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Allain M, Morel-Journel T, Condamine B, Gibeaux B, Gachet B, Gschwind R, Denamur E, Landraud L. IncC plasmid genome rearrangements influence the vertical and horizontal transmission tradeoff in Escherichia coli. Antimicrob Agents Chemother 2024; 68:e0055424. [PMID: 39194203 DOI: 10.1128/aac.00554-24] [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: 04/17/2024] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
It has been shown that an evolutionary tradeoff between vertical (host growth rate) and horizontal (plasmid conjugation) transmissions contributes to global plasmid fitness. As conjugative IncC plasmids are important for the spread of multidrug resistance (MDR), in a broad range of bacterial hosts, we investigated vertical and horizontal transmissions of two multidrug-resistant IncC plasmids according to their backbones and MDR-region rearrangements, upon plasmid entry into a new host. We observed plasmid genome deletions after conjugation in three diverse natural Escherichia coli clinical strains, varying from null to high number depending on the plasmid, all occurring in the MDR region. The plasmid burden on bacterial fitness depended more on the strain background than on the structure of the MDR region, with deletions appearing to have no impact. Besides, we observed an increase in plasmid transfer rate, from ancestral host to new clinical recipient strains, when the IncC plasmid was rearranged. Finally, using a second set of conjugation experiments, we investigated the evolutionary tradeoff of the IncC plasmid during the critical period of plasmid establishment in E. coli K-12, by correlating the transfer rates of deleted or non-deleted IncC plasmids and their costs on the recipient strain. Plasmid deletions strongly improved conjugation efficiency with no negative growth effect. Our findings indicate that the flexibility of the MDR-region of the IncC plasmids can promote their dissemination, and provide diverse opportunities to capture new resistance genes. In a broader view, they suggest that the vertical-horizontal transmission tradeoff can be manipulated by the plasmid to improve its fitness.
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Affiliation(s)
- Margaux Allain
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- AP-HP, Laboratoire de Microbiologie Hygiène, Hôpital Louis Mourier, Colombes, France
| | - Thibaut Morel-Journel
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Bénédicte Condamine
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Benoist Gibeaux
- AP-HP, Laboratoire de Microbiologie Hygiène, Hôpital Louis Mourier, Colombes, France
| | - Benoit Gachet
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Rémi Gschwind
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Erick Denamur
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Luce Landraud
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- AP-HP, Laboratoire de Microbiologie Hygiène, Hôpital Louis Mourier, Colombes, France
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Crettels L, Burlion N, Habets A, Taminiau B, Daube G, Delrée E, Mouchette AF, Thiry D. Exploring the presence, genomic traits, and pathogenic potential of extended-spectrum β-lactamase Escherichia coli in freshwater, wastewater, and hospital effluents. J Appl Microbiol 2024; 135:lxae144. [PMID: 38906843 DOI: 10.1093/jambio/lxae144] [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: 11/16/2023] [Revised: 05/30/2024] [Accepted: 06/20/2024] [Indexed: 06/23/2024]
Abstract
AIMS The purpose of this work was to study extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) in freshwaters, hospital effluents, and wastewaters during two sampling campaigns in 2021. METHODS AND RESULTS Water sampling was performed at 24 stations in the Ourthe watershed in Belgium. A total of 644 ESBL (n = 642) and AmpC (n = 2) E. coli strains were isolated. Disk-diffusion assays were performed following the EUCAST's recommendations. All strains were tested for the presence of blaCTX-M-1, blaCTX-M-2, and blaCTX-M-9 gene groups by PCR. Genes belonging to blaCTX-M-1 and blaCTX-M-9 groups were detected, respectively, in 73.6% and 14.9% of the strains. No blaCTX-M-2 group's gene was found. A subset of strains (n = 40) was selected for whole genome sequencing. Escherichia coli serotype O18: H7 ST 1463 was predominant (n = 14) in the sequenced strains and showed pathogenicity in the Galleria mellonella larvae model. β-lactamase genes identified were blaCTX-M (n = 21), with blaCTX-M-15 mostly represented (n = 15), as well as blaTEM (n = 11), blaOXA (n = 7), blaSHV (n = 9), and carbapenemase (CP) genes were observed in several strains-blaKPC-3 (n = 19), blaNDM-1 (n = 1), blaVIM-1 (n = 2), and blaOXA-244 (n = 2)-even from freshwaters. CONCLUSIONS ESBL-EC are widely distributed in the aquatic environment in Belgium and contain a variety of ESBL and CP genes.
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Affiliation(s)
- Leslie Crettels
- Department of Microbiology, Scientific Institute of Public Service (ISSeP), 4000 Liège, Belgium
- Veterinary bacteriology and bacterial animal diseases, Department of Parasitic and Infectious Diseases, Fundamental and Applied Research for Animals and Health Centre (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Nadine Burlion
- Department of Microbiology, Scientific Institute of Public Service (ISSeP), 4000 Liège, Belgium
| | - Audrey Habets
- Veterinary bacteriology and bacterial animal diseases, Department of Parasitic and Infectious Diseases, Fundamental and Applied Research for Animals and Health Centre (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Bernard Taminiau
- Department of Food Sciences-Microbiology, Fundamental and Applied Research for Animals and Health Centre (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Georges Daube
- Department of Food Sciences-Microbiology, Fundamental and Applied Research for Animals and Health Centre (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Elisa Delrée
- Department of Microbiology, Scientific Institute of Public Service (ISSeP), 4000 Liège, Belgium
| | | | - Damien Thiry
- Veterinary bacteriology and bacterial animal diseases, Department of Parasitic and Infectious Diseases, Fundamental and Applied Research for Animals and Health Centre (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
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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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Allain M, Mahérault AC, Gachet B, Martinez C, Condamine B, Magnan M, Kempf I, Denamur E, Landraud L. Dissemination of IncI plasmid encoding bla CTX-M-1 is not hampered by its fitness cost in the pig's gut. Antimicrob Agents Chemother 2023; 67:e0011123. [PMID: 37702541 PMCID: PMC10583664 DOI: 10.1128/aac.00111-23] [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: 02/02/2023] [Accepted: 07/01/2023] [Indexed: 09/14/2023] Open
Abstract
Multiresistance plasmids belonging to the IncI incompatibility group have become one of the most pervasive plasmid types in extended-spectrum beta-lactamase-producing Escherichia coli of animal origin. The extent of the burden imposed on the bacterial cell by these plasmids seems to modulate the emergence of "epidemic" plasmids. However, in vivo data in the natural environment of the strains are scarce. Here, we investigated the cost of a bla CTX-M-1-IncI1 epidemic plasmid in a commensal E. coli animal strain, UB12-RC, before and after oral inoculation of 15 6- to 8-week- old specific-pathogen-free pigs. Growth rate in rich medium was determined on (i) UB12-RC and derivatives, with or without plasmid, in vivo and/or in vitro evolved, and (ii) strains that acquired the plasmid in the gut during the experiment. Although bla CTX-M-1-IncI1 plasmid imposed no measurable burden on the recipient strain after conjugation and during the longitudinal carriage in the pig's gut, we observed a significant difference in the bacterial growth rate between IncI1 plasmid-carrying and plasmid-free isolates collected during in vivo carriage. Only a few mutations on the chromosome of the UB12-RC derivatives were detected by whole-genome sequencing. RNA-Seq analysis of a selected set of these strains showed that transcriptional responses to the bla CTX-M-1-IncI1 acquisition were limited, affecting metabolism, stress response, and motility functions. Our data suggest that the effect of IncI plasmid on host cells is limited, fitness cost being insufficient to act as a barrier to IncI plasmid spread among natural population of E. coli in the gut niche.
