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Mallawaarachchi S, Tonkin-Hill G, Pöntinen A, Calland J, Gladstone R, Arredondo-Alonso S, MacAlasdair N, Thorpe H, Top J, Sheppard S, Balding D, Croucher N, Corander J. Detecting co-selection through excess linkage disequilibrium in bacterial genomes. NAR Genom Bioinform 2024; 6:lqae061. [PMID: 38846349 PMCID: PMC11155488 DOI: 10.1093/nargab/lqae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/15/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Population genomics has revolutionized our ability to study bacterial evolution by enabling data-driven discovery of the genetic architecture of trait variation. Genome-wide association studies (GWAS) have more recently become accompanied by genome-wide epistasis and co-selection (GWES) analysis, which offers a phenotype-free approach to generating hypotheses about selective processes that simultaneously impact multiple loci across the genome. However, existing GWES methods only consider associations between distant pairs of loci within the genome due to the strong impact of linkage-disequilibrium (LD) over short distances. Based on the general functional organisation of genomes it is nevertheless expected that majority of co-selection and epistasis will act within relatively short genomic proximity, on co-variation occurring within genes and their promoter regions, and within operons. Here, we introduce LDWeaver, which enables an exhaustive GWES across both short- and long-range LD, to disentangle likely neutral co-variation from selection. We demonstrate the ability of LDWeaver to efficiently generate hypotheses about co-selection using large genomic surveys of multiple major human bacterial pathogen species and validate several findings using functional annotation and phenotypic measurements. Our approach will facilitate the study of bacterial evolution in the light of rapidly expanding population genomic data.
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Affiliation(s)
| | | | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Jessica K Calland
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | | | | | | | - Harry A Thorpe
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Janetta Top
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Samuel K Sheppard
- Ineos Oxford Institute of Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom
| | - David Balding
- Melbourne Integrative Genomics, School of BioSciences and School of Mathematics & Statistics, University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas J Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, United Kingdom
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
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2
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Wranne MS, Karami N, Sriram KK, Jaén-Luchoro D, Yazdanshenas S, Lin YL, Kabbinale A, Flach CF, Westerlund F, Åhrén C. Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden. Sci Rep 2024; 14:11880. [PMID: 38789462 PMCID: PMC11126669 DOI: 10.1038/s41598-024-62663-2] [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: 02/09/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024] Open
Abstract
Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009-2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.
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Affiliation(s)
- Moa S Wranne
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Nahid Karami
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden.
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden.
| | - K K Sriram
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Shora Yazdanshenas
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Yii-Lih Lin
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Arpitha Kabbinale
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Christina Åhrén
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
- Swedish Strategic Program Against Antimicrobial Resistance (Strama), Region Västra Götaland, Gothenburg, Sweden
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3
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Carrera Páez LC, Olivier M, Gambino AS, Poklepovich T, Aguilar AP, Quiroga MP, Centrón D. Sporadic clone Escherichia coli ST615 as a vector and reservoir for dissemination of crucial antimicrobial resistance genes. Front Cell Infect Microbiol 2024; 14:1368622. [PMID: 38741889 PMCID: PMC11089171 DOI: 10.3389/fcimb.2024.1368622] [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: 01/10/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
There is scarce information concerning the role of sporadic clones in the dissemination of antimicrobial resistance genes (ARGs) within the nosocomial niche. We confirmed that the clinical Escherichia coli M19736 ST615 strain, one of the first isolates of Latin America that harbors a plasmid with an mcr-1 gene, could receive crucial ARG by transformation and conjugation using as donors critical plasmids that harbor bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, or aadB genes. Escherichia coli M19736 acquired bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, and aadB genes, being only blaNDM-1 maintained at 100% on the 10th day of subculture. In addition, when the evolved MDR-E. coli M19736 acquired sequentially bla CTX-M-15 and bla NDM-1 genes, the maintenance pattern of the plasmids changed. In addition, when the evolved XDR-E. coli M19736 acquired in an ulterior step the paadB plasmid, a different pattern of the plasmid's maintenance was found. Interestingly, the evolved E. coli M19736 strains disseminated simultaneously the acquired conjugative plasmids in different combinations though selection was ceftazidime in all cases. Finally, we isolated and characterized the extracellular vesicles (EVs) from the native and evolved XDR-E. coli M19736 strains. Interestingly, EVs from the evolved XDR-E. coli M19736 harbored bla CTX-M-15 though the pDCAG1-CTX-M-15 was previously lost as shown by WGS and experiments, suggesting that EV could be a relevant reservoir of ARG for susceptible bacteria. These results evidenced the genetic plasticity of a sporadic clone of E. coli such as ST615 that could play a relevant transitional link in the clinical dynamics and evolution to multidrug/extensively/pandrug-resistant phenotypes of superbugs within the nosocomial niche by acting simultaneously as a vector and reservoir of multiple ARGs which later could be disseminated.
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Affiliation(s)
- Laura Camila Carrera Páez
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Martin Olivier
- The Research Institute of the McGill University Health Centre, McGill University, Montréal, QC, Canada
| | - Anahí Samanta Gambino
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Tomás Poklepovich
- Plataforma de Genómica y Bioinformática, Instituto Nacional de Enfermedades Infecciosas - La Administración Nacional de Laboratorios e Institutos de Salud (INEI-ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Andrea Pamela Aguilar
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
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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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5
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Wyrsch ER, Hoye BJ, Sanderson-Smith M, Gorman J, Maute K, Cummins ML, Jarocki VM, Marenda MS, Dolejska M, Djordjevic SP. The faecal microbiome of the Australian silver gull contains phylogenetically diverse ExPEC, aEPEC and Escherichia coli carrying the transmissible locus of stress tolerance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170815. [PMID: 38336047 DOI: 10.1016/j.scitotenv.2024.170815] [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: 12/05/2023] [Revised: 01/28/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Wildlife are implicated in the dissemination of antimicrobial resistance, but their roles as hosts for Escherichia coli that pose a threat to human and animal health is limited. Gulls (family Laridae) in particular, are known to carry diverse lineages of multiple-antibiotic resistant E. coli, including extra-intestinal pathogenic E. coli (ExPEC). Whole genome sequencing of 431 E. coli isolates from 69 healthy Australian silver gulls (Chroicocephalus novaehollandiae) sampled during the 2019 breeding season, and without antibiotic selection, was undertaken to assess carriage in an urban wildlife population. Phylogenetic analysis and genotyping resolved 123 sequence types (STs) representing most phylogroups, and identified diverse ExPEC, including an expansive phylogroup B2 cluster comprising 103 isolates (24 %; 31 STs). Analysis of the mobilome identified: i) widespread carriage of the Yersinia High Pathogenicity Island (HPI), a key ExPEC virulence determinant; ii) broad distribution of two novel phage elements, each carrying sitABCD and iii) carriage of the transmissible locus of stress tolerance (tLST), an element linked to sanitation resistance. Of the 169 HPI carrying isolates, 49 (48 %) represented diverse B2 isolates hosting FII-64 ColV-like plasmids that lacked iutABC and sitABC operons typical of ColV plasmids, but carried the serine protease autotransporter gene, sha. Diverse E. coli also carried archetypal ColV plasmids (52 isolates; 12 %). Clusters of closely related E. coli (<50 SNVs) from ST58, ST457 and ST746, sourced from healthy gulls, humans, and companion animals, were frequently identified. In summary, anthropogenically impacted gulls host an expansive E. coli population, including: i) putative ExPEC that carry ColV virulence gene cargo (101 isolates; 23.4 %) and HPI (169 isolates; 39 %); ii) atypical enteropathogenic E. coli (EPEC) (17 isolates; 3.9 %), and iii) E. coli that carry the tLST (20 isolates; 4.6 %). Gulls play an important role in the evolution and transmission of E. coli that impact human health.
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Affiliation(s)
- Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Bethany J Hoye
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Martina Sanderson-Smith
- Molecular Horizons Research Institute, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jody Gorman
- Molecular Horizons Research Institute, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Kimberly Maute
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Marc S Marenda
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC 3030, Australia
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Czech Republic; CEITEC VETUNI, University of Veterinary Sciences Brno, Czech Republic; Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Czech Republic; Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Pilsen, Czech Republic
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia.
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Phan MD, Schirra HJ, Nhu NTK, Peters KM, Sarkar S, Allsopp LP, Achard MES, Kappler U, Schembri MA. Combined functional genomic and metabolomic approaches identify new genes required for growth in human urine by multidrug-resistant Escherichia coli ST131. mBio 2024; 15:e0338823. [PMID: 38353545 PMCID: PMC10936160 DOI: 10.1128/mbio.03388-23] [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: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 03/14/2024] Open
Abstract
Urinary tract infections (UTIs) are one of the most common bacterial infections in humans, with ~400 million cases across the globe each year. Uropathogenic Escherichia coli (UPEC) is the major cause of UTI and increasingly associated with antibiotic resistance. This scenario has been worsened by the emergence and spread of pandemic UPEC sequence type 131 (ST131), a multidrug-resistant clone associated with extraordinarily high rates of infection. Here, we employed transposon-directed insertion site sequencing in combination with metabolomic profiling to identify genes and biochemical pathways required for growth and survival of the UPEC ST131 reference strain EC958 in human urine (HU). We identified 24 genes required for growth in HU, which mapped to diverse pathways involving small peptide, amino acid and nucleotide metabolism, the stringent response pathway, and lipopolysaccharide biosynthesis. We also discovered a role for UPEC resistance to fluoride during growth in HU, most likely associated with fluoridation of drinking water. Complementary nuclear magnetic resonance (NMR)-based metabolomics identified changes in a range of HU metabolites following UPEC growth, the most pronounced being L-lactate, which was utilized as a carbon source via the L-lactate dehydrogenase LldD. Using a mouse UTI model with mixed competitive infection experiments, we demonstrated a role for nucleotide metabolism and the stringent response in UPEC colonization of the mouse bladder. Together, our application of two omics technologies combined with different infection-relevant settings has uncovered new factors required for UPEC growth in HU, thus enhancing our understanding of this pivotal step in the UPEC infection pathway. IMPORTANCE Uropathogenic Escherichia coli (UPEC) cause ~80% of all urinary tract infections (UTIs), with increasing rates of antibiotic resistance presenting an urgent threat to effective treatment. To cause infection, UPEC must grow efficiently in human urine (HU), necessitating a need to understand mechanisms that promote its adaptation and survival in this nutrient-limited environment. Here, we used a combination of functional genomic and metabolomic techniques and identified roles for the metabolism of small peptides, amino acids, nucleotides, and L-lactate, as well as the stringent response pathway, lipopolysaccharide biosynthesis, and fluoride resistance, for UPEC growth in HU. We further demonstrated that pathways involving nucleotide metabolism and the stringent response are required for UPEC colonization of the mouse bladder. The UPEC genes and metabolic pathways identified in this study represent targets for the development of innovative therapeutics to prevent UPEC growth during human UTI, an urgent need given the rapidly rising rates of global antibiotic resistance.
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Affiliation(s)
- Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Horst Joachim Schirra
- School of Environment and Science, Griffith University, Nathan, Queensland, Australia
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Kate M. Peters
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Sohinee Sarkar
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Luke P. Allsopp
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Maud E. S. Achard
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Ulrike Kappler
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark A. Schembri
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
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7
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Yu K, Huang Z, Xiao Y, Gao H, Bai X, Wang D. Global spread characteristics of CTX-M-type extended-spectrum β-lactamases: A genomic epidemiology analysis. Drug Resist Updat 2024; 73:101036. [PMID: 38183874 DOI: 10.1016/j.drup.2023.101036] [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: 07/13/2023] [Revised: 10/18/2023] [Accepted: 12/15/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Extended-spectrum β-lactamases (ESBLs) producing bacteria have spread worldwide and become a global public health concern. Plasmid-mediated transfer of ESBLs is an important route for resistance acquisition. METHODS We collected 1345 complete sequences of plasmids containing CTX-Ms from public database. The global transmission pattern of plasmids and evolutionary dynamics of CTX-Ms have been inferred. We applied the pan-genome clustering based on plasmid genomes and evolution analysis to demonstrate the transmission events. FINDINGS Totally, 48 CTX-Ms genotypes and 186 incompatible types of plasmids were identified. The geographical distribution of CTX-Ms showed significant differences across countries and continents. CTX-M-14 and CTX-M-55 were found to be the dominant genotypes in Asia, while CTX-M-1 played a leading role in Europe. The plasmids can be divided into 12 lineages, some of which forming distinct geographical clusters in Asia and Europe, while others forming hybrid populations. The Inc types of plasmids are lineage-specific, with the CTX-M-1_IncI1-I (Alpha) and CTX-M-65_IncFII (pHN7A8)/R being the dominant patterns of cross-host and cross-regional transmission. The IncI-I (Alpha) plasmids with the highest number, were presumed to form communication groups in Europe-Asia and Asia-America-Oceania, showing the transmission model as global dissemination and regional microevolution. Meanwhile, the main kinetic elements of blaCTX-Ms showed genotypic preferences. ISEcpl and IS26 were most frequently involved in the transfer of CTX-M-14 and CTX-M-65, respectively. IS15 has become a crucial participant in mediating the dissemination of blaCTX-Ms. Interestingly, blaTEM and blaCTX-Ms often coexisted in the same transposable unit. Furthermore, antibiotic resistance genes associated with aminoglycosides, sulfonamides and cephalosporins showed a relatively high frequency of synergistic effects with CTX-Ms. CONCLUSIONS We recognized the dominant blaCTX-Ms and mainstream plasmids of different continents. The results of this study provide support for a more effective response to the risks associated with the evolution of blaCTX-Ms-bearing plasmids, and lay the foundation for genotype-specific epidemiological surveillance of resistance, which are of important public health implications.
