovine Pathogens. Front Microbiol 2022; 13:764760. [PMID: 35330764 PMCID: PMC8940275 DOI: 10.3389/fmicb.2022.764760] [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: 08/25/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The study of livestock microbiota has immediate benefits for animal health as well as mitigating food contamination and emerging pathogens. While prior research has indicated the gastrointestinal tract of cattle as the source for many zoonoses, including Shiga-toxin producing Escherichia coli and antibiotic resistant bacteria, the bovine urinary tract microbiota has yet to be thoroughly investigated. Here, we describe 5 E. coli and 4 Pseudomonas aeruginosa strains isolated from urine of dairy Gyr cattle. While both species are typically associated with urinary tract infections and mastitis, all of the animals sampled were healthy. The bovine urinary strains were compared to E. coli and P. aeruginosa isolates from other bovine samples as well as human urinary samples. While the bovine urinary E. coli isolates had genomic similarity to isolates from the gastrointestinal tract of cattle and other agricultural animals, the bovine urinary P. aeruginosa strains were most similar to human isolates suggesting niche adaptation rather than host adaptation. Examination of prophages harbored by these bovine isolates revealed similarity with prophages within distantly related E. coli and P. aeruginosa isolates from the human urinary tract. This suggests that related urinary phages may persist and/or be shared between mammals. Future studies of the bovine urinary microbiota are needed to ascertain if E. coli and P. aeruginosa are resident members of this niche and/or possible sources for emerging pathogens in humans.
Collapse
Affiliation(s)
- Silvia Giannattasio-Ferraz
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | - Vitor Júnio Gomes
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Cid Oliveira Queiroz
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Laura Maskeri
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
| | | | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Edel F Barbosa-Stancioli
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
20
|
Gatya Al-Mayahie SM, Al-Guranie DRT, Hussein AA, Bachai ZA. Prevalence of common carbapenemase genes and multidrug resistance among uropathogenic Escherichia coli phylogroup B2 isolates from outpatients in Wasit Province/ Iraq. PLoS One 2022; 17:e0262984. [PMID: 35077517 PMCID: PMC8789106 DOI: 10.1371/journal.pone.0262984] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 01/10/2022] [Indexed: 01/04/2023] Open
Abstract
Carbapenems are the last resort antimicrobials for the treatment of extended spectrum β-lactamases (ESBLs) producing Enterobacteriaceae. Emergence of carbapenems resistant group B2 uropathogenic E. coli (UPEC) is a major concern because of their high virulence. Prevalence of these enzymes and multidrug resistance (MDR) among B2 UPEC isolates from Iraqi outpatients with acute urinary tract infection (UTI) was evaluated in this research. Urine cultures were performed and the isolates were identified biochemically. Escherichia coli isolates were tested for phylogroup reference by quadraplex PCR, then B2 isolates were detected for antimicrobial resistance by disc diffusion test and carbapenemase genes by PCR. Escherichia coli was the most prevalent among Gram-negative isolates (66.6%) and B2 was the most detected phylogroup among E. coli isolates (33.9%). Most of B2 isolates showed high resistance rates to tested antimicrobials, especially β-lactams with MDR revealed in 100% of them. Whereas, low resistance rates were noted against carbapenems, aminoglycosides and nitrofurantoin. Carbapenemase genes were detected in 76.3% of B2 isolates. Of which, blaOXA-48 was the most frequent (57.8%), followed by blaPER (47.3%), blaKPC (15.7%), blaVEB and blaVIM (10.5%, for each). Whereas, blaGES and blaIMP genes were not found. Coproduction of these genes occurred among 17 isolates. The combination of blaOXA-48 and blaPER was the most frequent (41.1%). All carbapenemase producing isolates were MDR. These results revealed high prevalence of carbapenemase genes and MDR among B2 UPEC recovered in this study. In the study area. it is strongly advised to use aminoglycosides and nitrofurantoin for empirical treatment of UPEC.
Collapse
Affiliation(s)
| | | | - Aya Aziz Hussein
- Department of Biology, College of Science, Wasit University, Al-Kut City, Wasit Province, Iraq
| | - Zaineb Ali Bachai
- Department of Biology, College of Science, Wasit University, Al-Kut City, Wasit Province, Iraq
| |
Collapse
|
21
|
AB 5 Enterotoxin-Mediated Pathogenesis: Perspectives Gleaned from Shiga Toxins. Toxins (Basel) 2022; 14:toxins14010062. [PMID: 35051039 PMCID: PMC8779504 DOI: 10.3390/toxins14010062] [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: 12/27/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Foodborne diseases affect an estimated 600 million people worldwide annually, with the majority of these illnesses caused by Norovirus, Vibrio, Listeria, Campylobacter, Salmonella, and Escherichia coli. To elicit infections in humans, bacterial pathogens express a combination of virulence factors and toxins. AB5 toxins are an example of such toxins that can cause various clinical manifestations, including dehydration, diarrhea, kidney damage, hemorrhagic colitis, and hemolytic uremic syndrome (HUS). Treatment of most bacterial foodborne illnesses consists of fluid replacement and antibiotics. However, antibiotics are not recommended for infections caused by Shiga toxin-producing E. coli (STEC) because of the increased risk of HUS development, although there are conflicting views and results in this regard. Lack of effective treatment strategies for STEC infections pose a public health threat during outbreaks; therefore, the debate on antibiotic use for STEC infections could be further explored, along with investigations into antibiotic alternatives. The overall goal of this review is to provide a succinct summary on the mechanisms of action and the pathogenesis of AB5 and related toxins, as expressed by bacterial foodborne pathogens, with a primary focus on Shiga toxins (Stx). The role of Stx in human STEC disease, detection methodologies, and available treatment options are also briefly discussed.
Collapse
|
22
|
Specificities and Commonalities of Carbapenemase-Producing Escherichia coli Isolated in France from 2012 to 2015. mSystems 2022; 7:e0116921. [PMID: 35014866 PMCID: PMC8751382 DOI: 10.1128/msystems.01169-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Carbapenemase-producing Escherichia coli (CP-Ec) represents a major public health threat with a risk of dissemination in the community as has occurred for lineages producing extended-spectrum β-lactamases. To characterize the extent of CP-Ec spread in France, isolates from screening and infection samples received at the French National Reference Center (F-NRC) laboratory for carbapenemase-producing Enterobacterales were investigated. A total of 691 CP-Ec isolates collected between 2012 and 2015 and 22 isolates collected before 2012 were fully sequenced. Analysis of their genome sequences revealed some disseminating multidrug-resistant (MDR) lineages frequently acquiring diverse carbapenemase genes mainly belonging to clonal complex 23 (CC23) (sequence type 410 [ST410]) and CC10 (ST10 and ST167) and sporadic isolates, including rare ST131 isolates (n = 17). However, the most represented sequence type (ST) was ST38 (n = 92) with four disseminated lineages carrying blaOXA-48-like genes inserted in the chromosome. Globally, the most frequent carbapenemase gene (n = 457) was blaOXA-48. It was also less frequently associated with MDR isolates being the only resistance gene in 119 isolates. Thus, outside the ST38 clades, its acquisition was frequently sporadic with no sign of dissemination, reflecting the circulation of the IncL plasmid pOXA-48 in France and its high frequency of conjugation. In contrast, blaOXA-181 and blaNDM genes were often associated with the evolution of MDR E. coli lineages characterized by mutations in ftsI and ompC. IMPORTANCE Carbapenemase-producing Escherichia coli (CP-Ec) might be difficult to detect, as MICs can be very low. However, their absolute number and their proportion among carbapenem-resistant Enterobacterales have been increasing, as reported by WHO and national surveillance programs. This suggests a still largely uncharacterized community spread of these isolates. Here, we have characterized the diversity and evolution of CP-Ec isolated in France before 2016. We show that carbapenemase genes are associated with a wide variety of E. coli genomic backgrounds and a small number of dominant phylogenetic lineages. In a significant proportion of CP-Ec, the most frequent carbapenemase gene blaOXA-48, was detected in isolates lacking any other resistance gene, reflecting the dissemination of pOXA-48 plasmids, likely in the absence of any antibiotic pressure. In contrast, carbapenemase gene transfer may also occur in multidrug-resistant E. coli, ultimately giving rise to at-risk lineages encoding carbapenemases with a high potential of dissemination.