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Affiliation(s)
- Margaux Allain
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- AP-HP, Laboratoire de Microbiologie Hygiène, Hôpital Louis Mourier, Colombes, France
| | - Anne Claire Mahérault
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- AP-HP, Laboratoire de Microbiologie Hygiène, Hôpital Louis Mourier, Colombes, France
| | - Benoit Gachet
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Caroline Martinez
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Bénédicte Condamine
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Mélanie Magnan
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Isabelle Kempf
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Erick Denamur
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Luce Landraud
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- AP-HP, Laboratoire de Microbiologie Hygiène, Hôpital Louis Mourier, Colombes, France
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Choudhury A, Gachet B, Dixit Z, Faure R, Gill RT, Tenaillon O. Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs. Nat Commun 2023; 14:6319. [PMID: 37813857 PMCID: PMC10562459 DOI: 10.1038/s41467-023-41882-7] [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: 09/21/2023] [Indexed: 10/11/2023] Open
Abstract
RNA polymerase (RNAP) is emblematic of complex biological systems that control multiple traits involving trade-offs such as growth versus maintenance. Laboratory evolution has revealed that mutations in RNAP subunits, including RpoB, are frequently selected. However, we lack a systems view of how mutations alter the RNAP molecular functions to promote adaptation. We, therefore, measured the fitness of thousands of mutations within a region of rpoB under multiple conditions and genetic backgrounds, to find that adaptive mutations cluster in two modules. Mutations in one module favor growth over maintenance through a partial loss of an interaction associated with faster elongation. Mutations in the other favor maintenance over growth through a destabilized RNAP-DNA complex. The two molecular handles capture the versatile RNAP-mediated adaptations. Combining both interaction losses simultaneously improved maintenance and growth, challenging the idea that growth-maintenance tradeoff resorts only from limited resources, and revealing how compensatory evolution operates within RNAP.
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Affiliation(s)
- Alaksh Choudhury
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France.
- Laboratoire Biophysique et Évolution (LBE), UMR Chimie Biologie Innovation 8231, ESPCI Paris, Université PSL, CNRS, 75005, Paris, France.
| | - Benoit Gachet
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
| | - Zoya Dixit
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
- Université de Paris Cité, INSERM, CNRS, Institut Cochin, UMR 1016, 75014, Paris, France
| | - Roland Faure
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
- Université de Rennes, INRIA RBA, CNRS UMR 6074, Rennes, France
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Ryan T Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado-Boulder, Boulder, CO, 80309-0027, USA
- Novo Nordisk Foundation, Denmark Technical University, 2800 Kgs, Lyngby, Denmark
| | - Olivier Tenaillon
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France.
- Université de Paris Cité, INSERM, CNRS, Institut Cochin, UMR 1016, 75014, Paris, France.
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Farizqi MTI, Effendi MH, Adikara RTS, Yudaniayanti IS, Putra GDS, Khairullah AR, Kurniawan SC, Silaen OSM, Ramadhani S, Millannia SK, Kaben SE, Waruwu YKK. Detection of extended-spectrum β-lactamase-producing Escherichia coli genes isolated from cat rectal swabs at Surabaya Veterinary Hospital, Indonesia. Vet World 2023; 16:1917-1925. [PMID: 37859949 PMCID: PMC10583880 DOI: 10.14202/vetworld.2023.1917-1925] [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: 06/22/2023] [Accepted: 08/29/2023] [Indexed: 10/21/2023] Open
Abstract
Background and Aim Escherichia coli causes a bacterial illness that frequently affects cats. Diseases caused by E. coli are treated using antibiotics. Because of their proximity to humans, cats possess an extremely high risk of contracting antibiotic resistance genes when their owners touch cat feces containing E. coli that harbor resistance genes. This study was conducted to identify multidrug-resistant E. coli and extended-spectrum β-lactamase (ESBL)-producing genes from cat rectal swabs collected at Surabaya City Veterinary Hospital to determine antibiotic sensitivity. Materials and Methods Samples of cat rectal swabs were cultured in Brilliant Green Bile Lactose Broth medium and then streaked on eosin methylene blue agar medium for bacterial isolation, whereas Gram-staining and IMViC tests were conducted to confirm the identification results. The Kirby-Bauer diffusion test was used to determine antibiotic sensitivity, and the double-disk synergy test was used to determine ESBL-producing bacteria. Molecular detection of the genes TEM and CTX-M was performed using a polymerase chain reaction. Results Based on morphological culture, Gram-staining, and biochemical testing, the results of sample inspection showed that of the 100 cat rectal swab samples isolated, 71 (71%) were positive for E. coli. Furthermore, 23 E. coli isolates (32.39%) demonstrated the highest resistance to ampicillin. Four isolates were confirmed to be multidurg-resistant and ESBL-producing strains. Molecular examination revealed that three E. coli isolates harbored TEM and CTX-M. Conclusion In conclusion, pet owners must be educated on the use of antibiotics to improve their knowledge about the risks of antibiotic resistance.