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Affiliation(s)
- Keyi Yu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China; Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, China
| | - Zhenzhou Huang
- Hangzhou Center for Disease Control and Prevention, Hangzhou, Zhejiang 310021, China
| | - Yue Xiao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China; Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, China
| | - He Gao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China; Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, China
| | - Xuemei Bai
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China; Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, China
| | - Duochun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China; Center for Human Pathogenic Culture Collection, China CDC, Beijing 102206, China.
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8
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García-Meniño I, García V, Lumbreras-Iglesias P, Fernández J, Mora A. Fluoroquinolone resistance in complicated urinary tract infections: association with the increased occurrence and diversity of Escherichia coli of clonal complex 131, together with ST1193. Front Cell Infect Microbiol 2024; 14:1351618. [PMID: 38510968 PMCID: PMC10953827 DOI: 10.3389/fcimb.2024.1351618] [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: 12/06/2023] [Accepted: 02/02/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Urinary tract infections (UTIs) are one of the leading causes of multidrug-resistance (MDR) spread and infection-related deaths. Escherichia coli is by far the main causative agent. We conducted a prospective study on complicated urinary tract infections (cUTIs) i) to monitor the high-risk clones that could be compromising the therapeutic management and ii) to compare the cUTI etiology with uncomplicated infections (uUTIs) occurring in the same period and health area. Methods 154 non-duplicated E. coli recovered from cUTIs in 2020 at the Hospital Universitario Central de Asturias (Spain) constituted the study collection. Results Most cUTI isolates belonged to phylogroup B2 (72.1%) and met the uropathogenic (UPEC) status (69.5%) (≥3 of chuA, fyuA, vat, and yfcV genes). MDR was exhibited by 35.7% of the isolates, similarly to data observed in the uUTI collection. A significant difference observed in cUTI was the higher level of fluoroquinolone resistance (FQR) (47.4%), where the pandemic clonal groups B2-CC131 and B2-ST1193 (CH14-64) comprised 28% of the 154 E. coli, representing 52.1% of the FQR isolates. Other prevalent FQR clones were D-ST69 (CH35-27), D-ST405 (CH37-27), and B2-ST429 (CH40-20) (three isolates each). We uncovered an increased genetic and genomic diversity of the CC131: 10 different virotypes, 8 clonotypes (CH), and 2 STs. The presence of bla CTX-M-15 was determined in 12 (7.8%) isolates (all CC131), which showed 10 different core genome (cg)STs and 2 fimH types (fimH30 and fimH602) but the same set of chromosomal mutations conferring FQR (gyrA p.S83L, gyrA p.D87N, parC p.S80I, parC p.E84V, and parE p.I529L). In addition, the plasmidome analysis revealed 10 different IncF formulae in CC131 genomes. Conclusion We proved here that non-lactose fermenting screening, together with the detection of O25b (rfbO25b), H4 (fliCH4), and H5 (fliCH5) genes, and phylogroup and clonotyping assignation, is a reasonable approach that can be easily implemented for the surveillance of emerging high-risk clones associated with FQR spread in cUTIs, such as the uncommonly reported O25b:H4-B2-ST9126-CC131 (CH1267-30). Since E. coli CC131 and ST1193 are also involved in the community uUTIs of this health area, interventions to eradicate these MDR clones, along with surveillance for other emerging ones, are essential for antibiotic use optimization programs.
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Affiliation(s)
- Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Pilar Lumbreras-Iglesias
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Research and Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, Oviedo, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
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9
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Pitout JDD, Peirano G, Matsumura Y, DeVinney R, Chen L. Escherichia coli sequence type 410 with carbapenemases: a paradigm shift within E. coli toward multidrug resistance. Antimicrob Agents Chemother 2024; 68:e0133923. [PMID: 38193668 PMCID: PMC10869336 DOI: 10.1128/aac.01339-23] [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] [Indexed: 01/10/2024] Open
Abstract
Escherichia coli sequence type ST410 is an emerging carbapenemase-producing multidrug-resistant (MDR) high-risk One-Health clone with the potential to significantly increase carbapenem resistance among E. coli. ST410 belongs to two clades (ST410-A and ST410-B) and three subclades (ST410-B1, ST410-B2, and ST410-B3). After a fimH switch between clades ST410-A and ST410-B1, ST410-B2 and ST410-B3 subclades showed a stepwise progression toward developing MDR. (i) ST410-B2 initially acquired fluoroquinolone resistance (via homologous recombination) in the 1980s. (ii) ST410-B2 then obtained CMY-2, CTX-M-15, and OXA-181 genes on different plasmid platforms during the 1990s. (iii) This was followed by the chromosomal integration of blaCMY-2, fstl YRIN insertion, and ompC/ompF mutations during the 2000s to create the ST410-B3 subclade. (iv) An IncF plasmid "replacement" scenario happened when ST410-B2 transformed into ST410-B3: F36:31:A4:B1 plasmids were replaced by F1:A1:B49 plasmids (both containing blaCTX-M-15) followed by blaNDM-5 incorporation during the 2010s. User-friendly cost-effective methods for the rapid identification of ST410 isolates and clades are needed because limited data are available about the frequencies and global distribution of ST410 clades. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST410 (including the ability to acquire successive MDR determinants). Such information will aid with management and prevention strategies to curb the spread of carbapenem-resistant E. coli. The medical community can ill afford to ignore the spread of a global E. coli clone with the potential to end the carbapenem era.
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Affiliation(s)
- Johann D. D. Pitout
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Yasufumi Matsumura
- Kyoto University Graduate School of Medicine, Pretoria, Gauteng, South Africa
| | | | - Liang Chen
- Meridian Health Center for Discovery and Innovation, Kyoto, Japan
- Hackensack Meridian School of Medicine at Seton Hall University, Nutley, New Jersey, USA
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10
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Kim J, Cho Y, Lim SK, Seo MR, Sohn JW, Kim B, Rho M, Pai H. Comparative analyses of the faecal resistome against β-lactam and quinolone antibiotics in humans and livestock using metagenomic sequencing. Sci Rep 2023; 13:20993. [PMID: 38017092 PMCID: PMC10684531 DOI: 10.1038/s41598-023-48221-2] [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: 02/23/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
To assess the prevalence and abundance of antibiotic resistance genes in human and livestock gut microbiomes, 87 humans (healthy individuals and patients with Clostridioides difficile infection (CDI)) and 108 livestock (swine, cattle, and chickens) were enrolled. Gut microbiomes and fluoroquinolone-resistant Escherichia coli isolates were sequenced, and mobile genetic elements adjacent to the β-lactamase (bla) and transferable quinolone resistance (qnr) genes were compared using metagenomic contigs. Each group of humans and livestock exhibited distinctive microbiota and resistome compositions in the gut. Concerning the resistome of bla and qnr, the prevalence rates between chickens and patients with CDI were the most similar (R2 = 0.46); blaTEM, blaOXA, blaCTX-M, and qnrS were highly prevalent in both groups. According to genomic and phylogenetic analyses, blaCTX-M and blaOXA expressed lineage specificity to either humans or livestock, while qnrS and blaTEM displayed a shared lineage between humans and livestock. A qnrS1 mobilome comprising five genes, including two recombinases, a transposase, and a plasmid gene, is commonly found in human and chicken gut microbiomes. Humans and chickens showed the most similar gut resistomes to β-lactams and quinolones. QnrS and blaTEM displayed especially strong co-occurrence between the guts of humans and livestock.
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Affiliation(s)
- Jieun Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
| | - Youna Cho
- Department of Computer Science and Engineering, Hanyang University, Seoul, 04763, Republic of Korea
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeokin 8-ro, Gimcheon-si, Gyeongsangbuk-do, 39660, Republic of Korea
| | - Mi-Ran Seo
- ConnectaGen Inc., F 203, MisaCentumbiz 2F, Jojeong-Dearo, Hanam-si, Gyeonggi-do, 12918, Republic of Korea
| | - Jang Won Sohn
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
| | - Bongyoung Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
| | - Mina Rho
- Department of Computer Science and Engineering, Hanyang University, Seoul, 04763, Republic of Korea.
- Department of Biomedical Informatics, Hanyang University, Seoul, 04763, Republic of Korea.
| | - Hyunjoo Pai
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea.
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11
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Fuzi M, Sokurenko E. Commensal Fitness Advantage May Contribute to the Global Dissemination of Multidrug-Resistant Lineages of Bacteria-The Case of Uropathogenic E. coli. Pathogens 2023; 12:1150. [PMID: 37764958 PMCID: PMC10536240 DOI: 10.3390/pathogens12091150] [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: 06/14/2023] [Revised: 09/01/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
It is widely accepted that favorable fitness in commensal colonization is one of the prime facilitators of clonal dissemination in bacteria. The question arises as to what kind of fitness advantage may be wielded by uropathogenic strains of the two predominant fluoroquinolone- and multidrug-resistant clonal groups of E. coli-ST131-H30 and ST1193, which has permitted their unprecedented pandemic-like global expansion in the last few decades. The colonization-associated genes' content, carriage of low-cost plasmids, and integrons with weak promoters could certainly contribute to the fitness of the pandemic groups, although those genetic factors are common among other clonal groups as well. Also, ST131-H30 and ST1193 strains harbor fluoroquinolone-resistance conferring mutations targeting serine residues in DNA gyrase (GyrA-S83) and topoisomerase IV (ParC-S80) that, in those clonal backgrounds, might result in a commensal fitness benefit, i.e., beyond the antibiotic resistance per se. This fitness gain might have contributed not only to the widespread dissemination of these major clones in the healthcare setting but also to their long-term colonization of healthy individuals and, thus, circulation in the community, even in a low or no fluoroquinolone use environment. This evolutionary shift affecting commensal E. coli, initiated by mutations co-favorable in both antibiotics-treated patients and healthy individuals warrants more in-depth studies to monitor further changes in the epidemiological situation and develop effective measures to reduce the antibiotic resistance spread.
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Affiliation(s)
- Miklos Fuzi
- Independent Researcher, Seattle, WA 98195, USA
| | - Evgeni Sokurenko
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA 98195, USA;
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12
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Shropshire WC, Strope B, Selvaraj Anand S, Bremer J, McDaneld P, Bhatti MM, Flores AR, Kalia A, Shelburne SA. Temporal dynamics of genetically heterogeneous extended-spectrum cephalosporin-resistant Escherichia coli bloodstream infections. mSphere 2023; 8:e0018323. [PMID: 37427953 PMCID: PMC10449519 DOI: 10.1128/msphere.00183-23] [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: 04/10/2023] [Accepted: 05/24/2023] [Indexed: 07/11/2023] Open
Abstract
Extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R-Ec) is an urgent public health threat with sequence type clonal complex 131 (STc131), phylogroup B2 strains being particularly concerning as the dominant cause of ESC-R-Ec infections. To address the paucity of recent ESC-R-Ec molecular epidemiology data in the United States, we used whole-genome sequencing (WGS) to fully characterize a large cohort of invasive ESC-R-Ec at a tertiary care cancer center in Houston, Texas, collected from 2016 to 2020. During the study time frame, there were 1,154 index E. coli bloodstream infections (BSIs) of which 389 (33.7%) were ESC-R-Ec. Using time series analyses, we identified a temporal dynamic of ESC-R-Ec distinct from ESC-susceptible E. coli (ESC-S-Ec), with cases peaking in the last 6 months of the calendar year. WGS of 297 ESC-R-Ec strains revealed that while STc131 strains accounted for ~45% of total BSIs, the proportion of STc131 strains remained stable across the study time frame with infection peaks driven by genetically heterogeneous ESC-R-Ec clonal complexes. bla CTX-M variants accounted for most β-lactamases conferring the ESC-R phenotype (89%; 220/248 index ESC-R-Ec), and amplification of bla CTX-M genes was widely detected in ESC-R-Ec strains, particularly in carbapenem non-susceptible, recurrent BSI strains. Bla CTX-M-55 was significantly enriched within phylogroup A strains, and we identified bla CTX-M-55 plasmid-to-chromosome transmission occurring across non-B2 strains. Our data provide important information regarding the current molecular epidemiology of invasive ESC-R-Ec infections at a large tertiary care cancer center and provide novel insights into the genetic basis of observed temporal variability for these clinically important pathogens. IMPORTANCE Given that E. coli is the leading cause of worldwide ESC-R Enterobacterales infections, we sought to assess the current molecular epidemiology of ESC-R-Ec using a WGS analysis of many BSIs over a 5-year period. We identified fluctuating temporal dynamics of ESC-R-Ec infections, which have also recently been identified in other geographical regions such as Israel. Our WGS data allowed us to visualize the stable nature of STc131 over the study period and demonstrate a limited but genetically diverse group of ESC-R-Ec clonal complexes are detected during infection peaks. Additionally, we provide a widespread assessment of β-lactamase gene copy number in ESC-R-Ec infections and delineate mechanisms by which such amplifications are achieved in a diverse array of ESC-R-Ec strains. These data suggest that serious ESC-R-Ec infections are driven by a diverse array of strains in our cohort and impacted by environmental factors suggesting that community-based monitoring could inform novel preventative measures.