Collapse
|
23
|
Foster-Nyarko E, Pallen MJ. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6522174. [PMID: 35134909 PMCID: PMC9075585 DOI: 10.1093/femsre/fuac008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has a rich history as biology's ‘rock star’, driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance—including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
Collapse
Affiliation(s)
- Ebenezer Foster-Nyarko
- Corresponding author: Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom. E-mail:
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, United Kingdom
| |
Collapse
|
24
|
COSTA LETÍCIADAF, FALCÃO DAIANEA, GRASSOTTI TIELAT, CHRISTIANO FRANCIELED, FRAZZON JEVERSON, FRAZZON ANAPAULAG. Antimicrobial resistance of enterococci isolated from food in South Brazil: Comparing pre- and post-RDC 20/2011. AN ACAD BRAS CIENC 2022; 94:e20201765. [DOI: 10.1590/0001-3765202220201765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/15/2021] [Indexed: 11/22/2022] Open
|
25
|
A 21-Year Survey of Escherichia coli from Bloodstream Infections (BSI) in a Tertiary Hospital Reveals How Community-Hospital Dynamics of B2 Phylogroup Clones Influence Local BSI Rates. mSphere 2021; 6:e0086821. [PMID: 34935444 PMCID: PMC8722714 DOI: 10.1128/msphere.00868-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This is a longitudinal study comprising 649 Escherichia coli isolates representing all 7,165 E. coli bloodstream infection (BSI) episodes recorded in a hospital (1996 to 2016). Strain analysis included clonal identification (phylogenetic groups/subgroups, STc131 subclades, pulsed-field gel electrophoresis [PFGE], and whole-genome sequencing [WGS]), antibiotic susceptibility (13 antibiotics), and virulence-associated genes (VAGs; 29 genes). The incidence of E. coli BSI increased from 1996 to 2016 (5.5 to 10.8 BSI episodes/1,000 hospitalizations, average 7 to 8/1,000). B2 isolates predominate (53%), with subgroups B2-I (STc131), B2-II, B2-IX, and B2-VI representing 25%, 25%, 14%, and 9%, respectively. Intertwined waves of community-acquired (CA) plus health care-associated and community-onset health care-associated (HCA) and hospital-acquired (HA) episodes of both B2 and non-B2 phylogroups occurred. A remarkable increase was observed only for B2-I-STc131 (C1/C2 subclades), with oscillations for other B2 subgroups and phylogroups throughout the years. Epidemic and persistent clones (comprising isolates with highly similar/identical PFGE types and genomes differing in 6 to 173 single nucleotide polymorphisms [SNPs]) of B2-I (STc131), B2-II (STc73), B2-III (STc127), B2-IX (STc95), and B2-VI (STc12) were recovered from different patients, most at hospital admission, for long periods (2 to 17 years), and extended-spectrum beta-lactamase (ESBL) producers or resistance to ciprofloxacin in B2 isolates was almost restricted to B2-I (STc131) subclade C. STc131 contributed to increasing the B2 rates but only transiently altered the E. coli population structure. The increase of E. coli BSI was determined by waves of CA+HCA BSI episodes that predate the waves of HA BSI. Besides the risk of hospital transmission that led to temporal increases in BSI, this study suggests that E. coli populations/clones from community-based healthy individuals may occasionally have an epidemic structure and provide a source of transmissible strains influencing the HA BSI incidence. IMPORTANCE Sepsis is the third leading cause of mortality in Western countries and one of the Global Health Threats recognized by the WHO since 2017. Despite Escherichia coli constituting the most common cause of bloodstream infections (BSI), its epidemiology is not fully understood, in part due to the scarcity of local and longitudinal studies. Our work analyzes the long-term dynamics of E. coli causing bacteremia in a single institution and reveals waves of different clonal lineages that emerge periodically and successfully spread afterward in both the community and hospitals. Because the origin of E. coli bloodstream infections is the gut, the microbiota of healthy individuals might occasionally have an epidemic structure, providing a source of E. coli strains to influence the incidence of hospital BSI. The study complements previous fractionated observations focusing on specific E. coli lineages or antibiotic-resistant isolates in the last decades and helps to understand the epidemiology of E. coli BSI and the dynamics of pandemic clones.
Collapse
|
26
|
Tang-Fichaux M, Branchu P, Nougayrède JP, Oswald E. Tackling the Threat of Cancer Due to Pathobionts Producing Colibactin: Is Mesalamine the Magic Bullet? Toxins (Basel) 2021; 13:toxins13120897. [PMID: 34941734 PMCID: PMC8703417 DOI: 10.3390/toxins13120897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 12/15/2022] Open
Abstract
Colibactin is a genotoxin produced primarily by Escherichia coli harboring the genomic pks island (pks+ E. coli). Pks+ E. coli cause host cell DNA damage, leading to chromosomal instability and gene mutations. The signature of colibactin-induced mutations has been described and found in human colorectal cancer (CRC) genomes. An inflamed intestinal environment drives the expansion of pks+ E. coli and promotes tumorigenesis. Mesalamine (i.e., 5-aminosalycilic acid), an effective anti-inflammatory drug, is an inhibitor of the bacterial polyphosphate kinase (PPK). This drug not only inhibits the production of intestinal inflammatory mediators and the proliferation of CRC cells, but also limits the abundance of E. coli in the gut microbiota and diminishes the production of colibactin. Here, we describe the link between intestinal inflammation and colorectal cancer induced by pks+ E. coli. We discuss the potential mechanisms of the pleiotropic role of mesalamine in treating both inflammatory bowel diseases and reducing the risk of CRC due to pks+ E. coli.
Collapse
Affiliation(s)
- Min Tang-Fichaux
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, 31024 Toulouse, France; (M.T.-F.); (P.B.); (J.-P.N.)
| | - Priscilla Branchu
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, 31024 Toulouse, France; (M.T.-F.); (P.B.); (J.-P.N.)
| | - Jean-Philippe Nougayrède
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, 31024 Toulouse, France; (M.T.-F.); (P.B.); (J.-P.N.)
| | - Eric Oswald
- IRSD, Université de Toulouse, INSERM, INRAE, ENVT, UPS, 31024 Toulouse, France; (M.T.-F.); (P.B.); (J.-P.N.)
- Service de Bactériology-Hygiène, Hôpital Purpan, CHU de Toulouse, 31059 Toulouse, France
- Correspondence:
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Armand-Lefèvre L, Rondinaud E, Desvillechabrol D, Mullaert J, Clermont O, Petitjean M, Ruppe E, Cokelaer T, Bouchier C, Tenaillon O, Ma L, Nooroya Y, Matheron S, The Voyag-R Study Group, Andremont A, Denamur E, Kennedy SP. Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad. Microb Genom 2021; 7. [PMID: 34279212 PMCID: PMC8477403 DOI: 10.1099/mgen.0.000576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Travel to tropical regions is associated with high risk of acquiring extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) that are typically cleared in less than 3 months following return. The conditions leading to persistent carriage that exceeds 3 months in some travellers require investigation. Whole-genome sequencing (Illumina MiSeq) was performed on the 82 ESBL-E isolates detected upon return and 1, 2, 3, 6 and 12 months later from the stools of 11 long-term (>3 months) ESBL-E carriers following travel abroad. One to five different ESBL Escherichia coli strains were detected per traveller upon return, and this diminished to one after 3 months. Long-term carriage was due to the presence of the same ESBL E. coli strain, for more than 3 months, in 9 out of 11 travellers, belonging to epidemic sequence type complexes (STc 10, 14, 38, 69, 131 and 648). The mean carriage duration of strains belonging to phylogroups B2/D/F, associated with extra-intestinal virulence, was higher than that for commensal-associated A/B1/E phylogroups (3.5 vs 0.5 months, P=0.021). Genes encoding iron capture systems (fyuA, irp), toxins (senB, sat), adhesins (flu, daaF, afa/nfaE, pap, ecpA) and colicin (cjrA) were more often present in persistent strains than in transient ones. Single-nucleotide polymorphism (SNP) analysis in persistent strains showed a maximum divergence of eight SNPs over 12 months without signs of adaptation. Genomic plasticity was observed during the follow-up with the loss or gain of mobile genetic elements such as plasmids, integrons and/or transposons that may contain resistance genes at different points in the follow-up. Long-term colonization of ESBL-E following travel is primarily due to the acquisition of E. coli strains belonging to epidemic clones and harbouring ‘virulence genes’, allowing good adaptation to the intestinal microbiota.
Collapse
Affiliation(s)
- Laurence Armand-Lefèvre
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Emilie Rondinaud
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Dimitri Desvillechabrol
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France
| | - Jimmy Mullaert
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Olivier Clermont
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Marie Petitjean
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Etienne Ruppe
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Thomas Cokelaer
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France.,Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, F-75015 Paris, France
| | - Christiane Bouchier
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France
| | | | - Laurence Ma
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France
| | - Yasmine Nooroya
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Sophie Matheron
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France.,Service de Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France
| | | | - Antoine Andremont
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Erick Denamur
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France.,Laboratoire de Génétique Moléculaire, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France
| | - Sean P Kennedy
- Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, F-75015 Paris, France
| |
Collapse
|
29
|
Diversity and Adaptations of Escherichia coli Strains: Exploring the Intestinal Community in Crohn's Disease Patients and Healthy Individuals. Microorganisms 2021; 9:microorganisms9061299. [PMID: 34203637 PMCID: PMC8232093 DOI: 10.3390/microorganisms9061299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022] Open
Abstract
Crohn's disease (CD) is characterized by a chronic, progressive inflammation across the gastrointestinal tract with a series of exacerbations and remissions. A significant factor in the CD pathogenesis is an imbalance in gut microbiota composition, particularly the prevalence of Escherichia coli. In the present study, the genomes of sixty-three E. coli strains from the gut of patients with CD and healthy subjects were sequenced. In addition, eighteen E. coli-like metagenome-assembled genomes (MAGs) were reconstructed from the shotgun-metagenome sequencing data of fecal samples. The comparative analysis revealed the similarity of E. coli genomes regardless of the origin of the strain. The strains exhibited similar genetic patterns of virulence, antibiotic resistance, and bacteriocin-producing systems. The study showed antagonistic activity of E. coli strains and the metabolic features needed for their successful competition in the human gut environment. These observations suggest complex bacterial interactions within the gut which may affect the host and cause intestinal damage.
