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Tóth K, Damjanova I, Laczkó L, Buzgó L, Lesinszki V, Ungvári E, Jánvári L, Hanczvikkel A, Tóth Á, Szabó D. Genomic Epidemiology of C2/H30Rx and C1-M27 Subclades of Escherichia coli ST131 Isolates from Clinical Blood Samples in Hungary. Antibiotics (Basel) 2024; 13:363. [PMID: 38667039 PMCID: PMC11047377 DOI: 10.3390/antibiotics13040363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/10/2024] [Accepted: 04/14/2024] [Indexed: 04/29/2024] Open
Abstract
Extended-spectrum β-lactamase-producing Escherichia coli ST131 has become widespread worldwide. This study aims to characterize the virulome, resistome, and population structure of E. coli ST131 isolates from clinical blood samples in Hungary. A total of 30 C2/H30Rx and 33 C1-M27 ST131 isolates were selected for Illumina MiSeq sequencing and 30 isolates for MinION sequencing, followed by hybrid de novo assembly. Five C2/H30Rx and one C1-M27 cluster were identified. C1-M27 isolates harbored the F1:A2:B20 plasmid in 93.9% of cases. Long-read sequencing revealed that blaCTX-M-27 was on plasmids. Among the C2/H30Rx isolates, only six isolates carried the C2-associated F2:A1:B- plasmid type. Of 19 hybrid-assembled C2/H30Rx genomes, the blaCTX-M-15 gene was located on plasmid only in one isolate, while in the other isolates, ISEcp1 or IS26-mediated chromosomal integration of blaCTX-M-15 was detected in unique variations. In one isolate a part of F2:A1:B- plasmid integrated into the chromosome. These results suggest that CTX-M-15-producing C2/H30Rx and CTX-M-27-producing C1-M27 subclades may have emerged and spread in different ways in Hungary. While blaCTX-M-27 was carried mainly on the C1/H30R-associated F1:A2:B20 plasmid, the IncF-like plasmids of C2/H30Rx or its composite transposons have been incorporated into the chromosome through convergent evolutionary processes.
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Affiliation(s)
- Kinga Tóth
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Ivelina Damjanova
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Levente Laczkó
- One Health Institute, Faculty of Health Sciences, University of Debrecen, 4032 Debrecen, Hungary
- HUN-REN-DE Conservation Biology Research Group, University of Debrecen, 4032 Debrecen, Hungary
| | - Lilla Buzgó
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Virág Lesinszki
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Erika Ungvári
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Laura Jánvári
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Adrienn Hanczvikkel
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Ákos Tóth
- Department of Bacteriology, Parasitology and Mycology, National Center for Public Health and Pharmacy, 1097 Budapest, Hungary (L.B.); (L.J.); (Á.T.)
| | - Dóra Szabó
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, 1089 Budapest, Hungary
- HUN-REN-SE Human Microbiota Research Group, 1052 Budapest, Hungary
- Neurosurgical and Neurointervention Clinic, Semmelweis University, 1083 Budapest, Hungary
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Biguenet A, Bertrand X, Bourgeon M, Gnide DC, Gbaguidi-Haore H, Slekovec C. Population structure of community-acquired extended-spectrum beta-lactamase producing Escherichia coli and methicillin resistant Staphylococcus aureus in a French region showed no difference between urban and rural areas. PLoS One 2023; 18:e0294433. [PMID: 37972023 PMCID: PMC10653544 DOI: 10.1371/journal.pone.0294433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance is a global health issue and extended-spectrum β-lactamase producing Escherichia coli (ESBL-Ec) and methicillin-resistant Staphylococcus aureus (MRSA) are of particular concern. Whole genome sequencing analysis of isolates from the community is essential to understand the circulation of those multidrug-resistant bacteria. Our main objective was to determine the population structure of clinical ESBL-Ec and MRSA isolated in the community setting of a French region. For this purpose, isolates were collected from 23 sites belonging to 6 private medical biology laboratories in the Bourgogne-Franche-Comté region. One hundred ninety ESBL-Ec and 67 MRSA were sequenced using the Illumina technology. Genomic analyses were performed to determine the bacterial typing, presence of antibiotic resistance genes, metal resistance genes as well as virulence genes. Analysis showed that ST131 was the major ESBL-Ec clone circulating in the region, representing 42.1% of the ESBL-Ec isolates. The blaCTX-M genes represented 98% of blaESBL with the majority being blaCTX-M-15 (53.9%). MRSA population consisted of mainly of CC8 (50.7%) and CC5 (38.8%) clonal complexes. Interestingly, we found a prevalence of 40% of the zinc resistance gene czrC in our MRSA population. We observed no differences in our ESBL-Ec or MRSA populations between urban and rural areas in our French region, suggesting no impact of population density or rural environment.