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Affiliation(s)
- M. Thoriq Ihza Farizqi
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya, 60115, East Java, Indonesia
| | - Mustofa Helmi Effendi
- Division of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya, 60115, East Java, Indonesia
| | - R. Tatang Santanu Adikara
- Division of Veterinary Anatomy, Faculty of Veterinary Medicine, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya, 60115, East Java, Indonesia
| | - Ira Sari Yudaniayanti
- Division of Veterinary Clinic, Faculty of Veterinary Medicine, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabay, 60115, East Java, Indonesia
| | - Giovanni Dwi Syahni Putra
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya, 60115, East Java, Indonesia
| | - Aswin Rafif Khairullah
- Division of Animal Husbandry, Faculty of Veterinary Medicine, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya, 60115, East Java, Indonesia
| | - Shendy Canadya Kurniawan
- Department of Animal Sciences, Specialisation in Molecule, Cell and Organ Functioning, Wageningen University and Research. Wageningen, 6708 PB, Netherlands
| | - Otto Sahat Martua Silaen
- Department of Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya No. 6 Senen, Jakarta, 10430, Indonesia
| | - Safira Ramadhani
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya, 60115, East Java, Indonesia
| | - Saumi Kirey Millannia
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya, 60115, East Java, Indonesia
| | - Sergius Erikson Kaben
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya, 60115, East Java, Indonesia
| | - Yusac Kristanto Khoda Waruwu
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, Universitas Airlangga. Jl. Dr. Ir. H. Soekarno, Kampus C Mulyorejo, Surabaya, 60115, East Java, Indonesia
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dos Santos AMP, Panzenhagen P, Ferrari RG, de Jesus ACS, Portes AB, Ochioni AC, Rodrigues DDP, Conte-Junior CA. Genomic Characterization of Salmonella Isangi: A Global Perspective of a Rare Serovar. Antibiotics (Basel) 2023; 12:1309. [PMID: 37627729 PMCID: PMC10451742 DOI: 10.3390/antibiotics12081309] [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: 07/20/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Salmonella Isangi is an infrequent serovar that has recently been reported in several countries due to nosocomial infections. A considerable number of reports indicate Salmonella Isangi multidrug resistance, especially to cephalosporins, which could potentially pose a risk to public health worldwide. Genomic analysis is an excellent tool for monitoring the emergence of microorganisms and related factors. In this context, the aim of this study was to carry out a genomic analysis of Salmonella Isangi isolated from poultry in Brazil, and to compare it with the available genomes from the Pathogen Detection database and Sequence Read Archive. A total of 142 genomes isolated from 11 different countries were investigated. A broad distribution of extended-spectrum beta-lactamase (ESBL) genes was identified in the Salmonella Isangi genomes examined (blaCTX-M-15, blaCTX-M-2, blaDHA-1, blaNDM-1, blaOXA-10, blaOXA-1, blaOXA-48, blaSCO-1, blaSHV-5, blaTEM-131, blaTEM-1B), primarily in South Africa. Resistome analysis revealed predicted resistance to aminoglycoside, sulfonamide, macrolide, tetracycline, trimethoprim, phenicol, chloramphenicol, and quaternary ammonium. Additionally, PMQR (plasmid-mediated quinolone resistance) genes qnr19, qnrB1, and qnrS1 were identified, along with point mutations in the genes gyrAD87N, gyrAS83F, and gyrBS464F, which confer resistance to ciprofloxacin and nalidixic acid. With regard to plasmids, we identified 17 different incompatibility groups, including IncC, Col(pHAD28), IncHI2, IncHI2A, IncM2, ColpVC, Col(Ye4449), Col156, IncR, IncI1(Alpha), IncFIB (pTU3), Col(B5512), IncQ1, IncL, IncN, IncFIB(pHCM2), and IncFIB (pN55391). Phylogenetic analysis revealed five clusters grouped by sequence type and antimicrobial gene distribution. The study highlights the need for monitoring rare serovars that may become emergent due to multidrug resistance.
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Affiliation(s)
- Anamaria Mota Pereira dos Santos
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Veterinary Hygiene (PGHIGVET), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Niterói 24230-340, RJ, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
| | - Rafaela G. Ferrari
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
| | - Ana Carolina S. de Jesus
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
| | - Ana Beatriz Portes
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Veterinary Hygiene (PGHIGVET), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Niterói 24230-340, RJ, Brazil
| | - Alan Clavelland Ochioni
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
| | | | - Carlos Adam Conte-Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-598, RJ, Brazil; (A.M.P.d.S.); (R.G.F.); (A.C.S.d.J.); (A.B.P.); (A.C.O.); (C.A.C.-J.)
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Veterinary Hygiene (PGHIGVET), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Niterói 24230-340, RJ, Brazil
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
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8
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A Trade-Off for Maintenance of Multidrug-Resistant IncHI2 Plasmids in Salmonella enterica Serovar Typhimurium through Adaptive Evolution. mSystems 2022; 7:e0024822. [PMID: 36040022 PMCID: PMC9599605 DOI: 10.1128/msystems.00248-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Understanding the fitness costs associated with plasmid carriage is a key to better understanding the mechanisms of plasmid maintenance in bacteria. In the current work, we performed multiple serial passages (63 days, 627.8 generations) to identify the compensatory mechanisms that Salmonella enterica serovar Typhimurium ATCC 14028 utilized to maintain the multidrug-resistant (MDR) IncHI2 plasmid pJXP9 in the presence and absence of antibiotic selection. The plasmid pJXP9 was maintained for hundreds of generations even without drug exposure. Endpoint evolved (the endpoint of evolution) S. Typhimurium bearing evolved plasmids displayed decreased growth lag times and a competitive advantage over ancestral pJXP9 plasmid-carrying ATCC 14028 strains. Genomic and transcriptomic analyses revealed that the fitness costs of carrying pJXP9 were derived from both specific plasmid genes and particularly the MDR regions and conjugation transfer region I and conflicts resulting from chromosome-plasmid gene interactions. Correspondingly, plasmid deletions of these regions could compensate for the fitness cost that was due to the plasmid carriage. The deletion extent and range of large fragments on the evolved plasmids, as well as the trajectory of deletion mutation, were related to the antibiotic treatment conditions. Furthermore, it is also adaptive evolution that chromosomal gene mutations and altered mRNA expression correlated with changed physiological functions of the bacterium, such as decreased flagellar motility, increased oxidative stress, and fumaric acid synthesis but increased Cu resistance in a given niche. Our findings indicated that plasmid maintenance evolves via a plasmid-bacterium adaptative evolutionary process that is a trade-off between vertical and horizontal transmission costs along with associated alterations in host bacterial physiology. IMPORTANCE The current idea that compensatory evolution processes can account for the "plasmid paradox" phenomenon associated with the maintenance of large costly plasmids in host bacteria has attracted much attention. Although many compensatory mutations have been discovered through various plasmid-host bacterial evolution experiments, the basis of the compensatory mechanisms and the nature of the bacteria themselves to address the fitness costs remain unclear. In addition, the genetic backgrounds of plasmids and strains involved in previous research were limited and clinical drug resistance such as the poorly understood compensatory evolution among clinically dominant multidrug-resistant plasmids or clones was rarely considered. The IncHI2 plasmid is widely distributed in Salmonella Typhimurium and plays an important role in the emergence and rapid spread of its multidrug resistance. In this study, the predominant multidrug-resistant IncHI2 plasmid pJXP9 and the standard Salmonella Typhimurium ATCC 14028 bacteria were used for evolution experiments under laboratory conditions. Our findings indicated that plasmid maintenance through experimental evolution of plasmid-host bacteria is a trade-off between increasing plasmid vertical transmission and impairing its horizontal transmission and bacterial physiological phenotypes, in which compensatory mutations and altered chromosomal expression profiles collectively contribute to alleviating plasmid-borne fitness cost. These results provided potential insights into understanding the relationship of coexistence between plasmids encoding antibiotic resistance and their bacterial hosts and provided a clue to the adaptive forces that shaped the evolution of these plasmids within bacteria and to predicting the evolution trajectory of antibiotic resistance.
