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Mansoor MH, Lu X, Woksepp H, Sattar A, Humak F, Ali J, Li R, Bonnedahl J, Mohsin M. Detection and genomic characterization of Klebsiella pneumoniae and Escherichia coli harboring tet(X4) in black kites (Milvus migrans) in Pakistan. Sci Rep 2024; 14:9054. [PMID: 38643223 PMCID: PMC11032342 DOI: 10.1038/s41598-024-59201-5] [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: 09/27/2023] [Accepted: 04/08/2024] [Indexed: 04/22/2024] Open
Abstract
The emergence of plasmid-mediated tigecycline resistance gene tet(X4) among clinically relevant bacteria has promoted significant concerns, as tigecycline is considered a last-resort drug against serious infections caused by multidrug-resistant bacteria. We herein focused on the isolation and molecular characterization of tet(X4)-positive Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli) in wild bird populations with anthropogenic interaction in Faisalabad, Pakistan. A total of 150 birds including black kites (Milvus migrans) and house crows (Corvus splendens) were screened for the presence of tigecycline resistance K. pneumoniae and E. coli. We found two K. pneumoniae and one E. coli isolate carrying tet(X4) originating from black kites. A combination of short- and long-read sequencing strategies showed that tet(X4) was located on a broad host range IncFII plasmid family in K. pneumoniae isolates whereas on an IncFII-IncFIB hybrid plasmid in E. coli. We also found an integrative and conjugative element ICEKp2 in K. pneumoniae isolate KP8336. We demonstrate the first description of tet(X4) gene in the WHO critical-priority pathogen K. pneumoniae among wild birds. The convergence of tet(X4) and virulence associated ICEKp2 in a wild bird with known anthropogenic contact should be further investigated to evaluate the potential epidemiological implications. The potential risk of global transmission of tet(X4)-positive K. pneumoniae and E. coli warrant comprehensive evaluation and emphasizes the need for effective mitigation strategies to reduce anthropogenic-driven dissemination of AMR in the environment.
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Affiliation(s)
| | - Xiaoyu Lu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Hanna Woksepp
- Department of Development and Public Health, Kalmar County Hospital, 391 85, Kalmar, Sweden
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 392 31, Kalmar, Sweden
| | - Amna Sattar
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Farwa Humak
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Jabir Ali
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Jonas Bonnedahl
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden.
- Department of Infectious Diseases, Region Kalmar County, 391 85, Kalmar, Sweden.
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan.
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Nesporova K, Ruzickova M, Tarabai H, Krejci S, Masarikova M, Lausova J, Literak I, Dolejska M. Changing dynamics of antibiotic resistant Escherichia in Caspian gulls shows the importance of longitudinal environmental studies. ENVIRONMENT INTERNATIONAL 2024; 186:108606. [PMID: 38554502 DOI: 10.1016/j.envint.2024.108606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/01/2024]
Abstract
This study is focused on Escherichia spp. isolates resistant to critically important antibiotics (cefotaxime, ciprofloxacin and colistin) among Caspian gull's (Larus cachinnans) chicks nesting in the Nove Mlyny Water Reservoir, Czech Republic. The prevalence of antimicrobial resistance (AMR) in bacteria within wild birds is commonly evaluated using a single sampling event, capturing only a brief and momentary snapshot at a particular location. Therefore, the Caspian gulls in our study were sampled in May 2018 (n = 72) and May 2019 (n = 45), and a water sample was taken from the reservoir (2019). We obtained 197 isolates identified as E. coli by MALDI-TOF MS. A total of 158 representative isolates were whole-genome sequenced, 17 isolates were then reclassified to Escherichia albertii. We observed a higher (86 %; 62/72) occurrence of ESBL/AmpC-producing Escherichia spp. among gulls in 2018 compared to 38 % (17/45) in 2019 (p < 0.00001). The decrease in prevalence was linked to clonal lineage of E. coli ST11893 predominating in 2018 which carried blaCMY-2 and which was not recovered from the gulls in 2019. Oppositely, several Escherichia STs were found in gulls from both years as well as in the water sample including STs commonly recognized as internationally high-risk lineages such as ST10, ST58, ST88, ST117, ST648 or ST744. Phylogenetic analysis of E. coli from EnteroBase from countries where these particular gulls wander revealed that some STs are commonly found in various sources including humans and a portion of them is even closely related (up to 100 SNPs) to our isolates. We demonstrated that the occurrence of AMR in Escherichia can vary greatly in time in synanthropic birds and we detected both, a temporary prevalent lineage and several persistent STs. The close relatedness of isolates from gulls and isolates from EnteroBase highlights the need to further evaluate the risk connected to wandering birds.
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Affiliation(s)
- Kristina Nesporova
- CEITEC VETUNI Brno, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Michaela Ruzickova
- CEITEC VETUNI Brno, University of Veterinary Sciences Brno, Brno, Czech Republic; Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Hassan Tarabai
- CEITEC VETUNI Brno, University of Veterinary Sciences Brno, Brno, Czech Republic; Department of Parasitology, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Simon Krejci
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Martina Masarikova
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Jarmila Lausova
- CEITEC VETUNI Brno, University of Veterinary Sciences Brno, Brno, Czech Republic; Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Ivan Literak
- CEITEC VETUNI Brno, University of Veterinary Sciences Brno, Brno, Czech Republic; Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Monika Dolejska
- CEITEC VETUNI Brno, University of Veterinary Sciences Brno, Brno, Czech Republic; Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic; Biomedical Centre, Charles University, Pilsen, Czech Republic; Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Czech Republic.
