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Butters A, Jovel J, Gow S, Liljebjelke K, Waldner C, Checkley SL. PmrB Y358N, E123D amino acid substitutions are not associated with colistin resistance but with phylogeny in Escherichia coli. Microbiol Spectr 2024; 12:e0053224. [PMID: 39162501 PMCID: PMC11451601 DOI: 10.1128/spectrum.00532-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 07/16/2024] [Indexed: 08/21/2024] Open
Abstract
Colistin resistance in Escherichia coli is of public health significance for its use to treat multidrug-resistant Gram-negative infections. Amino acid variations in PmrB have been implicated in colistin resistance in E. coli. In this cross-sectional study, 288 generic E. coli isolates from surveillance of broiler chicken and feedlot cattle feces, retail meat, wastewater, and well water were whole-genome sequenced. Phylogroup designation and screening for two amino acid substitutions in PmrB putatively linked to colistin resistance (Y358N, E123D) were performed in silico. Three additional data sets of publicly available E. coli assemblies were similarly scrutinized: (i) E. coli isolates from studies identifying the Y358N or E123D substitutions, (ii) colistin-susceptible E. coli isolates reported in the literature, and (iii) a random sampling of 14,700 E. coli assemblies available in the National Center for Biotechnology Information public database. Within all data sets, ≥95% of phylogroup B1 and C isolates have the PmrB Y358N variation. The PmrB E123D amino acid substitution was only identified in phylogroup B2 isolates, of which 94%-100% demonstrate the substitution. Both PmrB amino acid variations were infrequent in other phylogroups. Among published colistin susceptible isolates, colistin minimum inhibitory concentrations (MICs) were not higher in isolates bearing the E123D and Y358N amino acid variations than in isolates without these PmrB substitutions. The E123D and Y358N PmrB amino acid substitutions in E. coli appear strongly associated with phylogroup. The previously observed associations between Y358N and E123D amino acid substitutions in PmrB and colistin resistance in E. coli may be spurious. IMPORTANCE Colistin is a critical last-resort treatment for extensively drug-resistant Gram-negative infections in humans. Therefore, accurate identification of the genetic mechanisms of resistance to this antimicrobial is crucial to effectively monitor and mitigate the spread of resistance. Examining over 16,000 whole-genome sequenced Escherichia coli isolates, this study identifies that PmrB E123D and Y358N amino acid substitutions previously associated with colistin resistance in E. coli are strongly associated with phylogroup and are alone not sufficient to confer a colistin-resistant phenotype. This is a critical clarification, as both substitutions are identified as putative mechanisms of colistin resistance in many publications and a common bioinformatic tool. Given the potential spurious nature of initial associations of these substitutions with colistin resistance, this study's findings emphasize the importance of appropriate experimental design and consideration of relevant biological factors such as phylogroup when ascribing causal mechanisms of resistance to chromosomal variations.
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Affiliation(s)
- Alyssa Butters
- Faculty of Veterinary
Medicine, University of Calgary,
Calgary, Alberta,
Canada
- AMR—One Health
Consortium, Calgary,
Alberta, Canada
| | - Juan Jovel
- Faculty of Veterinary
Medicine, University of Calgary,
Calgary, Alberta,
Canada
| | - Sheryl Gow
- Canadian Integrated
Program for Antimicrobial Resistance Surveillance/FoodNet, Public Health
Agency of Canada, Ottawa,
Ontario, Canada
- Department of Large
Animal Clinical Sciences, Western College of Veterinary Medicine,
University of Saskatchewan,
Saskatoon, Saskatchewan,
Canada
| | - Karen Liljebjelke
- Faculty of Veterinary
Medicine, University of Calgary,
Calgary, Alberta,
Canada
- AMR—One Health
Consortium, Calgary,
Alberta, Canada
| | - Cheryl Waldner
- Department of Large
Animal Clinical Sciences, Western College of Veterinary Medicine,
University of Saskatchewan,
Saskatoon, Saskatchewan,
Canada
| | - Sylvia L. Checkley
- Faculty of Veterinary
Medicine, University of Calgary,
Calgary, Alberta,
Canada
- AMR—One Health
Consortium, Calgary,
Alberta, Canada
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2
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Li X, Mowlaboccus S, Jackson B, Cai C, Coombs GW. Antimicrobial resistance among clinically significant bacteria in wildlife: An overlooked one health concern. Int J Antimicrob Agents 2024; 64:107251. [PMID: 38906487 DOI: 10.1016/j.ijantimicag.2024.107251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/30/2024] [Accepted: 06/07/2024] [Indexed: 06/23/2024]
Abstract
Antimicrobial resistance (AMR) has emerged as a critical global health challenge. However, the significance of AMR is not limited to humans and domestic animals but extends to wildlife and the environment. Based on the analysis of > 200 peer-reviewed papers, this review provides comprehensive and current insights into the detection of clinically significant antimicrobial resistant bacteria and resistance genes in wild mammals, birds and reptiles worldwide. The review also examines the overlooked roles of wildlife in AMR emergence and transmission. In wildlife, AMR is potentially driven by anthropogenic activity, agricultural and environmental factors, and natural evolution. This review highlights the significance of AMR surveillance in wildlife, identifies species and geographical foci and gaps, and demonstrates the value of multifaceted One Health strategies if further escalation of AMR globally is to be curtailed.