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9
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Palkovicova J, Sukkar I, Delafuente J, Valcek A, Medvecky M, Jamborova I, Bitar I, Phan MD, San Millan A, Dolejska M. Fitness effects of blaCTX-M-15-harbouring F2:A1:B- plasmids on their native Escherichia coli ST131 H30Rx hosts. J Antimicrob Chemother 2022; 77:2960-2963. [PMID: 35880751 DOI: 10.1093/jac/dkac250] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/27/2022] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES To investigate the fitness effects of large blaCTX-M-15-harbouring F2:A1:B- plasmids on their native Escherichia coli ST131 H30Rx hosts. METHODS We selected five E. coli ST131 H30Rx isolates of diverse origin, each carrying an F2:A1:B- plasmid with the blaCTX-M-15 gene. The plasmid was eliminated from each isolate by displacement using an incompatible curing plasmid, pMDP5_cureEC958. WGS was performed to obtain complete chromosome and plasmid sequences of original isolates and to detect chromosomal mutations in 'cured' clones. High-throughput competition assays were conducted to determine the relative fitness of cured clones compared with the corresponding original isolates. RESULTS We were able to successfully eliminate the F2:A1:B- plasmids from all five original isolates using pMDP5_cureEC958. The F2:A1:B- plasmids produced non-significant fitness effects in three isolates and moderate reductions in relative fitness (3%-4%) in the two remaining isolates. CONCLUSIONS We conclude that F2:A1:B- plasmids pose low fitness costs in their E. coli ST131 H30Rx hosts. This plasmid-host fitness compatibility is likely to promote the maintenance of antibiotic resistance in this clinically important E. coli lineage.
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Affiliation(s)
- Jana Palkovicova
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic.,Department of Biology and Wildlife Diseases, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Iva Sukkar
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Javier Delafuente
- Department of Microbiology, Hospital Universitario Ramon y Cajal (IRYCIS), Madrid, Spain
| | - Adam Valcek
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic.,Microbial Resistance and Drug Discovery, VIB-VUB Centre for Structural Biology, VIB, Flanders Institute for Biotechnology, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Matej Medvecky
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ivana Jamborova
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Ibrahim Bitar
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Minh Duy Phan
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Monika Dolejska
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic.,Department of Biology and Wildlife Diseases, University of Veterinary Sciences Brno, Brno, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.,Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czech Republic
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10
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Spreading Advantages of Coresident Plasmids blaCTX-M-Bearing IncFII and mcr-1-Bearing IncI2 in Escherichia coli. Microbiol Spectr 2022; 10:e0170621. [PMID: 35171014 PMCID: PMC8849077 DOI: 10.1128/spectrum.01706-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two diverse conjugative plasmids can interact within bacterial cells. However, to the best of our knowledge, the interaction between blaCTX-M-bearing IncFII plasmid and mcr-1-carrying IncI2 plasmid colocated on the same bacterial host has not been reported. This study was initiated to explore the interaction and to analyze the reasons that these two plasmids are often coresident in multidrug-resistant Escherichia coli. To assess the interactions on plasmid stabilities, fitness costs, and transfer rates, we constructed two groups of isogenic derivatives, C600FII, C600I2, and C600FII+I2 of E. coli C600 and J53FII, J53I2, and J53FII+I2 of E. coli J53, respectively. We found that carriage of FII and I2 plasmids, independently and together, had not impaired the growth of the bacterial host. It was difficult for the single plasmid FII or I2 in E. coli C600 to reach stable persistence for a long time in an antibiotic-free environment, while the stability would be striking improved when they coresided. Meanwhile, plasmids FII and I2, whether together or apart, could notably enhance the fitness advantage of the host; moreover, E. coli coharboring plasmids FII and I2 presented more obvious fitness advantage than that carrying single plasmid FII. Coresident plasmids FII and I2 could accelerate horizontal cotransfer by conjugation. The transfer rates from a strain carrying coresident FII and I2 plasmids increased significantly when it mated with a recipient cell carrying one of them. Our findings highlight the advantages of coinhabitant FII and I2 plasmids in E. coli to drive the persistence and spread of plasmid-carried blaCTX-M and mcr-1 genes, although the molecular mechanisms of their coresidence warrant further study. IMPORTANCE More and more Enterobacteriaceae carry both blaCTX-M and mcr-1, which are usually located on IncFII-type and IncI2-type plasmids in the same bacterial host, respectively. However, the study on advantages of coresident plasmids in bacterial host is still sparse. Here, we investigated the stability, fitness cost, and cotransfer traits associated with coresident IncFII-type and IncI2-type plasmids in E. coli. Our results show that coinhabitant plasmids in E. coli are more stable, confer more fitness advantages, and are easier to transfer and cotransfer than a single plasmid IncFII or IncI2. Our findings confirm the advantages of coresident plasmids of blaCTX-M-bearing IncFII and mcr-1-bearing IncI2 in clinical E. coli, which will pose a serious threat to clinical therapy and public health.
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11
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Chen S, Wan L, Wei DD, Du F, Huang QS, Liu Y. High Prevalence and Fitness of IncFrepB Carrying qnrS1 in Hypervirulent Klebsiella pneumoniae Isolates. Microb Drug Resist 2022; 28:361-369. [PMID: 35021884 DOI: 10.1089/mdr.2021.0241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Objective: This study aimed to reveal the prevalence and fitness of qnrS1-carrying plasmids in hypervirulent Klebsiella pneumoniae (hvKP) isolates. Materials and Methods: Two hundred ninety-nine hvKP strains carrying qnrS1 were collected and screened for resistance genes using PCR and sequencing. The location of qnrS1 and rmpA2 was identified by Southern blotting. The transferability and fitness of qnrS1-carrying plasmids were analyzed by conjugation experiments and plasmid stability assay. Result: In 299 hvKP isolates, the most frequently detected capsular serotype was K64 (81.9%, 245/299), followed by K1 (4.7%, 14/299) and K2 (3.7%, 11/299). All K64-hvKP were sequence type (ST) 11. The qnrS1 and rmpA2 gene mainly was located on the ∼70-210 kb IncFrepB and ∼170-220 kb IncFIB plasmid, respectively. QnrS1-carrying plasmids could be transferred into Escherichia coli J53. However, the plasmid was transferred at a low rate of 13.4% (40/299). The 40 donor isolates belong to 4 STs-ST11, ST700, ST592, and ST86, and none contains the CRISPR-Cas loci. CRISPR-Cas loci were mainly found in ST23 K. pneumoniae. The relative fitness (RF) of qnrS1-carrying plasmids in ST86 and ST11 (cotransfer with blaTEM-1 genes) was more than one and enhanced during cultivation, especially in ST86. However, the RF of qnrS1-carrying plasmids in ST592 and ST700 showed a high fitness cost. Whole-genome sequencing showed that the qnrS1-carrying plasmids in ST86 harbored more maintenance modules (SOS inhibitor protein psiB, parA, and parB partition systems) and insertion sequence (IS) elements (IS91, IS481-like, IS1380), indicating that the qnrS1-carrying plasmid in ST86 is more stable than the other types of qnrS1-carrying plasmids. Conclusion: QnrS1-carrying IncFrepB plasmids were highly prevalent and show polymorphism in hvKP strains. The qnrS1-carrying IncFrepB plasmid in ST86 hvKP should be highlighted due to its remarkable adaptability advantages.