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3
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Sacristán-Soriano O, Jarma D, Sánchez MI, Romero N, Alonso E, Green AJ, Sànchez-Melsió A, Hortas F, Balcázar JL, Peralta-Sánchez JM, Borrego CM. Winged resistance: Storks and gulls increase carriage of antibiotic resistance by shifting from paddy fields to landfills. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169946. [PMID: 38199372 DOI: 10.1016/j.scitotenv.2024.169946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
Waterbirds are vectors for the dissemination of antimicrobial resistance across environments, with some species increasingly reliant on highly anthropized habitats for feeding. However, data on the impact of their feeding habits on the carriage of antibiotic resistance genes (ARGs) are still scarce. To fill this gap, we examined the microbiota (16S rRNA amplicon gene sequencing) and the prevalence of ARG (high-throughput qPCR of 47 genes) in faeces from white storks (Ciconia ciconia) and lesser black-backed gulls (Larus fuscus) feeding in highly (landfill) and less (paddy fields) polluted habitats. Faecal bacterial richness and diversity were higher in gulls feeding upon landfills and showed a greater abundance of potential pathogens, such as Staphylococcus. In contrast, faecal bacterial communities from storks were similar regardless of habitat preferences, maybe due to a less intense habitat use compared to gulls. In addition, birds feeding in the landfill carried a higher burden of ARGs compared to the surrounding soil and surface waters. Network analysis revealed strong correlations between ARGs and potential pathogens, particularly between tetM (resistance to tetracyclines), blaCMY (beta-lactam resistance), sul1 (sulfonamide resistance) and members of the genera Streptococcus, Peptostreptococcus, and Peptoclostridium. Our work demonstrates how transitioning from paddy fields to landfills fosters the carriage of ARGs and potential pathogens in the bird gut, shedding light on the ecological role of these avian vectors in antimicrobial resistance dissemination.
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Affiliation(s)
| | - Dayana Jarma
- Departamento de Biología de la Conservación y Cambio Global, Estación Biológica de Doñana EBD-CSIC, Avda. Américo Vespucio 26, 41092, Sevilla, Spain; Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Avda. República Saharaui, s/n, 11510, Puerto Real, Cádiz, Spain.
| | - Marta I Sánchez
- Departamento de Biología de la Conservación y Cambio Global, Estación Biológica de Doñana EBD-CSIC, Avda. Américo Vespucio 26, 41092, Sevilla, Spain
| | - Noelia Romero
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012 Sevilla, Spain
| | - Esteban Alonso
- Departamento de Química Analítica, Escuela Politécnica Superior, Universidad de Sevilla, C/Virgen de África, 7, 41011 Sevilla, Spain
| | - Andy J Green
- Departamento de Biología de la Conservación y Cambio Global, Estación Biológica de Doñana EBD-CSIC, Avda. Américo Vespucio 26, 41092, Sevilla, Spain
| | | | - Francisco Hortas
- Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Avda. República Saharaui, s/n, 11510, Puerto Real, Cádiz, Spain
| | - José Luis Balcázar
- Institut Català de Recerca de l'Aigua (ICRA), Emili Grahit 101, E-17003 Girona, Spain
| | - Juan Manuel Peralta-Sánchez
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012 Sevilla, Spain; Departamento de Zoología, Universidad de Sevilla, Avda. Reina Mercedes s/n, 41012 Sevilla, Spain
| | - Carles M Borrego
- Institut Català de Recerca de l'Aigua (ICRA), Emili Grahit 101, E-17003 Girona, Spain; Grup d'Ecologia Microbiana Molecular, Institut d'Ecologia Aquàtica, Universitat de Girona, Campus de Montilivi, E-17003 Girona, Spain
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Tarabai H, Krejci S, Karyakin I, Bitar I, Literak I, Dolejska M. Clinically relevant antibiotic resistance in Escherichia coli from black kites in southwestern Siberia: a genetic and phenotypic investigation. mSphere 2023; 8:e0009923. [PMID: 37310717 PMCID: PMC10449506 DOI: 10.1128/msphere.00099-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/27/2023] [Indexed: 06/14/2023] Open
Abstract
Wild birds including raptors can act as vectors of clinically relevant bacteria with antibiotic resistance. The aim of this study was to investigate the occurrence of antibiotic-resistant Escherichia coli in black kites (Milvus migrans) inhabiting localities in proximity to human-influenced environments in southwestern Siberia and investigate their virulence and plasmid contents. A total of 51 E. coli isolates mostly with multidrug resistance (MDR) profiles were obtained from cloacal swabs of 35 (64%, n = 55) kites. Genomic analyses of 36 whole genome sequenced E. coli isolates showed: (i) high prevalence and diversity of their antibiotic resistance genes (ARGs) and common association with ESBL/AmpC production (27/36, 75%), (ii) carriage of mcr-1 for colistin resistance on IncI2 plasmids in kites residing in proximity of two large cities, (iii) frequent association with class one integrase (IntI1, 22/36, 61%), and (iv) presence of sequence types (STs) linked to avian-pathogenic (APEC) and extra-intestinal pathogenic E. coli (ExPEC). Notably, numerous isolates had significant virulence content. One E. coli with APEC-associated ST354 carried qnrE1 encoding fluoroquinolone resistance on IncHI2-ST3 plasmid, the first detection of such a gene in E. coli from wildlife. Our results implicate black kites in southwestern Siberia as reservoirs for antibiotic-resistant E. coli. It also highlights the existing link between proximity of wildlife to human activities and their carriage of MDR bacteria including pathogenic STs with significant and clinically relevant antibiotic resistance determinants. IMPORTANCE Migratory birds have the potential to acquire and disperse clinically relevant antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs) through vast geographical regions. The opportunistic feeding behavior associated with some raptors including black kites and the growing anthropogenic influence on their natural habitats increase the transmission risk of multidrug resistance (MDR) and pathogenic bacteria from human and agricultural sources into the environment and wildlife. Thus, monitoring studies investigating antibiotic resistance in raptors may provide essential data that facilitate understanding the fate and evolution of ARB and ARGs in the environment and possible health risks for humans and animals associated with the acquisition of these resistance determinants by wildlife.