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Affiliation(s)
- Xing Li
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia; Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Perth, Australia
| | - Bethany Jackson
- School of Veterinary Medicine, Murdoch University, Perth, Australia
| | - Chang Cai
- School of Information Technology, College of Science, Technology, Engineering and Mathematics, Murdoch University, Perth, Australia
| | - Geoffrey Wallace Coombs
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia; Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Perth, Australia.
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3
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dos Santos EJE, Lopes ATS, Fehlberg HF, Rocha JM, Brito Júnior PDA, Bernardes FCS, Costa TDSO, Guilherme EA, Vleeschouwer KMD, Oliveira LDC, Rosa BF, de Amorim BS, Filho LMC, Rios EO, Ferreira SS, Rodrigues DDP, Albuquerque GR, Miranda FR, Alvarez MRDV, Orrico VGD, Rezende RP, Nogueira SSDC, Pizauro LJL, Maciel BM. Low Occurrence of Salmonella spp. in Wild Animals in Bahia, Brazil-Population Assessment and Characterization in the Caatinga and Atlantic Forest Biomes. Animals (Basel) 2023; 14:21. [PMID: 38200752 PMCID: PMC10778494 DOI: 10.3390/ani14010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/06/2023] [Accepted: 09/09/2023] [Indexed: 01/12/2024] Open
Abstract
Salmonella spp. are known to persist in the environment. Wild animals are believed to act as important reservoirs, with antimicrobial resistance frequently occurring in the environment. However, little is known about the role of the wildlife in Bahia as a reservoir for Salmonella in Brazil. This study aimed to isolate and characterize Salmonella spp. from wildlife in the Atlantic Forest and Caatinga biomes considering indicators such as the animal species, degree of anthropization, sampling area, and feeding habits. Convenience wildlife sampling and characterization were conducted, followed by microbiological and molecular identification of Salmonella isolates, serotyping, and antimicrobial susceptibility testing. A total of 674 fecal samples were collected from 12 municipalities during 2015-2021, and 4 were positive for the following Salmonella species: Salmonella enterica subspecies enterica serovar Agona (n = 1), Salmonella enterica subsp. enterica serogroup O:16 (n = 2), and Salmonella enterica subsp. enterica serovar Muenchen (n = 1). Antimicrobial susceptibility analysis revealed that one isolate was resistant to six antibiotics, including extended-spectrum penicillins and beta-lactamase inhibitors. These results indicated a low frequency of Salmonella spp. in the sampled forest fragments. The presence of Salmonella in wild animals increases the risk to public health and biodiversity and indicates that they can act as sentinels of environmental contamination or indicators of preservation.