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Affiliation(s)
- Si Chen
- Department of Bacteriology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China.,School of Public Health, Nanchang University, Nanchang, P.R. China
| | - Lagen Wan
- Department of Bacteriology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China
| | - Dan-Dan Wei
- Department of Bacteriology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China
| | - Fanglin Du
- Department of Bacteriology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China
| | - Qi-Seng Huang
- Department of Bacteriology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China.,School of Public Health, Nanchang University, Nanchang, P.R. China
| | - Yang Liu
- Department of Bacteriology, The First Affiliated Hospital of Nanchang University, Nanchang, P.R. China
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12
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Milenkov M, Rasoanandrasana S, Rahajamanana LV, Rakotomalala RS, Razafindrakoto CA, Rafalimanana C, Ravelomandranto E, Ravaoarisaina Z, Westeel E, Petitjean M, Mullaert J, Clermont O, Raskine L, Samison LH, Endtz H, Andremont A, Denamur E, Komurian-Pradel F, Armand-Lefevre L. Prevalence, Risk Factors, and Genetic Characterization of Extended-Spectrum Beta-Lactamase Escherichia coli Isolated From Healthy Pregnant Women in Madagascar. Front Microbiol 2021; 12:786146. [PMID: 35003019 PMCID: PMC8740230 DOI: 10.3389/fmicb.2021.786146] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial resistance is a major public health concern worldwide affecting humans, animals and the environment. However, data is lacking especially in developing countries. Thus, the World Health Organization developed a One-Health surveillance project called Tricycle focusing on the prevalence of ESBL-producing Escherichia coli in humans, animals, and the environment. Here we present the first results of the human community component of Tricycle in Madagascar. From July 2018 to April 2019, rectal swabs from 492 pregnant women from Antananarivo, Mahajanga, Ambatondrazaka, and Toamasina were tested for ESBL-E. coli carriage. Demographic, sociological and environmental risk factors were investigated, and E. coli isolates were characterized (antibiotic susceptibility, resistance and virulence genes, plasmids, and genomic diversity). ESBL-E. coli prevalence carriage in pregnant women was 34% varying from 12% (Toamasina) to 65% (Ambatondrazaka). The main risk factor associated with ESBL-E. coli carriage was the rainy season (OR = 2.9, 95% CI 1.3-5.6, p = 0.009). Whole genome sequencing was performed on 168 isolates from 144 participants. bla CTX-M-15 was the most frequent ESBL gene (86%). One isolate was resistant to carbapenems and carried the bla NDM-5 gene. Most isolates belonged to commensalism associated phylogenetic groups A, B1, and C (90%) and marginally to extra-intestinal virulence associated phylogenetic groups B2, D and F (10%). Multi locus sequence typing showed 67 different sequence types gathered in 17 clonal complexes (STc), the most frequent being STc10/phylogroup A (35%), followed distantly by the emerging STc155/phylogroup B1 (7%), STc38/phylogroup D (4%) and STc131/phylogroup B2 (3%). While a wide diversity of clones has been observed, SNP analysis revealed several genetically close isolates (n = 34/168) which suggests human-to-human transmissions. IncY plasmids were found with an unusual prevalence (23%), all carrying a bla CTX-M-15. Most of them (85%) showed substantial homology (≥85%) suggesting a dissemination of IncY ESBL plasmids in Madagascar. This large-scale study reveals a high prevalence of ESBL-E. coli among pregnant women in four cities in Madagascar associated with warmth and rainfall. It shows the great diversity of E. coli disseminating throughout the country but also transmission of specific clones and spread of plasmids. This highlights the urgent need of public-health interventions to control antibiotic resistance in the country.
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Affiliation(s)
- Milen Milenkov
- Fondation Mérieux, Lyon, France
- Université de Paris, IAME, INSERM UMR 1137, Paris, France
| | - Saida Rasoanandrasana
- Laboratoire de Bactériologie, CHU Joseph Raseta Befelatanana, RESAMAD Network, Antananarivo, Madagascar
| | | | | | | | - Christian Rafalimanana
- Laboratoire de Bactériologie, CHU Joseph Ravoahangy Andrianavalona, RESAMAD Network, Antananarivo, Madagascar
| | - Emile Ravelomandranto
- Laboratoire de Bactériologie, CHRR Alaotra Mangoro, RESAMAD Network, Ambatondrazaka, Madagascar
| | | | | | | | - Jimmy Mullaert
- Université de Paris, IAME, INSERM UMR 1137, Paris, France
| | | | | | - Luc Hervé Samison
- Centre d’Infectiologie Charles Mérieux, University of Antananarivo, Antananarivo, Madagascar
| | - Hubert Endtz
- Fondation Mérieux, Lyon, France
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, Netherlands
| | | | - Erick Denamur
- Université de Paris, IAME, INSERM UMR 1137, Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, Paris, France
| | | | - Laurence Armand-Lefevre
- Université de Paris, IAME, INSERM UMR 1137, Paris, France
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, Paris, France
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13
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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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14
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Suzuki M, Norizuki C, Wachino JI, Kawamura K, Nagano N, Nagano Y, Hayashi W, Kimura K, Doi Y, Arakawa Y. Dissecting the clonality of I1 plasmids using ORF-based binarized structure network analysis of plasmids (OSNAp). J Infect Chemother 2021; 28:473-479. [PMID: 34916137 DOI: 10.1016/j.jiac.2021.12.003] [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: 09/29/2021] [Revised: 11/18/2021] [Accepted: 12/05/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVES We aimed to elucidate the relationship among blaCTX-M-carrying plasmids and their transmission between humans and domestic animals. METHODS Phylogenetic relationship of 90 I1 plasmids harboring blaCTX-M genes encoding extended-spectrum β-lactamase (ESBL) was analyzed using the ORF-based binarized structure network analysis of plasmids (OSNAp). RESULTS The majority of plasmids carrying blaCTX-M-1 or blaCTX-M-8 belonged to a single lineage, respectively, and were primarily associated with domestic animals especially chickens. On the other hand, plasmids carrying blaCTX-M-14 or blaCTX-M-15, identified from both humans and domestic animals, were distributed in two or more lineages. CONCLUSION OSNAp has revealed the phylogenetic relationships and diversity of plasmids carrying blaCTX-M more distinctly than pMLST. The findings suggest that circulation of I1 plasmids between humans and animals may contribute to their diversity.