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Affiliation(s)
- William C. Shropshire
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Benjamin Strope
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Selvalakshmi Selvaraj Anand
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Jordan Bremer
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Patrick McDaneld
- Division of Pharmacy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Micah M. Bhatti
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anthony R. Flores
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA
| | - Awdhesh Kalia
- Program in Diagnostic Genetics and Genomics, MD Anderson Cancer Center School of Health Professions, Houston, Texas, USA
| | - Samuel A. Shelburne
- Department of Infectious Diseases and Infection Control, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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13
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Cave R, Ter-Stepanyan MM, Mkrtchyan HV. Short- and Long-Read Sequencing Reveals the Presence and Evolution of an IncF Plasmid Harboring blaCTX-M-15 and blaCTX-M-27 Genes in Escherichia coli ST131. Microbiol Spectr 2023; 11:e0035623. [PMID: 37466446 PMCID: PMC10433869 DOI: 10.1128/spectrum.00356-23] [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: 01/23/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Escherichia coli sequence type 131 (ST131) has contributed to the spread of extended-spectrum beta-lactamase (ESBL) and has emerged as the dominant cause of hospital- and community-acquired urinary tract infections. Here, we report for the first time an in-depth analysis of whole-genome sequencing (WGS) of 4 ESBL-producing E. coli ST131 isolates recovered from patients in two hospitals in Armenia using Illumina short-read sequencing for accurate base calling to determine their genotype and to infer their phylogeny and using Oxford Nanopore Technologies long-read sequencing to resolve plasmid and chromosomal genetic elements. Genotypically, the four Armenian isolates were identified as part of the H30Rx/clade C2 (n = 2) and H41/clade A (n = 2) lineages and were phylogenetically closely related to isolates from the European Nucleotide Archive (ENA) database previously recovered from patients in the United States, Australia, and New Zealand. The Armenian isolates recovered in this study had chromosomal integration of the blaCTX-M-15 gene in the H30Rx isolates and a high number of virulence genes found in the H41 isolates associated with the carriage of a rare genomic island (in the context of E. coli ST131) containing the S fimbrial, salmochelin siderophore, and microcin H47 virulence genes. Furthermore, our data show the evolution of the IncF[2:A2:B20] plasmid harboring both blaCTX-M-15 and blaCTX-M-27 genes, derived from the recombination of genes from an IncF[F2:A-:B-] blaCTX-M-15-associated plasmid into the IncF[F1:A2:B20] blaCTX-M-27-associated plasmid backbone seen in two genetically closely related H41 Armenian isolates. IMPORTANCE Combining short and long reads from whole-genome sequencing analysis provided a genetic context for uncommon genes of clinical importance to better understand transmission and evolutionary features of ESBL-producing uropathogenic E. coli (UPEC) ST131 isolates recovered in Armenia. Using hybrid genome assembly in countries lacking genomic surveillance studies can inform us about new lineages not seen in other countries with genes encoding high virulence and antibiotic resistance harbored on mobile genetic elements.
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Affiliation(s)
- Rory Cave
- School of Biomedical Sciences, University of West London, London, United Kingdom
| | - Mary M. Ter-Stepanyan
- Yerevan State Medical University after M. Heratsi, Faculty of Public Health, Department of Epidemiology, Yerevan, Republic of Armenia
- Research Center of Maternal and Child Health Protection, Yerevan, Armenia
| | - Hermine V. Mkrtchyan
- School of Biomedical Sciences, University of West London, London, United Kingdom
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14
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Rodrigues C, Lanza VF, Peixe L, Coque TM, Novais Â. Phylogenomics of Globally Spread Clonal Groups 14 and 15 of Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0339522. [PMID: 37098951 PMCID: PMC10269502 DOI: 10.1128/spectrum.03395-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/26/2023] [Indexed: 04/27/2023] Open
Abstract
Klebsiella pneumoniae sequence type 14 (ST14) and ST15 caused outbreaks of CTX-M-15 and/or carbapenemase producers worldwide, but their phylogeny and global dynamics remain unclear. We clarified the evolution of K. pneumoniae clonal group 14 (CG14) and CG15 by analyzing the capsular locus (KL), resistome, virulome, and plasmidome of public genomes (n = 481) and de novo sequences (n = 9) representing main sublineages circulating in Portugal. CG14 and CG15 evolved independently within 6 main subclades defined according to the KL and the accessory genome. The CG14 (n = 65) clade was structured in two large monophyletic subclades, CG14-I (KL2, 86%) and CG14-II (KL16, 14%), whose emergences were dated to 1932 and 1911, respectively. Genes encoding extended-spectrum β-lactamase (ESBL), AmpC, and/or carbapenemases were mostly observed in CG14-I (71% versus 22%). CG15 clade (n = 170) was segregated into subclades CG15-IA (KL19/KL106, 9%), CG15-IB (variable KL types, 6%), CG15-IIA (KL24, 43%) and CG15-IIB (KL112, 37%). Most CG15 genomes carried specific GyrA and ParC mutations and emerged from a common ancestor in 1989. CTX-M-15 was especially prevalent in CG15 (68% CG15 versus 38% CG14) and in CG15-IIB (92%). Plasmidome analysis revealed 27 predominant plasmid groups (PG), including particularly pervasive and recombinant F-type (n = 10), Col (n = 10), and new plasmid types. While blaCTX-M-15 was acquired multiple times by a high diversity of F-type mosaic plasmids, other antibiotic resistance genes (ARGs) were dispersed by IncL (blaOXA-48) or IncC (blaCMY/TEM-24) plasmids. We first demonstrate an independent evolutionary trajectory for CG15 and CG14 and how the acquisition of specific KL, quinolone-resistance determining region (QRDR) mutations (CG15), and ARGs in highly recombinant plasmids could have shaped the expansion and diversification of particular subclades (CG14-I and CG15-IIA/IIB). IMPORTANCE Klebsiella pneumoniae represents a major threat in the burden of antibiotic resistance (ABR). Available studies to explain the origin, the diversity, and the evolution of certain ABR K. pneumoniae populations have mainly been focused on a few clonal groups (CGs) using phylogenetic analysis of the core genome, the accessory genome being overlooked. Here, we provide unique insights into the phylogenetic evolution of CG14 and CG15, two poorly characterized CGs which have contributed to the global dissemination of genes responsible for resistance to first-line antibiotics such as β-lactams. Our results point out an independent evolution of these two CGs and highlight the existence of different subclades structured by the capsular type and the accessory genome. Moreover, the contribution of a turbulent flux of plasmids (especially multireplicon F type and Col) and adaptive traits (antibiotic resistance and metal tolerance genes) to the pangenome reflect the exposure and adaptation of K. pneumoniae under different selective pressures.
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Affiliation(s)
- Carla Rodrigues
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Val F. Lanza
- Unidad de Genómica Traslacional Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Luísa Peixe
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M. Coque
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Ângela Novais
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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15
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Negeri AA, Mamo H, Gahlot DK, Gurung JM, Seyoum ET, Francis MS. Characterization of plasmids carrying bla CTX-M genes among extra-intestinal Escherichia coli clinical isolates in Ethiopia. Sci Rep 2023; 13:8595. [PMID: 37237011 DOI: 10.1038/s41598-023-35402-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
CTX-Ms are encoded by blaCTX-M genes and are widely distributed extended-spectrum β-lactamases (ESBLs). They are the most important antimicrobial resistance (AMR) mechanism to β-lactam antibiotics in the Enterobacteriaceae. However, the role of transmissible AMR plasmids in the dissemination of blaCTX-M genes has scarcely been studied in Africa where the burden of AMR is high and rapidly spreading. In this study, AMR plasmid transmissibility, replicon types and addiction systems were analysed in CTX-M-producing Escherichia coli clinical isolates in Ethiopia with a goal to provide molecular insight into mechanisms underlying such high prevalence and rapid dissemination. Of 100 CTX-Ms-producing isolates obtained from urine (84), pus (10) and blood (6) from four geographically distinct healthcare settings, 75% carried transmissible plasmids encoding for CTX-Ms, with CTX-M-15 being predominant (n = 51). Single IncF plasmids with the combination of F-FIA-FIB (n = 17) carried the bulk of blaCTX-M-15 genes. In addition, IncF plasmids were associated with multiple addiction systems, ISEcp1 and various resistance phenotypes for non-cephalosporin antibiotics. Moreover, IncF plasmid carriage is associated with the international pandemic E. coli ST131 lineage. Furthermore, several CTX-M encoding plasmids were associated with serum survival of the strains, but less so with biofilm formation. Hence, both horizontal gene transfer and clonal expansion may contribute to the rapid and widespread distribution of blaCTX-M genes among E. coli populations in Ethiopian clinical settings. This information is relevant for local epidemiology and surveillance, but also for global understanding of the successful dissemination of AMR gene carrying plasmids.
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Affiliation(s)
- Abebe Aseffa Negeri
- National Clinical Bacteriology and Mycology Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Hassen Mamo
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dharmender K Gahlot
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Jyoti M Gurung
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Eyasu Tigabu Seyoum
- Global One Health Initiative of the Ohio State University, East African Regional Office, Addis Ababa, Ethiopia
| | - Matthew S Francis
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.
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Coque TM, Cantón R, Pérez-Cobas AE, Fernández-de-Bobadilla MD, Baquero F. Antimicrobial Resistance in the Global Health Network: Known Unknowns and Challenges for Efficient Responses in the 21st Century. Microorganisms 2023; 11:1050. [PMID: 37110473 PMCID: PMC10144039 DOI: 10.3390/microorganisms11041050] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the Global Health challenges of the 21st century. The inclusion of AMR on the global map parallels the scientific, technological, and organizational progress of the healthcare system and the socioeconomic changes of the last 100 years. Available knowledge about AMR has mostly come from large healthcare institutions in high-income countries and is scattered in studies across various fields, focused on patient safety (infectious diseases), transmission pathways and pathogen reservoirs (molecular epidemiology), the extent of the problem at a population level (public health), their management and cost (health economics), cultural issues (community psychology), and events associated with historical periods (history of science). However, there is little dialogue between the aspects that facilitate the development, spread, and evolution of AMR and various stakeholders (patients, clinicians, public health professionals, scientists, economic sectors, and funding agencies). This study consists of four complementary sections. The first reviews the socioeconomic factors that have contributed to building the current Global Healthcare system, the scientific framework in which AMR has traditionally been approached in such a system, and the novel scientific and organizational challenges of approaching AMR in the fourth globalization scenario. The second discusses the need to reframe AMR in the current public health and global health contexts. Given that the implementation of policies and guidelines are greatly influenced by AMR information from surveillance systems, in the third section, we review the unit of analysis ("the what" and "the who") and the indicators (the "operational units of surveillance") used in AMR and discuss the factors that affect the validity, reliability, and comparability of the information to be applied in various healthcare (primary, secondary, and tertiary), demographic, and economic contexts (local, regional, global, and inter-sectorial levels). Finally, we discuss the disparities and similarities between distinct stakeholders' objectives and the gaps and challenges of combatting AMR at various levels. In summary, this is a comprehensive but not exhaustive revision of the known unknowns about how to analyze the heterogeneities of hosts, microbes, and hospital patches, the role of surrounding ecosystems, and the challenges they represent for surveillance, antimicrobial stewardship, and infection control programs, which are the traditional cornerstones for controlling AMR in human health.