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Affiliation(s)
| | | | | | - Josiane Moreira Rocha
- Graduate Program in Animal Science, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil; (E.J.E.d.S.)
| | | | | | | | - Elisa Arcanjo Guilherme
- Undergraduate Program in Veterinary Medicine, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | | | | | - Beatris Felipe Rosa
- Graduate Program in Zoology, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | | | | | - Elson Oliveira Rios
- Mammals Collection Alexandre Rodrigues Ferreira (CMARF-UESC), Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | - Suelen Sanches Ferreira
- North Fluminense Foundation for Regional Development, Campos dos Goytacazes 28053-100, RJ, Brazil
| | | | - George Rêgo Albuquerque
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | - Flávia Regina Miranda
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | | | | | - Rachel Passos Rezende
- Department of Biological Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | | | - Lucas Jose Luduverio Pizauro
- Department of Agricultural and Environmental Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
| | - Bianca Mendes Maciel
- Department of Biological Sciences, Santa Cruz State University, Ilhéus 45662-900, BA, Brazil
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4
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Oludairo OO, Kwaga JKP, Kabir J, Abdu PA, Gitanjali A, Perrets A, Cibin V, Lettini AA, Aiyedun JO. Ecology and epidemiology of Salmonella spp. isolated from the environment and the roles played by wild animals in their maintenance. INTERNATIONAL JOURNAL OF ONE HEALTH 2023. [DOI: 10.14202/ijoh.2023.1-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Salmonella is a ubiquitous organism of public health importance that causes diarrhea and other systemic disease syndromes. The ecology and epidemiology of the organism in addition to the roles played by wild animals are important in understanding its disease. Relevant published peer-reviewed literature was obtained after imputing the study's keywords into the Google search engine. The publications were thereafter saved for the study. The study revealed the ecology of Salmonella is directly related to its epidemiology. These were found to be either positively or negatively influenced by the living and non-living parts of the environment. Free-ranging and captive wild animals can serve as asymptomatic carriers of Salmonella, therefore, help to maintain the cycle of the disease since wildlife serves as reservoir hosts to over 70% of emerging zoonotic diseases. Cockroaches transmit Salmonella through their feces, and body parts and when ingested by birds and animals. The statistically significant over 83% of Salmonella isolation in lizards suggests the reptile could be a source of Salmonella distribution. Snakes, foxes, badgers, rodents, and raccoons have been reported to have Salmonella as a natural component of their gut with the ability to shed the organism often. The high occurrence (>45%) of diverse Salmonella serovars coupled with the fact that some of these animals were handled, kept as pets and consumed by man portends these animals as potential sources of transmission of the organism and the disease. The etiology and epidemiology of Salmonella are overtly affected by several environmental factors which also determine their survival and maintenance. The roles played by wild animals in the relationship, transmission, growth or interaction within and between Salmonella spp., the occurrence, prevalence, and distribution of the organism help maintain the organism in the environment. An understanding of the roles played by the different parts of the environment and wild animals in the ecology and epidemiology of Salmonella can help make informed decisions on the prevention and control of the diseases it causes. This review aimed to investigate the relationship between ecology, epidemiology, and environment, including the roles played by wild animals in the maintenance of the organism and its disease.
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Affiliation(s)
- Oladapo Oyedeji Oludairo
- Department of Veterinary Public Health and Preventive Medicine, University of Ilorin, Ilorin, Nigeria
| | - Jacob K. P. Kwaga
- Department of Veterinary Public Health and Preventive Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Junaid Kabir
- Department of Veterinary Public Health and Preventive Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Paul A. Abdu
- Department of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Arya Gitanjali
- OIE Salmonella Reference Laboratory, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Ann Perrets
- OIE Salmonella Reference Laboratory, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Veronica Cibin
- Salmonella Reference Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie Viale dell'Università, Legnaro (PD), Italy
| | - Antonia Anna Lettini
- Salmonella Reference Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie Viale dell'Università, Legnaro (PD), Italy
| | - Julius O. Aiyedun
- Department of Veterinary Public Health and Preventive Medicine, University of Ilorin, Ilorin, Nigeria
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5
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Commensal Rodents: Still a Current Threat. Pathogens 2022; 11:pathogens11121483. [PMID: 36558816 PMCID: PMC9780816 DOI: 10.3390/pathogens11121483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Commensal rodents live in human habitats where they can find essential elements, including food, water, shelter, and space [...].