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Affiliation(s)
- Adrien Biguenet
- Université de Franche-Comté, UMR-CNRS 6249 Chrono-Environnement, Besançon, France
- CHU de Besançon, Hygiène Hospitalière, Besançon, France
| | - Xavier Bertrand
- Université de Franche-Comté, UMR-CNRS 6249 Chrono-Environnement, Besançon, France
- CHU de Besançon, Hygiène Hospitalière, Besançon, France
| | - Marilou Bourgeon
- CHU de Besançon, Centre de Ressources Biologiques - Filière Microbiologique, Besançon, France
| | - Dossi Carine Gnide
- CHU de Besançon, Bioinformatique et Big Data Au Service de La Santé, Besançon, France
| | - Houssein Gbaguidi-Haore
- Université de Franche-Comté, UMR-CNRS 6249 Chrono-Environnement, Besançon, France
- CHU de Besançon, Hygiène Hospitalière, Besançon, France
| | - Céline Slekovec
- Université de Franche-Comté, UMR-CNRS 6249 Chrono-Environnement, Besançon, France
- CHU de Besançon, Hygiène Hospitalière, Besançon, France
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Biggel M, Hoehn S, Frei A, Dassler K, Jans C, Stephan R. Dissemination of ESBL-producing E. coli ST131 through wastewater and environmental water in Switzerland. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122476. [PMID: 37659628 DOI: 10.1016/j.envpol.2023.122476] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/06/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023]
Abstract
The E. coli lineage ST131 is a major cause of multidrug-resistant urinary tract and bloodstream infections worldwide. Recently emerged ST131 sublineages spread globally within few years, but their dissemination routes are incompletely understood. In this study, we investigate the potential role of wastewater and surface water in the spread of extended-spectrum β-lactamase (ESBL)-producing ST131. Streams, lakes, and two wastewater treatment plants (WWTPs) in the canton of Zug, Switzerland, were consecutively sampled over 1.5 years. ST131 was detected in 38% of the samples taken downstream (1-5 km) of WWTP discharge sites, but usually absent in water bodies distant from urban areas or WWTP discharge. Specific strains were repeatedly isolated (≤5 pairwise cgSNP distance) from wastewater or river sites downstream of effluent discharge, indicating their repeated entry or persistence in WWTPs in large concentrations. Genetic characterization of the ESBL-producing water isolates revealed a predominance of clades A and C1 and an emerging ciprofloxacin-resistant sublineage with mutations in quinolone resistance determining regions (QRDR) within clade A. Multiple isolates belonged to internationally circulating sublineages, including C1-M27 and papGII + sublineages with chromosomally encoded ESBLs. This study demonstrates that the clinically relevant E. coli lineage ST131 pollutes river ecosystems, representing a significant challenge to public health and to technologies to minimize their entry into the water environment.
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Affiliation(s)
- Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland.
| | - Sarah Hoehn
- Amt für Verbraucherschutz, Kanton Zug, Steinhausen, Switzerland.
| | - Andrea Frei
- Amt für Verbraucherschutz, Kanton Zug, Steinhausen, Switzerland.
| | - Kira Dassler
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland.
| | - Christoph Jans
- Amt für Verbraucherschutz, Kanton Zug, Steinhausen, Switzerland.
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Switzerland.