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Affiliation(s)
- Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan.
| | - Chihiro Norizuki
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Jun-Ichi Wachino
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Kumiko Kawamura
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Noriyuki Nagano
- Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Nagano, Japan
| | - Yukiko Nagano
- Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Nagano, Japan
| | - Wataru Hayashi
- Department of Medical Sciences, Shinshu University Graduate School of Medicine, Science and Technology, Nagano, Japan
| | - Kouji Kimura
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Yohei Doi
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan; Department of Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan; Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Aichi, Japan
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15
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Interplay between Bacterial Clones and Plasmids in the Spread of Antibiotic Resistance Genes in the Gut: Lessons from a Temporal Study in Veal Calves. Appl Environ Microbiol 2021; 87:e0135821. [PMID: 34613750 DOI: 10.1128/aem.01358-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli is a frequent, increasing, and worrying phenomenon, but little is known about the molecular scenario and the evolutionary forces at play. We screened 45 veal calves, known to have high prevalence of carriage, for ESBL-producing E. coli on 514 rectal swabs (one randomly selected colony per sample) collected over 6 months. We characterized the bacterial clones and plasmids carrying blaESBL genes with a combination of genotyping methods, whole genome sequencing, and conjugation assays. One hundred and seventy-three ESBL-producing E. coli isolates [blaCTX-M-1 (64.7%), blaCTX-M-14 (33.5%), or blaCTX-M-15 (1.8%)] were detected, belonging to 32 bacterial clones, mostly of phylogroup A. Calves were colonized successively by different clones with a trend in decreasing carriage. The persistence of a clone in a farm was significantly associated with the number of calves colonized. Despite a high diversity of E. coli clones and blaCTX-M-carrying plasmids, few blaCTX-M gene/plasmid/chromosomal background combinations dominated, due to (i) efficient colonization of bacterial clones and/or (ii) successful plasmid spread in various bacterial clones. The scenario "clone versus plasmid spread" depended on the farm. Thus, epistatic interactions between resistance genes, plasmids, and bacterial clones contribute to optimize fitness in specific environments. IMPORTANCE The gut microbiota is the epicenter of the emergence of resistance. Considerable amount of knowledge on the molecular mechanisms of resistance has been accumulated, but the ecological and evolutionary forces at play in nature are less studied. In this context, we performed a field work on temporal intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli in veal farms. Veal calves are animals with one of the highest levels of ESBL producing E. coli fecal carriage, due to early high antibiotic exposure. We were able to show that calves were colonized successively by different ESBL-producing E. coli clones, and that two main scenarios were at play in the spread of blaCTX-M genes among calves: efficient colonization of several calves by a few bacterial clones and successful plasmid spread in various bacterial clones. Such knowledge should help develop new strategies to fight the emergence of antibiotic-resistance.
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Mitra SD, Irshad P, Anusree M, Rekha I, Shailaja S, Suresh J, Aishwarya G, Shrestha S, Shome BR. Whole genome global insight of antibiotic resistance gene repertoire and virulome of high - risk multidrug-resistant Uropathogenic Escherichiacoli. Microb Pathog 2021; 161:105256. [PMID: 34695556 DOI: 10.1016/j.micpath.2021.105256] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/06/2021] [Accepted: 10/14/2021] [Indexed: 12/17/2022]
Abstract
Elucidation of genetic determinants via whole genome sequence (WGS) analyses can help understand the high risk multidrug-resistant (MDR) Uropathogenic Escherichia coli (UPEC) associated with urinary tract infections (UTI) and its evasion strategies from treatment. We investigated the WGS of 30 UPEC strains from UTI samples across the world (2016-2019) and found 25 UPEC strains carrying 2-23 antibiotic resistance genes (ARGs) scattered across 1-3 plasmids per strain. Different ARGs (blaTEM, blaCTXM, blaNDM, blaOXA, blaCMY) encoding extended-spectrum beta-lactamases (TEM, CTXM, CMY) and carbapenemases (NDM, OXA) were found in 24/30, ARGs encoding aminoglycoside modifying enzymes (AAC, APH, AAD) variants in 23/30, trimethoprim ARGs (dfrA17, dfrA12, dfrA5, dfrB4 variants) encoding dihydrofolate reductase in 19/30 and sulfonamide ARGs (sul1, sul2, sul3) encoding dihydropteroate synthase and macrolide ARGs (mph1) encoding macrolide 2' phosphotransferase in 15/30 UPEC strains. Collectively the ARGs were distributed in different combinations in 40 plasmids across UPEC strains with 20 plasmids displaying co-occurrence of multiple ARGs conferring resistance to beta lactam, aminoglycoside, sulfonamide, trimethoprim and macrolide antibiotics. These resistance plasmids belonged to seven incompatibility groups (IncF, IncI, IncC, IncH, IncN, IncB and Col), with IncFI and IncFII being the predominant resistance plasmids. Additionally, we observed co-occurrence of specific mutation pattern in quinolone resistance determining region (QRDR) viz., DNA gyrase (gyrA: S83L, D87N), and topoisomerase IV (parC: S80I, E84V; parE: I529L) in 18/30 strains. The strains also harbored diverse virulence genes, such as fimH, gad, iss, iha, ireA, iroN, cnf1 and san. Multilocus sequence typing (MLST) reconfirmed ST131(n = 10) as the predominant global high-risk clonal strain causing UTI. In summary, our findings contribute to better understand the plasmid mediated ARGs and its encoded enzymes that may contribute in antibiotic inactivation/modification or alteration in the antibiotic target site in high risk MDR hypervirulent UPEC strains causing UTI. The study reinforces the need to characterize and design appropriate inhibitors to counterattack different enzymes and devise strategies to curtail resistance plasmid.
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Affiliation(s)
- Susweta Das Mitra
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India.
| | - Pir Irshad
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - M Anusree
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Injeti Rekha
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - S Shailaja
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Janshi Suresh
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - G Aishwarya
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Smeeta Shrestha
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Bibek Ranjan Shome
- ICAR- National Institute of Veterinary Epidemiology & Disease Informatics, Bangalore, India
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17
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Armand-Lefèvre L, Rondinaud E, Desvillechabrol D, Mullaert J, Clermont O, Petitjean M, Ruppe E, Cokelaer T, Bouchier C, Tenaillon O, Ma L, Nooroya Y, Matheron S, The Voyag-R Study Group, Andremont A, Denamur E, Kennedy SP. Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad. Microb Genom 2021; 7. [PMID: 34279212 PMCID: PMC8477403 DOI: 10.1099/mgen.0.000576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Travel to tropical regions is associated with high risk of acquiring extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) that are typically cleared in less than 3 months following return. The conditions leading to persistent carriage that exceeds 3 months in some travellers require investigation. Whole-genome sequencing (Illumina MiSeq) was performed on the 82 ESBL-E isolates detected upon return and 1, 2, 3, 6 and 12 months later from the stools of 11 long-term (>3 months) ESBL-E carriers following travel abroad. One to five different ESBL Escherichia coli strains were detected per traveller upon return, and this diminished to one after 3 months. Long-term carriage was due to the presence of the same ESBL E. coli strain, for more than 3 months, in 9 out of 11 travellers, belonging to epidemic sequence type complexes (STc 10, 14, 38, 69, 131 and 648). The mean carriage duration of strains belonging to phylogroups B2/D/F, associated with extra-intestinal virulence, was higher than that for commensal-associated A/B1/E phylogroups (3.5 vs 0.5 months, P=0.021). Genes encoding iron capture systems (fyuA, irp), toxins (senB, sat), adhesins (flu, daaF, afa/nfaE, pap, ecpA) and colicin (cjrA) were more often present in persistent strains than in transient ones. Single-nucleotide polymorphism (SNP) analysis in persistent strains showed a maximum divergence of eight SNPs over 12 months without signs of adaptation. Genomic plasticity was observed during the follow-up with the loss or gain of mobile genetic elements such as plasmids, integrons and/or transposons that may contain resistance genes at different points in the follow-up. Long-term colonization of ESBL-E following travel is primarily due to the acquisition of E. coli strains belonging to epidemic clones and harbouring ‘virulence genes’, allowing good adaptation to the intestinal microbiota.