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Falay D, Hardy L, Tanzito J, Lunguya O, Bonebe E, Peeters M, Mattheus W, Van Geet C, Verheyen E, Akaibe D, Katuala P, Ngbonda D, Weill FX, Pardos de la Gandara M, Jacobs J. Urban rats as carriers of invasive Salmonella Typhimurium sequence type 313, Kisangani, Democratic Republic of Congo. PLoS Negl Trop Dis 2022; 16:e0010740. [PMID: 36067238 PMCID: PMC9481155 DOI: 10.1371/journal.pntd.0010740] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/16/2022] [Accepted: 08/13/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Invasive non-typhoidal Salmonella (iNTS-mainly serotypes Enteritidis and Typhimurium) are major causes of bloodstream infections in children in sub-Saharan Africa, but their reservoir remains unknown. We assessed iNTS carriage in rats in an urban setting endemic for iNTS carriage and compared genetic profiles of iNTS from rats with those isolated from humans. METHODOLOGY/PRINCIPAL FINDINGS From April 2016 to December 2018, rats were trapped in five marketplaces and a slaughterhouse in Kisangani, Democratic Republic of the Congo. After euthanasia, blood, liver, spleen, and rectal content were cultured for Salmonella. Genetic relatedness between iNTS from rats and humans-obtained from blood cultures at Kisangani University Hospital-was assessed with multilocus variable-number tandem repeat (VNTR) analysis (MLVA), multilocus sequence typing (MLST) and core-genome MLST (cgMLST). 1650 live-capture traps yielded 566 (34.3%) rats (95.6% Rattus norvegicus, 4.4% Rattus rattus); 46 (8.1%) of them carried Salmonella, of which 13 had more than one serotype. The most common serotypes were II.42:r:- (n = 18 rats), Kapemba (n = 12), Weltevreden and Typhimurium (n = 10, each), and Dublin (n = 8). Salmonella Typhimurium belonged to MLST ST19 (n = 7 rats) and the invasive ST313 (n = 3, isolated from deep organs but not from rectal content). Sixteen human S. Typhimurium isolates (all ST313) were available for comparison: MLVA and cgMLST revealed two distinct rat-human clusters involving both six human isolates, respectively, i.e. in total 12/16 human ST313 isolates. All ST313 Typhimurium isolates from rats and humans clustered with the ST313 Lineage 2 isolates and most were multidrug resistant; the remaining isolates from rats including S. Typhimurium ST19 were pan-susceptible. CONCLUSION The present study provides evidence of urban rats as potential reservoirs of S. Typhimurium ST313 in an iNTS endemic area in sub-Saharan Africa.
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Affiliation(s)
- Dadi Falay
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, the Democratic Republic of the Congo
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Liselotte Hardy
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jacques Tanzito
- Biodiversity Monitoring Center (Centre de Surveillance de la Biodiversité, CSB), Faculty of Science, University of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Octavie Lunguya
- Department of Medical Biology, National Institute for Biomedical Research, Kinshasa, the Democratic Republic of the Congo
- Department of Microbiology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Edmonde Bonebe
- Department of Medical Biology, National Institute for Biomedical Research, Kinshasa, the Democratic Republic of the Congo
| | - Marjan Peeters
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Wesley Mattheus
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, Brussels, Belgium
| | - Chris Van Geet
- Department of Cardiovascular Sciences and Pediatrics, KU Leuven and University Hospital Leuven, Leuven, Belgium
| | - Erik Verheyen
- OD Taxonomy & Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Evolutionary Ecology, University of Antwerp, Antwerp, Belgium
| | - Dudu Akaibe
- Biodiversity Monitoring Center (Centre de Surveillance de la Biodiversité, CSB), Faculty of Science, University of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Pionus Katuala
- Biodiversity Monitoring Center (Centre de Surveillance de la Biodiversité, CSB), Faculty of Science, University of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Dauly Ngbonda
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des bactéries pathogènes entériques, Paris, France
| | | | - Jan Jacobs
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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7
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Binsker U, Käsbohrer A, Hammerl JA. Global colistin use: A review of the emergence of resistant Enterobacterales and the impact on their genetic basis. FEMS Microbiol Rev 2021; 46:6382128. [PMID: 34612488 PMCID: PMC8829026 DOI: 10.1093/femsre/fuab049] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
The dramatic global rise of MDR and XDR Enterobacterales in human medicine forced clinicians to the reintroduction of colistin as last-resort drug. Meanwhile, colistin is used in the veterinary medicine since its discovery, leading to a steadily increasing prevalence of resistant isolates in the livestock and meat-based food sector. Consequently, transmission of resistant isolates from animals to humans, acquisition via food and exposure to colistin in the clinic are reasons for the increased prevalence of colistin-resistant Enterobacterales in humans in the last decades. Initially, resistance mechanisms were caused by mutations in chromosomal genes. However, since the discovery in 2015, the focus has shifted exclusively to mobile colistin resistances (mcr). This review will advance the understanding of chromosomal-mediated resistance mechanisms in Enterobacterales. We provide an overview about genes involved in colistin resistance and the current global situation of colistin-resistant Enterobacterales. A comparison of the global colistin use in veterinary and human medicine highlights the effort to reduce colistin sales in veterinary medicine under the One Health approach. In contrast, it uncovers the alarming rise in colistin consumption in human medicine due to the emergence of MDR Enterobacterales, which might be an important driver for the increasing emergence of chromosome-mediated colistin resistance.
