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Karpenko A, Shelenkov A, Manzeniuk I, Kulikova N, Gevorgyan A, Mikhaylova Y, Akimkin V. Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance. Microbiol Spectr 2024:e0075124. [PMID: 39166856 DOI: 10.1128/spectrum.00751-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/19/2024] [Indexed: 08/23/2024] Open
Abstract
The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid. IMPORTANCE Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.
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Affiliation(s)
- Anna Karpenko
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Andrey Shelenkov
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Igor Manzeniuk
- Administrative and Management Department - Directorate, Central Research Institute of Epidemiology, Moscow, Russia
| | - Nina Kulikova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Arman Gevorgyan
- Republican Veterinary and Phytosanitary Laboratory Services Center, Yerevan, Armenia
| | - Yulia Mikhaylova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
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Costache C, Colosi I, Toc DA, Daian K, Damacus D, Botan A, Toc A, Pana AG, Panaitescu P, Neculicioiu V, Schiopu P, Iordache D, Butiuc-Keul A. CRISPR-Cas System, Antimicrobial Resistance, and Enterococcus Genus-A Complicated Relationship. Biomedicines 2024; 12:1625. [PMID: 39062198 PMCID: PMC11274382 DOI: 10.3390/biomedicines12071625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/07/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
(1) Background: The rise in antibiotic resistant bacteria poses a significant threat to public health worldwide, necessitating innovative solutions. This study explores the role of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) in the context of antibiotic resistance among different species from the Enterococcus genus. (2) Methods: The genomes of Enterococcus included in the study were analyzed using CRISPRCasFinder to distinguish between CRISPR-positive (level 4 CRISPR) and CRISPR-negative genomes. Antibiotic resistance genes were identified, and a comparative analysis explored potential associations between CRISPR presence and antibiotic resistance profiles in Enterococcus species. (3) Results: Out of ten antibiotic resistance genes found in Enterococcus species, only one, the efmA gene, showed a strong association with CRISPR-negative isolates, while the others did not significantly differ between CRISPR-positive and CRISPR-negative Enterococcus genomes. (4) Conclusion: These findings indicate that the efmA gene may be more prevalent in CRISPR-negative Enterococcus genomes, and they may contribute to a better understanding of the molecular mechanisms underlying the acquisition of antibiotic resistance genes in Enterococcus species.
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Affiliation(s)
- Carmen Costache
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
- Cluj County Emergency Hospital, 400000 Cluj-Napoca, Romania
| | - Ioana Colosi
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
| | - Dan-Alexandru Toc
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
- Cluj County Emergency Hospital, 400000 Cluj-Napoca, Romania
| | - Karla Daian
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - David Damacus
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Alexandru Botan
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Adelina Toc
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Adrian Gabriel Pana
- Faculty of Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Paul Panaitescu
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
| | - Vlad Neculicioiu
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
| | - Pavel Schiopu
- Department of Microbiology, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania (I.C.)
| | - Dumitrana Iordache
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 400084 Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
| | - Anca Butiuc-Keul
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeş-Bolyai University, 400084 Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babes-Bolyai University, 400006 Cluj-Napoca, Romania
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Costa-Júnior SD, Ferreira YLA, Agreles MAA, Alves ÁEF, Melo de Oliveira MB, Cavalcanti IMF. Gram-negative bacilli carrying mcr gene in Brazil: a pathogen on the rise. Braz J Microbiol 2023:10.1007/s42770-023-00948-w. [PMID: 36943639 PMCID: PMC10028778 DOI: 10.1007/s42770-023-00948-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/04/2023] [Indexed: 03/23/2023] Open
Abstract
The incidence of infections caused by resistant Gram-negative pathogens has become a critical factor in public health due to the limitation of therapeutic options for the control of infections caused, especially, by Enterobacteriaceae (Escherichia coli and Klebsiella pneumoniae), Pseudomonas spp., and Acinetobacter spp. Thus, given the increase in resistant pathogens and the reduction of therapeutic options, polymyxins were reintroduced into the clinic. As the last treatment option, polymyxins were regarded as the therapeutic key, since they were one of the few classes of antimicrobials that had activity against multidrug-resistant Gram-negative bacilli. Nonetheless, over the years, the frequent use of this antimicrobial has led to reports of resistance cases. In 2015, mcr (mobile colistin resistance), a colistin resistance gene, was described in China. Due to its location on carrier plasmids, this gene is characterized by rapid spread through conjugation. It has thus been classified as a rising threat to public health worldwide. In conclusion, based on several reports that show the emergence of mcr in different regional and climatic contexts and species of isolates, this work aims to review the literature on the incidence of the mcr gene in Brazil in different regions, types of samples identified, species of isolates, and type of carrier plasmid.