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Affiliation(s)
- Teresa M. Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana Elena Pérez-Cobas
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Miguel D. Fernández-de-Bobadilla
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, 28029 Madrid, Spain
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17
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Pitout JD, Peirano G, DeVinney R. The contributions of multidrug resistant clones to the success of pandemic extra-intestinal Pathogenic Escherichia coli. Expert Rev Anti Infect Ther 2023; 21:343-353. [PMID: 36822840 DOI: 10.1080/14787210.2023.2184348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
INTRODUCTION High-risk multidrug (MDR) clones have played essential roles in the global emergence and spread of antimicrobial resistance (AMR), especially among Extra-intestinal Escherichia coli (ExPEC). AREAS COVERED Successful global ExPEC MDR clones are linked with the acquisition of fluoroquinolone resistance, CTX-M enzymes, and with carbapenemases. This article described the underlying mechanisms of fluoroquinolone resistance, the acquisition of CTX-M and carbapenemase genes among three global ExPEC high-risk MDR clones, namely i) ST1193 as being an example of a fluoroquinolone resistant clone. ii) ST131 as an example of a fluoroquinolone resistant and CTX-M clone. iii) ST410 as an example of a fluoroquinolone resistant, CTX-M and carbapenemase clone. This article also highlighted the contributions of these MDR determinants in the evolution of these high-risk MDR clones. EXPERT OPINION There is an enormous public health burden due to E. coli MDR high-risk clones such as ST1193, ST131 and ST410. These clones have played pivotal roles in the global spread of AMR. Sparse information is available on which specific features of these high-risk MDR clones have enabled them to become such successful global pathogens in relative short time periods.
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Affiliation(s)
- Johann Dd Pitout
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada.,University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada
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18
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Pitout JDD, Chen L. The Significance of Epidemic Plasmids in the Success of Multidrug-Resistant Drug Pandemic Extraintestinal Pathogenic Escherichia coli. Infect Dis Ther 2023; 12:1029-1041. [PMID: 36947392 PMCID: PMC10147871 DOI: 10.1007/s40121-023-00791-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Epidemic IncF plasmids have been pivotal in the selective advantage of multidrug-resistant (MDR) extraintestinal pathogenic Escherichia coli (ExPEC). These plasmids have offered several advantages to their hosts that allowed them to coevolve with the bacterial host genomes and played an integral role in the success of ExPEC. IncF plasmids are large, mosaic, and often contain various types of antimicrobial resistance (AMR) and virulence associated factor (VAF) genes. The presence of AMR, VAF genes, several addition/restriction systems combined with truncated transfer regions, led to the fixation of IncF plasmids in certain ExPEC MDR clones, such as ST131 and ST410. IncF plasmids entered the ST131 ancestral lineage in the mid 1900s and different ST131 clade/CTX-M plasmid combinations coevolved over time. The IncF_CTX-M-15/ST131-C2 subclade combination emerged during the early 2000s, spread rapidly across the globe, and is one of the greatest clone/plasmid successes of the millennium. The ST410-B3 subclade containing blaCTX-M-15 incorporated the NDM-5 carbapenemase gene into existing IncF platforms, providing an additional positive selective advantage that included the carbapenems. A "plasmid-replacement" clade scenario occurred in the histories of ST131 and ST410 as different subclades gained different AMR genes on different IncF platforms. The use of antimicrobial agents will generate selection pressures that enhance the risks for the continuous emergence of MDR ExPEC clone/IncF plasmid combinations. The reasons for clade/IncF replacements and associations between certain clades and specific IncF plasmid types are unknown. Such information will aid in designing management and prevention strategies to combat AMR.
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Affiliation(s)
- Johann D D Pitout
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, AB, T2L 2K8, Canada.
- Dynacare Laboratories, Alberta, Canada.
- University of Pretoria, Pretoria, Gauteng, South Africa.
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, NJ, USA
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19
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Couturier A, Virolle C, Goldlust K, Berne-Dedieu A, Reuter A, Nolivos S, Yamaichi Y, Bigot S, Lesterlin C. Real-time visualisation of the intracellular dynamics of conjugative plasmid transfer. Nat Commun 2023; 14:294. [PMID: 36653393 PMCID: PMC9849209 DOI: 10.1038/s41467-023-35978-3] [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: 10/05/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Conjugation is a contact-dependent mechanism for the transfer of plasmid DNA between bacterial cells, which contributes to the dissemination of antibiotic resistance. Here, we use live-cell microscopy to visualise the intracellular dynamics of conjugative transfer of F-plasmid in E. coli, in real time. We show that the transfer of plasmid in single-stranded form (ssDNA) and its subsequent conversion into double-stranded DNA (dsDNA) are fast and efficient processes that occur with specific timing and subcellular localisation. Notably, the ssDNA-to-dsDNA conversion determines the timing of plasmid-encoded protein production. The leading region that first enters the recipient cell carries single-stranded promoters that allow the early and transient synthesis of leading proteins immediately upon entry of the ssDNA plasmid. The subsequent conversion into dsDNA turns off leading gene expression, and activates the expression of other plasmid genes under the control of conventional double-stranded promoters. This molecular strategy allows for the timely production of factors sequentially involved in establishing, maintaining and disseminating the plasmid.
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Affiliation(s)
- Agathe Couturier
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Chloé Virolle
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Kelly Goldlust
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Annick Berne-Dedieu
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Audrey Reuter
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Sophie Nolivos
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France
| | - Yoshiharu Yamaichi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sarah Bigot
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France.
| | - Christian Lesterlin
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, 69007, Lyon, France.
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20
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Tonkin-Hill G, Gladstone RA, Pöntinen AK, Arredondo-Alonso S, Bentley SD, Corander J. Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe. Genome Res 2023; 33:129-140. [PMID: 36669850 PMCID: PMC9977150 DOI: 10.1101/gr.277340.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 12/14/2022] [Indexed: 01/21/2023]
Abstract
Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.
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Affiliation(s)
- Gerry Tonkin-Hill
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway;,Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
| | | | - Anna K. Pöntinen
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway;,Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
| | - Stephen D. Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, 0372 Blindern, Norway;,Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1RQ, United Kingdom;,Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
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21
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Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122077. [PMID: 36556442 PMCID: PMC9780897 DOI: 10.3390/life12122077] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Multiresistant Escherichia coli has been disseminated worldwide, and it is one of the major causative agents of nosocomial infections. E. coli has a remarkable and complex genomic plasticity for taking up and accumulating genetic elements; thus, multiresistant high-risk clones can evolve. In this review, we summarise all available data about internationally disseminated extraintestinal pathogenic high-risk E. coli clones based on whole-genome sequence (WGS) data and confirmed outbreaks. Based on genetic markers, E. coli is clustered into eight phylogenetic groups. Nowadays, the E. coli ST131 clone from phylogenetic group B2 is the predominant high-risk clone worldwide. Currently, strains of the C1-M27 subclade within clade C of ST131 are circulating and becoming prominent in Canada, China, Germany, Hungary and Japan. The C1-M27 subclade is characterised by blaCTX-M-27. Recently, the ST1193 clone has been reported as an emerging high-risk clone from phylogenetic group B2. ST38 clone carrying blaOXA-244 (a blaOXA-48-like carbapenemase gene) caused several outbreaks in Germany and Switzerland. Further high-risk international E. coli clones include ST10, ST69, ST73, ST405, ST410, ST457. High-risk E. coli strains are present in different niches, in the human intestinal tract and in animals, and persist in environment. These strains can be transmitted easily within the community as well as in hospital settings. WGS analysis is a useful tool for tracking the dissemination of resistance determinants, the emergence of high-risk mulitresistant E. coli clones and to analyse changes in the E. coli population on a genomic level.
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22
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Chen L, Peirano G, Kreiswirth BN, Devinney R, Pitout JDD. Acquisition of genomic elements were pivotal for the success of Escherichia coli ST410. J Antimicrob Chemother 2022; 77:3399-3407. [PMID: 36204996 PMCID: PMC10205468 DOI: 10.1093/jac/dkac329] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/05/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Escherichia coli ST410 is an emerging MDR clone linked to blaCTX-M-15 and blaOXA-181. Limited comprehensive data about the global distribution of ST410 clades and mobile genetic elements associated with different β-lactamases are available. METHODS Short- and long-read WGS were performed on a collection of ST410 producing carbapenemases (n = 45) obtained from 11 countries. The evolutionary history of global E. coli ST410 was also investigated. RESULTS OXA-181 and NDM-5 were the most frequent carbapenemases and used different underlying strategies to ensure their successful association with ST410 clades. Our phylogenetic analysis of publicly available ST410 genomes amended the previously published ST410 B subclades: ST410-B1 is identical to B1/H24, ST410-B2 includes B2/H24R and B3/H24Rx, while ST410-B3 corresponds to B4/H24RxC. Long-read WGS identified the following genomic events that likely shaped the evolution of ST410-B3: (i) gyrA and parC mutations were acquired via homologous recombination events; (ii) chromosomal integration of blaCMY-2 among ST410-B3; (iii) the emergence of ST410-B3 from ST410-B2 was accompanied by the replacement of IncFII plasmids harbouring blaCTX-M-15 (i.e. F36:31:A4:B1 in ST410-B2 with F1:A1:B49 plasmids in ST410-B3); and (iv) the NDM-5 gene was integrated within F1:A1:B49 plasmids over time. CONCLUSIONS The global ST410 population producing carbapenemases is dominated by the ST410-B2 and B3 subclades with varied geographical distribution that requires ongoing genomic surveillance. We provided an updated timeline of pivotal genomic events that have shaped the success of the ST410-B3 subclade.
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Affiliation(s)
- Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Gisele Peirano
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, T2L 2K8 Calgary, Alberta, Canada
| | - Barry N Kreiswirth
- Hackensack Meridian Health Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Rebekah Devinney
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, T2L 2K8 Calgary, Alberta, Canada
| | - Johann D D Pitout
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, T2L 2K8 Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
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23
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Burgess SA, Moinet M, Brightwell G, Cookson AL. Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites. Microb Genom 2022; 8. [PMID: 36200854 DOI: 10.1099/mgen.0.000893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Extended-spectrum beta lactamase (ESBL)-producing Escherichia coli are often isolated from humans with urinary tract infections and may display a multidrug-resistant phenotype. These pathogens represent a target for a One Health surveillance approach to investigate transmission between humans, animals and the environment. This study examines the multidrug-resistant phenotype and whole genome sequence data of four ESBL-producing E. coli isolated from freshwater in New Zealand. All four isolates were obtained from a catchment with a mixed urban and pastoral farming land-use. Three isolates were sequence type (ST) 131 (CTX-M-27-positive) and the other ST69 (CTX-M-15-positive); a phylogenetic comparison with other locally isolated strains demonstrated a close relationship with New Zealand clinical isolates. Genes associated with resistance to antifolates, tetracyclines, aminoglycosides and macrolides were identified in all four isolates, together with fluoroquinolone resistance in two isolates. The ST69 isolate harboured the bla CTX-M-15 gene on a IncHI2A plasmid, and two of the three ST131 isolates harboured the bla CTX-M-27 genes on IncF plasmids. The last ST131 isolate harboured bla CTX-M-27 on the chromosome in a unique site between gspC and gspD. These data highlight a probable human origin of the isolates with subsequent transmission from urban centres through wastewater to the wider environment.
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Affiliation(s)
- Sara A Burgess
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand
| | - Marie Moinet
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North 4410, New Zealand
| | - Gale Brightwell
- AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North 4410, New Zealand.,New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Adrian L Cookson
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North 4410, New Zealand.,AgResearch Ltd, Hopkirk Research Institute, Massey University, Palmerston North 4410, New Zealand
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24
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Convergence of virulence and antimicrobial resistance in increasingly prevalent Escherichia coli ST131 papGII+ sublineages. Commun Biol 2022; 5:752. [PMID: 35902767 PMCID: PMC9334617 DOI: 10.1038/s42003-022-03660-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/29/2022] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli lineage ST131 is an important cause of urinary tract and bloodstream infections worldwide and is highly resistant to antimicrobials. Specific ST131 lineages carrying invasiveness-associated papGII pathogenicity islands (PAIs) were previously described, but it is unknown how invasiveness relates to the acquisition of antimicrobial resistance (AMR). In this study, we analysed 1638 ST131 genomes and found that papGII+ isolates carry significantly more AMR genes than papGII-negative isolates, suggesting a convergence of virulence and AMR. The prevalence of papGII+ isolates among human clinical ST131 isolates increased dramatically since 2005, accounting for half of the recent E. coli bloodstream isolates. Emerging papGII+ lineages within clade C2 were characterized by a chromosomally integrated blaCTX-M-15 and the loss and replacement of F2:A1:B- plasmids. Convergence of virulence and AMR is worrying, and further dissemination of papGII+ ST131 lineages may lead to a rise in severe and difficult-to-treat extraintestinal infections. Genomic analyses indicate that the ST131 lineage of E. coli, responsible for urinary and bloodstream infections globally, is evolving towards both increased virulence and increased resistance to antimicrobials.