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Affiliation(s)
- Ulrike Binsker
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Annemarie Käsbohrer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Department for Farm Animals and Veterinary Public Health, Institute of Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Jens A Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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8
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Skarżyńska M, Zaja C M, Bomba A, Bocian Ł, Kozdruń W, Polak M, Wia Cek J, Wasyl D. Antimicrobial Resistance Glides in the Sky-Free-Living Birds as a Reservoir of Resistant Escherichia coli With Zoonotic Potential. Front Microbiol 2021; 12:656223. [PMID: 33897669 PMCID: PMC8062882 DOI: 10.3389/fmicb.2021.656223] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most important global health concerns; therefore, the identification of AMR reservoirs and vectors is essential. Attention should be paid to the recognition of potential hazards associated with wildlife as this field still seems to be incompletely explored. In this context, the role of free-living birds as AMR carriers is noteworthy. Therefore, we applied methods used in AMR monitoring, supplemented by colistin resistance screening, to investigate the AMR status of Escherichia coli from free-living birds coming from natural habitats and rescue centers. Whole-genome sequencing (WGS) of strains enabled to determine resistance mechanisms and investigate their epidemiological relationships and virulence potential. As far as we know, this study is one of the few that applied WGS of that number (n = 71) of strains coming from a wild avian reservoir. The primary concerns arising from our study relate to resistance and its determinants toward antimicrobial classes of the highest priority for the treatment of critical infections in people, e.g., cephalosporins, quinolones, polymyxins, and aminoglycosides, as well as fosfomycin. Among the numerous determinants, bla CTX-M-15, bla CMY-2, bla SHV-12, bla TEM-1B, qnrS1, qnrB19, mcr-1, fosA7, aac(3)-IIa, ant(3")-Ia, and aph(6)-Id and chromosomal gyrA, parC, and parE mutations were identified. Fifty-two sequence types (STs) noted among 71 E. coli included the global lineages ST131, ST10, and ST224 as well as the three novel STs 11104, 11105, and 11194. Numerous virulence factors were noted with the prevailing terC, gad, ompT, iss, traT, lpfA, and sitA. Single E. coli was Shiga toxin-producing. Our study shows that the clonal spread of E. coli lineages of public and animal health relevance is a serious avian-associated hazard.
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Affiliation(s)
- Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Magdalena Zaja C
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Arkadiusz Bomba
- Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
| | - Łukasz Bocian
- Department of Epidemiology and Risk Assessment, National Veterinary Research Institute, Puławy, Poland
| | - Wojciech Kozdruń
- Department of Poultry Diseases, National Veterinary Research Institute, Puławy, Poland
| | - Marcin Polak
- Department of Zoology and Nature Protection, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Jarosław Wia Cek
- Department of Zoology and Nature Protection, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland.,Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
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9
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Gwenzi W, Chaukura N, Muisa-Zikali N, Teta C, Musvuugwa T, Rzymski P, Abia ALK. Insects, Rodents, and Pets as Reservoirs, Vectors, and Sentinels of Antimicrobial Resistance. Antibiotics (Basel) 2021; 10:antibiotics10010068. [PMID: 33445633 PMCID: PMC7826649 DOI: 10.3390/antibiotics10010068] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
This paper reviews the occurrence of antimicrobial resistance (AMR) in insects, rodents, and pets. Insects (e.g., houseflies, cockroaches), rodents (rats, mice), and pets (dogs, cats) act as reservoirs of AMR for first-line and last-resort antimicrobial agents. AMR proliferates in insects, rodents, and pets, and their skin and gut systems. Subsequently, insects, rodents, and pets act as vectors that disseminate AMR to humans via direct contact, human food contamination, and horizontal gene transfer. Thus, insects, rodents, and pets might act as sentinels or bioindicators of AMR. Human health risks are discussed, including those unique to low-income countries. Current evidence on human health risks is largely inferential and based on qualitative data, but comprehensive statistics based on quantitative microbial risk assessment (QMRA) are still lacking. Hence, tracing human health risks of AMR to insects, rodents, and pets, remains a challenge. To safeguard human health, mitigation measures are proposed, based on the one-health approach. Future research should include human health risk analysis using QMRA, and the application of in-silico techniques, genomics, network analysis, and ’big data’ analytical tools to understand the role of household insects, rodents, and pets in the persistence, circulation, and health risks of AMR.