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Affiliation(s)
- Hassan Tarabai
- Central European Institute of Technology (CEITEC), University of Veterinary Sciences, Brno, Czech Republic
- Department of Parasitology, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Simon Krejci
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences, Brno, Czech Republic
| | | | - Ibrahim Bitar
- Biomedical Center, Charles University, Prague, Czech Republic
| | - Ivan Literak
- Central European Institute of Technology (CEITEC), University of Veterinary Sciences, Brno, Czech Republic
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences, Brno, Czech Republic
| | - Monika Dolejska
- Central European Institute of Technology (CEITEC), University of Veterinary Sciences, Brno, Czech Republic
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences, Brno, Czech Republic
- Biomedical Center, Charles University, Prague, Czech Republic
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital, Brno, Czech Republic
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Fuentes-Castillo D, Castro-Tardón D, Esposito F, Neves I, Rodrigues L, Fontana H, Fuga B, Catão-Dias JL, Lincopan N. Genomic evidences of gulls as reservoirs of critical priority CTX-M-producing Escherichia coli in Corcovado Gulf, Patagonia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162564. [PMID: 36870482 DOI: 10.1016/j.scitotenv.2023.162564] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Extended spectrum β-lactamase (ESBL)-producing Enterobacterales has spread rapidly around the world, reaching remote areas. In this regard, wild birds that acquire ESBL producers from anthropogenically impacted areas can become reservoirs, contributing to further dissemination of antimicrobial-resistant bacteria categorized as critical priority pathogens to remote environments, during migration seasons. We have conducted a microbiological and genomic investigation on the occurrence and features of ESBL-producing Enterobacterales in wild birds from the remote Acuy Island, in the Gulf of Corcovado, at Chilean Patagonia. Strikingly, five ESBL-producing Escherichia coli were isolated from migratory and resident gulls. Whole-genome sequencing (WGS) analysis revealed the presence of two E. coli clones belonging to international sequence types (STs) ST295 and ST388, producing CTX-M-55 and CTX-M-1 ESBLs, respectively. Moreover, E. coli carried a wide resistome and virulome associated with human and animal infections. Phylogenomic analysis of global and publicly genomes of E. coli ST388 (n = 51) and ST295 (n = 85) clustered gulls isolates along to E. coli strains isolated from the environment, companion animal and livestock in the United States of America, within or close to the migratory route of Franklin's gull, suggesting a possible trans hemispheric movement of international clones of WHO critical priority ESBL producing pathogens.
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Affiliation(s)
- Danny Fuentes-Castillo
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile; Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
| | - Daniela Castro-Tardón
- Escuela de Medicina Veterinaria, Facultad de Recursos Naturales y Medicina Veterinaria, Universidad Santo Tomás, Talca, Chile
| | - Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Ingrith Neves
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Larissa Rodrigues
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - José L Catão-Dias
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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López-Calderón C, Martín-Vélez V, Blas J, Höfle U, Sánchez MI, Flack A, Fiedler W, Wikelski M, Green AJ. White stork movements reveal the ecological connectivity between landfills and different habitats. MOVEMENT ECOLOGY 2023; 11:18. [PMID: 36978169 PMCID: PMC10045253 DOI: 10.1186/s40462-023-00380-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Connections between habitats are key to a full understanding of anthropic impacts on ecosystems. Freshwater habitats are especially biodiverse, yet depend on exchange with terrestrial habitats. White storks (Ciconia ciconia) are widespread opportunists that often forage in landfills and then visit wetlands, among other habitats. It is well known that white storks ingest contaminants at landfills (such as plastics and antibiotic resistant bacteria), which can be then deposited in other habitats through their faeces and regurgitated pellets. METHODS We characterized the role of white storks in habitat connectivity by analyzing GPS data from populations breeding in Germany and wintering from Spain to Morocco. We overlaid GPS tracks on a land-use surface to construct a spatially-explicit network in which nodes were sites, and links were direct flights. We then calculated centrality metrics, identified spatial modules, and quantified overall connections between habitat types. For regional networks in southern Spain and northern Morocco, we built Exponential Random Graph Models (ERGMs) to explain network topologies as a response to node habitat. RESULTS For Spain and Morocco combined, we built a directed spatial network with 114 nodes and 370 valued links. Landfills were the habitat type most connected to others, as measured by direct flights. The relevance of landfills was confirmed in both ERGMs, with significant positive effects of this habitat as a source of flights. In the ERGM for southern Spain, we found significant positive effects of rice fields and salines (solar saltworks) as sinks for flights. By contrast, in the ERGM for northern Morocco, we found a significant positive effect of marshes as a sink for flights. CONCLUSIONS These results illustrate how white storks connect landfills with terrestrial and aquatic habitats, some of which are managed for food production. We identified specific interconnected habitat patches across Spain and Morocco that could be used for further studies on biovectoring of pollutants, pathogens and other propagules.