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Balbuena-Alonso MG, Camps M, Cortés-Cortés G, Carreón-León EA, Lozano-Zarain P, Rocha-Gracia RDC. Strain belonging to an emerging, virulent sublineage of ST131 Escherichia coli isolated in fresh spinach, suggesting that ST131 may be transmissible through agricultural products. Front Cell Infect Microbiol 2023; 13:1237725. [PMID: 37876872 PMCID: PMC10591226 DOI: 10.3389/fcimb.2023.1237725] [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: 06/09/2023] [Accepted: 09/15/2023] [Indexed: 10/26/2023] Open
Abstract
Food contamination with pathogenic Escherichia coli can cause severe disease. Here, we report the isolation of a multidrug resistant strain (A23EC) from fresh spinach. A23EC belongs to subclade C2 of ST131, a virulent clone of Extraintestinal Pathogenic E. coli (ExPEC). Most A23EC virulence factors are concentrated in three pathogenicity islands. These include PapGII, a fimbrial tip adhesin linked to increased virulence, and CsgA and CsgB, two adhesins known to facilitate spinach leaf colonization. A23EC also bears TnMB1860, a chromosomally-integrated transposon with the demonstrated potential to facilitate the evolution of carbapenem resistance among non-carbapenemase-producing enterobacterales. This transposon consists of two IS26-bound modular translocatable units (TUs). The first TU carries aac(6')-lb-cr, bla OXA-1, ΔcatB3, aac(3)-lle, and tmrB, and the second one harbors bla CXT-M-15. A23EC also bears a self-transmissible plasmid that can mediate conjugation at 20°C and that has a mosaic IncF [F(31,36):A(4,20):B1] and Col156 origin of replication. Comparing A23EC to 86 additional complete ST131 sequences, A23EC forms a monophyletic cluster with 17 other strains that share the following four genomic traits: (1) virotype E (papGII+); (2) presence of a PAI II536-like pathogenicity island with an additional cnf1 gene; (3) presence of chromosomal TnMB1860; and (4) frequent presence of an F(31,36):A(4,20):B1 plasmid. Sequences belonging to this cluster (which we named "C2b sublineage") are highly enriched in septicemia samples and their associated genetic markers align with recent reports of an emerging, virulent sublineage of the C2 subclade, suggesting significant pathogenic potential. This is the first report of a ST131 strain belonging to subclade C2 contaminating green leafy vegetables. The detection of this uropathogenic clone in fresh food is alarming. This work suggests that ST131 continues to evolve, gaining selective advantages and new routes of transmission. This highlights the pressing need for rigorous epidemiological surveillance of ExPEC in vegetables with One Health perspective.
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Affiliation(s)
- Maria G. Balbuena-Alonso
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Manel Camps
- Departament of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, United States
| | - Gerardo Cortés-Cortés
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
- Departament of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, United States
| | - Eder A. Carreón-León
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Chihuahua, Mexico
| | - Patricia Lozano-Zarain
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Rosa del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
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Qamar MU, Ejaz H, Mohsin M, Hadjadj L, Karadeniz A, Rolain JM, Saleem Z, Diene SM. Co-existence of NDM-, aminoglycoside- and fluoroquinolone-resistant genes in carbapenem-resistant Escherichia coli clinical isolates from Pakistan. Future Microbiol 2023; 18:959-969. [PMID: 37656032 DOI: 10.2217/fmb-2023-0068] [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] [Indexed: 09/02/2023] Open
Abstract
Background: To determine the prevalence of antimicrobial-resistant genes in carbapenem-resistant Escherichia coli (CRECO). Methods: A total of 290 carbapenem-resistant bacteria were collected from tertiary care hospitals in Lahore (Pakistan). These isolates were confirmed by VITEK 2 and matrix-assisted laser desorption/ionization time of flight. The minimum inhibitory concentration was performed by VITEK 2. Sequence typing, resistant gene identification, DNA hybridization and replicate typing were also performed. Results: 33 out of 290 (11.3%) were CRECO and carried blaNDM; 69, 18 and 12% were NDM-1, NDM-5 and NDM-7, respectively, with 100% resistance to β-lactams and β-lactam inhibitors. ST405 and ST468 were mostly identified. NDM-ECO carried approximately 50-450 kb of plasmids and 16 (55%) were associated with IncA/C. Conclusion: NDM-1-producing E. coli are highly prevalent in clinical settings.
