Polymyxin Resistance in Salmonella: Exploring Mutations and Genetic Determinants of Non-Human Isolates
Abstract
:1. Introduction
2. Results
3. Discussion
4. Materials and Methods
- Bacterial isolates
- Colistin drop test
- Minimum inhibitory concentrations
- PCR amplification
- DNA Extraction, Whole-Genome Sequencing, and Assembly
- Annotation, Resistome and Virulome Detection, Serotype Prediction, and MLST
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Landers, T.F.; Cohen, B.; Wittum, T.E.; Larson, E.L. A review of antibiotic use in food animals: Perspective, policy, and potential. Public Health Rep. 2012, 127, 4–22. [Google Scholar] [CrossRef] [PubMed]
- Li, Y.; Ed-Dra, A.; Tang, B.; Kang, X.; Muller, A.; Kehrenberg, C.; Jia, C.; Pan, H.; Yang, H.; Yue, M. Higher tolerance of predominant Salmonella serovars circulating in the antibiotic-free feed farms to environmental stresses. J. Hazard. Mater. 2022, 438, 129476. [Google Scholar] [CrossRef] [PubMed]
- Imran, M.; Das, K.R.; Naik, M.M. Co-selection of multi-antibiotic resistance in bacterial pathogens in metal and microplastic contaminated environments: An emerging health threat. Chemosphere 2019, 215, 846–857. [Google Scholar] [CrossRef] [PubMed]
- Sharma, J.; Sharma, D.; Singh, A.; Sunita, K. Colistin resitance and management of drug resistant infections. Can. J. Infect. Dis. Med. Microbiol. 2022, 2022, 4315030. [Google Scholar] [CrossRef] [PubMed]
- Poirel, L.; Jayol, A.; Nordmann, P. Polymyxins: Antibacterial activity, susceptibility testing, and resistance mechanisms encoded by plasmids or chromosomes. Clin. Microbiol. Rev. 2017, 30, 557–596. [Google Scholar] [CrossRef] [PubMed]
- Sun, J.; Zhang, H.; Liu, Y.H.; Feng, Y. Towards Understanding MCR-like Colistin Resistance. Trends Microbiol. 2018, 26, 794–808. [Google Scholar] [CrossRef]
- Olaitan, A.O.; Morand, S.; Rolain, J.M. Mechanisms of polymyxin resistance: Acquired and intrinsic resistance in bacteria. Front. Microbiol. 2014, 5, 643. [Google Scholar] [CrossRef]
- Rolain, J.M.; Olaitan, A.O. Plasmid-mediated colistin resistance: The final blow to colistin? Int. J. Antimicrob. Agents 2016, 47, 4–5. [Google Scholar] [CrossRef]
- Liu, Y.; Wang, Y.; Wash, T.R.; Yi, L.X.; Zhang, R.; Spencer, J.; Doi, Y.; Tian, G.; Dong, B.; Huang, X.; et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: A microbiological and molecular biological study. Lancet Infect. Dis. 2016, 16, 161–168. [Google Scholar] [CrossRef]
- Ling, Z.; Yin, W.; Shen, Z.; Wang, Y.; Shen, J.; Walsh, T.R. Epidemiology of mobile colistin resistance genes mcr-1 to mcr-9. J. Antimicrob. Chemother. 2020, 75, 3087–3095. [Google Scholar] [CrossRef]
- Santos, C.A.; Cunha, M.P.V.; Bertani, A.M.J.; Almeida, E.A.; Gonçalves, C.R.; Sacchi, C.T.; Paiva, J.B.; Camargo, C.H.; Tiba-Casas, M.R. Detection of multidrug- and colistin-resistant Salmonella Choleraesuis causing bloodstream infection. J. Antimicrob. Chemother. 2020, 75, 2009–2010. [Google Scholar] [CrossRef] [PubMed]
- Ferrari, R.G.; Rosario, D.K.A.; Cunha-Neto, A.; Mano, S.B.; Figueiredo, E.E.S.; Conte Júnior, C.A. Worldwide Epidemiology of Salmonella Serovars in Animal-Based Foods: A Meta-analysis. Appl. Environ. Microbiol. 2019, 85, 00591-19. [Google Scholar] [CrossRef]
- Fernandes, S.A.; Tavechio, A.T.; Ghilardi, A.C.R.; Almeida, E.A.; Silva, J.M.L.; Camargo, C.H.; Tiba-Casas, M.R. Salmonella enterica serotypes from human and nonhuman sources in Sao Paulo State, Brazil, 2004–2020. Rev. Inst. Med. Trop Sao Paulo. 2022, 30, e66. [Google Scholar] [CrossRef] [PubMed]
- MAPA (Ministério da Agricultura, Pecuária e Abastecimento) Instrução Normativa No20, of 21 of October 2016. Available online: https://www.gov.br/agricultura/pt-br/assuntos/sanidade-animal-e-vegetal/saude-animal/programas-de-saude-animal/pnsa/in20-2016-en-atualizada2017.pdf/ (accessed on 10 July 2023).