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Affiliation(s)
- Cosme López-Calderón
- Department of Wetland Ecology, Estación Biológica de Doñana CSIC, Seville, Spain.
| | - Víctor Martín-Vélez
- Department of Wetland Ecology, Estación Biológica de Doñana CSIC, Seville, Spain
| | - Julio Blas
- Department of Conservation Biology, Estación Biológica de Doñana CSIC, Seville, Spain
| | - Ursula Höfle
- SaBio Health and Biotechnology Research Group, Institute for Game and Wildlife Research (IREC), CSIC-UCLM-JCCM, Ciudad Real, Spain
| | - Marta I Sánchez
- Department of Wetland Ecology, Estación Biológica de Doñana CSIC, Seville, Spain
| | - Andrea Flack
- Collective Migration Group, Max Planck Institute of Animal Behavior, 78315, Radolfzell, Germany
- Department of Migration and Immuno-Ecology, Max Planck Institute of Animal Behaviour, Radolfzell, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78468, Constance, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Wolfgang Fiedler
- Department of Migration and Immuno-Ecology, Max Planck Institute of Animal Behaviour, Radolfzell, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78468, Constance, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Martin Wikelski
- Department of Migration and Immuno-Ecology, Max Planck Institute of Animal Behaviour, Radolfzell, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78468, Constance, Germany
- Department of Biology, University of Konstanz, Constance, Germany
| | - Andy J Green
- Department of Wetland Ecology, Estación Biológica de Doñana CSIC, Seville, Spain
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Ewbank AC, Fuentes-Castillo D, Sacristán C, Esposito F, Fuga B, Cardoso B, Godoy SN, Zamana RR, Gattamorta MA, Catão-Dias JL, Lincopan N. World Health Organization critical priority Escherichia coli clone ST648 in magnificent frigatebird (Fregata magnificens) of an uninhabited insular environment. Front Microbiol 2022; 13:940600. [PMID: 36033868 PMCID: PMC9410367 DOI: 10.3389/fmicb.2022.940600] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance is an ancient natural phenomenon increasingly pressured by anthropogenic activities. Escherichia coli has been used as markers of environmental contamination and human-related activity. Seabirds may be bioindicators of clinically relevant bacterial pathogens and their antimicrobial resistance genes, including extended-spectrum-beta-lactamase (ESBL) and/or plasmid-encoded AmpC (pAmpC), in anthropized and remote areas. We evaluated cloacal swabs of 20 wild magnificent frigatebirds (Fregata magnificens) of the Alcatrazes Archipelago, the biggest breeding colony of magnificent frigatebirds in the southern Atlantic and a natural protected area with no history of human occupation, located in the anthropized southeastern Brazilian coast. We characterized a highly virulent multidrug-resistant ST648 (O153:H9) pandemic clone, harboring blaCTX–M–2, blaCMY–2, qnrB, tetB, sul1, sul2, aadA1, aac(3)-VIa and mdfA, and virulence genes characteristic of avian pathogenic (APEC) (hlyF, iroN, iss, iutA, and ompT) and other extraintestinal E. coli (ExPEC) (chuA, kpsMII, and papC). To our knowledge, this is the first report of ST648 E. coli co-producing ESBL and pAmpC in wild birds inhabiting insular environments. We suggest this potentially zoonotic and pathogenic lineage was likely acquired through indirect anthropogenic contamination of the marine environment, ingestion of contaminated seafood, or by intra and/or interspecific contact. Our findings reinforce the role of wild birds as anthropization sentinels in insular environments and the importance of wildlife surveillance studies on pathogens of critical priority classified by the World Health Organization.
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Affiliation(s)
- Ana Carolina Ewbank
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
- *Correspondence: Ana Carolina Ewbank,
| | - Danny Fuentes-Castillo
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Carlos Sacristán
- Centro de Investigación en Sanidad Animal (CISA-INIA), CSIC, Valdeolmos-Alalpardo, Spain
| | - Fernanda Esposito
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Brenda Cardoso
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Silvia Neri Godoy
- Refúgio de Vida Silvestre do Arquipélago de Alcatrazes – Instituto Chico Mendes de Conservação da Biodiversidade, São Paulo, Brazil
| | - Roberta Ramblas Zamana
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Marco Aurélio Gattamorta
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Luiz Catão-Dias
- Laboratory of Wildlife Comparative Pathology, Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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8
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Athanasakopoulou Z, Diezel C, Braun SD, Sofia M, Giannakopoulos A, Monecke S, Gary D, Krähmer D, Chatzopoulos DC, Touloudi A, Birtsas P, Palli M, Georgakopoulos G, Spyrou V, Petinaki E, Ehricht R, Billinis C. Occurrence and Characteristics of ESBL- and Carbapenemase- Producing Escherichia coli from Wild and Feral Birds in Greece. Microorganisms 2022; 10:1217. [PMID: 35744734 PMCID: PMC9227375 DOI: 10.3390/microorganisms10061217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/04/2022] [Accepted: 06/12/2022] [Indexed: 11/16/2022] Open
Abstract
Wild and feral birds are known to be involved in the maintenance and dissemination of clinically-important antimicrobial-resistant pathogens, such as extended-spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacteriaceae. The aim of our study was to evaluate the presence of ESBL- and carbapenemase-producing Escherichia coli among wild and feral birds from Greece and to describe their antimicrobial resistance characteristics. In this context, fecal samples of 362 birds were collected and cultured. Subsequently, the antimicrobial resistance pheno- and geno-type of all the obtained E. coli isolates were determined. A total of 12 multidrug-resistant (MDR), ESBL-producing E. coli were recovered from eight different wild bird species. Eleven of these isolates carried a blaCTX-M-1 group gene alone or in combination with blaTEM and one carried only blaTEM. AmpC, fluoroquinolone, trimethoprim/sulfamethoxazole, aminoglycoside and macrolide resistance genes were also detected. Additionally, one carbapenemase-producing E. coli was identified, harboring blaNDM along with a combination of additional resistance genes. This report describes the occurrence of ESBL- and carbapenemase-producing E. coli among wild avian species in Greece, emphasizing the importance of incorporating wild birds in the assessment of AMR circulation in non-clinical settings.
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Affiliation(s)
- Zoi Athanasakopoulou
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (A.G.); (A.T.)
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (C.D.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07745 Jena, Germany
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (C.D.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07745 Jena, Germany
| | - Marina Sofia
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (A.G.); (A.T.)
| | - Alexios Giannakopoulos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (A.G.); (A.T.)