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Affiliation(s)
- Muhammad Usman Qamar
- Institute of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, 38000, Pakistan
| | - Hasan Ejaz
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Saudi Arabia
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Linda Hadjadj
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Pharmacie, Marseille, France
| | - Aylin Karadeniz
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Pharmacie, Marseille, France
| | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Pharmacie, Marseille, France
| | - Zikria Saleem
- Department of Pharmacy Practice, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Seydina M Diene
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Faculté de Pharmacie, Marseille, France
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Bhattacharjee A, Sands K, Mitra S, Basu R, Saha B, Clermont O, Dutta S, Basu S. A Decade-Long Evaluation of Neonatal Septicaemic Escherichia coli: Clonal Lineages, Genomes, and New Delhi Metallo-Beta-Lactamase Variants. Microbiol Spectr 2023; 11:e0521522. [PMID: 37367488 PMCID: PMC10434172 DOI: 10.1128/spectrum.05215-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/27/2023] [Indexed: 06/28/2023] Open
Abstract
Longitudinal studies of extraintestinal pathogenic Escherichia coli (ExPEC) and epidemic clones of E. coli in association with New Delhi metallo-β-lactamase (blaNDM) in septicaemic neonates are rare. This study captured the diversity of 80 E. coli isolates collected from septicaemic neonates in terms of antibiotic susceptibility, resistome, phylogroups, sequence types (ST), virulome, plasmids, and integron types over a decade (2009 to 2019). Most of the isolates were multidrug-resistant and, 44% of them were carbapenem-resistant, primarily due to blaNDM. NDM-1 was the sole NDM-variant present in conjugative IncFIA/FIB/FII replicons until 2013, and it was subsequently replaced by other variants, such as NDM-5/-7 found in IncX3/FII. A core genome analysis for blaNDM+ve isolates showed the heterogeneity of the isolates. Fifty percent of the infections were caused by isolates of phylogroups B2 (34%), D (11.25%), and F (4%), whereas the other half were caused by phylogroups A (25%), B1 (11.25%), and C (14%). The isolates were further distributed in approximately 20 clonal complexes (STC), including five epidemic clones (ST131, ST167, ST410, ST648, and ST405). ST167 and ST131 (subclade H30Rx) were dominant, with most of the ST167 being blaNDM+ve and blaCTX-M-15+ve. In contrast, the majority of ST131 isolates were blaNDM-ve but blaCTX-M-15+ve, and they possessed more virulence determinants than did ST167. A single nucleotide polymorphism (SNP)-based comparative genome analysis of epidemic clones ST167 and ST131 in a global context revealed that the study isolates were present in close proximity but were distant from global isolates. The presence of antibiotic-resistant epidemic clones causing sepsis calls for a modification of the recommended antibiotics with which to treat neonatal sepsis. IMPORTANCE Multidrug-resistant and virulent ExPEC causing sepsis in neonates is a challenge to neonatal health. The presence of enzymes, such as carbapenemases (blaNDM) that hydrolyze most β-lactam antibiotic compounds, result in difficulties when treating neonates. The characterization of ExPECs collected over 10 years showed that 44% of ExPECs were carbapenem-resistant, possessing transmissible blaNDM genes. The isolates belonged to different phylogroups that are considered to be either commensals or virulent. The isolates were distributed in around 20 clonal complexes (STC), including two predominant epidemic clones (ST131 and ST167). ST167 possessed few virulence determinants but was blaNDM+ve. In contrast, ST131 harbored several virulence determinants but was blaNDM-ve. A comparison of the genomes of these epidemic clones in a global context revealed that the study isolates were present in close proximity but were distant from global isolates. The presence of epidemic clones in a vulnerable population with contrasting characteristics and the presence of resistance genes call for strict vigilance.
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Affiliation(s)
- Amrita Bhattacharjee
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Kirsty Sands
- Division of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, United Kingdom
- Ineos Oxford Institute of Antimicrobial Research, Department of Biology, University of Oxford, United Kingdom
| | - Shravani Mitra
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Ritojeet Basu
- Department of Economics, University of Warwick, Coventry, United Kingdom
| | - Bijan Saha
- Department of Neonatology, Institute of Post-Graduate Medical Education & Research and SSKM Hospital, Kolkata, West Bengal, India
| | - Olivier Clermont
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- Université Sorbonne Paris Nord, IAME, Paris, France
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
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Burgaya J, Marin J, Royer G, Condamine B, Gachet B, Clermont O, Jaureguy F, Burdet C, Lefort A, de Lastours V, Denamur E, Galardini M, Blanquart F. The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans. PLoS Genet 2023; 19:e1010842. [PMID: 37531401 PMCID: PMC10395866 DOI: 10.1371/journal.pgen.1010842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 08/04/2023] Open
Abstract
Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostic, prevention and treatment is still lacking. We used a collection of 912 BSI and 370 commensal E. coli isolates collected in France over a 17-year period (2000-2017). We compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity continuously increased through 1980, 2000, to 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.
