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Carrera Páez LC, Olivier M, Gambino AS, Poklepovich T, Aguilar AP, Quiroga MP, Centrón D. Sporadic clone Escherichia coli ST615 as a vector and reservoir for dissemination of crucial antimicrobial resistance genes. Front Cell Infect Microbiol 2024; 14:1368622. [PMID: 38741889 PMCID: PMC11089171 DOI: 10.3389/fcimb.2024.1368622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
There is scarce information concerning the role of sporadic clones in the dissemination of antimicrobial resistance genes (ARGs) within the nosocomial niche. We confirmed that the clinical Escherichia coli M19736 ST615 strain, one of the first isolates of Latin America that harbors a plasmid with an mcr-1 gene, could receive crucial ARG by transformation and conjugation using as donors critical plasmids that harbor bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, or aadB genes. Escherichia coli M19736 acquired bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, and aadB genes, being only blaNDM-1 maintained at 100% on the 10th day of subculture. In addition, when the evolved MDR-E. coli M19736 acquired sequentially bla CTX-M-15 and bla NDM-1 genes, the maintenance pattern of the plasmids changed. In addition, when the evolved XDR-E. coli M19736 acquired in an ulterior step the paadB plasmid, a different pattern of the plasmid's maintenance was found. Interestingly, the evolved E. coli M19736 strains disseminated simultaneously the acquired conjugative plasmids in different combinations though selection was ceftazidime in all cases. Finally, we isolated and characterized the extracellular vesicles (EVs) from the native and evolved XDR-E. coli M19736 strains. Interestingly, EVs from the evolved XDR-E. coli M19736 harbored bla CTX-M-15 though the pDCAG1-CTX-M-15 was previously lost as shown by WGS and experiments, suggesting that EV could be a relevant reservoir of ARG for susceptible bacteria. These results evidenced the genetic plasticity of a sporadic clone of E. coli such as ST615 that could play a relevant transitional link in the clinical dynamics and evolution to multidrug/extensively/pandrug-resistant phenotypes of superbugs within the nosocomial niche by acting simultaneously as a vector and reservoir of multiple ARGs which later could be disseminated.
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Affiliation(s)
- Laura Camila Carrera Páez
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Martin Olivier
- The Research Institute of the McGill University Health Centre, McGill University, Montréal, QC, Canada
| | - Anahí Samanta Gambino
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Tomás Poklepovich
- Plataforma de Genómica y Bioinformática, Instituto Nacional de Enfermedades Infecciosas - La Administración Nacional de Laboratorios e Institutos de Salud (INEI-ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Andrea Pamela Aguilar
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
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Guidotti-Takeuchi M, Melo RTD, Ribeiro LNDM, Dumont CF, Ribeiro RAC, Brum BDA, de Amorim Junior TLIF, Rossi DA. Interference with Bacterial Conjugation and Natural Alternatives to Antibiotics: Bridging a Gap. Antibiotics (Basel) 2023; 12:1127. [PMID: 37508224 PMCID: PMC10376302 DOI: 10.3390/antibiotics12071127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Horizontal gene transfer (HGT) in food matrices has been investigated under conditions that favor gene exchange. However, the major challenge lies in determining the specific conditions pertaining to the adapted microbial pairs associated with the food matrix. HGT is primarily responsible for enhancing the microbial repertoire for the evolution and spread of antimicrobial resistance and is a major target for controlling pathogens of public health concern in food ecosystems. In this study, we investigated Salmonella Heidelberg (SH) and Escherichia coli (EC) regarding gene exchange under conditions mimicking the industrial environment, with the coproducts whey (SL) and chicken juice (CJ). The S. Heidelberg strain was characterized by antibiotic susceptibility standards and PCR to detect the blaTEM gene. A concentration of 0.39 mg/mL was determined to evaluate the anti-conjugation activity of nanostructured lipid nanocarriers (NLCs) of essential oils to mitigate β-lactam resistance gene transfer. The results showed that the addition of these coproducts promoted an increase of more than 3.5 (whey) and 2.5 (chicken juice) orders of magnitude in the conjugation process (p < 0.01), and NLCs of sage essential oil significantly reduced the conjugation frequency (CF) by 74.90, 90.6, and 124.4 times when compared to the transfers in the absence of coproducts and the presence of SL and CJ, respectively. For NLCs from olibanum essential oil, the decrease was 4.46-fold for conjugations without inhibitors and 3.12- and 11.3-fold in the presence of SL and CJ. NLCs associated with sage and olibanum essential oils effectively control the transfer of antibiotic resistance genes and are a promising alternative for use at industrial levels.