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (C.D.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07745 Jena, Germany
| | - Dominik Gary
- fzmb GmbH, Forschungszentrum für Medizintechnik und Biotechnologie, 99947 Bad Langensalza, Germany; (D.G.); (D.K.)
| | - Domenique Krähmer
- fzmb GmbH, Forschungszentrum für Medizintechnik und Biotechnologie, 99947 Bad Langensalza, Germany; (D.G.); (D.K.)
| | | | - Antonia Touloudi
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (A.G.); (A.T.)
| | - Periklis Birtsas
- Faculty of Forestry, Wood Science and Design, 43100 Karditsa, Greece;
| | - Matina Palli
- Wildlife Protection & Rehabilitation Center, 24400 Gargalianoi, Greece; (M.P.); (G.G.)
| | | | - Vassiliki Spyrou
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece;
| | | | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (C.D.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07745 Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller-University, 07745 Jena, Germany
| | - Charalambos Billinis
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (A.G.); (A.T.)
- Faculty of Public and One Health, University of Thessaly, 43100 Karditsa, Greece;
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9
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Islam MS, Sobur MA, Rahman S, Ballah FM, Ievy S, Siddique MP, Rahman M, Kafi MA, Rahman MT. Detection of bla TEM, bla CTX-M, bla CMY, and bla SHV Genes Among Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated from Migratory Birds Travelling to Bangladesh. MICROBIAL ECOLOGY 2022; 83:942-950. [PMID: 34312710 PMCID: PMC8313370 DOI: 10.1007/s00248-021-01803-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/18/2021] [Indexed: 06/02/2023]
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli cause severe health hazards. Migratory birds are reservoirs and transmitters of many pathogens including ESBL-producing E. coli. To examine migratory birds as potential carriers of ESBL-producing E. coli and E. coli-carrying antibiotic resistance genes, 55 PCR-positive E. coli isolates were screened using the disk diffusion method, double-disk synergy test, and further polymerase chain reaction (PCR) tests. Genes encoding resistance to tetracycline [tetA, 100% (35/35); tetB, 31.43% (11/35)], fluoroquinolone [qnrA, 35.71% (10/28); qnrB, 25% (7/28)], and streptomycin [aadA1, 90.24% (37/41)] were detected in the isolated E. coli. Of the 55 E. coli isolates, 21 (38.18%) were ESBL producers, and all of them were multidrug resistant. All the ESBL-producing E. coli isolates harbored at least two or more beta-lactamase genes, of which blaTEM, blaCMY, blaCTX-M, and blaSHV were detected in 95.24%, 90.48%, 85.71%, and 42.86% of isolates, respectively. All the beta-lactamase genes were present in four of the ESBL-producing E. coli isolates. Furthermore, 95.24% of ESBL-producing E. coli isolates were positive for one or more antibiotic resistance genes. To the best of our knowledge, this is the first study to detect E. coli-carrying antibiotic resistance genes including beta-lactamase blaCMY and blaSHV originating from migratory birds in Bangladesh. These results suggest that migratory birds are potential carriers of ESBL-producing E. coli along with other clinically important antibiotic resistance genes which may have detrimental impacts on human health.
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Affiliation(s)
- Md Saiful Islam
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Abdus Sobur
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Saifur Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Fatimah Mohammed Ballah
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Samina Ievy
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Mahbubul Pratik Siddique
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Marzia Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Abdul Kafi
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
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10
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Duxbury SJN, Alderliesten JB, Zwart MP, Stegeman A, Fischer EAJ, de Visser JAGM. Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli. Proc Biol Sci 2021; 288:20212027. [PMID: 34727719 PMCID: PMC8564601 DOI: 10.1098/rspb.2021.2027] [Citation(s) in RCA: 3] [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: 09/11/2021] [Accepted: 10/12/2021] [Indexed: 12/17/2022] Open
Abstract
Plasmid-mediated antimicrobial resistance is a major contributor to the spread of resistance genes within bacterial communities. Successful plasmid spread depends upon a balance between plasmid fitness effects on the host and rates of horizontal transmission. While these key parameters are readily quantified in vitro, the influence of interactions with other microbiome members is largely unknown. Here, we investigated the influence of three genera of lactic acid bacteria (LAB) derived from the chicken gastrointestinal microbiome on the spread of an epidemic narrow-range ESBL resistance plasmid, IncI1 carrying blaCTX-M-1, in mixed cultures of isogenic Escherichia coli strains. Secreted products of LAB decreased E. coli growth rates in a genus-specific manner but did not affect plasmid transfer rates. Importantly, we quantified plasmid transfer rates by controlling for density-dependent mating opportunities. Parametrization of a mathematical model with our in vitro estimates illustrated that small fitness costs of plasmid carriage may tip the balance towards plasmid loss under growth conditions in the gastrointestinal tract. This work shows that microbial interactions can influence plasmid success and provides an experimental-theoretical framework for further study of plasmid transfer in a microbiome context.
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Affiliation(s)
| | - Jesse B. Alderliesten
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Mark P. Zwart
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Arjan Stegeman
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Egil A. J. Fischer
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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11
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Ramey AM. Antimicrobial resistance: Wildlife as indicators of anthropogenic environmental contamination across space and through time. Curr Biol 2021; 31:R1385-R1387. [PMID: 34699802 DOI: 10.1016/j.cub.2021.08.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Prior assessments support wildlife as indicators of anthropogenically influenced antimicrobial resistance across the landscape. A ground-breaking new study suggests that wildlife may also provide information on antimicrobial resistance in the environment through time.
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Affiliation(s)
- Andrew M Ramey
- US Geological Survey Alaska Science Center, Anchorage, AK 99508, USA.