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25
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Escherichia coli ST1193: Following in the Footsteps of E. coli ST131. Antimicrob Agents Chemother 2022; 66:e0051122. [PMID: 35658504 DOI: 10.1128/aac.00511-22] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Escherichia coli ST1193 is an emerging global multidrug (MDR) high-risk clone and an important cause of community-onset urinary and bloodstream infections. ST1193 is imitating E. coli ST131, the most successful MDR clone of all time. Both clones emerged in the early 1990s by acquiring quinolone resistance-determining region (QRDR) mutations, IncF plasmids, virulence factors, and type 1 pilus (fimH) recombination. They are the only MDR clones that are dominant among unselected E. coli populations. ST131 is the most frequent clone and ST1193 the second most frequent clone among fluoroquinolone/cephalosporin-resistant E. coli isolates. Both clones have played pivotal roles in the global spread of MDR E. coli. ST1193 originated from ST clonal complex 14 (STc14), is lactose nonfermenting, belongs to phylogenetic group B2, and contains the O type O75. Global ST1193 prevalence has been increasing since 2012, even replacing ST131 in certain regions. blaCTX-M genes are rapidly expanding among ST1193 isolates, a scenario that occurred with ST131 during the 2000s. A validated PCR will enable global surveys to determine the extent of ST1193 among One Health E. coli isolates. The rapid emergence of ST1193 is concerning and is adding to the public health burden of MDR E. coli clones. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST1193. Such information will aid with management and prevention strategies. The medical community can ill afford to ignore the spread of another global successful MDR high-risk E. coli clone, especially one that is following in the footsteps of E. coli ST131.
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26
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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.
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27
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Salamzade R, Manson AL, Walker BJ, Brennan-Krohn T, Worby CJ, Ma P, He LL, Shea TP, Qu J, Chapman SB, Howe W, Young SK, Wurster JI, Delaney ML, Kanjilal S, Onderdonk AB, Bittencourt CE, Gussin GM, Kim D, Peterson EM, Ferraro MJ, Hooper DC, Shenoy ES, Cuomo CA, Cosimi LA, Huang SS, Kirby JE, Pierce VM, Bhattacharyya RP, Earl AM. Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance. Genome Med 2022; 14:37. [PMID: 35379360 PMCID: PMC8981930 DOI: 10.1186/s13073-022-01040-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/22/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms. METHODS To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years. RESULTS Our CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment. CONCLUSIONS Collectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.
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Affiliation(s)
- Rauf Salamzade
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.14003.360000 0001 2167 3675Present Address: Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Abigail L. Manson
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Bruce J. Walker
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,Applied Invention, Cambridge, MA 02139 USA
| | - Thea Brennan-Krohn
- grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Colin J. Worby
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Peijun Ma
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Lorrie L. He
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Terrance P. Shea
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - James Qu
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Sinéad B. Chapman
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Whitney Howe
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Sarah K. Young
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Jenna I. Wurster
- grid.38142.3c000000041936754XDepartment of Ophthalmology, Department of Microbiology, Harvard Medical School and Massachusetts Eye and Ear Infirmary, 240 Charles St., Boston, MA 02114 USA
| | - Mary L. Delaney
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Sanjat Kanjilal
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Population Medicine, Harvard Medical School and Harvard Pilgrim Healthcare Institute, Boston, MA 02215 USA
| | - Andrew B. Onderdonk
- grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Cassiana E. Bittencourt
- grid.266093.80000 0001 0668 7243Department of Pathology and Laboratory Medicine, University of California Irvine School of Medicine, Orange, CA 92868 USA
| | - Gabrielle M. Gussin
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - Diane Kim
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - Ellena M. Peterson
- grid.266093.80000 0001 0668 7243Department of Pathology and Laboratory Medicine, University of California Irvine School of Medicine, Orange, CA 92868 USA
| | - Mary Jane Ferraro
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - David C. Hooper
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Erica S. Shenoy
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Christina A. Cuomo
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Lisa A. Cosimi
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.38142.3c000000041936754XDivision of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | - Susan S. Huang
- grid.266093.80000 0001 0668 7243Division of Infectious Diseases, University of California Irvine School of Medicine, Irvine, CA 92617 USA
| | - James E. Kirby
- grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Virginia M. Pierce
- grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Roby P. Bhattacharyya
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Massachusetts General Hospital, Boston, MA 02114 USA
| | - Ashlee M. Earl
- grid.66859.340000 0004 0546 1623Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
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Plasmid Replicon Diversity of Clinical Uropathogenic Escherichia coli Isolates from Riyadh, Saudi Arabia. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.51] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to identify and compare the plasmid replicons of clinical uropathogenic Escherichia coli (UPEC) isolates, involving extended spectrum β-lactamase (ESBL)-positive and ESBL-negative, E. coli ST131 and non-ST131 and various ST131 subclones. Plasmid replicon typing on 24 clinical UPEC isolates was carried out using polymerase chain reaction-based replicon typing. A statistical analysis was performed to assess the associations between plasmid replicon types and ESBL carriage, and to evaluate the link between ST131 isolates and high replicon carriage. Eight replicons, I1α, N2, Iγ, X1, FIIS, K, FIA, and FII were detected. The FII was the most common replicon identified here. ESBL-positive E. coli isolates were highly associated with I1α, N2, Iγ, X1, and FIIS replicons, while FIA was present only in ESBL-negative group. ST131 isolates were highly associated with I1α and N2 replicons compared to non-ST131. No link was found between replicon carriage and the number or type of ESBLs in E. coli isolates. The diversity observed in replicon patterns of our clinical E. coli isolates indicates that they might be originated from different sources. The presence of replicons reported previously in animal sources suggests a possible transfer of antimicrobial resistance between animal and human bacterial isolates.
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Hertz FB, Marvig RL, Frimodt-Møller N, Nielsen KL. In vitro Relative Fitness, in vivo Intestinal Colonization and Genomic Differences of Escherichia coli of ST131 Carrying blaCTX–M–15. Front Microbiol 2022; 12:798473. [PMID: 35250906 PMCID: PMC8894762 DOI: 10.3389/fmicb.2021.798473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction Extended-spectrum beta-lactamase (ESBL) producing Escherichia coli have become prevalent worldwide, with E. coli of sequence type 131 (ST131) as the dominant genotype. E. coli ST131 predominantly exhibits the serotype O25, is associated with the ESBL CTX-M-15 and belongs to a well-defined subclade within the FimH30-R clade, FimH30-Rx/C2. Multidrug resistance may have fitness costs for the bacteria. The aim of the current study was to investigate the fitness burden compared to a susceptible ST131 isolate without resistance genes in vitro and in vivo and describe genetic differences between fit and less fit isolates. Materials and methods From a collection of clinical ESBL and non-ESBL E. coli isolates from urinary tract infection, we selected 16 blaCTX–M–15-positive isolates of ST131. The in vitro fitness was examined, and relative bacterial fitness (fitt) was determined by direct competition with a fully susceptible ST131 isolate and illustrated in percent, with <100% resulting in a lower fitness, compared to the susceptible reference isolate. The isolates were subjected to whole-genome sequencing and analyzed for resistance markers, plasmids, phage content, and serotype. In vivo competition was tested in a mouse colonization model. Results The majority (12 out of 16) of the CTX-M-15-producing isolates had a slightly lower relative fitness compared to the susceptible ST131 isolate (mean, 97.6%; range, 82.6–108%) in vitro. Three isolates had a better fitness than the susceptible ST131 isolate, and one isolate had an identical fitness to the susceptible ST131 isolate. The in vitro fitness showed no correlation to the number of plasmids, number of phages, number of resistances, or genome size. For the in vivo competition assays, all three ESBL-producing isolates showed better colonization of the ESBL-resistant ST131 isolates compared to the susceptible ST131 isolate. Conclusion This study shows that ESBL-producing ST131/H30-Rx are not necessarily burdened by multidrug resistance, however, have a better in vitro fitness than the susceptible isolate. These data contribute to the understanding of the success of ST131/H30-Rx, although they do not indicate ways to overcome this highly fit, virulent, and antimicrobial-resistant clone.
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Affiliation(s)
| | - Rasmus L. Marvig
- Department of Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Niels Frimodt-Møller
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- *Correspondence: Niels Frimodt-Møller,
| | - Karen Leth Nielsen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
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Tóth K, Tóth Á, Kamotsay K, Németh V, Szabó D. Population snapshot of the extended-spectrum β-lactamase-producing Escherichia coli invasive strains isolated from a Hungarian hospital. Ann Clin Microbiol Antimicrob 2022; 21:3. [PMID: 35144632 PMCID: PMC8829994 DOI: 10.1186/s12941-022-00493-8] [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: 05/17/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022] Open
Abstract
Background This study was carried out to determine the prevalence and the genetic background of extended-spectrum β-lactamase-producing Escherichia coli invasive isolates obtained from a tertiary-care hospital in Budapest, Hungary. Methods Between October–November 2018, all invasive ESBL-producing E. coli isolates were collected from Central Hospital of Southern Pest. The antimicrobial susceptibility testing was performed according to the EUCAST guidelines. The possible clonal relationships were investigated by core genome (cg)MLST (SeqSphere +) using whole-genome sequencing (WGS) data of isolates obtained from Illumina 251-bp paired-end sequencing. From WGS data acquired antimicrobial resistance genes, virulence genes and replicon types were retrieved using ResFinder3.1, PlasmidFinder2.1, pMLST-2.0, VirulenceFinder2.0 and Virulence Factors Database online tools. Results Overall, six E. coli isolates proved to be resistant to third-generation cephalosporins and ESBL-producers in the study period. Full genome sequence analysis showed that five E. coli isolates belonged to the ST131 clone: two to C1-M27 subclade with blaCTX-M-27 and three to C2/H30Rx subclade with blaCTX-M-15. One isolate belonged to ST1193 with blaCTX-M-27. According to cgMLST, all C2/H30Rx isolates formed a cluster (≤ 6 allele differences), while the blaCTX-M-27-producing C1-M27 isolates differed at least 35 alleles from each other. Both C2/H30Rx and C1-M27 ST131 isolates harbored similar antimicrobial resistance gene sets. However, only C2/H30Rx isolates had the qnrB and aac(3)-IIa. The isolates carried similar extraintestinal virulence gene set but differed in some genes encoding siderophores, protectins and toxins. Moreover, only one C2/H30Rx isolate carried salmochelin siderophore system and showed virotype B. All isolates showed resistance against ceftriaxone, cefotaxime, and ciprofloxacin, and the C2/H30Rx isolates were also resistant to gentamicin, tobramycin, and ceftazidime. Conclusions Out of six ESBL-producing E. coli, five belonged to the ST131 clone. This study indicates, that the C2/H30Rx and C1-M27 subclades of the ST131 appear to be the dominant clones collected in a Hungarian hospital.
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Affiliation(s)
- Kinga Tóth
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary. .,Department of Bacteriology, Mycology, and Parasitology, National Public Health Center, Budapest, Hungary.
| | - Ákos Tóth
- Department of Bacteriology, Mycology, and Parasitology, National Public Health Center, Budapest, Hungary
| | - Katalin Kamotsay
- Central Microbiology Laboratory, Central Hospital of Southern Pest National Institute of Hematology and Infectious Disease, Budapest, Hungary
| | - Viktória Németh
- Central Microbiology Laboratory, Central Hospital of Southern Pest National Institute of Hematology and Infectious Disease, Budapest, Hungary
| | - Dóra Szabó
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
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F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses. mSystems 2022; 7:e0121221. [PMID: 35076267 PMCID: PMC8788324 DOI: 10.1128/msystems.01212-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Escherichia coli sequence type 95 (ST95) is an extraintestinal pathogenic E. coli (ExPEC) renowned for its ability to cause significant morbidity and mortality in humans and poultry. A core genome analysis of 668 ST95 isolates generated 10 clades (A to J), 5 of which are reported here for the first time. F plasmid replicon sequence typing showed that almost a third (178/668 [27%]) of the collection carry pUTI89 (F29:B10) and were restricted to clade A and a sublineage of clade B. In contrast, almost half (328/668 [49%]) of the collection across multiple clades harbor ColV plasmids (multiple F types). Strikingly, ST95 lineages with pUTI89 were almost exclusively from humans, while ColV+ ST95 lineages were sourced from poultry and humans. Clade I was notable because it comprises temporally and geographically matched ColV+ isolates sourced from human and retail poultry meat, suggesting interspecies transmission via food. Clade F contained ST95 isolates of bovine origin, none of which carried ColV or pUTI89 plasmids. Remarkably, an analysis of a cohort of 34,176 E. coli isolates comprising 2,570 sequence types mirrored what was observed in ST95: (i) pUTI89 was overwhelmingly linked to E. coli sourced from humans but almost entirely absent from 13,027 E. coli isolates recovered from poultry, pigs, and cattle, and (ii) E. coli isolates harboring ColV plasmids were from multiple sources, including humans, poultry, and swine. Overall, our data suggest that F plasmids influence E. coli host range, clade structure, and zoonotic potential in ST95 and ExPEC more broadly. IMPORTANCEE. coli ST95 is one of five dominant ExPEC lineages globally and noted for causing urinary tract and bloodstream infections and neonatal meningitis in humans and colibacillosis in poultry. Using high-resolution phylogenomics, we show that F replicon sequence type is linked to ST95 clade structure and zoonotic potential. Specifically, human centric ST95 clades overwhelmingly harbor F29:B10 (pUTI89) plasmids, while clades carrying both human- and poultry-sourced isolates are typically ColV+ with multiple replicon types. Importantly, several clades identified clonal ColV+ ST95 isolates from human and poultry sources, but clade I, which housed temporally and spatially matched isolates, provided the most robust evidence. Notably, patterns of association of F replicon types with E. coli host were mirrored within a diverse collection of 34,176 E. coli genomes. Our studies indicate that the role of food animals as a source of human ExPEC disease is complex and warrants further investigation.