Collapse
|
30
|
Royer G, Darty MM, Clermont O, Condamine B, Laouenan C, Decousser JW, Vallenet D, Lefort A, de Lastours V, Denamur E. Phylogroup stability contrasts with high within sequence type complex dynamics of Escherichia coli bloodstream infection isolates over a 12-year period. Genome Med 2021; 13:77. [PMID: 33952335 PMCID: PMC8097792 DOI: 10.1186/s13073-021-00892-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/22/2021] [Indexed: 11/12/2022] Open
Abstract
Background Escherichia coli is the leading cause of bloodstream infections, associated with a significant mortality. Recent genomic analyses revealed that few clonal lineages are involved in bloodstream infections and captured the emergence of some of them. However, data on within sequence type (ST) population genetic structure evolution are rare. Methods We compared whole genome sequences of 912 E. coli isolates responsible for bloodstream infections from two multicenter clinical trials that were conducted in the Paris area, France, 12 years apart, in teaching hospitals belonging to the same institution (“Assistance Publique-Hôpitaux de Paris”). We analyzed the strains at different levels of granularity, i.e., the phylogroup, the ST complex (STc), and the within STc clone taking into consideration the evolutionary history, the resistance, and virulence gene content as well as the antigenic diversity of the strains. Results We found a mix of stability and changes overtime, depending on the level of comparison. Overall, we observed an increase in antibiotic resistance associated to a restricted number of genetic determinants and in strain plasmidic content, whereas phylogroup distribution and virulence gene content remained constant. Focusing on STcs highlighted the pauci-clonality of the populations, with only 11 STcs responsible for more than 73% of the cases, dominated by five STcs (STc73, STc131, STc95, STc69, STc10). However, some STcs underwent dramatic variations, such as the global pandemic STc131, which replaced the previously predominant STc95. Moreover, within STc131, 95 and 69 genomic diversity analysis revealed a highly dynamic pattern, with reshuffling of the population linked to clonal replacement sometimes coupled with independent acquisitions of virulence factors such as the pap gene cluster bearing a papGII allele located on various pathogenicity islands. Additionally, STc10 exhibited huge antigenic diversity evidenced by numerous O:H serotype/fimH allele combinations, whichever the year of isolation. Conclusions Altogether, these data suggest that the bloodstream niche is occupied by a wide but specific phylogenetic diversity and that highly specialized extra-intestinal clones undergo frequent turnover at the within ST level. Additional worldwide epidemiological studies overtime are needed in different geographical and ecological contexts to assess how generalizable these data are. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00892-0.
Collapse
Affiliation(s)
- Guilhem Royer
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France.,Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - Mélanie Mercier Darty
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - Olivier Clermont
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France
| | | | - Cédric Laouenan
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Département d'épidémiologie, biostatistiques et recherche clinique, Hôpital Bichat, AP-HP, F-75018, Paris, France
| | - Jean-Winoc Decousser
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, F-94000, Créteil, France
| | - David Vallenet
- LABGeM, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Paris-Saclay, Evry, France
| | - Agnès Lefort
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, F-92100, Clichy, France
| | - Victoire de Lastours
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France.,Service de Médecine Interne, Hôpital Beaujon, AP-HP, F-92100, Clichy, France
| | - Erick Denamur
- Université de Paris, IAME, UMR 1137, INSERM, F-75018, Paris, France. .,Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, F-75018, Paris, France.
| | | |
Collapse
|
31
|
Birgy A, Madhi F, Jung C, Levy C, Cointe A, Bidet P, Hobson CA, Bechet S, Sobral E, Vuthien H, Ferroni A, Aberrane S, Cuzon G, Beraud L, Gajdos V, Launay E, Pinquier D, Haas H, Desmarest M, Dommergues MA, Cohen R, Bonacorsi S. Diversity and trends in population structure of ESBL-producing Enterobacteriaceae in febrile urinary tract infections in children in France from 2014 to 2017. J Antimicrob Chemother 2021; 75:96-105. [PMID: 31617912 DOI: 10.1093/jac/dkz423] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/21/2019] [Accepted: 09/10/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The population structure of extraintestinal pathogenic Escherichia coli evolves over time, notably due to the emergence of antibiotic-resistant clones such as ESBL-producing Enterobacteriaceae (ESBL-E). OBJECTIVES To analyse by WGS the genetic diversity of a large number of ESBL-E isolated from urinary tract infections in children from paediatric centres across France between 2014 and 2017 and collected by the National Observatory of febrile urinary tract infection (FUTI) caused by ESBL-E. METHODS A total of 40 905 Enterobacteriaceae-positive urine cultures were identified. ESBL-E were found in 1983 samples (4.85%). WGS was performed on 251 ESBL-E causing FUTI. STs, core genome MLST (cgMLST), serotype, fimH allele, ESBL genes and presence of papGII key virulence factor were determined. RESULTS E. coli and Klebsiella pneumoniae were found in 86.9% (218/251) and 11.2% (28/251) of cases, respectively. Several STs predominate among E. coli such as ST131, ST38, ST69, ST73, ST95, ST405, ST12 and ST1193, while no ST emerged in K. pneumoniae. E. coli ST131, ST38 and ST1193 increased during the study period, with a heterogeneity in papGII prevalence (64.5%, 35% and 20% respectively). Most isolates harboured the CTX-M type (97%) with a predominance of blaCTX-M-15. blaCTX-M-27, an emerging variant in E. coli, is found in various STs. cgMLST enabled discrimination of clusters within the main STs. CONCLUSIONS The predominance of ST131, and the emergence of other STs such as ST38 and ST1193 combined with ESBL genes deserves close epidemiological surveillance considering their high threat in infectious disease. cgMLST could be a discriminant complementary tool for the analyses.
Collapse
Affiliation(s)
- André Birgy
- Université de Paris, IAME, INSERM, F-75018, Paris, France.,AP-HP, Hôpital Robert Debré, Service de Microbiologie, F-75019, Paris, France
| | - Fouad Madhi
- Service de Pédiatrie Générale, Centre Hospitalier Intercommunal de Créteil, France.,Groupe de Pathologie Infectieuse Pédiatrique (GPIP), Paris, France.,Centre de Recherche Clinique, Centre Hospitalier Intercommunal de Créteil, France
| | - Camille Jung
- Service de Pédiatrie Générale, Centre Hospitalier Intercommunal de Créteil, France.,Centre de Recherche Clinique, Centre Hospitalier Intercommunal de Créteil, France
| | - Corinne Levy
- Groupe de Pathologie Infectieuse Pédiatrique (GPIP), Paris, France.,Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Saint Maur des Fossés, France.,Université Paris Est, IMRB-GRC GEMINI, ACTIV, 94000, Créteil, France
| | - Aurélie Cointe
- Université de Paris, IAME, INSERM, F-75018, Paris, France.,AP-HP, Hôpital Robert Debré, Service de Microbiologie, F-75019, Paris, France
| | - Philippe Bidet
- Université de Paris, IAME, INSERM, F-75018, Paris, France.,AP-HP, Hôpital Robert Debré, Service de Microbiologie, F-75019, Paris, France
| | | | - Stéphane Bechet
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Saint Maur des Fossés, France
| | - Elsa Sobral
- Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Saint Maur des Fossés, France
| | - Hoang Vuthien
- AP-HP, HU-Est Parisien site Trousseau, Service de Bactériologie, F-75012, Paris, France
| | - Agnès Ferroni
- AP-HP, Hopital Necker, Service de Microbiologie, University Paris Descartes, Paris, France
| | - Saïd Aberrane
- Microbiology Laboratory, Créteil Hospital, Créteil, France
| | - Gaëlle Cuzon
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France.,Université Paris Sud, LabEx LERMIT, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France.,Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur, APHP-Université Paris Sud, Paris, France
| | - Laetitia Beraud
- Centre National de Référence des Légionelles, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Vincent Gajdos
- Service de Pédiatrie, Antoine Béclère University Hospital, Assistance Publique-Hôpitaux de Paris, Clamart, France.,Centre for Research in Epidemiology and Population Health, Villejuif, France
| | - Elise Launay
- Service de Pédiatrie Générale et Infectiologie Pédiatrique, Hôpital Femme-Enfant-Adolescent, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Didier Pinquier
- Unité de Pneumologie et Allergologie pédiatriques & CRCM mixte, Pédiatrie Médicale, CHU Charles Nicolle, Rouen, France
| | - Hervé Haas
- Hôpitaux pédiatriques CHU Lenval, Nice, France
| | - Marie Desmarest
- Service d'Accueil des Urgences Pédiatriques, AP-HP, Hôpital Robert Debré, Paris, France
| | - Marie-Aliette Dommergues
- Groupe de Pathologie Infectieuse Pédiatrique (GPIP), Paris, France.,Service de pédiatrie, centre hospitalier de Versailles, Le Chesnay, France
| | - Robert Cohen
- Groupe de Pathologie Infectieuse Pédiatrique (GPIP), Paris, France.,Centre de Recherche Clinique, Centre Hospitalier Intercommunal de Créteil, France.,Association Clinique Thérapeutique Infantile du Val de Marne (ACTIV), Saint Maur des Fossés, France.,Université Paris Est, IMRB-GRC GEMINI, ACTIV, 94000, Créteil, France.,Unité Court Séjour, Petits Nourrisson, Service de Néonatologie, Centre Hospitalier Intercommunal de Créteil, France
| | - Stéphane Bonacorsi
- Université de Paris, IAME, INSERM, F-75018, Paris, France.,AP-HP, Hôpital Robert Debré, Service de Microbiologie, F-75019, Paris, France
| | | |
Collapse
|
32
|
Oliero M, Calvé A, Fragoso G, Cuisiniere T, Hajjar R, Dobrindt U, Santos MM. Oligosaccharides increase the genotoxic effect of colibactin produced by pks+ Escherichia coli strains. BMC Cancer 2021; 21:172. [PMID: 33596864 PMCID: PMC7890614 DOI: 10.1186/s12885-021-07876-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/03/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Colibactin is a genotoxin that induces DNA double-strand breaks that may lead to carcinogenesis and is produced by Escherichia coli strains harboring the pks island. Human and animal studies have shown that colibactin-producing gut bacteria promote carcinogenesis and enhance the progression of colorectal cancer through cellular senescence and chromosomal abnormalities. In this study, we investigated the impact of prebiotics on the genotoxicity of colibactin-producing E. coli strains Nissle 1917 and NC101. METHODS Bacteria were grown in medium supplemented with 20, 30 and 40 mg/mL of prebiotics inulin or galacto-oligosaccharide, and with or without 5 μM, 25 μM and 125 μM of ferrous sulfate. Colibactin expression was assessed by luciferase reporter assay for the clbA gene, essential for colibactin production, in E. coli Nissle 1917 and by RT-PCR in E. coli NC101. The human epithelial colorectal adenocarcinoma cell line, Caco-2, was used to assess colibactin-induced megalocytosis by methylene blue binding assay and genotoxicity by γ-H2AX immunofluorescence analysis. RESULTS Inulin and galacto-oligosaccharide enhanced the expression of clbA in pks+ E. coli. However, the addition of 125 μM of ferrous sulfate inhibited the expression of clbA triggered by oligosaccharides. In the presence of either oligosaccharide, E. coli NC101 increased dysplasia and DNA double-strand breaks in Caco-2 cells compared to untreated cells. CONCLUSION Our results suggest that, in vitro, prebiotic oligosaccharides exacerbate DNA damage induced by colibactin-producing bacteria. Further studies are necessary to establish whether oligosaccharide supplementation may lead to increased colorectal tumorigenesis in animal models colonized with pks+ E. coli.