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12
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Kurittu P, Khakipoor B, Brouwer MS, Heikinheimo A. Plasmids conferring resistance to extended-spectrum beta-lactamases including a rare IncN+IncR multireplicon carrying blaCTX-M-1 in Escherichia coli recovered from migrating barnacle geese ( Branta leucopsis). OPEN RESEARCH EUROPE 2021; 1:46. [PMID: 37645149 PMCID: PMC10446048 DOI: 10.12688/openreseurope.13529.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/23/2021] [Indexed: 08/31/2023]
Abstract
Background: Increasing antimicrobial resistance (AMR) is a global threat and wild migratory birds may act as mediators of resistant bacteria across country borders. Our objective was to study extended-spectrum beta-lactamase (ESBL) and plasmid-encoded AmpC (pAmpC) producing Escherichia coli in barnacle geese using whole genome sequencing (WGS) and to identify plasmids harboring bla genes. Methods: Barnacle geese feces (n=200) were collected during fall 2017 and spring 2018 from an urban area in Helsinki, Finland. ESBL/AmpC-producing E. coli were recovered from nine samples (4.5%) and isolates were subjected to WGS on both short- and long-read sequencers, enabling hybrid assembly and determination of the genomic location of bla genes. Results: A rare multireplicon IncN+IncR was recovered from one isolate carrying bla CTX-M-1 in addition to aadA2b, lnu(F), and qnrS1. Moreover, rarely detected IncY plasmids in two isolates were found to harbor multiple resistance genes in addition to the human-associated bla CTX-M-15. Poultry-associated bla CMY-2 was identified from the widely distributed IncI1 and IncK plasmids from four different isolates. One isolate harbored an IncI1 plasmid with bla CTX-M-1 and flor. A chromosomal point mutation in the AmpC promoter was identified in one of the isolates. WGS analysis showed isolates carried multiple resistance and virulence genes and harbored multiple different plasmid replicons in addition to bla-carrying plasmids. Conclusions: Our findings suggest that wild migratory birds serve as a limited source of ESBL/AmpC-producing E. coli and may act as disseminators of the epidemic plasmid types IncI1 and IncK but also rarely detected plasmid types carrying multidrug resistance. Human and livestock-associated ESBL enzyme types were recovered from samples, suggesting a potential for interspecies transmission. WGS offers a thorough method for studying AMR from different sources and should be implemented more widely in the future for AMR surveillance and detection. Understanding plasmid epidemiology is vital for efforts to mitigate global AMR spread.
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Affiliation(s)
- Paula Kurittu
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Banafsheh Khakipoor
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Laboratory and Research Division, Microbiology Unit, Finnish Food Authority, Seinäjoki, Finland
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13
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Lin Z, Yuan T, Zhou L, Cheng S, Qu X, Lu P, Feng Q. Impact factors of the accumulation, migration and spread of antibiotic resistance in the environment. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:1741-1758. [PMID: 33123928 DOI: 10.1007/s10653-020-00759-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance is a great concern, which leads to global public health risks and ecological and environmental risks. The presence of antibiotic-resistant genes and antibiotic-resistant bacteria in the environment exacerbates the risk of spreading antibiotic resistance. Among them, horizontal gene transfer is an important mode in the spread of antibiotic resistance genes, and it is one of the reasons that the antibiotic resistance pollution has become increasingly serious. At the same time, free antibiotic resistance genes and resistance gene host bacterial also exist in the natural environment. They can not only affect horizontal gene transfer, but can also migrate and aggregate among environmental media in many ways and then continue to affect the proliferate and transfer of antibiotic resistance genes. All this shows the seriousness of antibiotic resistance pollution. Therefore, in this review, we reveal the sensitive factors affecting the distribution and spread of antibiotic resistance through three aspects: the influencing factors of horizontal gene transfer, the host bacteria of resistance genes and the migration of antibiotic resistance between environmental media. This review reveals the huge role of environmental migration in the spread of antibiotic resistance, and the environmental behavior of antibiotic resistance deserves wider attention. Meanwhile, extracellular antibiotic resistance genes and intracellular antibiotic resistance genes play different roles, so they should be studied separately.
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Affiliation(s)
- Zibo Lin
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Tao Yuan
- Department of Construction Equipment and Municipal Engineering, Jiangsu Vocational Institute of Architectural Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
- Jiangsu Collaborative Innovation Center for Building Energy Saving and Construct Technology, Xuzhou, 221116, China
| | - Lai Zhou
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Sen Cheng
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Xu Qu
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
| | - Ping Lu
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China.
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China.
| | - Qiyan Feng
- School of Environmental Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221000, Jiangsu, China
- Jiangsu Key Laboratory of Coal-based Greenhouse Gas Control and Utilization, China University of Mining and Technology, Xuzhou, 221008, China
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14
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Ahlstrom CA, van Toor ML, Woksepp H, Chandler JC, Reed JA, Reeves AB, Waldenström J, Franklin AB, Douglas DC, Bonnedahl J, Ramey AM. Evidence for continental-scale dispersal of antimicrobial resistant bacteria by landfill-foraging gulls. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:144551. [PMID: 33385653 DOI: 10.1016/j.scitotenv.2020.144551] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Anthropogenic inputs into the environment may serve as sources of antimicrobial resistant bacteria and alter the ecology and population dynamics of synanthropic wild animals by providing supplemental forage. In this study, we used a combination of phenotypic and genomic approaches to characterize antimicrobial resistant indicator bacteria, animal telemetry to describe host movement patterns, and a novel modeling approach to combine information from these diverse data streams to investigate the acquisition and long-distance dispersal of antimicrobial resistant bacteria by landfill-foraging gulls. Our results provide evidence that gulls acquire antimicrobial resistant bacteria from anthropogenic sources, which they may subsequently disperse across and between continents via migratory movements. Furthermore, we introduce a flexible modeling framework to estimate the relative dispersal risk of antimicrobial resistant bacteria in western North America and adjacent areas within East Asia, which may be adapted to provide information on the risk of dissemination of other organisms and pathogens maintained by wildlife through space and time.