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Affiliation(s)
- Laurence Armand-Lefèvre
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Emilie Rondinaud
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Dimitri Desvillechabrol
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France
| | - Jimmy Mullaert
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Olivier Clermont
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Marie Petitjean
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Etienne Ruppe
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Thomas Cokelaer
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France.,Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, F-75015 Paris, France
| | - Christiane Bouchier
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France
| | | | - Laurence Ma
- Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, F-75015 Paris, France
| | - Yasmine Nooroya
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Sophie Matheron
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France.,Service de Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France
| | | | - Antoine Andremont
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France.,Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France
| | - Erick Denamur
- Université de Paris, IAME, INSERM UMR 1137, F-75018 Paris, France.,Laboratoire de Génétique Moléculaire, Hôpital Bichat-Claude Bernard, AP-HP Nord-Université de Paris, F-75018 Paris, France
| | - Sean P Kennedy
- Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, F-75015 Paris, France
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18
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Minja CA, Shirima G, Mshana SE. Conjugative Plasmids Disseminating CTX-M-15 among Human, Animals and the Environment in Mwanza Tanzania: A Need to Intensify One Health Approach. Antibiotics (Basel) 2021; 10:antibiotics10070836. [PMID: 34356757 PMCID: PMC8300620 DOI: 10.3390/antibiotics10070836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 11/30/2022] Open
Abstract
Background: Globally, blaCTX-M-15 beta-lactamases are the most popular extended spectrum beta-lactamase alleles that are widely distributed due its mobilisation by mobile genetic elements in several compartments. We aimed to determine the conjugation frequencies and replicon types associated with plasmids carrying blaCTX-M-15 gene from Extended Spectrum Beta-lactamase producing isolates in order to understand the dissemination of resistance genes in different compartments. Material and methods: A total of 51 archived isolates carrying blaCTX-M-15 beta-lactamases were used as donors in this study. Antibiotic susceptibility tests were performed as previously described for both donors and transconjugants. Conjugation experiment was performed by a modified protocol of the plate mating experiment, and plasmid replicon types were screened among donor and transconjugant isolates by multiplex Polymerase Chain Reaction in a set of three primer panels. Results: The conjugation efficiency of plasmids carrying blaCTX-M-15 was 88.2% (45/51) with conjugation frequencies in the order of 10−1 to 10−9 and a 100% transfer efficiency observed among E. coli of animal origin. Majority of donors (n = 21) and transconjugants (n = 14) plasmids were typed as either Inc FIA or Inc FIB. Resistance to non-beta-lactam antibiotics was transferrable in 34/45 (75.6%) of events. Ciprofloxacin, tetracycline and sulphamethoxazole-trimethoprim resistance was co-transferred in 29/34 (85.3%) such events. Gentamicin resistance was transferred in 17/34 (50%) of events. Conclusions: Majority of plasmids carrying blaCTX-M-15 were conjugatively transferred by IncF plasmids along with non-beta lactam resistance. There is a need for more research on plasmids to understand how plasmids especially multi replicon plasmids interact and the effect of such interaction on conjugation. One Health approach is to be intensified to address antimicrobial resistance which is a public health threat.
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Affiliation(s)
- Caroline A. Minja
- School of Life Sciences, Department of Global Health and Biomedical Sciences, Nelson Mandela African Institution of Science and Technology, Arusha 23306, Tanzania;
- Correspondence:
| | - Gabriel Shirima
- School of Life Sciences, Department of Global Health and Biomedical Sciences, Nelson Mandela African Institution of Science and Technology, Arusha 23306, Tanzania;
| | - Stephen E. Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza 33109, Tanzania;
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Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces. Proc Natl Acad Sci U S A 2021; 118:2024464118. [PMID: 34161269 DOI: 10.1073/pnas.2024464118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While it is well recognized that the environmental resistome is global, diverse, and augmented by human activities, it has been difficult to assess risk because of the inability to culture many environmental organisms, and it is difficult to evaluate risk from current sequence-based environmental methods. The four most important criteria to determine risk are whether the antibiotic-resistance genes (ARGs) are a complete, potentially functional complement; if they are linked with other resistances; whether they are mobile; and the identity of their host. Long-read sequencing fills this important gap between culture and short sequence-based methods. To address these criteria, we collected feces from a ceftiofur-treated cow, enriched the samples in the presence of antibiotics to favor ARG functionality, and sequenced long reads using Nanopore and PacBio technologies. Multidrug-resistance genes comprised 58% of resistome abundance, but only 0.8% of them were plasmid associated; fluroquinolone-, aminoglycoside-, macrolide-lincosamide-streptogramin (MLS)-, and β-lactam-resistance genes accounted for 2.7 to 12.3% of resistome abundance but with 19 to 78% located on plasmids. A variety of plasmid types were assembled, some of which share low similarity to plasmids in current databases. Enterobacteriaceae were dominant hosts of antibiotic-resistant plasmids; physical linkage of extended-spectrum β-lactamase genes (CTX-M, TEM, CMY, and CARB) was largely found with aminoglycoside-, MLS-, tetracycline-, trimethoprim-, phenicol-, sulfonamide-, and mercury-resistance genes. A draft circular chromosome of Vagococcus lutrae was assembled; it carries MLS-, tetracycline- (including tetM and tetL on an integrative conjugative element), and trimethoprim-resistance genes flanked by many transposase genes and insertion sequences, implying that they remain transferrable.
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20
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Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo. THE ISME JOURNAL 2021; 15:862-878. [PMID: 33149210 PMCID: PMC8026971 DOI: 10.1038/s41396-020-00819-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/15/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023]
Abstract
Horizontal gene transfer, mediated by conjugative plasmids, is a major driver of the global rise of antibiotic resistance. However, the relative contributions of factors that underlie the spread of plasmids and their roles in conjugation in vivo are unclear. To address this, we investigated the spread of clinical Extended Spectrum Beta-Lactamase (ESBL)-producing plasmids in the absence of antibiotics in vitro and in the mouse intestine. We hypothesised that plasmid properties would be the primary determinants of plasmid spread and that bacterial strain identity would also contribute. We found clinical Escherichia coli strains natively associated with ESBL-plasmids conjugated to three distinct E. coli strains and one Salmonella enterica serovar Typhimurium strain. Final transconjugant frequencies varied across plasmid, donor, and recipient combinations, with qualitative consistency when comparing transfer in vitro and in vivo in mice. In both environments, transconjugant frequencies for these natural strains and plasmids covaried with the presence/absence of transfer genes on ESBL-plasmids and were affected by plasmid incompatibility. By moving ESBL-plasmids out of their native hosts, we showed that donor and recipient strains also modulated transconjugant frequencies. This suggests that plasmid spread in the complex gut environment of animals and humans can be predicted based on in vitro testing and genetic data.