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Affiliation(s)
- Judit Burgaya
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - Julie Marin
- Université Sorbonne Paris Nord, INSERM, IAME, Bobigny, France
| | - Guilhem Royer
- Université Paris Cité, INSERM, IAME, Paris, France
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, Créteil, France
- Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Institut Pasteur, UMR CNRS 6047, Université Paris-Cité, Paris, France
| | | | | | | | | | | | - Agnès Lefort
- Université Paris Cité, INSERM, IAME, Paris, France
| | | | - Erick Denamur
- Université Paris Cité, INSERM, IAME, Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, Paris, France
| | - Marco Galardini
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - François Blanquart
- Center for Interdisciplinary Research in Biology, Collège de France, CNRS UMR7241 / INSERM U1050, PSL Research University, Paris, France
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Jaén-Luchoro D, Kahnamouei A, Yazdanshenas S, Lindblom A, Samuelsson E, Åhrén C, Karami N. Comparative Genomic Analysis of ST131 Subclade C2 of ESBL-Producing E. coli Isolates from Patients with Recurrent and Sporadic Urinary Tract Infections. Microorganisms 2023; 11:1622. [PMID: 37512795 PMCID: PMC10384980 DOI: 10.3390/microorganisms11071622] [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] [Received: 05/03/2023] [Revised: 05/31/2023] [Accepted: 06/17/2023] [Indexed: 07/30/2023] Open
Abstract
The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is a major threat to human health. ESBL-E. coli sequence type (ST) 131 is the dominating clone worldwide, especially its subclade C2. Patients developing recurrent UTI (RUTI) due to ST131 subclade C2 appear to have an increased risk of recurrent infections. We have thus compared the whole genome of ST131 subclade C2 isolates from 14 patients with RUTI to those from 14 patients with sporadic UTI (SUTI). We aimed to elucidate if isolates causing RUTI can be associated with specific genomic features. Paired isolates from patients with RUTI were identical, presenting 2-18 single nucleotide polymorphism (SNP) differences for all six patients investigated. Comparative genomic analyses, including virulence factors, antibiotic resistance, pangenome and SNP analyses did not find any pattern associated with isolates causing RUTI. Despite extensive whole genome analyses, an increased risk of recurrences seen in patients with UTI due to ST131 subclade C2 isolates could not be explained by bacterial genetic differences in the two groups of isolates. Hence, additional factors that could aid in identifying bacterial properties contributing to the increased risk of RUTI due to ESBL-E. coli ST131 subclade C2 remains to be explored.
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Affiliation(s)
- Daniel Jaén-Luchoro
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
| | - Arezou Kahnamouei
- Department of Life Sciences and Systems Biology, University of Turin, 10124 Turin, Italy
| | - Shora Yazdanshenas
- Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, 41345 Gothenburg, Sweden
| | - Anna Lindblom
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
- Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, 41345 Gothenburg, Sweden
| | - Emma Samuelsson
- Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Region Västra Götaland, 41345 Gothenburg, Sweden
| | - Christina Åhrén
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
- Swedish Strategic Program against Antimicrobial Resistance (Strama), Region Västra Götaland, 40544 Gothenburg, Sweden
| | - Nahid Karami
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
- Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, 41345 Gothenburg, Sweden
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Soni V, Rosenn EH, Venkataraman R. Insights into the central role of N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU) in peptidoglycan metabolism and its potential as a therapeutic target. Biochem J 2023; 480:1147-1164. [PMID: 37498748 DOI: 10.1042/bcj20230173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023]
Abstract
Several decades after the discovery of the first antibiotic (penicillin) microbes have evolved novel mechanisms of resistance; endangering not only our abilities to combat future bacterial pandemics but many other clinical challenges such as acquired infections during surgeries. Antimicrobial resistance (AMR) is attributed to the mismanagement and overuse of these medications and is complicated by a slower rate of the discovery of novel drugs and targets. Bacterial peptidoglycan (PG), a three-dimensional mesh of glycan units, is the foundation of the cell wall that protects bacteria against environmental insults. A significant percentage of drugs target PG, however, these have been rendered ineffective due to growing drug resistance. Identifying novel druggable targets is, therefore, imperative. Uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) is one of the key building blocks in PG production, biosynthesized by the bifunctional enzyme N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU). UDP-GlcNAc metabolism has been studied in many organisms, but it holds some distinctive features in bacteria, especially regarding the bacterial GlmU enzyme. In this review, we provide an overview of different steps in PG biogenesis, discuss the biochemistry of GlmU, and summarize the characteristic structural elements of bacterial GlmU vital to its catalytic function. Finally, we will discuss various studies on the development of GlmU inhibitors and their significance in aiding future drug discoveries.