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Affiliation(s)
- Christina A Ahlstrom
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK 99508, USA.
| | - Mariëlle L van Toor
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Stuvaregatan 2, Kalmar 392 31, Sweden.
| | - Hanna Woksepp
- Department of Development and Public Health, Kalmar County Hospital, Kalmar 391 85, Sweden.
| | - Jeffrey C Chandler
- USDA/APHIS/WS, National Wildlife Research Center, 4101 Laporte Ave, Fort Collins, CO 80521, USA.
| | - John A Reed
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK 99508, USA.
| | - Andrew B Reeves
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK 99508, USA.
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Stuvaregatan 2, Kalmar 392 31, Sweden.
| | - Alan B Franklin
- USDA/APHIS/WS, National Wildlife Research Center, 4101 Laporte Ave, Fort Collins, CO 80521, USA.
| | - David C Douglas
- Alaska Science Center, U.S. Geological Survey, 250 Egan Drive, Juneau, AK 99801, USA.
| | - Jonas Bonnedahl
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping 581 83, Sweden; Department of Infectious Diseases, Region Kalmar County, Kalmar 391 85, Sweden.
| | - Andrew M Ramey
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK 99508, USA.
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15
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Selection of Resistant Bacteria in Mallards Exposed to Subinhibitory Concentrations of Ciprofloxacin in Their Water Environment. Antimicrob Agents Chemother 2021; 65:AAC.01858-20. [PMID: 33318021 DOI: 10.1128/aac.01858-20] [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] [Received: 09/01/2020] [Accepted: 12/10/2020] [Indexed: 12/22/2022] Open
Abstract
Emergence and selection of antibiotic resistance following exposure to high antibiotic concentrations have been repeatedly shown in clinical and agricultural settings, whereas the role of the weak selective pressures exerted by antibiotic levels below the MIC (sub-MIC) in aquatic environments due to anthropogenic contamination remains unclear. Here, we studied how exposure to sub-MIC levels of ciprofloxacin enriches for Escherichia coli with reduced susceptibility to ciprofloxacin using a mallard colonization model. Mallards were inoculated with two isogenic extended-spectrum-β-lactamase (ESBL)-encoding E. coli strains, differing only by a gyrA mutation that results in increased MICs of ciprofloxacin, and exposed to different levels of ciprofloxacin in their swimming water. Changes in the ratios of mutant to parental strains excreted in feces over time and ESBL plasmid spread within the gut microbiota from individual birds were investigated. Results show that in vivo selection of gyrA mutants occurred in mallards during exposure to ciprofloxacin at concentrations previously found in aquatic environments. During colonization, resistance plasmids were readily transferred between strains in the intestines of the mallards, but conjugation frequencies were not affected by ciprofloxacin exposure. Our results highlight the potential for enrichment of resistant bacteria in wildlife and underline the importance of reducing antibiotic pollution in the environment.
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16
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Blanco G, López-Hernández I, Morinha F, López-Cerero L. Intensive farming as a source of bacterial resistance to antimicrobial agents in sedentary and migratory vultures: Implications for local and transboundary spread. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 739:140356. [PMID: 32758969 DOI: 10.1016/j.scitotenv.2020.140356] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
The role of wild birds in the carriage and transmission of human and food animal bacteria with resistant genotypes has repeatedly been highlighted. However, few studies have focussed on the specific exposure sources and places of acquisition and selection for antimicrobial-resistant bacteria in vultures relying on livestock carcasses across large areas and different continents. The occurrence of bacterial resistance to antimicrobial agents was assessed in the faecal microbiota of sedentary Griffon vultures (Gyps fulvus) and trans-Saharan migratory Egyptian vultures (Neophron percnopterus) in central Spain. High rates (generally >50%) of resistant Escherichia coli and other enterobacteria to amoxicillin, cotrimoxazole and tetracycline were found. About 25-30% of samples were colonised by extended-spectrum beta-lactamases (ESBL) producing bacteria, while 5-17% were positive for plasmid mediated quinolone resistance (PMQR) phenotypes, depending on vulture species and age. In total, nine ESBL types were recorded (7 in griffon vultures and 5 in Egyptian vultures), with CTX-M-1 the most prevalent in both species. The most prevalent PMQR was mediated by qnrS genes. We found no clear differences in the occurrence of antimicrobial resistance in adult vultures of each species, or between nestling and adult Egyptian vultures. This supports the hypothesis that antimicrobial resistance is acquired in the European breeding areas of both species. Bacterial resistance can directly be driven by the regular ingestion of multiple active antimicrobials found in medicated livestock carcasses from factory farms, which should be not neglected as a contributor to the emergence of novel resistance clones. The One Health framework should consider the potential transboundary carriage and spread of epidemic resistance from high-income European to low-income African countries via migratory birds.