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Affiliation(s)
- Micaela Guidotti-Takeuchi
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | - Roberta Torres de Melo
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | | | - Carolyne Ferreira Dumont
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | | | - Bárbara de Araújo Brum
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | | | - Daise Aparecida Rossi
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
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Lian ZJ, Phan MD, Hancock SJ, Nhu NTK, Paterson DL, Schembri MA. Genetic basis of I-complex plasmid stability and conjugation. PLoS Genet 2023; 19:e1010773. [PMID: 37347771 DOI: 10.1371/journal.pgen.1010773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/05/2023] [Indexed: 06/24/2023] Open
Abstract
Plasmids are major drivers of increasing antibiotic resistance, necessitating an urgent need to understand their biology. Here we describe a detailed dissection of the molecular components controlling the genetics of I-complex plasmids, a group of antibiotic resistance plasmids found frequently in pathogenic Escherichia coli and other Enterobacteriaceae that cause significant human disease. We show these plasmids cluster into four distinct subgroups, with the prototype IncI1 plasmid R64 subgroup displaying low nucleotide sequence conservation to other I-complex plasmids. Using pMS7163B, an I-complex plasmid distantly related to R64, we performed a high-resolution transposon-based genetic screen and defined genes involved in replication, stability, and conjugative transfer. We identified the replicon and a partitioning system as essential for replication/stability. Genes required for conjugation included the type IV secretion system, relaxosome, and several uncharacterised genes located in the pMS7163B leading transfer region that exhibited an upstream strand-specific transposon insertion bias. The overexpression of these genes severely impacted host cell growth or reduced fitness during mixed competitive growth, demonstrating that their expression must be controlled to avoid deleterious impacts. These genes were present in >80% of all I-complex plasmids and broadly conserved across multiple plasmid incompatibility groups, implicating an important role in plasmid dissemination.
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Affiliation(s)
- Zheng Jie Lian
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Minh-Duy Phan
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Steven J Hancock
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - David L Paterson
- The University of Queensland Centre for Clinical Research, Brisbane, Australia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
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Qi Q, Kamruzzaman M, Iredell JR. A Streamlined Approach for Fluorescence Labelling of Low-Copy-Number Plasmids for Determination of Conjugation Frequency by Flow Cytometry. Microorganisms 2023; 11:microorganisms11040878. [PMID: 37110299 PMCID: PMC10144549 DOI: 10.3390/microorganisms11040878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
Bacterial conjugation plays a major role in the dissemination of antibiotic resistance and virulence traits through horizontal transfer of plasmids. Robust measurement of conjugation frequency of plasmids between bacterial strains and species is therefore important for understanding the transfer dynamics and epidemiology of conjugative plasmids. In this study, we present a streamlined experimental approach for fluorescence labelling of low-copy-number conjugative plasmids that allows plasmid transfer frequency during filter mating to be measured by flow cytometry. A blue fluorescent protein gene is inserted into a conjugative plasmid of interest using a simple homologous recombineering procedure. A small non-conjugative plasmid, which carries a red fluorescent protein gene with a toxin–antitoxin system that functions as a plasmid stability module, is used to label the recipient bacterial strain. This offers the dual advantage of circumventing chromosomal modifications of recipient strains and ensuring that the red fluorescent protein gene-bearing plasmid can be stably maintained in recipient cells in an antibiotic-free environment during conjugation. A strong constitutive promoter allows the two fluorescent protein genes to be strongly and constitutively expressed from the plasmids, thus allowing flow cytometers to clearly distinguish between donor, recipient, and transconjugant populations in a conjugation mix for monitoring conjugation frequencies more precisely over time.