- Jouy, E.; Haenni, M.L.; Devendec, L.L.; Roux, A.L.; Châtre, P.; Madec, J.Y.; Kempf, I. Improvement in routine detection of colistin resistance in E. coli isolated in veterinary diagnostic laboratories. J. Microbiol. Methods 2017, 132, 125–127. [Google Scholar] [CrossRef] [PubMed]
- Pasteran, F.; Danze, D.; Menocal, A.; Cabrera, C.; Castillo, I.; Albornoz, E.; Lucero, C.; Rapoport, M.; Ceriana, P.; Corso, A. Simple Phenotypic Tests To Improve Accuracy in Screening Chromosomal and Plasmid-Mediated Colistin Resistance in Gram-Negative Bacilli. J. Clin. Microbiol. 2021, 59, e01701-20. [Google Scholar] [CrossRef]
- Bardet, L.; Rolain, J.M. Development of New Tools to Detect Colistin-Resistance among Enterobacteriaceae Strains. Can. J. Infect. Dis. Med. Microbiol. 2018, 2018, 3095249. [Google Scholar] [CrossRef]
- Conceição-Neto, O.C.; Aires, C.A.M.; Pereira, N.F.; Silvia, L.H.J.; Picão, R.C.; Siqueira, B.N.; Albano, R.M.; Asensi, M.D.; Caralho-Assef, A.P. Detection of the plasmid-mediated mcr-1 gene in clinical KPC-2-producing Escherichia coli isolates in Brazil. J. Antimicrob. Agents 2017, 50, 282–284. [Google Scholar] [CrossRef]
- Rau, R.B.; Lima-Morales, D.; Wink, P.L.; Ribeiro, A.R.; Barth, A.L. Salmonella enterica mcr-1 Positive from Food in Brazil: Detection and Characterization. Foodborne Pathog. Dis. 2020, 17, 202–208. [Google Scholar] [CrossRef]
- Moreno, L.Z.; Gomes, V.T.M.; Moreira, J.; Oliveira, C.H.; Peres, B.P.; Silva, A.P.S.; Thakur, S.; La Ragione, R.M.; Moreno, A.M. First report of mcr-1-harboring Salmonella enterica serovar Schwarzengrund isolated from poultry meat in Brazil. Diagn. Microbiol. Infect. Dis. 2019, 93, 376–379. [Google Scholar] [CrossRef]
- Leite, E.L.; Araújo, W.J.; Vieira, T.R.; Zenato, K.S.; Vasconcelos, P.C.; Cibulski, S.; Givisiez, P.E.N.; Cardoso, M.R.I.; Oliveira, C.J.B. First reported genome of an mcr-9-mediated colistin-resistant Salmonella Typhimurium isolate from Brazilian livestock. J. Glob. Antimicrob. Resist. 2020, 23, 394–397. [Google Scholar] [CrossRef]
- Braga, P.R.C.; Santos, C.A.; Bertani, A.M.J.; Viera, T.; Amarante, A.F.; Reis, A.D.; Sacchi, C.T.; Camargo, C.H.; Ribeiro, M.G.; Borges, A.S.; et al. Detection and genomic characterization of a multidrug-resistant Salmonella Newport co-harbouring blaCMY-2, qnrB19 and mcr-9 from the diarrheic faeces of a foal. J. Glob. Antimicrob. Resist. 2023, 35, 198–201. [Google Scholar] [CrossRef]