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Affiliation(s)
- Willis Gwenzi
- Biosystems and Environmental Engineering Research Group, Department of Agricultural and Biosystems Engineering, University of Zimbabwe, Mount. Pleasant, Harare P.O. Box MP167, Zimbabwe
- Correspondence: or (W.G.); or (A.L.K.A.)
| | - Nhamo Chaukura
- Department of Physical and Earth Sciences, Sol Plaatje University, Kimberley 8300, South Africa;
| | - Norah Muisa-Zikali
- Department of Environmental Sciences and Technology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Private Bag, Chinhoyi 7724, Zimbabwe; or
| | - Charles Teta
- Future Water Institute, Faculty of Engineering & Built Environment, University of Cape Town, Cape Town 7700, South Africa;
| | - Tendai Musvuugwa
- Department of Biological and Agricultural Sciences, Sol Plaatje University, Kimberley 8300, South Africa;
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 60-806 Poznan, Poland;
- Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), 60-806 Poznań, Poland
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
- Correspondence: or (W.G.); or (A.L.K.A.)
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10
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Skarżyńska M, Leekitcharoenphon P, Hendriksen RS, Aarestrup FM, Wasyl D. A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more. PLoS One 2020; 15:e0242987. [PMID: 33270717 PMCID: PMC7714112 DOI: 10.1371/journal.pone.0242987] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is a complex subject, why one need to look at this phenomenon from a wider and holistic perspective. The extensive use of the same antimicrobial classes in human and veterinary medicine as well as horticulture is one of the main drivers for the AMR selection. Here, we applied shotgun metagenomics to investigate the AMR epidemiology in several animal species including farm animals, which are often exposed to antimicrobial treatment opposed to an unique set of wild animals that seems not to be subjected to antimicrobial pressure. The comparison of the domestic and wild animals allowed to investigate the possible anthropogenic impact on AMR spread. Inclusion of animals with different feeding behaviors (carnivores, omnivores) enabled to further assess which AMR genes that thrives within the food chain. We tested fecal samples not only of intensively produced chickens, turkeys, and pigs, but also of wild animals such as wild boars, red foxes, and rodents. A multi-directional approach mapping obtained sequences to several databases provided insight into the occurrence of the different AMR genes. The method applied enabled also analysis of other factors that may influence AMR of intestinal microbiome such as diet. Our findings confirmed higher levels of AMR in farm animals than in wildlife. The results also revealed the potential of wildlife in the AMR dissemination. Particularly in red foxes, we found evidence of several AMR genes conferring resistance to critically important antimicrobials like quinolones and cephalosporins. In contrast, the lowest abundance of AMR was observed in rodents originating from natural environment with presumed limited exposure to antimicrobials. Shotgun metagenomics enabled us to demonstrate that discrepancies between AMR profiles found in the intestinal microbiome of various animals probably resulted from the different antimicrobial exposure, habitats, and behavior of the tested animal species.
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Affiliation(s)
- Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Pimlapas Leekitcharoenphon
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens, Food and Agriculture Organization Reference Laboratory for Antimicrobial Resistance, and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rene S. Hendriksen
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens, Food and Agriculture Organization Reference Laboratory for Antimicrobial Resistance, and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- National Food Institute, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens, Food and Agriculture Organization Reference Laboratory for Antimicrobial Resistance, and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
- Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
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