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Affiliation(s)
- Vijay Soni
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065, U.S.A
| | - Eric H Rosenn
- Tel Aviv University School of Medicine, Tel Aviv 6997801, Israel
| | - Ramya Venkataraman
- Laboratory of Innate Immunity, National Institute of Immunology, New Delhi 110067, India
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Nurjadi D, Tkadlec J, Boutin S, Vandenesch F. Editorial: "Omics"- revolution in elucidating the virulence and resistance in Staphylococcus aureus. Front Cell Infect Microbiol 2023; 13:1209671. [PMID: 37265498 PMCID: PMC10230050 DOI: 10.3389/fcimb.2023.1209671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Affiliation(s)
- Dennis Nurjadi
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Jan Tkadlec
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czechia
| | - Sébastien Boutin
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique (CNRS), UMR5308, École Normale Supérieure (ENS) de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
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Li R, Xu H, Tang H, Shen J, Xu Y. The Characteristics of Extended-Spectrum β-Lactamases (ESBLs)-Producing Escherichia coli in Bloodstream Infection. Infect Drug Resist 2023; 16:2043-2060. [PMID: 37056484 PMCID: PMC10086224 DOI: 10.2147/idr.s400170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/16/2023] [Indexed: 04/08/2023] Open
Abstract
Background Bloodstream infection (BSI) is a common type of infection frequently diagnosed in clinics. The emergence and spread of ESBLs-producing Escherichia coli (E. coli) has emerged as one of the biggest challenges in global community health. Methods The production of ESBLs was determined by the composite disk diffusion method. The expression of the various resistance and virulence genes were detected by PCR and sequencing. Multi-locus sequence typing (MLST) and phylogenetic groups were used for the classification. The transfer of resistant plasmids was determined by conjugation assay. The statistical differences were analyzed using Statistical Product and Service Solutions (SPSS) version 23.0. Results A total of 60 strains of ESBLs-producing E. coli were collected. The resistance genes that were identified included bla CTX-M, bla TEM, bla SHV, bla OXA-1 and mcr-1. The most common one was the bla CTX-M including bla CTX-M-27 (n = 16), bla CTX-M-14 (n = 15), bla CTX-M-15 (n = 11), bla CTX-M-55 (n = 14) and bla CTX-M-65 (n = 5). A total of 31 STs were detected, and the most abundant among which was ST131 (n = 16, 26.7%). Most of the E. coli (n = 46, 76.7%) belonged to the groups B2 and D. And some virulence genes were related to the classification of the E. coli. Among them, the detection rates of hek/hra, kpsMII and papGII-III in groups B2 and D were higher than those in groups A and B1. The detection rates of cnf1, iucC and papGII-III in ST131 were higher than those in non-ST131. And the distributions of hek/hra, iroN, iucC, kpsMII and papGII-III were related to the bla CTX-M subtypes. Finally, most bacterial (n = 32, 53.3%) resistance genes could be transferred between the bacteria by plasmids, especially IncFIB. Conclusion ESBLs-producing E. coli in BSI exhibited had high resistance rates and carried a variety of virulence factors (VFs). This is necessary to strengthen the monitoring of ESBLs-producing isolates in the medical environment.