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Affiliation(s)
- Qin Qi
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, NSW 2145, Australia
| | - Muhammad Kamruzzaman
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, NSW 2145, Australia
- Correspondence: (M.K.); (J.R.I.)
| | - Jonathan R. Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, NSW 2145, Australia
- Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
- Correspondence: (M.K.); (J.R.I.)
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DelaFuente J, Toribio-Celestino L, Santos-Lopez A, León-Sampedro R, Alonso-Del Valle A, Costas C, Hernández-García M, Cui L, Rodríguez-Beltrán J, Bikard D, Cantón R, San Millan A. Within-patient evolution of plasmid-mediated antimicrobial resistance. Nat Ecol Evol 2022; 6:1980-1991. [PMID: 36303001 PMCID: PMC7613874 DOI: 10.1038/s41559-022-01908-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/12/2022] [Indexed: 12/15/2022]
Abstract
Antimicrobial resistance (AMR) in bacteria is a major threat to public health; one of the key elements in the spread and evolution of AMR in clinical pathogens is the transfer of conjugative plasmids. The drivers of AMR evolution have been studied extensively in vitro but the evolution of plasmid-mediated AMR in vivo remains poorly explored. Here, we tracked the evolution of the clinically relevant plasmid pOXA-48, which confers resistance to the last-resort antibiotics carbapenems, in a large collection of enterobacterial clones isolated from the gut of hospitalized patients. Combining genomic and experimental approaches, we first characterized plasmid diversity and the genotypic and phenotypic effects of multiple plasmid mutations on a common genetic background. Second, using cutting-edge genomic editing in wild-type multidrug-resistant enterobacteria, we dissected three cases of within-patient plasmid-mediated AMR evolution. Our results revealed compensatory evolution of plasmid-associated fitness cost and the evolution of enhanced plasmid-mediated AMR in bacteria evolving in the gut of hospitalized patients. Crucially, we observed that the evolution of pOXA-48-mediated AMR in vivo involves a pivotal trade-off between resistance levels and bacterial fitness. This study highlights the need to develop new evolution-informed approaches to tackle plasmid-mediated AMR dissemination.
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Affiliation(s)
- Javier DelaFuente
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain.
| | - Laura Toribio-Celestino
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Alfonso Santos-Lopez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Ricardo León-Sampedro
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Integrative Biology, Department of Environmental Systems Science, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Aida Alonso-Del Valle
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Coloma Costas
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Marta Hernández-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Lun Cui
- Institut Pasteur, Universite de Paris Cité, Centre National de la Recherche Scientifique Unité Mixte de Recherche 6047, Synthetic Biology, Paris, France
| | - Jerónimo Rodríguez-Beltrán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - David Bikard
- Institut Pasteur, Universite de Paris Cité, Centre National de la Recherche Scientifique Unité Mixte de Recherche 6047, Synthetic Biology, Paris, France
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alvaro San Millan
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain.
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain.
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A Broad-Host-Range Plasmid Outbreak: Dynamics of IncL/M Plasmids Transferring Carbapenemase Genes. Antibiotics (Basel) 2022; 11:antibiotics11111641. [DOI: 10.3390/antibiotics11111641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
IncL/M broad-host-range conjugative plasmids are involved in the global spread of blaOXA-48 and the emergence of blaNDM-1. The aim of this study was to evaluate the transmission potential of plasmids encoding the emergent NDM-1 carbapenemase compared to the pandemic OXA-48. The conjugation rate and fitness cost of IncM2 and IncL plasmids encoding these carbapenemase genes were tested using a variety of host bacteria. Genomic analysis of uropathogenic Escherichia coli SAP1756 revealed that blaNDM-1 was encoded on an IncM2 plasmid, which also harboured blaTEM-1, bleMBL and sul1 and was highly similar to plasmids isolated from the same geographical area. Conjugation experiments demonstrated that NDM-1 and OXA-48-carrying plasmids transfer successfully between different Enterobacterales species, both in vitro and in vivo. Interestingly, E. coli isolates tested as recipients belonging to phylogroups A, B1, D and F were able to receive IncM2 plasmid pSAP1756, while phylogroups B2, C, E and G were not permissive to its acquisition. In general, the IncL OXA-48-carrying plasmids tested transferred at higher rates than IncM2 harbouring NDM-1 and imposed a lower burden to their host, possibly due to the inactivation of the tir fertility inhibition gene and reflecting their worldwide dissemination. IncM2 plasmids carrying blaNDM-1 are considered emergent threats that need continuous monitoring. In addition to sequencing efforts, phenotypic analysis of conjugation rates and fitness cost are effective methods for estimating the pandemic potential of antimicrobial resistance plasmids.