Collapse
Affiliation(s)
- Manon Oliero
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), 900 Rue Saint Denis, Montreal, QC H2X 0A9 Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, 2900 boulevard Édouard-Montpetit, Montréal, QC H3T 1J4 Canada
| | - Annie Calvé
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), 900 Rue Saint Denis, Montreal, QC H2X 0A9 Canada
| | - Gabriela Fragoso
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), 900 Rue Saint Denis, Montreal, QC H2X 0A9 Canada
| | - Thibault Cuisiniere
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), 900 Rue Saint Denis, Montreal, QC H2X 0A9 Canada
| | - Roy Hajjar
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), 900 Rue Saint Denis, Montreal, QC H2X 0A9 Canada
- Department of Surgery, Faculty of Medicine, Université de Montréal, 2900 boulevard Édouard-Montpetit, Montréal, QC H3T 1J4 Canada
| | - Ulrich Dobrindt
- Institute of Hygiene, Section Microbial Genome Plasticity, University of Münster, Mendelstraße 7, 48149 Münster, Germany
| | - Manuela M. Santos
- Nutrition and Microbiome Laboratory, Institut du cancer de Montréal, Centre de recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), 900 Rue Saint Denis, Montreal, QC H2X 0A9 Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, 2900 boulevard Édouard-Montpetit, Montréal, QC H3T 1J4 Canada
| |
Collapse
|
33
|
Nji E, Kazibwe J, Hambridge T, Joko CA, Larbi AA, Damptey LAO, Nkansa-Gyamfi NA, Stålsby Lundborg C, Lien LTQ. High prevalence of antibiotic resistance in commensal Escherichia coli from healthy human sources in community settings. Sci Rep 2021; 11:3372. [PMID: 33564047 PMCID: PMC7873077 DOI: 10.1038/s41598-021-82693-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 01/21/2021] [Indexed: 01/30/2023] Open
Abstract
Antibiotic resistance is a global health crisis that requires urgent action to stop its spread. To counteract the spread of antibiotic resistance, we must improve our understanding of the origin and spread of resistant bacteria in both community and healthcare settings. Unfortunately, little attention is being given to contain the spread of antibiotic resistance in community settings (i.e., locations outside of a hospital inpatient, acute care setting, or a hospital clinic setting), despite some studies have consistently reported a high prevalence of antibiotic resistance in the community settings. This study aimed to investigate the prevalence of antibiotic resistance in commensal Escherichia coli isolates from healthy humans in community settings in LMICs. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we synthesized studies conducted from 1989 to May 2020. A total of 9363 articles were obtained from the search and prevalence data were extracted from 33 articles and pooled together. This gave a pooled prevalence of antibiotic resistance (top ten antibiotics commonly prescribed in LMICs) in commensal E. coli isolates from human sources in community settings in LMICs of: ampicillin (72% of 13,531 isolates, 95% CI: 65-79), cefotaxime (27% of 6700 isolates, 95% CI: 12-44), chloramphenicol (45% of 7012 isolates, 95% CI: 35-53), ciprofloxacin (17% of 10,618 isolates, 95% CI: 11-25), co-trimoxazole (63% of 10,561 isolates, 95% CI: 52-73), nalidixic acid (30% of 9819 isolates, 95% CI: 21-40), oxytetracycline (78% of 1451 isolates, 95% CI: 65-88), streptomycin (58% of 3831 isolates, 95% CI: 44-72), tetracycline (67% of 11,847 isolates, 95% CI: 59-74), and trimethoprim (67% of 3265 isolates, 95% CI: 59-75). Here, we provided an appraisal of the evidence of the high prevalence of antibiotic resistance by commensal E. coli in community settings in LMICs. Our findings will have important ramifications for public health policy design to contain the spread of antibiotic resistance in community settings. Indeed, commensal E. coli is the main reservoir for spreading antibiotic resistance to other pathogenic enteric bacteria via mobile genetic elements.
Collapse
Affiliation(s)
- Emmanuel Nji
- BioStruct-Africa, Vårby, 143 43, Stockholm, Sweden.
| | - Joseph Kazibwe
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Thomas Hambridge
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, 3015 GD, Rotterdam, The Netherlands
| | - Carolyn Alia Joko
- BioStruct-Africa, Vårby, 143 43, Stockholm, Sweden
- Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Amma Aboagyewa Larbi
- BioStruct-Africa, Vårby, 143 43, Stockholm, Sweden
- Department of Biochemistry and Biotechnology, College of Science, Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana
| | | | | | - Cecilia Stålsby Lundborg
- Health Systems and Policy (HSP): Improving the Use of Medicines, Department of Global Public Health, Karolinska Institutet, Tomtebodavägen 18A, 17177, Stockholm, Sweden
| | - La Thi Quynh Lien
- Department of Pharmaceutical Management and Pharmaco-Economics, Hanoi University of Pharmacy, 13-15 Le Thanh Tong, Hoan Kiem District, Hanoi, 110403, Vietnam
| |
Collapse
|
34
|
Foster-Nyarko E, Alikhan NF, Ikumapayi UN, Sarwar G, Okoi C, Tientcheu PEM, Defernez M, O'Grady J, Antonio M, Pallen MJ. Genomic diversity of Escherichia coli from healthy children in rural Gambia. PeerJ 2021; 9:e10572. [PMID: 33505796 PMCID: PMC7796664 DOI: 10.7717/peerj.10572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/23/2020] [Indexed: 01/21/2023] Open
Abstract
Little is known about the genomic diversity of Escherichia coli in healthy children from sub-Saharan Africa, even though this is pertinent to understanding bacterial evolution and ecology and their role in infection. We isolated and whole-genome sequenced up to five colonies of faecal E. coli from 66 asymptomatic children aged three-to-five years in rural Gambia (n = 88 isolates from 21 positive stools). We identified 56 genotypes, with an average of 2.7 genotypes per host. These were spread over 37 seven-allele sequence types and the E. coli phylogroups A, B1, B2, C, D, E, F and Escherichia cryptic clade I. Immigration events accounted for three-quarters of the diversity within our study population, while one-quarter of variants appeared to have arisen from within-host evolution. Several isolates encode putative virulence factors commonly found in Enteropathogenic and Enteroaggregative E. coli, and 53% of the isolates encode resistance to three or more classes of antimicrobials. Thus, resident E. coli in these children may constitute reservoirs of virulence- and resistance-associated genes. Moreover, several study strains were closely related to isolates that caused disease in humans or originated from livestock. Our results suggest that within-host evolution plays a minor role in the generation of diversity compared to independent immigration and the establishment of strains among our study population. Also, this study adds significantly to the number of commensal E. coli genomes, a group that has been traditionally underrepresented in the sequencing of this species.