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Affiliation(s)
- Guillermo Blanco
- Department of Evolutionary Ecology, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain.
| | - Inmaculada López-Hernández
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
| | - Francisco Morinha
- Department of Evolutionary Ecology, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Lorena López-Cerero
- Unidad de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
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17
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Blanco G, Bautista LM. Avian Scavengers as Bioindicators of Antibiotic Resistance due to Livestock Farming Intensification. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17103620. [PMID: 32455739 PMCID: PMC7277293 DOI: 10.3390/ijerph17103620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 11/25/2022]
Abstract
Industrial food animal production uses huge amounts of antibiotics worldwide. Livestock, their excreta used for manure and meat subproducts not intended for human consumption can all play important roles in the transmission of bacterial resistance to wildlife. Vultures and other scavengers can be directly exposed to active antibiotics ingested while feeding on livestock carcasses. This study evaluates whether bacterial resistance in the red kite (Milvus milvus) differs between two wintering areas selected based on patent differences in farming practices—particularly in the industrial production of food animals (primarily swine and poultry) vs. scarce and declining sheep herding. The results support the hypothesis that intensification in food animal production is associated with increased bacterial multidrug resistance in wildlife. Resistance was positively correlated with time elapsed since the beginning of the commercial application of each antibiotic in human and veterinary medicine, with clear differences depending on farming intensification between areas. Monitoring programs are encouraged to use red kites and other avian scavengers as valuable sentinels of contamination by antibiotics and clinically relevant resistant pathogens from livestock operations of variable intensities. Farms authorized for supplementary feeding of threatened scavengers should avoid supplying carcasses with active antibiotic residues to avoid bacterial resistance in scavenger wildlife.
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18
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Zhou Z, Alikhan NF, Mohamed K, Fan Y, Achtman M. The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res 2020; 30:138-152. [PMID: 31809257 PMCID: PMC6961584 DOI: 10.1101/gr.251678.119] [Citation(s) in RCA: 478] [Impact Index Per Article: 119.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 12/03/2019] [Indexed: 01/08/2023]
Abstract
EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. Here, we provide an overview of how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridioides, Helicobacter, Vibrio, and Moraxella and genotyped those assemblies by core genome multilocus sequence typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case Study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports single nucleotide polymorphism (SNP) calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by Case Study 2 which summarizes the microevolution of Yersinia pestis over the last 5000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by Case Study 3, which presents a novel, global overview of the population structure of all of the species, subspecies, and clades within Escherichia.
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Role of wastewater treatment plants on environmental abundance of Antimicrobial Resistance Genes in Chilean rivers. Int J Hyg Environ Health 2019; 223:56-64. [PMID: 31722832 DOI: 10.1016/j.ijheh.2019.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/04/2019] [Accepted: 10/12/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Point sources such as wastewater treatment plants (WWTPs) commonly discharge their effluent into rivers. Their waste may include antibiotic residues, disinfectants, antibiotic resistant bacteria (ARB), and Antimicrobial Resistance Genes (ARG). There is evidence that ARG can be found in the natural environment, but attribution to specific point sources is lacking. OBJECTIVES The goal of this study was to assess the release and dissemination of ARG from three WWTPs in southern Chile via two pathways: through the river systems, and through wild birds. METHODS A longitudinal study was conducted, collecting river sediment samples at different distances both upstream and downstream from each WWTP. Wild birds were sampled from around one of the WWTPs once a month for 13 months. A microfluidic q-PCR approach was used to quantify 48 genes covering different molecular mechanisms of resistance, and data was analyzed using ordination methods and linear mixed regression models. RESULTS There was a statistically significant increase downstream from the WWTPs (p < 0.05) for 17 ARG, but the downstream dissemination through the rivers was not clear. Beta-lactamase genes blaKPC, blaTEM, and blaSHV were the most abundant in birds, with higher abundance of blaSHV in migratory species compared to resident species (p < 0.05). The gene profile was more similar between the migratory and resident bird groups compared to the WWTP gene profile. CONCLUSIONS While results from this study indicate an influence of WWTPs on ARG abundance in the rivers, the biological significance of this increase and the extent of the WWTPs influence are unclear. In addition, wild birds were found to play a role in disseminating ARG, although association to the specific WWTP could not be ascertained.
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Zou H, Zheng B, Sun M, Ottoson J, Li Y, Berglund B, Chi X, Ji X, Li X, Stålsby Lundborg C, Nilsson LE. Evaluating Dissemination Mechanisms of Antibiotic-Resistant Bacteria in Rural Environments in China by Using CTX-M-Producing Escherichia coli as an Indicator. Microb Drug Resist 2019; 25:975-984. [PMID: 30942653 DOI: 10.1089/mdr.2018.0431] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
It is becoming increasingly recognized that the environment plays an important role both in the emergence and in dissemination of antibiotic-resistant bacteria (ARB), Mechanisms and factors facilitating this development are, however, not yet well understood. The high detection rate of CTX-M genes in environmental sources provides an opportunity to explore this issue. In this study, 88 CTX-M-producing Escherichia coli were isolated from 30 pig feces samples from 30 pig farms and 201 environmental samples. CTX-M-producing E. coli was detected with the following frequencies in the different types of samples: pig feces, 73%; river water, 64%; river sediment, 52%; wastewater, 31%; drinking water, 23%; outlet sediment, 21%; soil, 17%; and vegetables, 4.4%. Dissemination of CTX-M-producing E. coli to different environmental matrices was evaluated by analyzing the genetic relatedness of isolates from different environmental sources, and putative transmission routes through bird feces, pig feces, drinking water, river sediment, river water, and wastewater were hypothesized. Dissemination through these routes is likely facilitated by anthropogenic activities and environmental factors. Wild birds as potential vectors for dissemination of CTX-M-producing E. coli have the capacity to spread ARB across long distances. Regional dissemination between different environmental matrices of CTX-M-producing E. coli increases the exposure risk of humans and animals in the area.
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Affiliation(s)
- Huiyun Zou
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Mingli Sun
- Center of Disease Prevention and Control, Zhucheng City, Shandong Province, China
| | - Jakob Ottoson
- National Food Agency, Department of Risk and Benefit Assessment, Uppsala, Sweden
| | - Yubo Li
- Center of Disease Prevention and Control, Zhucheng City, Shandong Province, China
| | - Björn Berglund
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Xiaohui Chi
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Xiang Ji
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Xuewen Li
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Cecilia Stålsby Lundborg
- Global Health-Health Systems and Policy: Medicines, Focusing Antibiotics, Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Lennart E Nilsson
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
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