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32
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Hu D, Fuller NR, Caterson ID, Holmes AJ, Reeves PR. Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome. Cell Rep 2022; 38:110239. [PMID: 35021078 DOI: 10.1016/j.celrep.2021.110239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/17/2021] [Accepted: 12/17/2021] [Indexed: 02/01/2023] Open
Abstract
Gut microbiome is of major interest due to its close relationship to health and disease. Bacteria usually vary in gene content, leading to functional variations within species, so resolution higher than species-level methods is needed for ecological and clinical relevance. We design a protocol to identify strains in selected species with high discrimination and in high numbers by amplicon sequencing of the flagellin gene. We apply the protocol to fecal samples from a human diet trial, targeting Escherichia coli. Across the 119 samples from 16 individuals, there are 1,532 amplicon sequence variants (ASVs), but only 32 ASVs are dominant in one or more fecal samples, despite frequent dominant strain turnover. Major strains in an intestine are found to be commonly accompanied by a large number of satellite cells, and many are identified as potential extraintestinal pathogens. The protocol could be used to track epidemics or investigate the intra- or inter-host diversity of pathogens.
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Affiliation(s)
- Dalong Hu
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia
| | - Nicholas R Fuller
- The Boden Institute, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia; Metabolism and Obesity Services, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Ian D Caterson
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia; The Boden Institute, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia; Metabolism and Obesity Services, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Andrew J Holmes
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia
| | - Peter R Reeves
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia.
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Li D, Wyrsch ER, Elankumaran P, Dolejska M, Marenda MS, Browning GF, Bushell RN, McKinnon J, Chowdhury PR, Hitchick N, Miller N, Donner E, Drigo B, Baker D, Charles IG, Kudinha T, Jarocki VM, Djordjevic SP. Genomic comparisons of Escherichia coli ST131 from Australia. Microb Genom 2021; 7:000721. [PMID: 34910614 PMCID: PMC8767332 DOI: 10.1099/mgen.0.000721] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron-integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462-1014 bp), highlighting the ongoing evolution of this element. The module intI1-dfrA17-aadA5-qacEΔ1-sul1-ORF-chrA-padR-IS1600-mphR-mrx-mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically blaCTX-M-15 and blaCTX-M-27. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate that the the ST131 population in Australia carries diverse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across diverse reservoirs.
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Affiliation(s)
- Dmitriy Li
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Ethan R. Wyrsch
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Monika Dolejska
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czech Republic,Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Czech Republic,Biomedical Center, Charles University, Czech Republic,Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic
| | - Marc S. Marenda
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Glenn F. Browning
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Rhys N. Bushell
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Victoria, Australia
| | - Jessica McKinnon
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | | | - Nola Hitchick
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - Natalie Miller
- San Pathology, Sydney Adventist Hospital, Wahroonga, NSW 2076, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | | | | | - Timothy Kudinha
- Central West Pathology Laboratory, Charles Sturt University, Orange, NSW, 2800, Australia
| | - Veronica M. Jarocki
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia,*Correspondence: Veronica M. Jarocki,
| | - Steven Philip Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia,*Correspondence: Steven Philip Djordjevic,
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Hapuarachchi IU, Hannaway RF, Roman T, Biswas A, Dyet K, Morgan X, Ussher JE. Genetic evaluation of ESBL-producing Escherichia coli urinary isolates in Otago, New Zealand. JAC Antimicrob Resist 2021; 3:dlab147. [PMID: 34778763 PMCID: PMC8578626 DOI: 10.1093/jacamr/dlab147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES The incidence of infections with ESBL-producing Escherichia coli (ESBL-Ec) in New Zealand is increasing. ESBL-Ec most commonly cause urinary tract infections and are seen in both community and hospitalized patients. The reason for the increasing incidence of ESBL-Ec infections is unknown. METHODS In this study, 65 urinary ESBL-Ec isolates from the Otago region in 2015 were fully genetically characterized to understand the mechanisms of transmission. The ESBL gene, E. coli STs, plasmid types and genetic context (e.g. insertion sequences) of ESBL genes were determined by a combination of whole genome and plasmid sequencing. The phylogenetic relationships of the isolates were compared with ESBL-Ec isolates sequenced as part of the 2016 nationwide survey. RESULTS Significant diversity of E. coli strains, plasmids, and the genetic context of ESBL genes was seen. However, there was evidence of common mobile genetic elements in unrelated ESBL-Ec. CONCLUSIONS Multiple introductions of ESBL resistance genes or resistant bacterial strains with limited horizontal transmission of mobile genetic elements accounts for the increased incidence of ESBL-Ec in this low prevalence area. Future studies should investigate modes of transmission of ESBL-Ec in the Otago region.
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Affiliation(s)
- Isuri U Hapuarachchi
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rachel F Hannaway
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Tabatha Roman
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ambarish Biswas
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- AgResearch, Palmerston North, New Zealand
| | | | - Xochitl Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James E Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Southern Community Laboratories, Dunedin, New Zealand
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35
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Hall RJ, Whelan FJ, Cummins EA, Connor C, McNally A, McInerney JO. Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility. Microb Genom 2021; 7. [PMID: 34499026 PMCID: PMC8715431 DOI: 10.1099/mgen.0.000650] [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] [Indexed: 12/31/2022] Open
Abstract
The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships.
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Affiliation(s)
- Rebecca J Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.,School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Fiona J Whelan
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.,School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Christopher Connor
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - James O McInerney
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
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Arrangements of Mobile Genetic Elements among Virotype E Subpopulation of Escherichia coli Sequence Type 131 Strains with High Antimicrobial Resistance and Virulence Gene Content. mSphere 2021; 6:e0055021. [PMID: 34431692 PMCID: PMC8386418 DOI: 10.1128/msphere.00550-21] [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: 11/21/2022] Open
Abstract
Escherichia coli sequence type 131 (ST131) is known for its contribution to multidrug resistance and the worldwide spread of this clone has become a global problem. Understanding the trends among ST131 clades will help design strategies to prevent its rapid dissemination. In this study, 72 ST131 strains were subjected to comparative genomic analysis and 64 clade C strains were compared with clade C strains reported from other regions using publicly available whole-genome sequencing data. C1 (n = 31 [48.4%]) and C2 (n = 33 [%51.5]) strains had the same prevalence in our collection, and C1-M27 (n = 22) strains were closely related, carried a unique plasmid type (F1:A2:B20), and exhibited virotype C. Removal of 11 C2 strains with varied virotype patterns and the heterogeneous IncF type identified 22 closely related virotype E/F strains with replicon type F31/F36:A4:B1, forming what we denote as the “C2-subset.” In a global context, the C2-subset constituted a distinct cluster with international virotype E strains and harbored a genomic island, GI-pheU. Association of cnf1/hlyCABD genes with 1 to 7 mobile genetic elements, mostly IS682/ISKpn37 combination within GI-pheU was identified. The C2-subset accounted for excess resistance/virulence of subclade C2 relative to C1 strains. In addition, a conserved chromosomal IS26-mediated composite transposon (IS15DIV-ISEcp1-blaCTX-M-15-WbuC cupin fold metalloprotein-Tn2-IS15DIV) was observed in the C2-subset. The local spread of the C2-subset in the hospital studied, with the carriage of higher virulence/resistance markers and a peculiar F-type plasmid, demonstrates the potential for diversification of the ST131 lineage and the emergence of subpopulations with higher survival potential to cause health care-associated outbreaks. IMPORTANCEEscherichia coli sequence type 131 (ST131) is a globally dominant multidrug-resistant clone that is commonly associated with extraintestinal infections. Specific sublineages have been shown to have emerged and spread within ST131, highlighting the complex nature of ST131 epidemiology. This study systematically compared the Iranian ST131 population to those reported from other countries and found a subpopulation harboring virotype E, a homogeneous profile of plasmid Inc-F type F31/F36:A4:B1 harboring cnf1/hemolysin genes on the genomic island GI-pheU, and up to seven mobile genetic elements (MGEs) flanking cnf1/hemolysin virulence markers. The results of this study highlight the importance of MGEs for virulence gene acquisition and the formation of new subpopulations among pandemic clones such as E. coli ST131.
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Huang J, Zhang S, Zhao Z, Chen M, Cao Y, Li B. Acquisition of a Stable and Transferable bla NDM-5-Positive Plasmid With Low Fitness Cost Leading to Ceftazidime/Avibactam Resistance in KPC-2-Producing Klebsiella pneumoniae During Treatment. Front Cell Infect Microbiol 2021; 11:658070. [PMID: 34354959 PMCID: PMC8329419 DOI: 10.3389/fcimb.2021.658070] [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: 01/25/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
The emergence and prevalence of carbapenem-resistant Enterobacteriaceae (CRE) have drawn worldwide attention. Ceftazidime/avibactam (CAZ/AVI) gives us a valuable alternative strategy to treat CRE infections. Unfortunately, CAZ/AVI resistance could occur during CAZ/AVI treatment. The CAZ/AVI-resistant Carbapenem-resistant Klebsiella pneumoniae (CR-KP) (KP137060) and earlier CAZ/AVI-susceptible isolate (KP135194) from the same hospitalized patient were collected at Fujian Medical University Union Hospital between October and November 2019. In this study, CAZ/AVI MICs of CAZ/AVI-susceptible and -resistant isolates (KP135194 and KP137060) were 4 mg/L and 128 mg/L, respectively; and the two isolates had the same antibiotic resistance pattern to other carbapenems. Two strains were then submitted for whole-genome sequencing and bioinformatic analysis. ompK36 was not detected in two isolates. No mutation was observed in bla KPC-2, ompK35 and ompK37 in this study and there was no significant difference of the expression in bla KPC-2, ompK35 and ompK37 between the two isolates (p>0.05). Two isolates were sequence type 11 and harbored bla KPC-2, bla SHV-182 and bla TEM-1B. Compared with KP135194, KP137060 harbored an additional bla NDM-5 positive plasmid. bla NDM-5 gene could be successfully transferred into E. coli J53 at a conjugation frequency of 1.14×10-4. Plasmid stability testing showed that bla KPC-2- and bla NDM-5-harboring plasmids were still stably maintained in the hosts. Growth assay and growth competition experiments showed there was no significant difference in fitness cost between two CR-KP isolates. Our study described the acquisition of a bla NDM-5-harboring plasmid leading to resistance to ceftazidime/avibactam in KPC-2-producing Klebsiella pneumoniae during treatment. This phenomenon deserves further exploration.