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Affiliation(s)
- Rongrong Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People’s Republic of China
- Department of Pathogen Biology and Provincial Laboratories of Pathogen Biology and Zoonoses, Anhui Medical University, Hefei, People’s Republic of China
| | - Huaming Xu
- The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, People’s Republic of China
| | - Hao Tang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, People’s Republic of China
| | - Jilu Shen
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People’s Republic of China
- Anhui Public Health Clinical Center, Hefei, People’s Republic of China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People’s Republic of China
- Correspondence: Yuanhong Xu, Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, People’s Republic of China, Tel +86 13505694447, Email
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Xing Y, Clark JR, Chang JD, Chirman DM, Green S, Zulk JJ, Jelinski J, Patras KA, Maresso AW. Broad protective vaccination against systemic Escherichia coli with autotransporter antigens. PLoS Pathog 2023; 19:e1011082. [PMID: 36800400 PMCID: PMC9937491 DOI: 10.1371/journal.ppat.1011082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/26/2022] [Indexed: 02/18/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of adult life-threatening sepsis and urinary tract infections (UTI). The emergence and spread of multidrug-resistant (MDR) ExPEC strains result in a considerable amount of treatment failure and hospitalization costs, and contribute to the spread of drug resistance amongst the human microbiome. Thus, an effective vaccine against ExPEC would reduce morbidity and mortality and possibly decrease carriage in healthy or diseased populations. A comparative genomic analysis demonstrated a gene encoding an invasin-like protein, termed sinH, annotated as an autotransporter protein, shows high prevalence in various invasive ExPEC phylogroups, especially those associated with systemic bacteremia and UTI. Here, we evaluated the protective efficacy and immunogenicity of a recombinant SinH-based vaccine consisting of either domain-3 or domains-1,2, and 3 of the putative extracellular region of surface-localized SinH. Immunization of a murine host with SinH-based antigens elicited significant protection against various strains of the pandemic ExPEC sequence type 131 (ST131) as well as multiple sequence types in two distinct models of infection (colonization and bacteremia). SinH immunization also provided significant protection against ExPEC colonization in the bladder in an acute UTI model. Immunized cohorts produced significantly higher levels of vaccine-specific serum IgG and urinary IgG and IgA, findings consistent with mucosal protection. Collectively, these results demonstrate that autotransporter antigens such as SinH may constitute promising ExPEC phylogroup-specific and sequence-type effective vaccine targets that reduce E. coli colonization and virulence.
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Affiliation(s)
- Yikun Xing
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Justin R. Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - James D. Chang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Dylan M. Chirman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sabrina Green
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jacob J. Zulk
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph Jelinski
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kathryn A. Patras
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anthony W. Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
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Kudinha T, Kong F. Possible step-up in prevalence for Escherichia coli ST131 from fecal to clinical isolates: inferred virulence potential comparative studies within phylogenetic group B2. J Biomed Sci 2022; 29:78. [PMID: 36207707 PMCID: PMC9547475 DOI: 10.1186/s12929-022-00862-7] [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: 08/22/2022] [Accepted: 09/28/2022] [Indexed: 11/18/2022] Open
Abstract
Background Escherichia coli sequence type (ST)131 is an important urinary tract pathogen, and is responsible for considerable healthcare-associated problems and costs worldwide. A better understanding of the factors that contribute to its rapid worldwide spread may help in arresting its continual spread. We studied a large collection of fecal and urinary E. coli ST131 and E. coli non-ST131 phylogenetic group B2 isolates, from women, men and children, in regional NSW, Australia. Results We found out that there was a step up in ST131 prevalence (and possibly in virulence) from fecal to clinical (urinary) isolates in general, and specifically among ciprofloxacin resistant isolates, in the 3 host groups. Furthermore, our results revealed that the inferred virulence potential of the ST131 isolates (as measured by VF gene scores) was much higher than that of non-ST131 phylogenetic group B2 isolates, and this was much more pronounced amongst the urinary isolates. This finding suggests presence of possible E. coli phylogenetic B2 subgroups with varying levels of virulence, with ST131 being much more virulent compared to others. A strong association between ST131 and fluoroquinolone (FQ) resistance was also demonstrated, suggesting that FQ use is related to ST131 emergence and spread. Specifically, about 77% of ST131 isolates from women and men, and 47% from children, were extended spectrum β- lactamase (ESBL) producers. Moreover, FQ resistant ST131 ESBL isolates on average harbored more VF genes than all other isolates. Conclusions The strong association between ST131 prevalence and FQ resistance amongst the studied isolates suggests that FQ use is related to ST131 emergence and spread. Furthermore, our results demonstrate that FQ resistance and a plurality of VF genes can exist together in ST131, something that has traditionally been regarded as being inversely related. This may partly contribute to the emergence and worldwide spread of ST131. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-022-00862-7.
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Affiliation(s)
- Timothy Kudinha
- NSW Health Pathology, Regional and Rural, Orange Hospital, Orange, NSW, Australia. .,School of Biomedical Sciences, Charles Sturt University, Leeds Parade, Orange, NSW, 2800, Australia.
| | - Fanrong Kong
- NSW Health Pathology, CIDMLS, Westmead Hospital, Westmead, NSW, 2145, Australia
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