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Ezzeroug Ezzraimi A, Hannachi N, Mariotti A, Rolland C, Levasseur A, Baron SA, Rolain JM, Camoin-Jau L. The Antibacterial Effect of Platelets on Escherichia coli Strains. Biomedicines 2022; 10:biomedicines10071533. [PMID: 35884840 PMCID: PMC9313237 DOI: 10.3390/biomedicines10071533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/02/2023] Open
Abstract
Platelets play an important role in defense against pathogens; however, the interaction between Escherichia coli and platelets has not been well described and detailed. Our goal was to study the interaction between platelets and selected strains of E. coli in order to evaluate the antibacterial effect of platelets and to assess bacterial effects on platelet activation. Washed platelets and supernatants of pre-activated platelets were incubated with five clinical colistin-resistant and five laboratory colistin-sensitive strains of E. coli in order to study bacterial growth. Platelet activation was measured with flow cytometry by evaluating CD62P expression. To identify the difference in strain behavior toward platelets, a pangenome analysis using Roary and O-antigen serotyping was carried out. Both whole platelets and the supernatant of activated platelets inhibited growth of three laboratory colistin-sensitive strains. In contrast, platelets promoted growth of the other strains. There was a negative correlation between platelet activation and bacterial growth. The Roary results showed no logical clustering to explain the mechanism of platelet resistance. The diversity of the responses might be due to strains of different types of O-antigen. Our results show a bidirectional interaction between platelets and E. coli whose expression is dependent on the bacterial strain involved.
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Affiliation(s)
- Amina Ezzeroug Ezzraimi
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
| | - Nadji Hannachi
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- Département de Pharmacie, Faculté de Médecine, Université Ferhat Abbas Sétif I, Sétif 19000, Algeria
| | - Antoine Mariotti
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Laboratoire d’Hématologie, Hôpital de la Timone, APHM, Boulevard Jean-Moulin, 13385 Marseille, France
| | - Clara Rolland
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Aix Marseille University, IRD, SSA, APHM, VITROME, IHU Méditerranée Infection, 13385 Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Aix Marseille University, IRD, SSA, APHM, VITROME, IHU Méditerranée Infection, 13385 Marseille, France
| | - Sophie Alexandra Baron
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
| | - Jean-Marc Rolain
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
| | - Laurence Camoin-Jau
- Aix Marseille University, IRD, APHM, MEPHI, IHU Méditerranée Infection, 13385 Marseille, France; (A.E.E.); (N.H.); (A.M.); (S.A.B.); (J.-M.R.)
- IHU Méditerranée Infection, Boulevard Jean Moulin, 13385 Marseille, France; (C.R.); (A.L.)