Collapse
Affiliation(s)
- Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom.,Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Usman N Ikumapayi
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Golam Sarwar
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Catherine Okoi
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Marianne Defernez
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom
| | - Justin O'Grady
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom.,School of Veterinary Medicine, University of Surrey, Surrey, United Kingdom
| |
Collapse
|
35
|
Mota R, Pinto M, Palmeira J, Gonçalves D, Ferreira H. Multidrug-resistant bacteria as intestinal colonizers and evolution of intestinal colonization in healthy university students in Portugal. Access Microbiol 2020; 3:acmi000182. [PMID: 33997613 PMCID: PMC8115976 DOI: 10.1099/acmi.0.000182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/02/2020] [Indexed: 12/18/2022] Open
Abstract
Multidrug-resistant bacteria have been increasingly described in healthcare institutions, however community resistance also seems to be emerging. Escherichia coli an intestinal commensal bacteria, is also a pathogen and represents an important intestinal reservoir of resistance. Our aim was the study of the intestinal colonization and of the persistence of antibiotic resistant intestinal bacteria in healthy university students of Porto, in the north of Portugal. Samples from 30 university students were collected and analysed. Two E. coli isolates were randomly obtained from each student and Gram-negative bacilli resistant to antibiotics were studied. In addition, we evaluated changes in the Gram-negative intestinal colonization of ten university students in a short period of time. Molecular characterization showed a high presence of bla TEM in commensal E. coli . Gram-negative bacteria with intrinsic and extrinsic resistance were isolated, namely Pseudomonas spp., Enterobacter spp. and Pantoea spp. We isolated three ESBL-producing E. coli from two students. These isolates showed bla CTX-M group 1 (n=1), bla CTX-M group 9 (n=2), bla TEM (n=2), bla SHV (n=1) and tetA (n=2) genes. Additionally, they showed specific virulence factors and conjugational transfer of antibiotic resistance and virulence genes. One Pseudomonas spp. isolate resistant to carbapenems was detected colonizing one student. Our results confirm that healthy young adults may be colonized with commensals showing clinically relevant antibiotic resistance mechanisms, creating a risk of silent spread of these bacteria in the community.
Collapse
Affiliation(s)
- Raquel Mota
- UCIBIO, Microbiology, Faculty of Pharmacy of University of Porto, Portugal.,Microbiology, Faculty of Pharmacy of University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Marisa Pinto
- UCIBIO, Microbiology, Faculty of Pharmacy of University of Porto, Portugal.,Microbiology, Faculty of Pharmacy of University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Josman Palmeira
- UCIBIO, Microbiology, Faculty of Pharmacy of University of Porto, Portugal.,Microbiology, Faculty of Pharmacy of University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Daniela Gonçalves
- UCIBIO, Microbiology, Faculty of Pharmacy of University of Porto, Portugal.,Microbiology, Faculty of Pharmacy of University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.,Instituto Superior de Saúde, Rua Castelo de Almourol, 4720-155 Amares, Portugal
| | - Helena Ferreira
- UCIBIO, Microbiology, Faculty of Pharmacy of University of Porto, Portugal.,Microbiology, Faculty of Pharmacy of University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| |
Collapse
|
36
|
Galardini M, Clermont O, Baron A, Busby B, Dion S, Schubert S, Beltrao P, Denamur E. Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study. PLoS Genet 2020; 16:e1009065. [PMID: 33112851 PMCID: PMC7592755 DOI: 10.1371/journal.pgen.1009065] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/20/2020] [Indexed: 11/18/2022] Open
Abstract
The genus Escherichia is composed of several species and cryptic clades, including E. coli, which behaves as a vertebrate gut commensal, but also as an opportunistic pathogen involved in both diarrheic and extra-intestinal diseases. To characterize the genetic determinants of extra-intestinal virulence within the genus, we carried out an unbiased genome-wide association study (GWAS) on 370 commensal, pathogenic and environmental strains representative of the Escherichia genus phylogenetic diversity and including E. albertii (n = 7), E. fergusonii (n = 5), Escherichia clades (n = 32) and E. coli (n = 326), tested in a mouse model of sepsis. We found that the presence of the high-pathogenicity island (HPI), a ~35 kbp gene island encoding the yersiniabactin siderophore, is highly associated with death in mice, surpassing other associated genetic factors also related to iron uptake, such as the aerobactin and the sitABCD operons. We confirmed the association in vivo by deleting key genes of the HPI in E. coli strains in two phylogenetic backgrounds. We then searched for correlations between virulence, iron capture systems and in vitro growth in a subset of E. coli strains (N = 186) previously phenotyped across growth conditions, including antibiotics and other chemical and physical stressors. We found that virulence and iron capture systems are positively correlated with growth in the presence of numerous antibiotics, probably due to co-selection of virulence and resistance. We also found negative correlations between virulence, iron uptake systems and growth in the presence of specific antibiotics (i.e. cefsulodin and tobramycin), which hints at potential “collateral sensitivities” associated with intrinsic virulence. This study points to the major role of iron capture systems in the extra-intestinal virulence of the genus Escherichia. Bacterial isolates belonging to the genus Escherichia can be human commensals but also opportunistic pathogens, with the ability to cause extra-intestinal infection. There is therefore the need to identify the genetic elements that favour extra-intestinal virulence, so that virulent bacterial isolates can be identified through genome analysis and potential treatment strategies be developed. To reduce the influence of host variability on virulence, we have used a mouse model of sepsis to characterize the virulence of 370 strains belonging to the genus Escherichia, for which whole genome sequences were also available. We have used a statistical approach called Genome-Wide Association Study (GWAS) to show how the presence of genes that encode for iron scavenging are significantly associated with the propensity of a bacterial isolate to cause extra-intestinal infections. Taking advantage of previously generated growth data on a subset of the strains and its correlation to virulence we generated hypothesis on the relationship between iron scavenging and growth in the presence of various antimicrobials, which could have implications for developing new treatment strategies.
Collapse
Affiliation(s)
- Marco Galardini
- EMBL-EBI, Wellcome Genome Campus, Cambridge, United Kingdom
- * E-mail: (MG); (ED)
| | | | | | - Bede Busby
- Genome Biology Unit, EMBL, Heidelberg, Germany
| | - Sara Dion
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
| | - Sören Schubert
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Germany
| | - Pedro Beltrao
- EMBL-EBI, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Erick Denamur
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
- * E-mail: (MG); (ED)
| |
Collapse
|
37
|
Kamal SM, Cimdins-Ahne A, Lee C, Li F, Martín-Rodríguez AJ, Seferbekova Z, Afasizhev R, Wami HT, Katikaridis P, Meins L, Lünsdorf H, Dobrindt U, Mogk A, Römling U. A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid. Mol Microbiol 2020; 115:255-271. [PMID: 32985020 PMCID: PMC7984374 DOI: 10.1111/mmi.14614] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/29/2022]
Abstract
The ubiquitous human commensal Escherichia coli has been well investigated through its model representative E. coli K‐12. In this work, we initially characterized E. coli Fec10, a recently isolated human commensal strain of phylogroup A/sequence type ST10. Compared to E. coli K‐12, the 4.88 Mbp Fec10 genome is characterized by distinct single‐nucleotide polymorphisms and acquisition of genomic islands. In addition, E. coli Fec10 possesses a 155.86 kbp IncY plasmid, a composite element based on phage P1. pFec10 harbours multiple cargo genes such as coding for a tetrathionate reductase and its corresponding regulatory two‐component system. Among the cargo genes is also the Transmissible Locus of Protein Quality Control (TLPQC), which mediates tolerance to lethal temperatures in bacteria. The disaggregase ClpGGI of TLPQC constitutes a major determinant of the thermotolerance of E. coli Fec10. We confirmed stand‐alone disaggregation activity, but observed distinct biochemical characteristics of ClpGGI‐Fec10 compared to the nearly identical Pseudomonas aeruginosa ClpGGI‐SG17M. Furthermore, we noted a unique contribution of ClpGGI‐Fec10 to the exquisite thermotolerance of E. coli Fec10, suggesting functional differences between both disaggregases in vivo. Detection of thermotolerance in 10% of human commensal E. coli isolates hints to the successful establishment of food‐borne heat‐resistant strains in the human gut.
Collapse
Affiliation(s)
- Shady Mansour Kamal
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences & Pharmaceutical Industries, Future University in Egypt, Cairo, Egypt
| | | | - Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Fengyang Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Zaira Seferbekova
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Robert Afasizhev
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
| | | | - Panagiotis Katikaridis
- Center for Molecular Biology, University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Lena Meins
- Center for Molecular Biology, University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Axel Mogk
- Center for Molecular Biology, University of Heidelberg (ZMBH), German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
38
|
Martak D, Henriot CP, Broussier M, Couchoud C, Valot B, Richard M, Couchot J, Bornette G, Hocquet D, Bertrand X. High Prevalence of Human-Associated Escherichia coli in Wetlands Located in Eastern France. Front Microbiol 2020; 11:552566. [PMID: 33013784 PMCID: PMC7498643 DOI: 10.3389/fmicb.2020.552566] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/18/2020] [Indexed: 02/03/2023] Open
Abstract
Escherichia coli that are present in the rivers are mostly brought by human and animal feces. Contamination occurs mostly through wastewater treatment plant (WWTP) outflows and field amendment with sewage sludge or manure. However, the survival of these isolates in river-associated wetlands remains unknown. Here, we assessed E. coli population structure in low-anthropized wetlands located along three floodplains to identify the major source of contamination of wetlands, whose functioning is different from the rivers. We retrieved 179 E. coli in water samples collected monthly from 19 sites located in eastern France over 1 year. Phylogroups B1 and B2 were dominant in the E. coli population, while phylogroup A was dominant in isolates resistant to third-generation cephalosporins, which harbored the extended-spectrum β-lactamase (ESBL) encoding genes blaCTX–M–15 and blaCTX–M–27 in half of the cases. The high proportion of isolates from human source can be attributed to WWTP outflows and the spread of sewage sludge. We analyzed the distribution of the isolates belonging to the most human-associated phylogroups (B2 and D) on a phylogenetic tree of the whole species and compared it with that of isolates retrieved from patients and from WWTP outflows. The distribution of the three E. coli populations was similar, suggesting the absence of a specific population in the environment. Our results suggest that a high proportion of E. coli isolates that reach and survive in low-anthropized environments such as wetlands are from human source. To the best of our knowledge, this is the first study assessing E. coli contamination and resistance genes in natural freshwater wetlands.