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21
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Cheng K, Fang LX, Ge QW, Wang D, He B, Lu JQ, Zhong ZX, Wang XR, Yu Y, Lian XL, Liao XP, Sun J, Liu YH. Emergence of fosA3 and bla CTX-M- 14 in Multidrug-Resistant Citrobacter freundii Isolates From Flowers and the Retail Environment in China. Front Microbiol 2021; 12:586504. [PMID: 33613474 PMCID: PMC7893115 DOI: 10.3389/fmicb.2021.586504] [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: 07/23/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
We examined the prevalence and transmission of the fosA3 gene among Citrobacter freundii isolates from flowers and the retail environments. We identified 11 fosfomycin-resistant C. freundii strains (>256 μg/mL) from 270 samples that included petals (n = 7), leaves (n = 2), dust (n = 1) and water (n = 1). These 11 isolates were multidrug-resistant and most were simultaneously resistant to fosfomycin, cefotaxime, ciprofloxacin and amikacin. Consistently, all 11 isolates also possessed blaCTX–M–14, blaCMY–65/122, aac(6’)-Ib-cr, qnrS1, qnrB13/6/38 and rmtB. These fosA3-positive isolates were assigned to two distinct PFGE patterns and one (n = 9) predominated indicating clonal expansion of fosA3-positive isolates across flower markets and shops. Correspondingly, fosA3 was co-transferred with blaCTX–M–14via two plasmid types by conjugation possessing sizes of 110 kb (n = 9) and 260 kb (n = 2). Two representatives were fully sequenced and p12-1 and pS39-1 possessed one and two unclassified replicons, respectively. These plasmids shared a distinctive and conserved backbone in common with fosA3-carrying C. freundii and other Enterobacteriaceae from human and food animals. However, the fosA3-blaCTX–M–14-containing multidrug resistance regions on these untypable plasmids were highly heterogeneous. To the best of our knowledge, this is the first report of fosA3 and blaCTX–M–14 that were present in bacterial contaminants from flower shops and markets. These findings underscore a public health threat posed by untypable and transferable p12-1-like and pS39-1-like plasmids bearing fosA3-blaCTX–M–14 that could circulate among Enterobacteriaceae species and in particular C. freundi in environmental isolates.
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Affiliation(s)
- Ke Cheng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Qian-Wen Ge
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Dong Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Bing He
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Jia-Qi Lu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Zi-Xing Zhong
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Xi-Ran Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Yang Yu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xin-Lei Lian
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
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22
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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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23
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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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24
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OXA-48 Carbapenemase in Klebsiella pneumoniae Sequence Type 307 in Ecuador. Microorganisms 2020; 8:microorganisms8030435. [PMID: 32204571 PMCID: PMC7143988 DOI: 10.3390/microorganisms8030435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/10/2020] [Accepted: 03/17/2020] [Indexed: 01/04/2023] Open
Abstract
Antibiotic resistance is on the rise, leading to an increase in morbidity and mortality due to infectious diseases. Klebsiella pneumoniae is a Gram-negative bacterium that causes bronchopneumonia, abscesses, urinary tract infection, osteomyelitis, and a wide variety of infections. The ubiquity of this microorganism confounds with the great increase in antibiotic resistance and have bred great concern worldwide. K. pneumoniae sequence type (ST) 307 is a widespread emerging clone associated with hospital-acquired infections, although sporadic community infections have also been reported. The aim of our study is to describe the first case of Klebsiella pneumoniae (ST) 307 harboring the blaOXA-48-like gene in Ecuador. We characterized a new plasmid that carry OXA-48 and could be the source of future outbreaks. The strain was recovered from a patient with cancer previously admitted in a Ukrainian hospital, suggesting that this mechanism of resistance could be imported. These findings highlight the importance of programs based on active molecular surveillance for the intercontinental spread of multidrug-resistant microorganisms with emergent carbapenemases.
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Meta-analysis of Pandemic Escherichia coli ST131 Plasmidome Proves Restricted Plasmid-clade Associations. Sci Rep 2020; 10:36. [PMID: 31913346 PMCID: PMC6949217 DOI: 10.1038/s41598-019-56763-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023] Open
Abstract
Extraintestinal multidrug resistant Escherichia coli sequence type (ST) 131 is a worldwide pandemic pathogen and a major cause of urinary tract and bloodstream infections. The role of this pandemic lineage in multidrug resistance plasmid dissemination is still scarce. We herein performed a meta-analysis on E. coli ST131 whole-genome sequence (WGS) databases to unravel ST131 plasmidome and specifically to decipher CTX-M encoding plasmids-clade associations. We mined 880 ST131 WGS data and proved that CTX-M-27-encoding IncF[F1:A2:B20] (Group1) plasmids are strictly found in clade C1, whereas CTX-M-15-encoding IncF[F2:A1:B-] (Group2) plasmids exist only in clade C2 suggesting strong plasmid-clade adaptations. Specific Col-like replicons (Col156, Col(MG828), and Col8282) were also found to be clade C1-associated. BLAST-based search revealed that Group1 and Group2 plasmids are narrow-host-range and restricted to E.coli. Among a collection of 20 newly sequenced Israeli ST131 CTX-M-encoding plasmids (2003–2016), Group1 and Group2 plasmids were dominant and associated with the expected clades. We found, for the first time in ST131, a CTX-M-15-encoding phage-like plasmid group (Group3) and followed its spread in the WGS data. This study offers a comprehensive way to decipher plasmid-bacterium associations and demonstrates that the CTX-M-encoding ST131 Group1 and Group2 plasmids are clade-restricted and presumably less transmissible, potentially contributing to ST131 clonal superiority.
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A large self-transmissible resistance plasmid from Nigeria contains genes that ameliorate a carrying cost. Sci Rep 2019; 9:19624. [PMID: 31873110 PMCID: PMC6927977 DOI: 10.1038/s41598-019-56064-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance is rapidly expanding, in a large part due to mobile genetic elements. We screened 94 fecal fluoroquinolone-resistant Escherichia coli isolates from Nigeria for six plasmid-mediated quinolone resistance (PMQR) genes. Sixteen isolates harbored at least one of the PMQR genes and four were positive for aac-6-Ib-cr. In one strain, aac-6-Ib-cr was mapped to a 125 Kb self-transmissible IncFII plasmid, pMB2, which also bears blaCTX-M-15, seven other functional resistance genes and multiple resistance pseudogenes. Laboratory strains carrying pMB2 grew faster than isogenic strains lacking the plasmid in both rich and minimal media. We excised a 32 Kb fragment containing transporter genes and several open-reading frames of unknown function. The resulting 93 Kb mini-plasmid conferred slower growth rates and lower fitness than wildtype pMB2. Trans-complementing the deletion with the cloned sitABCD genes confirmed that they accounted for the growth advantage conferred by pMB2 in iron-depleted media. pMB2 is a large plasmid with a flexible resistance region that contains loci that can account for evolutionary success in the absence of antimicrobials. Ancillary functions conferred by resistance plasmids can mediate their retention and transmissibility, worsening the trajectory for antimicrobial resistance and potentially circumventing efforts to contain resistance through restricted use.
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