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Romero-Oraá L, Pulido MR, Galán F, Palacios MVG, Pascual A, López-Cerero L. Genetic features of BEL-1-producing and KPC-2-producing E. coli from hospital wastewater: human source or sewages adaptation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:43896-43902. [PMID: 38913264 PMCID: PMC11252172 DOI: 10.1007/s11356-024-33875-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/28/2024] [Indexed: 06/25/2024]
Abstract
Hospital sewage is an ecosystem that facilitates the transfer of antibiotic and heavy metal resistance genes and the interaction of human and environmental bacteria. In this environment, we have detected the presence of 7 KPC-2 and BEL-1 co-producing E. coli isolates of two different clones over a 10-month period in the same hospital. All isolates carried blaKPC-2 and the operon mer on the same IncP plasmid of similar size and an IncN plasmid of different size each clone carrying blaBEL-1. Both IncN-blaBEL-1 plasmids shared a 77 kb region containing blaBEL-1 alongside with fosE, bla OXA-10 and aac(6')-1b genes in a class 3 integron within a Tn3 transposon. The major IncN plasmid contained in addition a region homolog to P1-like bacteriophage RCS47, including the lytic RepL and lysogenic proteins, but other phage regions were incomplete. The characters such as the temporal persistence in sewage, the absence of colonized patients in the hospital or in the region, the presence of a p1 phage-plasmid fusion and the infrequent class 3 integron as genetic platform would indicate that BEL-1-producing isolates could have been generated in situ by adaptation to human sewage. Part of the microbiota in these discharges could be explained by the interactions of sewage ecosystems and not derive directly from the hospital.
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Affiliation(s)
- Laura Romero-Oraá
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Instituto de Biomedicina de Sevilla IBIS, Seville, Spain
| | - Marina R Pulido
- Departamento de Microbiología, Universidad de Sevilla, Avda Dr. Fedriani S/N. 41009, Seville, Spain
| | - Fatima Galán
- Unidad de Microbiología, Hospital Universitario Puerta del Mar, Cádiz, Spain
| | | | - Alvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Instituto de Biomedicina de Sevilla IBIS, Seville, Spain
- Departamento de Microbiología, Universidad de Sevilla, Avda Dr. Fedriani S/N. 41009, Seville, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Lorena López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Virgen Macarena, Instituto de Biomedicina de Sevilla IBIS, Seville, Spain.
- Departamento de Microbiología, Universidad de Sevilla, Avda Dr. Fedriani S/N. 41009, Seville, Spain.
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
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Hennequin C, Forestier C, Traore O, Debroas D, Bricheux G. Plasmidome analysis of a hospital effluent biofilm: Status of antibiotic resistance. Plasmid 2022; 122:102638. [PMID: 35691511 DOI: 10.1016/j.plasmid.2022.102638] [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: 11/16/2021] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022]
Abstract
Plasmids are widely involved in the dissemination of characteristics within bacterial communities. Their genomic content can be assessed by high-throughput sequencing of the whole plasmid fraction of an environment, the plasmidome. In this study, we analyzed the plasmidome of a biofilm formed in the effluents of the teaching hospital of Clermont-Ferrand (France). Our analysis discovered >350 new complete plasmids, with a length ranging from 1219 to 40,193 bp. Forty-two plasmid incompatibility (Inc) groups were found among all the plasmid contigs. Ten large plasmids, described here in detail, were reconstructed from plasmid contigs, seven of which carried antibiotic resistance genes. Four plasmids potentially confer resistance to numerous families of antibiotics, including carbapenems, aminoglycosides, colistin, and chloramphenicol. Most of these plasmids were affiliated to Proteobacteria, a phylum of Gram-negative bacteria. This study therefore illustrates the composition of an environmental mixed biofilm in terms of plasmids and antibiotic resistance genes.
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Affiliation(s)
- Claire Hennequin
- CHU Clermont-Ferrand, Service de Bactériologie Clinique, 58 rue Montalembert, 63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France; Laboratoire Microorganismes: Génome et Environnement, Campus Universitaire des Cézeaux, TSA 60026 - CS 60026, 1, impasse Amélie Murat, 63178 Aubière, France
| | - Christiane Forestier
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
| | - Ousmane Traore
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
| | - Didier Debroas
- Laboratoire Microorganismes: Génome et Environnement, Campus Universitaire des Cézeaux, TSA 60026 - CS 60026, 1, impasse Amélie Murat, 63178 Aubière, France
| | - Geneviève Bricheux
- Laboratoire Microorganismes: Génome et Environnement, Campus Universitaire des Cézeaux, TSA 60026 - CS 60026, 1, impasse Amélie Murat, 63178 Aubière, France.
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Böhm ME, Razavi M, Flach CF, Larsson DGJ. A Novel, Integron-Regulated, Class C β-Lactamase. Antibiotics (Basel) 2020; 9:antibiotics9030123. [PMID: 32183280 PMCID: PMC7148499 DOI: 10.3390/antibiotics9030123] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/26/2022] Open
Abstract
AmpC-type β-lactamases severely impair treatment of many bacterial infections, due to their broad spectrum (they hydrolyze virtually all β-lactams, except fourth-generation cephalosporins and carbapenems) and the increasing incidence of plasmid-mediated versions. The original chromosomal AmpCs are often tightly regulated, and their expression is induced in response to exposure to β-lactams. Regulation of mobile ampC expression is in many cases less controlled, giving rise to constitutively resistant strains with increased potential for development or acquisition of additional resistances. We present here the identification of two integron-encoded ampC genes, blaIDC-1 and blaIDC-2 (integron-derived cephalosporinase), with less than 85% amino acid sequence identity to any previously annotated AmpC. While their resistance pattern identifies them as class C β-lactamases, their low isoelectric point (pI) values make differentiation from other β-lactamases by isoelectric focusing impossible. To the best of our knowledge, this is the first evidence of an ampC gene cassette within a class 1 integron, providing a mobile context with profound potential for transfer and spread into clinics. It also allows bacteria to adapt expression levels, and thus reduce fitness costs, e.g., by cassette-reshuffling. Analyses of public metagenomes, including sewage metagenomes, show that the discovered ampCs are primarily found in Asian countries.
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Affiliation(s)
- Maria-Elisabeth Böhm
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; (M.-E.B.); (M.R.); (C.-F.F.)
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Mohammad Razavi
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; (M.-E.B.); (M.R.); (C.-F.F.)
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; (M.-E.B.); (M.R.); (C.-F.F.)
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - D. G. Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; (M.-E.B.); (M.R.); (C.-F.F.)
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence:
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Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution. Drug Resist Updat 2019; 44:100640. [PMID: 31492517 DOI: 10.1016/j.drup.2019.07.002] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.
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