Collapse
Affiliation(s)
- Daniel Martak
- Service d'Hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France
| | - Charles P Henriot
- UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France
| | - Marion Broussier
- Service d'Hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France
| | - Charlotte Couchoud
- Service d'Hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France
| | - Benoit Valot
- UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France.,Bioinformatique et big data au service de la santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
| | - Marion Richard
- Service d'Hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France
| | - Julie Couchot
- Service d'Hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France
| | - Gudrun Bornette
- UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France
| | - Didier Hocquet
- Service d'Hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France.,Bioinformatique et big data au service de la santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
| | - Xavier Bertrand
- Service d'Hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, CNRS-Université de Bourgogne Franche-Comté, Besançon, France
| |
Collapse
|
39
|
Moez NM, Mashouf RY, Sedighi I, Shokoohizadeh L, Taheri M. Phylogroup classification and investigation the relationships between phylogroups and antibiotic resistance patterns of uropathogenic E. coli isolated from pediatric urinary tract infection. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
40
|
Flament-Simon SC, de Toro M, Chuprikova L, Blanco M, Moreno-González J, Salas M, Blanco J, Redrejo-Rodríguez M. High diversity and variability of pipolins among a wide range of pathogenic Escherichia coli strains. Sci Rep 2020; 10:12452. [PMID: 32719405 PMCID: PMC7385651 DOI: 10.1038/s41598-020-69356-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/01/2020] [Indexed: 12/24/2022] Open
Abstract
Self-synthesizing transposons are integrative mobile genetic elements (MGEs) that encode their own B-family DNA polymerase (PolB). Discovered a few years ago, they are proposed as key players in the evolution of several groups of DNA viruses and virus–host interaction machinery. Pipolins are the most recent addition to the group, are integrated in the genomes of bacteria from diverse phyla and also present as circular plasmids in mitochondria. Remarkably, pipolins-encoded PolBs are proficient DNA polymerases endowed with DNA priming capacity, hence the name, primer-independent PolB (piPolB). We have now surveyed the presence of pipolins in a collection of 2,238 human and animal pathogenic Escherichia coli strains and found that, although detected in only 25 positive isolates (1.1%), they are present in E. coli strains from a wide variety of pathotypes, serotypes, phylogenetic groups and sequence types. Overall, the pangenome of strains carrying pipolins is highly diverse, despite the fact that a considerable number of strains belong to only three clonal complexes (CC10, CC23 and CC32). Comparative analysis with a set of 67 additional pipolin-harboring genomes from GenBank database spanning strains from diverse origin, further confirmed these results. The genetic structure of pipolins shows great flexibility and variability, with the piPolB gene and the attachment sites being the only common features. Most pipolins contain one or more recombinases that would be involved in excision/integration of the element in the same conserved tRNA gene. This mobilization mechanism might explain the apparent incompatibility of pipolins with other integrative MGEs such as integrons. In addition, analysis of cophylogeny between pipolins and pipolin-harboring strains showed a lack of congruence between several pipolins and their host strains, in agreement with horizontal transfer between hosts. Overall, these results indicate that pipolins can serve as a vehicle for genetic transfer among circulating E. coli and possibly also among other pathogenic bacteria.
Collapse
Affiliation(s)
- Saskia-Camille Flament-Simon
- Laboratorio de Referencia de E. Coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, CIBIR (Centro de Investigación Biomédica de La Rioja), La Rioja, 26006, Logroño, Spain
| | - Liubov Chuprikova
- Departamento de Bioquímica & Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain
| | - Miguel Blanco
- Laboratorio de Referencia de E. Coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - Juan Moreno-González
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Margarita Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de E. Coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - Modesto Redrejo-Rodríguez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Departamento de Bioquímica & Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain.
| |
Collapse
|
41
|
Virulence Potential of a Multidrug-Resistant Escherichia coli Strain Belonging to the Emerging Clonal Group ST101-B1 Isolated from Bloodstream Infection. Microorganisms 2020; 8:microorganisms8060827. [PMID: 32486334 PMCID: PMC7355805 DOI: 10.3390/microorganisms8060827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli EC121 is a multidrug-resistant (MDR) strain isolated from a bloodstream infection of an inpatient with persistent gastroenteritis and T-zone lymphoma that died due to septic shock. Despite causing an extraintestinal infection, previous studies showed that it did not have the usual characteristics of an extraintestinal pathogenic E. coli. Instead, it belonged to phylogenetic group B1 and harbored few known virulence genes. To evaluate the pathogenic potential of strain EC121, an extensive genome sequencing and in vitro characterization of various pathogenicity-associated properties were performed. The genomic analysis showed that strain EC121 harbors more than 50 complete virulence genetic clusters. It also displays the capacity to adhere to a variety of epithelial cell lineages and invade T24 bladder cells, as well as the ability to form biofilms on abiotic surfaces, and survive the bactericidal serum complement activity. Additionally, EC121 was shown to be virulent in the Galleria mellonella model. Furthermore, EC121 is an MDR strain harboring 14 antimicrobial resistance genes, including blaCTX-M-2. Completing the scenario, it belongs to serotype O154:H25 and to sequence type 101-B1, which has been epidemiologically linked to extraintestinal infections as well as to antimicrobial resistance spread. This study with E. coli strain EC121 shows that clinical isolates considered opportunistic might be true pathogens that go underestimated.
Collapse
|
42
|
Loayza F, Graham JP, Trueba G. Factors Obscuring the Role of E. coli from Domestic Animals in the Global Antimicrobial Resistance Crisis: An Evidence-Based Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E3061. [PMID: 32354184 PMCID: PMC7246672 DOI: 10.3390/ijerph17093061] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 01/01/2023]
Abstract
Recent studies have found limited associations between antimicrobial resistance (AMR) in domestic animals (and animal products), and AMR in human clinical settings. These studies have primarily used Escherichia coli, a critically important bacterial species associated with significant human morbidity and mortality. E. coli is found in domestic animals and the environment, and it can be easily transmitted between these compartments. Additionally, the World Health Organization has highlighted E. coli as a "highly relevant and representative indicator of the magnitude and the leading edge of the global antimicrobial resistance (AMR) problem". In this paper, we discuss the weaknesses of current research that aims to link E. coli from domestic animals to the current AMR crisis in humans. Fundamental gaps remain in our understanding the complexities of E. coli population genetics and the magnitude of phenomena such as horizontal gene transfer (HGT) or DNA rearrangements (transposition and recombination). The dynamic and intricate interplay between bacterial clones, plasmids, transposons, and genes likely blur the evidence of AMR transmission from E. coli in domestic animals to human microbiota and vice versa. We describe key factors that are frequently neglected when carrying out studies of AMR sources and transmission dynamics.
Collapse
Affiliation(s)
- Fernanda Loayza
- Microbiology Institute, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Diego de Robles y Pampite, Cumbayá-Quito P.O. BOX 170901, Ecuador
| | - Jay P. Graham
- Berkeley School of Public Health, University of California, 2121 Berkeley Way, Room 5302, Berkeley, CA 94720-7360, USA
| | - Gabriel Trueba
- Microbiology Institute, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Diego de Robles y Pampite, Cumbayá-Quito P.O. BOX 170901, Ecuador
| |
Collapse
|
43
|
MacFadden DR, Coburn B, Břinda K, Corbeil A, Daneman N, Fisman D, Lee RS, Lipsitch M, McGeer A, Melano RG, Mubareka S, Hanage WP. Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli. Antimicrob Agents Chemother 2020; 64:e02417-19. [PMID: 32152083 PMCID: PMC7179619 DOI: 10.1128/aac.02417-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/02/2020] [Indexed: 11/20/2022] Open
Abstract
The rising rates of antibiotic resistance increasingly compromise empirical treatment. Knowing the antibiotic susceptibility of a pathogen's close genetic relative(s) may improve empirical antibiotic selection. Using genomic and phenotypic data for Escherichia coli isolates from three separate clinically derived databases, we evaluated multiple genomic methods and statistical models for predicting antibiotic susceptibility, focusing on potentially rapidly available information, such as lineage or genetic distance from archived isolates. We applied these methods to derive and validate the prediction of antibiotic susceptibility to common antibiotics. We evaluated 968 separate episodes of suspected and confirmed infection with Escherichia coli from three geographically and temporally separated databases in Ontario, Canada, from 2010 to 2018. Across all approaches, model performance (area under the curve [AUC]) ranges for predicting antibiotic susceptibility were the greatest for ciprofloxacin (AUC, 0.76 to 0.97) and the lowest for trimethoprim-sulfamethoxazole (AUC, 0.51 to 0.80). When a model predicted that an isolate was susceptible, the resulting (posttest) probabilities of susceptibility were sufficient to warrant empirical therapy for most antibiotics (mean, 92%). An approach combining multiple models could permit the use of narrower-spectrum oral agents in 2 out of every 3 patients while maintaining high treatment adequacy (∼90%). Methods based on genetic relatedness to archived samples of E. coli could be used to predict antibiotic resistance and improve antibiotic selection.