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Affiliation(s)
- Jiangqing Huang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shengcen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zhichang Zhao
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, China
| | - Min Chen
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Yingping Cao
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Bin Li
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
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Comparative Pathogenomics of Escherichia coli: Polyvalent Vaccine Target Identification through Virulome Analysis. Infect Immun 2021; 89:e0011521. [PMID: 33941580 PMCID: PMC8281228 DOI: 10.1128/iai.00115-21] [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] [Indexed: 02/07/2023] Open
Abstract
Comparative genomics of bacterial pathogens has been useful for revealing potential virulence factors. Escherichia coli is a significant cause of human morbidity and mortality worldwide but can also exist as a commensal in the human gastrointestinal tract. With many sequenced genomes, it has served as a model organism for comparative genomic studies to understand the link between genetic content and potential for virulence. To date, however, no comprehensive analysis of its complete “virulome” has been performed for the purpose of identifying universal or pathotype-specific targets for vaccine development. Here, we describe the construction of a pathotype database of 107 well-characterized completely sequenced pathogenic and nonpathogenic E. coli strains, which we annotated for major virulence factors (VFs). The data are cross referenced for patterns against pathotype, phylogroup, and sequence type, and the results were verified against all 1,348 complete E. coli chromosomes in the NCBI RefSeq database. Our results demonstrate that phylogroup drives many of the “pathotype-associated” VFs, and ExPEC-associated VFs are found predominantly within the B2/D/F/G phylogenetic clade, suggesting that these phylogroups are better adapted to infect human hosts. Finally, we used this information to propose polyvalent vaccine targets with specificity toward extraintestinal strains, targeting key invasive strategies, including immune evasion (group 2 capsule), iron acquisition (FyuA, IutA, and Sit), adherence (SinH, Afa, Pap, Sfa, and Iha), and toxins (Usp, Sat, Vat, Cdt, Cnf1, and HlyA). While many of these targets have been proposed before, this work is the first to examine their pathotype and phylogroup distribution and how they may be targeted together to prevent disease.
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Genetic Environments of Plasmid-Mediated blaCTXM-15 Beta-Lactamase Gene in Enterobacteriaceae from Africa. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12020026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The most widely distributed blaCTX-M gene on a global scale is blaCTX-M-15. The dissemination has been associated with clonal spread and different types of mobile genetic elements. The objective of this review was to describe the genetic environments of the blaCTX-M-15 gene detected from Enterobacteriaceae in published literature from Africa. A literature search for relevant articles was performed through PubMed, AJOL, and Google Scholar electronic databases; 43 articles from 17 African countries were included in the review based on the eligibility criteria. Insertion sequences were reported as part of the genetic environment of blaCTX-M-15 gene in 32 studies, integrons in 13 studies, and plasmids in 23 studies. In this review, five insertion sequences including ISEcp1, IS26, orf447, IS903, and IS3 have been detected which are associated with the genetic environment of blaCTX-M-15 in Africa. Seven different genetic patterns were seen in the blaCTX-M-15 genetic environment. Insertion sequence ISEcp1 was commonly located upstream of the end of the blaCTX-M-15 gene, while the insertion sequence orf477 was located downstream. In some studies, ISEcp1 was truncated upstream of blaCTX-M-15 by insertion sequences IS26 and IS3. The class 1 integron (Intl1) was most commonly reported to be associated with blaCTX-M-15 (13 studies), with Intl1/dfrA17–aadA5 being the most common gene cassette array. IncFIA-FIB-FII multi-replicons and IncHI2 replicon types were the most common plasmid replicon types that horizontally transferred the blaCTX-M-15 gene. Aminoglycoside-modifying enzymes, and plasmid-mediated quinolone resistance genes were commonly collocated with the blaCTX-M-15 gene on plasmids. This review revealed the predominant role of ISEcp1, Intl1 and IncF plasmids in the mobilization and continental dissemination of the blaCTX-M-15 gene in Africa.
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Lopes R, Furlan JPR, Dos Santos LDR, Gallo IFL, Stehling EG. Colistin-Resistant mcr-1-Positive Escherichia coli ST131- H22 Carrying bla CTX-M-15 and qnrB19 in Agricultural Soil. Front Microbiol 2021; 12:659900. [PMID: 33897674 PMCID: PMC8062734 DOI: 10.3389/fmicb.2021.659900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/15/2021] [Indexed: 01/02/2023] Open
Abstract
The pandemic Escherichia coli sequence type 131 (ST131) carrying plasmid-mediated colistin resistance mcr genes has emerged worldwide causing extraintestinal infections, with lineages belonging to three major clades (A, B, and C). Clade B is the most prevalent in animals, contaminating associated meat products, and can be transmitted zoonotically. However, the blaCTX–M–15 gene has only been associated with C2 subclade so far. In this study, we performed a genomic investigation of an E. coli (strain S802) isolated from a kale crop in Brazil, which exhibited a multidrug-resistant (MDR) profile to clinically significant antimicrobials (i.e., polymyxin, broad-spectrum cephalosporins, aminoglycosides, and fluoroquinolones). Whole-genome sequencing analysis revealed that the S802 strain belonged to serotype O25:H4, ST131/CC131, phylogenetic group B2, and virotype D5. Furthermore, S802 carried the clade B-associated fimH22 allele, genes encoding resistance to clinically important antimicrobials, metals, and biocides, and was phylogenetically related to human, avian, and swine ST131-H22 strains. Additionally, IncHI2-IncQ1, IncF [F2:A-:B1], and ColE1-like plasmids were identified harboring mcr-1.1, blaCTX–M–15, and qnrB19, respectively. The emergence of the E. coli ST131-H22 sublineage carrying mcr-1.1, blaCTX–M–15, and qnrB19 in agricultural soil represents a threat to food and environmental safety. Therefore, a One Health approach to genomic surveillance studies is required to effectively detect and limit the spread of antimicrobial-resistant bacteria and their resistance genes.
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Affiliation(s)
- Ralf Lopes
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Inara Fernanda Lage Gallo
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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Yasugi M, Hatoya S, Motooka D, Matsumoto Y, Shimamura S, Tani H, Furuya M, Mie K, Miyake M, Nakamura S, Shimada T. Whole-genome analyses of extended-spectrum or AmpC β-lactamase-producing Escherichia coli isolates from companion dogs in Japan. PLoS One 2021; 16:e0246482. [PMID: 33544781 PMCID: PMC7864471 DOI: 10.1371/journal.pone.0246482] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/19/2021] [Indexed: 11/21/2022] Open
Abstract
The emergence and global spread of extended-spectrum or AmpC β-lactamase (ESBL/AmpC)-producing Enterobacteriaceae in companion animals have led to the hypothesis that companion animals might be reservoirs for cross-species transmission because of their close contact with humans. However, current knowledge in this field is limited; therefore, the role of companion animals in cross-species transmission remains to be elucidated. Herein, we studied ESBL/AmpC-producing Enterobacteriaceae, Escherichia coli in particular, isolated from extraintestinal sites and feces of companion dogs. Whole-genome sequencing analysis revealed that (i) extraintestinal E. coli isolates were most closely related to those isolated from feces from the same dog, (ii) chromosomal sequences in the ST131/C1-M27 clade isolated from companion dogs were highly similar to those in the ST131/C1-M27 clade of human origin, (iii) certain plasmids, such as IncFII/pMLST F1:A2:B20/blaCTX-M-27, IncI1/pMLST16/blaCTX-M-15, or IncI1/blaCMY-2 from dog-derived E. coli isolates, shared high homology with those from several human-derived Enterobacteriaceae, (iv) chromosomal blaCTX-M-14 was identified in the ST38 isolate from a companion dog, and (v) eight out of 14 tested ESBL/AmpC-producing E. coli isolates (i.e., ST131, ST68, ST405, and ST998) belonged to the human extraintestinal pathogenic E. coli (ExPEC) group. All of the bla-coding plasmids that were sequenced genome-wide were capable of horizontal transfer. These results suggest that companion dogs can spread ESBL/AmpC-producing ExPEC via their feces. Furthermore, at least some ESBL/AmpC-producing ExPECs and bla-coding plasmids can be transmitted between humans and companion dogs. Thus, companion dogs can act as an important reservoir for ESBL/AmpC-producing E. coli in the community.
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Affiliation(s)
- Mayo Yasugi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- Asian Health Science Research Institiute, Osaka Prefecture University, Izumisano, Osaka, Japan
- * E-mail:
| | - Shingo Hatoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Daisuke Motooka
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Yuki Matsumoto
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shunsuke Shimamura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Hiroyuki Tani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Masaru Furuya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Keiichiro Mie
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Masami Miyake
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Shota Nakamura
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Terumasa Shimada
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- Asian Health Science Research Institiute, Osaka Prefecture University, Izumisano, Osaka, Japan
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42
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Johnson TJ. Role of Plasmids in the Ecology and Evolution of "High-Risk" Extraintestinal Pathogenic Escherichia coli Clones. EcoSal Plus 2021; 9:eESP-0013-2020. [PMID: 33634776 PMCID: PMC11163845 DOI: 10.1128/ecosalplus.esp-0013-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/12/2021] [Indexed: 11/20/2022]
Abstract
Bacterial plasmids have been linked to virulence in Escherichia coli and Salmonella since their initial discovery. Though the plasmid repertoire of these bacterial species is extremely diverse, virulence-associated attributes tend to be limited to a small subset of plasmid types. This is particularly true for extraintestinal pathogenic E. coli, or ExPEC, where a handful of plasmids have been recognized to confer virulence- and fitness-associated traits. The purpose of this review is to highlight the biological and genomic attributes of ExPEC virulence-associated plasmids, with an emphasis on high-risk dominant ExPEC clones. Two specific plasmid types are highlighted to illustrate the independently evolved commonalities of these clones relative to plasmid content. Furthermore, the dissemination of these plasmids within and between bacterial species is examined. These examples demonstrate the evolution of high-risk clones toward common goals, and they show that rare transfer events can shape the ecological landscape of dominant clones within a pathotype.
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Affiliation(s)
- Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108
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Hernández-García M, Sánchez-López J, Martínez-García L, Becerra-Aparicio F, Morosini MI, Ruiz-Garbajosa P, Cantón R. Emergence of the New KPC-49 Variant Conferring an ESBL Phenotype with Resistance to Ceftazidime-Avibactam in the ST131-H30R1 Escherichia coli High-Risk Clone. Pathogens 2021; 10:pathogens10010067. [PMID: 33466574 PMCID: PMC7828710 DOI: 10.3390/pathogens10010067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 01/08/2023] Open
Abstract
We report the emergence of an isolate belonging to the sequence type (ST)131-Escherichia coli high-risk clone with ceftazidime-avibactam resistance recovered from a patient with bacteremia in 2019. Antimicrobial susceptibility was determined and whole genome sequencing (Illumina-NovaSeq6000) and cloning experiments were performed to investigate its resistance phenotype. A KPC-3-producing E. coli isolate susceptible to ceftazidime-avibactam (MIC = 0.5/4 mg/L) and with non-wild type MIC of meropenem (8 mg/L) was detected in a blood culture performed at hospital admission. Following 10-days of standard ceftazidime-avibactam dose treatment, a second KPC-producing E. coli isolate with a phenotype resembling an extended-spectrum β-lactamase (ESBL) producer (meropenem 0.5 mg/L, piperacillin-tazobactam 16/8 mg/L) but resistant to ceftazidime-avibactam (16/4 mg/L) was recovered. Both E. coli isolates belonged to ST131, serotype O25:H4 and sublineage H30R1. Genomics analysis showed a core genome of 5,203,887 base pair with an evolutionary distance of 6 single nucleotide polymorphisms. A high content of resistance and virulence genes was detected in both isolates. The novel KPC-49 variant, an Arg-163-Ser mutant of blaKPC-3, was detected in the isolate with resistance to ceftazidime-avibactam. Cloning experiments revealed that blaKPC-49 gene increases ceftazidime-avibactam MIC and decreases carbapenem MICs when using a porin deficient Klebsiella pneumoniae strain as a host. Both blaKPC-3 and blaKPC-49 genes were located on the transposon Tn4401a as a part of an IncF [F1:A2:B20] plasmid. The emergence of novel blaKPC genes conferring decreased susceptibility to ceftazidime-avibactam and resembling ESBL production in the epidemic ST131-H30R1-E. coli high-risk clone presents a new challenge in clinical practice.
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Affiliation(s)
- Marta Hernández-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (M.H.-G.); (J.S.-L.); (L.M.-G.); (F.B.-A.); (M.I.M.); (R.C.)
- Red Española de Investigación en Patología Infecciosa (REIPI), 28029 Madrid, Spain
| | - Javier Sánchez-López
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (M.H.-G.); (J.S.-L.); (L.M.-G.); (F.B.-A.); (M.I.M.); (R.C.)
- Red Española de Investigación en Patología Infecciosa (REIPI), 28029 Madrid, Spain
| | - Laura Martínez-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (M.H.-G.); (J.S.-L.); (L.M.-G.); (F.B.-A.); (M.I.M.); (R.C.)
- Red Española de Investigación en Patología Infecciosa (REIPI), 28029 Madrid, Spain
| | - Federico Becerra-Aparicio
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (M.H.-G.); (J.S.-L.); (L.M.-G.); (F.B.-A.); (M.I.M.); (R.C.)
- Red Española de Investigación en Patología Infecciosa (REIPI), 28029 Madrid, Spain
| | - María Isabel Morosini
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (M.H.-G.); (J.S.-L.); (L.M.-G.); (F.B.-A.); (M.I.M.); (R.C.)