- Laboratoire d’Hématologie, Hôpital de la Timone, APHM, Boulevard Jean-Moulin, 13385 Marseille, France
- Correspondence: ; Tel.: +33-4-13-73-24-01; Fax: +33-4-13-73-24-02
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He Z, Yang Y, Li W, Ma X, Zhang C, Zhang J, Sun B, Ding T, Tian GB. Comparative genomic analyses of Polymyxin-resistant Enterobacteriaceae strains from China. BMC Genomics 2022; 23:88. [PMID: 35100991 PMCID: PMC8805313 DOI: 10.1186/s12864-022-08301-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Mobile colistin resistance like gene (mcr-like gene) is a new type of polymyxin resistance gene that can be horizontally transferred in the Enterobacteriaceae. This has brought great challenges to the treatment of multidrug-resistant Escherichia coli and K. pneumoniae. RESULTS K. pneumoniae 16BU137 and E. coli 17MR471 were isolated from the bus and subway handrails in Guangzhou, China. K. pneumoniae 19PDR22 and KP20191015 were isolated from patients with urinary tract infection and severe pneumonia in Anhui, China. Sequence analysis indicated that the mcr-1.1 gene was present on the chromosome of E. coli 17MR471, and the gene was in the gene cassette containing pap2 and two copies of ISApl1.The mcr-1.1 was found in the putative IncX4 type plasmid p16BU137_mcr-1.1 of K. pneumoniae 16BU137, but ISApl1 was not found in its flanking sequence. Mcr-8 variants were found in the putative IncFIB/ IncFII plasmid pKP20191015_mcr-8 of K. pneumoniae KP20191015 and flanked by ISEcl1 and ISKpn26. CONCLUSION This study provides timely information on Enterobacteriaceae bacteria carrying mcr-like genes, and provides a reference for studying the spread of mcr-1 in China and globally.
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Affiliation(s)
- Zhien He
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China
| | - Yongqiang Yang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, 510006, China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China
| | - Xiaoling Ma
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China
| | - Changfeng Zhang
- Clinical Laboratory of the First Affiliated Hospital, Anhui University of Chinese Medicine, Hefei, 230031, Anhui, China
| | - Jingxiang Zhang
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Baolin Sun
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China.
| | - Tao Ding
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
- Xizang Minzu University School of Medicine, Xianyang, China.
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Baomo L, Lili S, Moran RA, van Schaik W, Chao Z. Temperature-Regulated IncX3 Plasmid Characteristics and the Role of Plasmid-Encoded H-NS in Thermoregulation. Front Microbiol 2022; 12:765492. [PMID: 35069472 PMCID: PMC8770905 DOI: 10.3389/fmicb.2021.765492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/17/2021] [Indexed: 12/03/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are a critical public health problem worldwide. Globally, IncX3-type plasmids have emerged as the predominant vehicles carrying the metallo-β-lactamase gene bla NDM. Although bla NDM-bearing IncX3 plasmids have been found in various hosts from diverse environments, whether their transfer and persistence properties vary under different conditions and what factors influence any variation is unknown. By observing the effects of different temperatures on IncX3 plasmid conjugation rates, stability, and effects on host fitness in Escherichia coli, we demonstrate that temperature is an important determinant of plasmid phenotypes. The IncX3 plasmid pGZIncX3 transferred at highest frequencies, was most stable and imposed lower fitness costs at 37°C. Temperature-regulated variation in pGZIncX3 properties involved a thermoregulated plasmid-encoded H-NS-like protein, which was produced at higher levels at 30°C and 42°C and inhibited the expression of type IV secretion system genes involved in conjugation. These findings suggest that bla NDM-bearing IncX3 plasmids are adapted to carriage by enterobacteria that colonize mammalian hosts and could explain the rapid dissemination of these plasmids among human-associated species, particularly in hospital settings.