Collapse
Affiliation(s)
- Derek R MacFadden
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Ottawa Hospital Research Institute, Ottawa, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
- University Health Network, Toronto, Canada
| | - Karel Břinda
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Antoine Corbeil
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Nick Daneman
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
| | - David Fisman
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Robyn S Lee
- Harvard Medical School, Boston, Massachusetts, USA
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Marc Lipsitch
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Allison McGeer
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Roberto G Melano
- Public Health Ontario Laboratory, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Samira Mubareka
- Division of Infectious Diseases, University of Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - William P Hanage
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| |
Collapse
|
44
|
Vega-Manriquez XD, Ubiarco-López A, Verdugo-Rodríguez A, Hernández-Chiñas U, Navarro-Ocaña A, Ahumada-Cota RE, Ramírez-Badillo D, Hernández-Díaz de León N, Eslava CA. Pet dogs potential transmitters of pathogenic Escherichia coli with resistance to antimicrobials. Arch Microbiol 2020; 202:1173-1179. [PMID: 32076735 DOI: 10.1007/s00203-020-01828-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 01/20/2020] [Accepted: 02/04/2020] [Indexed: 10/25/2022]
Abstract
Escherichia coli strains are part of the normal biota of humans and animals; however, several clinical reports have implicated E. coli as the etiological agent of diarrhea in humans and companion animals. Thus, the aim of the present study was to know if companion dogs in the city of San Luis Potosi are colonized with virulent potentially harmful E. coli strains. Rectal swabs from 30 dogs, 13 with and 17 without diarrhea were analyzed. Phylogenetic and virulence genes analysis was performed to the E. coli isolates. Additionally, the Kirby-Bauer test was used to analyze the sensitivity to 32 different antimicrobials from 14 families. Eighty-five isolates were identified as E. coli and detected in 97% of healthy and diarrheic dog samples. E. coli isolates from healthy dogs carried several virulence genes, in contrast with those from diarrheic animals that presented only eaeA. In healthy dogs, phylogenetic analysis showed that 57% and 43% of E. coli isolates belonged to commensal (A and B1) and virulent (B2 and D) groups respectively. Meanwhile, diarrheic dogs showed that 69% of the isolates were identified as virulent B2 and D phylogroups. Moreover, E. coli resistant to β-lactams, aminoglycosides, tetracycline, quinolones, and folate inhibitors were detected in both groups of dogs. The presence of E. coli with eaeA virulence gene in diarrheic dogs, suggest that these strains are associated with the animal´s condition. Finally, major attention must be drawn to the careful handling of dogs because of their capability to harbor and disseminate virulent E. coli strains.
Collapse
Affiliation(s)
- X D Vega-Manriquez
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, Potosí, Mexico
| | - A Ubiarco-López
- Laboratorio de Microbiología Molecular, Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico.,Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Public health Department/Research Division, Faculty of Medicine UNAM; Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children's Hospital of Mexico Federico Gómez/Faculty of Medicine UNAM, Dr. Márquez 162, Col. De los Doctores, CP 06720, Mexico City, Mexico
| | - A Verdugo-Rodríguez
- Laboratorio de Microbiología Molecular, Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - U Hernández-Chiñas
- Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Public health Department/Research Division, Faculty of Medicine UNAM; Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children's Hospital of Mexico Federico Gómez/Faculty of Medicine UNAM, Dr. Márquez 162, Col. De los Doctores, CP 06720, Mexico City, Mexico
| | - A Navarro-Ocaña
- Laboratorio de Bacteriología, Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - R E Ahumada-Cota
- Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Public health Department/Research Division, Faculty of Medicine UNAM; Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children's Hospital of Mexico Federico Gómez/Faculty of Medicine UNAM, Dr. Márquez 162, Col. De los Doctores, CP 06720, Mexico City, Mexico.,Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Mexico City, Mexico
| | - D Ramírez-Badillo
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, Potosí, Mexico
| | | | - C A Eslava
- Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Public health Department/Research Division, Faculty of Medicine UNAM; Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children's Hospital of Mexico Federico Gómez/Faculty of Medicine UNAM, Dr. Márquez 162, Col. De los Doctores, CP 06720, Mexico City, Mexico.
| |
Collapse
|
45
|
La Combe B, Clermont O, Messika J, Eveillard M, Kouatchet A, Lasocki S, Corvec S, Lakhal K, Billard-Pomares T, Fernandes R, Armand-Lefevre L, Bourdon S, Reignier J, Fihman V, de Prost N, Bador J, Goret J, Wallet F, Denamur E, Ricard JD. Pneumonia-Specific Escherichia coli with Distinct Phylogenetic and Virulence Profiles, France, 2012-2014. Emerg Infect Dis 2019; 25:710-718. [PMID: 30882313 PMCID: PMC6433033 DOI: 10.3201/eid2504.180944] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In a prospective, nationwide study in France of Escherichia coli responsible for pneumonia in patients receiving mechanical ventilation, we determined E. coli antimicrobial susceptibility, phylotype, O-type, and virulence factor gene content. We compared 260 isolates with those of 2 published collections containing commensal and bacteremia isolates. The preponderant phylogenetic group was B2 (59.6%), and the predominant sequence type complex (STc) was STc73. STc127 and STc141 were overrepresented and STc95 underrepresented in pneumonia isolates compared with bacteremia isolates. Pneumonia isolates carried higher proportions of virulence genes sfa/foc, papGIII, hlyC, cnf1, and iroN compared with bacteremia isolates. Virulence factor gene content and antimicrobial drug resistance were higher in pneumonia than in commensal isolates. Genomic and phylogenetic characteristics of E. coli pneumonia isolates from critically ill patients indicate that they belong to the extraintestinal pathogenic E. coli pathovar but have distinguishable lung-specific traits.
Collapse
|
46
|
Ahumada-Santos YP, Báez-Flores ME, Díaz-Camacho SP, Uribe-Beltrán MDJ, Eslava-Campos CA, Parra-Unda JR, Delgado-Vargas F. Association of phylogenetic distribution and presence of integrons with multidrug resistance in Escherichia coli clinical isolates from children with diarrhoea. J Infect Public Health 2019; 13:767-772. [PMID: 31859055 DOI: 10.1016/j.jiph.2019.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/29/2019] [Accepted: 11/26/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Escherichia coli strains include both commensal and virulent clones distributed in different phylogenetic groups. Antimicrobial resistance is an increasingly serious public health threat at the global level and integrons are important mobile genetic elements involved in resistance dissemination. This paper aims to determine the phylogenetic groups and presence of class 1 (intl1) and 2 (intl2) integrons in E. coli clinical isolates from children with diarrhoea, and to associate these characteristics with their antimicrobial resistance. METHODS Phylogeny and presence of integrons (intl1 and intl2) were analysed by PCR and amplicon sequencing in 70 E. coli isolates from children with and without diarrhoea (35 of each group) from Sinaloa, Mexico; these variables were analysed for correlation with the antimicrobial resistance profile of the isolates. RESULTS The most frequent phylogroups were A (42.9%) and B2 (15.7%). The E. coli isolates from children with diarrhoea were distributed in all phylogroups; while strains from children without diarrhoea were absent from phylogroups C, E, and clade I. The 17.1% of the isolates carried integrons (15.7% intI1 and 1.4% intI2); 28.6% of the isolates from children with diarrhoea showed the class 1 integron. Strains of phylogroup A showed the highest frequency of integrons (33.3%). The association of multidrug resistance and the presence of integrons was identified in 58.3% of strains isolated from children with diarrhoea included in phylogroups A and B2. The sequence analysis of intl1 and intl2 showed silent point mutations and similarities with plasmids of some APEC and AIEC strains. CONCLUSION Commensal E. coli strains are potential disseminators of antimicrobial resistance, and the improvement in the use of antimicrobials to treat childhood diarrhoea is essential for the control of such resistance.