- Red Española de Investigación en Patología Infecciosa (REIPI), 28029 Madrid, Spain
| | - Patricia Ruiz-Garbajosa
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (M.H.-G.); (J.S.-L.); (L.M.-G.); (F.B.-A.); (M.I.M.); (R.C.)
- Red Española de Investigación en Patología Infecciosa (REIPI), 28029 Madrid, Spain
- Correspondence:
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain; (M.H.-G.); (J.S.-L.); (L.M.-G.); (F.B.-A.); (M.I.M.); (R.C.)
- Red Española de Investigación en Patología Infecciosa (REIPI), 28029 Madrid, Spain
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Hastak P, Fourment M, Darling AE, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP, Roy Chowdhury P. Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex. Emerg Microbes Infect 2020; 9:1780-1792. [PMID: 32686595 PMCID: PMC7473005 DOI: 10.1080/22221751.2020.1797541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/14/2020] [Indexed: 11/25/2022]
Abstract
The H30Rx subclade of Escherichia coli ST131 is a clinically important, globally dispersed pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum β-lactams. Isolates EC233 and EC234, variants of ST131-H30Rx with a novel sequence type (ST) 8196, isolated from unrelated patients presenting with bacteraemia at a Sydney Hospital in 2014 are characterised here. EC233 and EC234 are phylogroup B2, serotype O25:H4A, and resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both harbour an IncFII_2 plasmid (pSPRC_Ec234-FII) that carries most of the resistance genes on an IS26 associated translocatable unit, two small plasmids and a novel IncI1 plasmid (pSPRC_Ec234-I). SNP-based phylogenetic analysis of the core genome of representatives within the ST131 clonal complex places both isolates in a subclade with three clinical Australian ST131-H30Rx clade-C isolates. A MrBayes phylogeny analysis of EC233 and EC234 indicates ST8196 share a most recent common ancestor with ST131-H30Rx strain EC70 isolated from the same hospital in 2013. Our study identified genomic hallmarks that define the ST131-H30Rx subclade in the ST8196 isolates and highlights a need for unbiased genomic surveillance approaches to identify novel high-risk MDR E. coli pathogens that impact healthcare facilities.
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Affiliation(s)
- Priyanka Hastak
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Mathieu Fourment
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Aaron E. Darling
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Elaine Cheong
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital, Concord, Australia
- Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Garry S. A. Myers
- The ithree institute, University of Technology Sydney, Ultimo, Australia
| | - Steven P. Djordjevic
- The ithree institute, University of Technology Sydney, Ultimo, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Broadway, Australia
| | - Piklu Roy Chowdhury
- The ithree institute, University of Technology Sydney, Ultimo, Australia
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Broadway, Australia
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45
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Hayashi M, Matsui M, Sekizuka T, Shima A, Segawa T, Kuroda M, Kawamura K, Suzuki S. Dissemination of IncF group F1:A2:B20 plasmid-harbouring multidrug-resistant Escherichia coli ST131 before the acquisition of bla CTX-M in Japan. J Glob Antimicrob Resist 2020; 23:456-465. [PMID: 33212283 DOI: 10.1016/j.jgar.2020.10.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/24/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022] Open
Abstract
OBJECTIVES The Escherichia coli O25-ST131 clone is responsible for global dissemination of the blaCTX-M gene. However, the prevalence of this clone in the digestive tract, devoid of antimicrobial selection, and its molecular epidemiology remain unclear. In this study, we examined the origin of blaCTX-M-positive E. coli O25-ST131 and its distribution. METHODS We separately sequenced the chromosomal and plasmid genomes of 50 E. coli O25 isolates obtained from faecal samples of patients with diarrhoea in Japan. RESULTS Although 36 (72%) of 50 E. coli O25 isolates were ST131, only 6 harboured blaCTX-M. According to the fimH and ybbW sequences and fluoroquinolone susceptibility, H30R1 isolates were dominant (27/36; 75%) and possessed IncFII-FIA-FIB with FAB formula subtype F1:A2:B20 plasmids at a high frequency (24/27; 89%). The F1:A2:B20 plasmids possessed more resistance genes such as blaTEM-1, aminoglycoside resistance genes and trimethoprim/sulfamethoxazole resistance genes compared with non-F1:A2:B20 plasmids. In contrast, only one blaCTX-M-14 gene was located on the F1:A2:B20 plasmids, whereas the other three were located on IncFII (F4:A-:B-) (n = 1) and IncZ (n = 2) plasmids. Two H30Rx-ST131 isolates harboured blaCTX-M-15: one was on the chromosome and the other on the IncFIA-R plasmid. The stability and conjugation ability of the F1:A2:B20 plasmids were compared with those of non-F1:A2:B20 plasmids, which revealed higher stability but lower conjugative ability. CONCLUSIONS These results suggest that E. coli H30R1-ST131 is a multidrug-resistant clone containing several resistance genes in the F1:A2:B20 plasmid, which were widely distributed before the acquisition of blaCTX-M.
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Affiliation(s)
- Michiko Hayashi
- Graduate School of Medicine, Nagoya University, Aichi, Japan; Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mari Matsui
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ayaka Shima
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takaya Segawa
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kumiko Kawamura
- Graduate School of Medicine, Nagoya University, Aichi, Japan
| | - Satowa Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
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Success of Escherichia coli O25b:H4 Sequence Type 131 Clade C Associated with a Decrease in Virulence. Infect Immun 2020; 88:IAI.00576-20. [PMID: 32989036 PMCID: PMC7671891 DOI: 10.1128/iai.00576-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 01/12/2023] Open
Abstract
Escherichia coli O25b:H4 sequence type 131 (ST131), which is resistant to fluoroquinolones and which is a producer of CTX-M-15, is globally one of the major extraintestinal pathogenic E. coli (ExPEC) lineages. Phylogenetic analyses showed that multidrug-resistant ST131 strains belong to clade C, which recently emerged from clade B by stepwise evolution. It has been hypothesized that features other than multidrug resistance could contribute to this dissemination since other major global ExPEC lineages (ST73 and ST95) are mostly antibiotic susceptible. Escherichia coli O25b:H4 sequence type 131 (ST131), which is resistant to fluoroquinolones and which is a producer of CTX-M-15, is globally one of the major extraintestinal pathogenic E. coli (ExPEC) lineages. Phylogenetic analyses showed that multidrug-resistant ST131 strains belong to clade C, which recently emerged from clade B by stepwise evolution. It has been hypothesized that features other than multidrug resistance could contribute to this dissemination since other major global ExPEC lineages (ST73 and ST95) are mostly antibiotic susceptible. To test this hypothesis, we compared early biofilm production, presence of ExPEC virulence factors (VFs), and in vivo virulence in a mouse sepsis model in 19 and 20 epidemiologically relevant strains of clades B and C, respectively. Clade B strains were significantly earlier biofilm producers (P < 0.001), carriers of more VFs (P = 4e−07), and faster killers of mice (P = 2e−10) than clade C strains. Gene inactivation experiments showed that the H30-fimB and ibeART genes were associated with in vivo virulence. Competition assays in sepsis, gut colonization, and urinary tract infection models between the most anciently diverged strain (B1 subclade), one C1 subclade strain, and a B4 subclade recombining strain harboring some clade C-specific genetic events showed that the B1 strain always outcompeted the C1 strain, whereas the B4 strain outcompeted the C1 strain, depending on the mouse niches. All these findings strongly suggest that clade C evolution includes a progressive loss of virulence involving multiple genes, possibly enhancing overall strain fitness by avoiding severe infections, even if it comes at the cost of a lower colonization ability.
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Wee BA, Muloi DM, van Bunnik BAD. Quantifying the transmission of antimicrobial resistance at the human and livestock interface with genomics. Clin Microbiol Infect 2020; 26:1612-1616. [PMID: 32979568 PMCID: PMC7721588 DOI: 10.1016/j.cmi.2020.09.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/05/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Livestock have been implicated as a reservoir for antimicrobial resistance (AMR) that can spread to humans. Close proximity and ecological interfaces involving livestock have been posited as risk factors for the transmission of AMR. In spite of this, there are sparse data and limited agreement on the transmission dynamics that occur. OBJECTIVES To identify how genome sequencing approaches can be used to quantify the dynamics of AMR transmission at the human-livestock interface, and where current knowledge can be improved to better understand the impact of transmission on the spread of AMR. SOURCES Key articles investigating various aspects of AMR transmission at the human-livestock interface are discussed, with a focus on Escherichia coli. CONTENT We recapitulate the current understanding of the transmission of AMR between humans and livestock based on current genomic and epidemiological approaches. We discuss how the use of well-designed, high-resolution genome sequencing studies can improve our understanding of the human-livestock interface. IMPLICATIONS A better understanding of the human-livestock interface will aid in the development of evidence-based and effective One Health interventions that can ultimately reduce the burden of AMR in humans.
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Affiliation(s)
- Bryan A Wee
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Dishon M Muloi
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom; International Livestock Research Institute, Nairobi, Kenya
| | - Bram A D van Bunnik
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Virulence and resistance properties of E. coli isolated from urine samples of hospitalized patients in Rio de Janeiro, Brazil - The role of mobile genetic elements. Int J Med Microbiol 2020; 310:151453. [PMID: 33045580 DOI: 10.1016/j.ijmm.2020.151453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 08/15/2020] [Accepted: 09/25/2020] [Indexed: 02/04/2023] Open
Abstract
Extraintestinal pathogenic E. coli (ExPEC) is the most frequent etiological agent of urinary tract infections (UTIs). Particular evolutionary successful lineages are associated with severe UTIs and higher incidences of multidrug resistance. Most of the resistance genes are acquired by horizontal transfer of plasmids and other mobile genetic elements (MGEs), and this process has been associated with the successful dissemination of particular lineages. Here, we identified the presence of MGEs and their role in virulence and resistance profiles of isolates obtained from the urine of hospitalized patients in Brazil. Isolates belonging to the successful evolutionary lineages of sequence type (ST) 131, ST405, and ST648 were found to be multidrug-resistant, while those belonging to ST69 and ST73 were often not. Among the ST131, ST405, and ST648 isolates with a resistant phenotype, a high number of mainly IncFII plasmids was identified. The plasmids contained resistance cassettes, and these were also found within phage-related sequences and the chromosome of the isolates. The resistance cassettes were found to harbor several resistance genes, including blaCTX-M-15. In addition, in ST131 isolates, diverse pathogenicity islands similar to those found in highly virulent ST73 isolates were detected. Also, a new genomic island associated with several virulence genes was identified in ST69 and ST131 isolates. In addition, several other MGEs present in the ST131 reference strain EC958 were identified in our isolates, most of them exclusively in ST131 isolates. In contrast, genomic islands present in this reference strain were only partially present or completely absent in our ST131 isolates. Of all isolates studied, ST73 and ST131 isolates had the most similar virulence profile. Overall, no clear association was found between the presence of specific MGEs and virulence profiles. Furthermore, the interplay between virulence and resistance by acquiring MGEs seemed to be lineage dependent. Although the acquisition of IncF plasmids, specific PAIs, GIs, and other MGEs seemed to be involved in the success of some lineages, it cannot explain the success of different lineages, also indicating other (host) factors are involved in this process. Nevertheless, the detection, identification, and surveillance of lineage-specific MGEs may be useful to monitor (new) emerging clones.
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Spankie TJ, Haywood AL, Dottorini T, Barrow PA, Hirst JD. Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid. J Mol Graph Model 2020; 101:107723. [PMID: 32927271 DOI: 10.1016/j.jmgm.2020.107723] [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: 06/22/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 10/23/2022]
Abstract
One promising strategy to combat antimicrobial resistance is to use bacteriophages that attach to the sex pili produced by transmissible antimicrobial resistance (AMR) plasmids, infect AMR bacteria and select for loss of the AMR plasmids, prolonging the life of existing antimicrobials. The maturation protein of the bacteriophage MS2 attaches to the pili produced by Incompatibility group F plasmid-containing bacteria. This interaction initiates delivery of the viral genetic material into the bacteria. Using protein-protein docking we constructed a model of the F pilus comprising a trimer of subunits binding to the maturation protein. Interactions between the maturation protein and the F pilus were investigated using molecular dynamics simulations. In silico alanine scanning and in silico single-point mutations were explored, with the longer term aim of increasing the affinity of the maturation protein to other Incompatibility group pili, without reducing the strength of binding to F pilin. We report our computational findings on which residues are required for the maturation protein and F pilin to interact, those which had no effect on the interaction and the mutations which led to a stronger interaction.
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Affiliation(s)
- Timothy J Spankie
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Alexe L Haywood
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE125RD, UK
| | - Paul A Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE125RD, UK
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK.
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Abstract
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times during E. coli evolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.
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