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Affiliation(s)
- Sérgio Dias Costa-Júnior
- Department of Physiology and Pathology, Federal University of Paraíba (UFPB), 58.051-900, João Pessoa, Brazil
| | | | | | | | - Maria Betânia Melo de Oliveira
- Department of Bio of Biochemistry, Center for Biosciences, Federal University of Pernambuco (UFPE), Av. Moraes Rego S/N, Recife, PE, Brazil
| | - Isabella Macário Ferro Cavalcanti
- Keizo Asami Institute, Federal University of Pernambuco (iLIKA/UFPE), 50.670-901, Recife, Brazil.
- Microbiology and Immunology Laboratory, Academic Center of Vitória, Federal University of Pernambuco (CAV/UFPE), Centro Acadêmico de Vitória, Rua Do Alto Do Reservatório S/N, Bela Vista, Vitória de Santo Antão, PE, 55608-680, Brazil.
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Jeamsripong S, Thaotumpitak V, Anuntawirun S, Roongrojmongkhon N, Atwill ER, Hinthong W. Molecular Epidemiology of Antimicrobial Resistance and Virulence Profiles of Escherichia coli, Salmonella spp., and Vibrio spp. Isolated from Coastal Seawater for Aquaculture. Antibiotics (Basel) 2022; 11:antibiotics11121688. [PMID: 36551345 PMCID: PMC9774326 DOI: 10.3390/antibiotics11121688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
The occurrence of waterborne antimicrobial-resistant (AMR) bacteria in areas of high-density oyster cultivation is an ongoing environmental and public health threat given the popularity of shellfish consumption, water-related human recreation throughout coastal Thailand, and the geographical expansion of Thailand's shellfish industry. This study characterized the association of phenotypic and genotypic AMR, including extended-spectrum β-lactamase (ESBL) production, and virulence genes isolated from waterborne Escherichia coli (E. coli) (n = 84), Salmonella enterica (S. enterica) subsp. enterica (n = 12), Vibrio parahaemolyticus (V. parahaemolyticus) (n = 249), and Vibrio cholerae (V. cholerae) (n = 39) from Thailand's coastal aquaculture regions. All Salmonella (100.0%) and half of V. cholerae (51.3%) isolates harbored their unique virulence gene, invA and ompW, respectively. The majority of isolates of V. parahaemolyticus and E. coli, ~25% of S. enterica subsp. enterica, and ~12% of V. cholerae, exhibited phenotypic AMR to multiple antimicrobials, with 8.9% of all coastal water isolates exhibiting multidrug resistance (MDR). Taken together, we recommend that coastal water quality surveillance programs include monitoring for bacterial AMR for food safety and recreational water exposure to water for Thailand's coastal water resources.
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Affiliation(s)
- Saharuetai Jeamsripong
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: ; Tel.: +662-218-9579
| | - Varangkana Thaotumpitak
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Saran Anuntawirun
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nawaphorn Roongrojmongkhon
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Edward R. Atwill
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
| | - Woranich Hinthong
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok 10210, Thailand
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Sellera FP, Cardoso B, Fuentes-Castillo D, Esposito F, Sano E, Fontana H, Fuga B, Goldberg DW, Seabra LAV, Antonelli M, Sandri S, Kolesnikovas CKM, Lincopan N. Genomic Analysis of a Highly Virulent NDM-1-Producing Escherichia coli ST162 Infecting a Pygmy Sperm Whale ( Kogia breviceps) in South America. Front Microbiol 2022; 13:915375. [PMID: 35755998 PMCID: PMC9231830 DOI: 10.3389/fmicb.2022.915375] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/18/2022] [Indexed: 11/29/2022] Open
Abstract
Carbapenemase-producing Enterobacterales are rapidly spreading and adapting to different environments beyond hospital settings. During COVID-19 lockdown, a carbapenem-resistant NDM-1-positive Escherichia coli isolate (BA01 strain) was recovered from a pygmy sperm whale (Kogia breviceps), which was found stranded on the southern coast of Brazil. BA01 strain belonged to the global sequence type (ST) 162 and carried the blaNDM–1, besides other medically important antimicrobial resistance genes. Additionally, genes associated with resistance to heavy metals, biocides, and glyphosate were also detected. Halophilic behavior (tolerance to > 10% NaCl) of BA01 strain was confirmed by tolerance tests of NaCl minimal inhibitory concentration, whereas halotolerance associated genes katE and nhaA, which encodes for catalase and Na+/H+ antiporter cytoplasmic membrane, respectively, were in silico confirmed. Phylogenomics clustered BA01 with poultry- and human-associated ST162 lineages circulating in European and Asian countries. Important virulence genes, including the astA (a gene encoding an enterotoxin associated with human and animal infections) were detected, whereas in vivo experiments using the Galleria mellonella infection model confirmed the virulent behavior of the BA01 strain. WHO critical priority carbapenemase-producing pathogens in coastal water are an emerging threat that deserves the urgent need to assess the role of the aquatic environment in its global epidemiology.
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Affiliation(s)
- Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Brenda Cardoso
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Danny Fuentes-Castillo
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - 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
| | - Elder Sano
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- 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 Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | | | - Lourdes A V Seabra
- School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | | | | | | | - Nilton Lincopan
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
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