Collapse
Affiliation(s)
- Yesmi Patricia Ahumada-Santos
- School of Chemical and Biological Sciences, Autonomous University of Sinaloa, Ciudad Universitaria, Culiacan, Sinaloa, Mexico
| | - María Elena Báez-Flores
- School of Chemical and Biological Sciences, Autonomous University of Sinaloa, Ciudad Universitaria, Culiacan, Sinaloa, Mexico
| | - Sylvia Páz Díaz-Camacho
- Research Unit in Environment and Health, Autonomous University of Occident, Culiacan, Sinaloa, Mexico
| | | | - Carlos Alberto Eslava-Campos
- School of Medicine, National Autonomous University of Mexico, Ciudad Universitaria, Coyoacan, 04510, Ciudad de Mexico, Mexico; Laboratory of Bacterial Pathogenicity, Hemato Oncology and Research Unit, Hospital Infantil de Mexico Federico Gomez 06720, Ciudad de Mexico, Mexico
| | - Jesús Ricardo Parra-Unda
- School of Chemical and Biological Sciences, Autonomous University of Sinaloa, Ciudad Universitaria, Culiacan, Sinaloa, Mexico
| | - Francisco Delgado-Vargas
- School of Chemical and Biological Sciences, Autonomous University of Sinaloa, Ciudad Universitaria, Culiacan, Sinaloa, Mexico.
| |
Collapse
|
47
|
Escherichia coli B2 Phylogenetic Subgroups in the Infant Gut Microbiota: Predominance of Uropathogenic Lineages in Swedish Infants and Enteropathogenic Lineages in Pakistani Infants. Appl Environ Microbiol 2019; 85:AEM.01681-19. [PMID: 31562173 DOI: 10.1128/aem.01681-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/19/2019] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli segregates into phylogenetic groups, with group B2 containing both extraintestinal pathogenic E. coli (ExPEC) and enteropathogenic E. coli (EPEC) strains. Ten main B2 subgroups (subgroups I to X)/sequence type complexes (STcs), as well as EPEC lineages, have been identified. In the current study, we characterized ExPEC and EPEC strains of E. coli B2 phylogenetic subgroups/STcs that colonize Swedish and Pakistani infants. Gut commensal E. coli B2 strains, 120 from Swedish infants (n = 87) and 19 from Pakistani infants (n = 12), were assigned to B2 subgroups. Carriage of the bundle-forming pili and intimin adhesin was examined in the EPEC lineages. The ExPEC virulence markers and the time of persistence of the strains in the microbiota were previously determined. In total, 84% of the Swedish strains and 47% of the Pakistani strains belonged to 1 of the 10 main B2 subgroups (P = 0.001). Among the Swedish strains, the most common B2 subgroups were IX/STc95 (19%), II/STc73 (17%), VI/STc12 (13%), and III/STc127 (11%), with each subgroup carrying distinctive sets of ExPEC virulence markers. EPEC lineages with few ExPEC features constituted 47% of the Pakistani B2 strains but only 7% of the Swedish B2 strains (P = 0.0001). The subgroup distribution within phylogenetic group B2 strains colonizing the gut differed between Swedish and Pakistani infants. B2 subgroups with uropathogenic characteristics dominated the gut microbiota of Swedish infants, while EPEC lineage 1 strains frequently colonized the intestines of Pakistani infants. Moreover, within the B2 subgroups, ExPEC virulence genes were more prevalent in Swedish strains than in Pakistani strains. Thus, ExPEC traits exemplify the intestinal B2 strains from Western populations.IMPORTANCE The intestinal microbiota is an important reservoir for bacteria that cause extraintestinal infections. Escherichia coli is found ubiquitously in the gut microbiota, and it also causes urinary tract infections, infantile septicemia, and meningitis. Urinary tract infections are usually caused by E. coli strains that originate in the intestinal microbiota. E. coli also causes gastrointestinal infections and is a major cause of diarrhea in infants worldwide. The abilities of certain E. coli strains to cause infections are attributed to their virulence factors, i.e., bacterial components that contribute to the development of different diseases. Our study shows that different subtypes of potentially pathogenic E. coli strains dominate in the gut microbiota of infants in different geographical areas and expands our knowledge of the interplay between bacterial commensalism and pathogenicity.
Collapse
|
48
|
Katongole P, Bulwadda Kisawuzi D, Kyobe Bbosa H, Patrick Kateete D, Florence Najjuka C. Phylogenetic groups and antimicrobial susceptibility patterns of uropathogenic Escherichia coli clinical isolates from patients at Mulago National Referral Hospital, Kampala, Uganda. F1000Res 2019. [DOI: 10.12688/f1000research.20930.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Introduction: Uropathogenic Escherichia coli (UPEC) remains the most common cause of urinary tract infections (UTIs). They account for over 80-90% of all community-acquired and 30-50% of all hospital-acquired UTIs. E. coli strains have been found to belong to evolutionary origins known as phylogenetic groups. In 2013, Clermont classified E. coli strains into eight phylogenetic groups using the quadruplex PCR method. The aim of this study was to identify the phylogenetic groups of UPEC strains in Uganda using Clermont’s quadruplex PCR method and to assess their antibiotic susceptibility patterns in Uganda. Methods: In this cross-sectional study, 140 stored uropathogenic E. coli isolates from the Clinical Microbiology Laboratory, Department of Medical Microbiology, College of Health Sciences Makerere University were subjected to phylogenetic typing by a quadruplex PCR method. Antimicrobial susceptibility testing was performed by disk diffusion method according to Clinical & Laboratory Standards Institute (CLSI) guidelines. Phenotypic detection of extended-spectrum beta-lactamase, AmpC and carbapenemases was done according to CLSI guidelines and Laboratory SOPs. Results: Phylogenetic group B2 (40%) was the most predominant, followed by A (6.23%), clade I and II (5%), D and E (each 2.14%), B1 (1.43%) and F and C (each 0.71%). The most common resistant antibiotic was trimethoprim-sulphamethoxazole (90.71%) and the least was imipenem (1.43%). In total, 73.57% of isolates were multi-drug resistant (MDR). Antibiotic resistance was mainly detected in phylogenetic group B2 (54%). Conclusions: Our findings showed the high prevalence of MDR E. coli isolates, with the dominance of phylogenetic group B2. About 9% of E. coli isolates belonged to the newly described phylogroups C, E, F, and clade I and II.
Collapse
|
49
|
Ghalayini M, Magnan M, Dion S, Zatout O, Bourguignon L, Tenaillon O, Lescat M. Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon. Mol Ecol 2019; 28:4470-4485. [PMID: 31482587 DOI: 10.1111/mec.15232] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/24/2019] [Indexed: 02/02/2023]
Abstract
In vitro experimental evolution has taught us many lessons on the molecular bases of adaptation. To move towards more natural settings, evolution in the mice gut has been successfully performed. Yet, these experiments suffered from the use of laboratory strains as well as the use of axenic or streptomycin-treated mice to maintain the inoculated strains. To circumvent these limitations, we conducted a one-year experimental evolution in vivo using a natural isolate of E. coli, strain 536, in conditions mimicking as much as possible natural environment with mother-to-offspring microbiota transmission. Mice were then distributed in 24 independent cages and separated into two different diets: a regular one (chow diet, CD) and high-fat and high-sugar one (Western Diet, WD). Genome sequences revealed an early and rapid selection during the breastfeeding period that selected the constitutive expression of the well-characterized lactose operon. E. coli was lost significantly more in CD than WD; however, we could not detect any genomic signature of selection, nor any diet specificities during the later part of the experiments. The apparently neutral evolution presumably due to low population size maintained nevertheless at high frequency the early selected mutations affecting lactose regulation. The rapid loss of lactose operon regulation challenges the idea that plastic gene expression is both optimal and stable in the wild.
Collapse
Affiliation(s)
- Mohamed Ghalayini
- IAME, INSERM, Université Paris 13, Bobigny, France.,Service de Réanimation Médico-Chirurgicale, Hôpital Avicenne, AP - HP, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Melanie Magnan
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Sara Dion
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | | | - Lucie Bourguignon
- IAME, INSERM, Université de Paris, Paris, France.,École de l'Inserm Liliane Bettencourt, Paris, France
| | - Olivier Tenaillon
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France
| | - Mathilde Lescat
- IAME, INSERM, Université Paris 13, Bobigny, France.,IAME, INSERM, Université de Paris, Paris, France.,Service de Microbiologie, Hôpital Avicenne, AP - HP, Bobigny, France
| |
Collapse
|
50
|
Clermont O, Dixit OVA, Vangchhia B, Condamine B, Dion S, Bridier-Nahmias A, Denamur E, Gordon D. Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential. Environ Microbiol 2019; 21:3107-3117. [PMID: 31188527 DOI: 10.1111/1462-2920.14713] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/31/2019] [Accepted: 06/09/2019] [Indexed: 12/22/2022]
Abstract
The phylogeny of the Escherichia coli species, with the identification of seven phylogroups (A, B1, B2, C, D, E and F), is linked to the lifestyle of the strains. With the accumulation of whole genome sequence data, it became clear that some strains belong to a group intermediate between the F and B2 phylogroups, designated as phylogroup G. Here, we studied the complete sequences of 112 strains representative of the G phylogroup diversity and showed that it is composed of one main sequence type complex (STc)117 and four other STcs (STc657, STc454, STc738 and STc174). STc117, which phylogeny is characterized by very short internal branches, exhibits extensive O diversity, but little H-type and fimH allele diversity, whereas the other STcs are characterized by a main O, H and fimH type. STc117 strains possess many traits associated with extra-intestinal virulence, are virulent in a mouse sepsis model and exhibit multi-drug resistance such as CTX-M production. Epidemiologic data on 4,524 Australian and French strains suggest that STc117 is a poultry-associated lineage that can also establish in humans and cause extra-intestinal diseases. We propose an easy identification method that will help to trace this potentially virulent and resistant phylogroup in epidemiologic studies.
Collapse
Affiliation(s)
- Olivier Clermont
- IAME, UMR 1137, INSERM, Université de Paris, Paris, 75018, France
| | - Ojas V A Dixit
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Belinda Vangchhia
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia.,Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Aizawl, 796014, India
| | | | - Sara Dion
- IAME, UMR 1137, INSERM, Université de Paris, Paris, 75018, France
| | | | - Erick Denamur
- IAME, UMR 1137, INSERM, Université de Paris, Paris, 75018, France.,Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, 75018, France
| | - David Gordon
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| |
Collapse
|