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Affiliation(s)
- Liu Baomo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shui Lili
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Robert A. Moran
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Zhuo Chao
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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10
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Apiwatsiri P, Pupa P, Yindee J, Niyomtham W, Sirichokchatchawan W, Lugsomya K, Shah AA, Prapasarakul N. Anticonjugation and Antibiofilm Evaluation of Probiotic Strains Lactobacillus plantarum 22F, 25F, and Pediococcus acidilactici 72N Against Escherichia coli Harboring mcr-1 Gene. Front Vet Sci 2021; 8:614439. [PMID: 34179153 PMCID: PMC8225926 DOI: 10.3389/fvets.2021.614439] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/30/2021] [Indexed: 11/13/2022] Open
Abstract
Several species of lactic acid bacteria (LAB) are commonly used as probiotics and as an alternative to antibiotics in various industries, especially in the livestock industry. This study aimed to investigate the anticonjugation and antibiofilm activity of cell-free supernatant (CFS) of Thai LAB strains (Lactobacillus plantarum 22F, 25F, and Pediococcus acidilactici 72N) against colistin-resistant Escherichia coli isolates. A total of six colistin-resistant E. coli strains were isolated from different sources, including pigs, farmers, and farmhouse environments. The E. coli were characterized by plasmid profiling, PCR detection of mcr-1 gene, and antibiotic susceptibility patterns. The CFS at dilutions ≥1:16 was chosen as the proper dilution for anticonjugation assay. Besides, it could significantly reduce the transfer frequencies of resistance gene mcr-1 up to 100 times compared to the neutralizing CFS (pH 6.5). The biofilm production in the planktonic stage was reduced by non-neutralizing and neutralizing CFS determining with crystal violet staining assay up to 82 and 60%, respectively. Moreover, the non-neutralizing CFS also inhibited the biofilm formation in the sessile stage up to 52%. The biofilm illustration was confirmed by scanning electron microscopy (SEM). These results agreed with the findings of the crystal violet technique, which showed a significant reduction in cell density, aggregation, and extracellular polysaccharide (EPS) matrix. The application of Thai LAB may serve as an attractive alternative to antibiotics for reducing biofilm formation and limiting the proliferation of antibiotic-resistant genes.
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Affiliation(s)
- Prasert Apiwatsiri
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Pawiya Pupa
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Jitrapa Yindee
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Waree Niyomtham
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Kittitat Lugsomya
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Asad Ali Shah
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Nuvee Prapasarakul
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Diagnosis and Monitoring of Animal Pathogens Research Unit (DMAP), Bangkok, Thailand
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11
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Alonso-Del Valle A, León-Sampedro R, Rodríguez-Beltrán J, DelaFuente J, Hernández-García M, Ruiz-Garbajosa P, Cantón R, Peña-Miller R, San Millán A. Variability of plasmid fitness effects contributes to plasmid persistence in bacterial communities. Nat Commun 2021; 12:2653. [PMID: 33976161 PMCID: PMC8113577 DOI: 10.1038/s41467-021-22849-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/25/2021] [Indexed: 02/03/2023] Open
Abstract
Plasmid persistence in bacterial populations is strongly influenced by the fitness effects associated with plasmid carriage. However, plasmid fitness effects in wild-type bacterial hosts remain largely unexplored. In this study, we determined the fitness effects of the major antibiotic resistance plasmid pOXA-48_K8 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. Our results show that although pOXA-48_K8 produced an overall reduction in bacterial fitness, it produced small effects in most bacterial hosts, and even beneficial effects in several isolates. Moreover, genomic results showed a link between pOXA-48_K8 fitness effects and bacterial phylogeny, helping to explain plasmid epidemiology. Incorporating our fitness results into a simple population dynamics model revealed a new set of conditions for plasmid stability in bacterial communities, with plasmid persistence increasing with bacterial diversity and becoming less dependent on conjugation. These results help to explain the high prevalence of plasmids in the greatly diverse natural microbial communities.
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Affiliation(s)
- Aida Alonso-Del Valle
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Ricardo León-Sampedro
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red. Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red. Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier DelaFuente
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Marta Hernández-García
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa. Instituto de Salud Carlos III, Madrid, Spain
| | - Patricia Ruiz-Garbajosa
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa. Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa. Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Peña-Miller
- Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
| | - Alvaro San Millán
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.
- Centro de Investigación Biológica en Red. Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain.
- Centro Nacional de Biotecnología-CSIC, Madrid, Spain.
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12
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León-Sampedro R, DelaFuente J, Díaz-Agero C, Crellen T, Musicha P, Rodríguez-Beltrán J, de la Vega C, Hernández-García M, López-Fresneña N, Ruiz-Garbajosa P, Cantón R, Cooper BS, San Millán Á. Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients. Nat Microbiol 2021; 6:606-616. [PMID: 33782584 PMCID: PMC7610705 DOI: 10.1038/s41564-021-00879-y] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/12/2021] [Indexed: 01/31/2023]
Abstract
Infections caused by carbapenemase-producing enterobacteria (CPE) are a major concern in clinical settings worldwide. Two fundamentally different processes shape the epidemiology of CPE in hospitals: the dissemination of CPE clones from patient to patient (between-patient transfer), and the transfer of carbapenemase-encoding plasmids between enterobacteria in the gut microbiota of individual patients (within-patient transfer). The relative contribution of each process to the overall dissemination of carbapenem resistance in hospitals remains poorly understood. Here, we used mechanistic models combining epidemiological data from more than 9,000 patients with whole genome sequence information from 250 enterobacteria clones to characterize the dissemination routes of a pOXA-48-like carbapenemase-encoding plasmid in a hospital setting over a 2-yr period. Our results revealed frequent between-patient transmission of high-risk pOXA-48-carrying clones, mostly of Klebsiella pneumoniae and sporadically Escherichia coli. The results also identified pOXA-48 dissemination hotspots within the hospital, such as specific wards and individual rooms within wards. Using high-resolution plasmid sequence analysis, we uncovered the pervasive within-patient transfer of pOXA-48, suggesting that horizontal plasmid transfer occurs in the gut of virtually every colonized patient. The complex and multifaceted epidemiological scenario exposed by this study provides insights for the development of intervention strategies to control the in-hospital spread of CPE.
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Affiliation(s)
- Ricardo León-Sampedro
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red, Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Javier DelaFuente
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Cristina Díaz-Agero
- Servicio de Medicina Preventiva y Salud Pública, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Thomas Crellen
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Patrick Musicha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jerónimo Rodríguez-Beltrán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red, Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen de la Vega
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Marta Hernández-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa, Instituto de Salud Carlos III, Madrid, Spain
| | - Nieves López-Fresneña
- Servicio de Medicina Preventiva y Salud Pública, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Patricia Ruiz-Garbajosa
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa, Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa, Instituto de Salud Carlos III, Madrid, Spain
| | - Ben S Cooper
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Álvaro San Millán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.
- Centro de Investigación Biológica en Red, Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain.
- Centro Nacional de Biotecnología-CSIC, Madrid, Spain.
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13
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Virulence Potential of a Multidrug-Resistant Escherichia coli Strain Belonging to the Emerging Clonal Group ST101-B1 Isolated from Bloodstream Infection. Microorganisms 2020; 8:microorganisms8060827. [PMID: 32486334 PMCID: PMC7355805 DOI: 10.3390/microorganisms8060827] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli EC121 is a multidrug-resistant (MDR) strain isolated from a bloodstream infection of an inpatient with persistent gastroenteritis and T-zone lymphoma that died due to septic shock. Despite causing an extraintestinal infection, previous studies showed that it did not have the usual characteristics of an extraintestinal pathogenic E. coli. Instead, it belonged to phylogenetic group B1 and harbored few known virulence genes. To evaluate the pathogenic potential of strain EC121, an extensive genome sequencing and in vitro characterization of various pathogenicity-associated properties were performed. The genomic analysis showed that strain EC121 harbors more than 50 complete virulence genetic clusters. It also displays the capacity to adhere to a variety of epithelial cell lineages and invade T24 bladder cells, as well as the ability to form biofilms on abiotic surfaces, and survive the bactericidal serum complement activity. Additionally, EC121 was shown to be virulent in the Galleria mellonella model. Furthermore, EC121 is an MDR strain harboring 14 antimicrobial resistance genes, including blaCTX-M-2. Completing the scenario, it belongs to serotype O154:H25 and to sequence type 101-B1, which has been epidemiologically linked to extraintestinal infections as well as to antimicrobial resistance spread. This study with E. coli strain EC121 shows that clinical isolates considered opportunistic might be true pathogens that go underestimated.
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