- Kieffer, N.; Royer, G.; Decousser, J.W.; Bourrel, A.S.; Palmieri, M.; De La Rosa, J.M.; Jacquier, H.; Denamur, E.; Nordmann, P.; Poirel, L. mcr-9, an inducible gene encoding an acquired phosphoethanolamine transferase in Escherichia coli, and its origin, Antimicrob. Agents Chemother. 2019, 63, e00965-19. [Google Scholar] [CrossRef]
- Wang, X.; Ling, Z.; Sun, N.; Liu, Y.; Huang, J.; Wang, L. Molecular genetic characteristics of mcr-9-harbouring Salmonella enterica serotype Typhimurium isolated from raw milk. Int. J. Antimicrob. Agents 2021, 57, 106332. [Google Scholar] [CrossRef] [PubMed]
- MAPA (Ministério da Agricultura, Pecuária e Abastecimento) Instrução Normativa No45, of 22 of november 2016. Available online: https://www.gov.br/agricultura/pt-br/assuntos/insumos-agropecuarios/insumos-pecuarios/alimentacao-animal/arquivos-alimentacao-animal/legislacao/instrucao-normativa-no-45-de-22-de-novembro-de-2016.pdf/view/ (accessed on 10 July 2023).
- Walsh, T.R.; Wu, Y. China bans colistin as a feed additive for animals. Lancet Infect. Dis. 2016, 16, 1102–1103. [Google Scholar] [CrossRef]
- Sun, S.; Negrea, A.; Rhen, M.; Andersson, D.I. Genetic analysis of colistin resistance in Salmonella enterica serovar Typhimurium. J. Antimicrob. Chemother. 2009, 53, 2298–2305. [Google Scholar] [CrossRef] [PubMed]
- Agersø, Y.; Torpdahl, M.; Zachariasen, C.; Seyfarth, A.; Hammerum, A.M.; Nielsen, E.M. Tentative colistin epidemiological cut-off value for Salmonella spp. Foodborne Pathog. Dis. 2012, 9, 367–369. [Google Scholar] [CrossRef] [PubMed]
- Luo, Q.; Niu, T.; Wang, Y.; Yin, J.; Wan, F.; Kyao, M.; Lu, H.; Xiao, Y.; Li, L. In vitro reduction of colistin susceptibility and comparative genomics reveals multiple differences between MCR-positive and MCR-negative colistin-resistant Escherichia Coli. Infect. Drug Resist. 2019, 12, 1665–1674. [Google Scholar] [CrossRef]
- Sevilla, E.; Vico, J.P.; Delgado-Blas, J.F.; González-Zorn, B.; Marin, C.M.; Uruén, C.; Martin-Burriel, I.; Bolea, R.; Mainar-Jaime, R.C. Resistance to colistin and production of extended-spectrum β-lactamases and/or AmpC enzymes in Salmonella isolates collected from healthy pigs in Northwest Spain in two periods: 2008–2009 and 2018. Int. J. Food Microbiol. 2021, 338, 108967. [Google Scholar] [CrossRef]
- Matchawe, C.; Machuka, E.M.; Kyallo, M.; Bonny, P.; Nkeunen, G.; Njaci, I.; Esemu, S.N.; Githae, D.; Juma, J.; Nfor, B.M.; et al. Detection of Antimicrobial Resistance, Pathogenicity, and Virulence Potentials of Non-Typhoidal Salmonella Isolates at the Yaounde Abattoir Using Whole-Genome Sequencing Technique. Pathogens 2022, 11, 502. [Google Scholar] [CrossRef]
- Ricci, V.; Zhang, D.; Teale, C.; Piddock, L.J.V. The O-Antigen Epitope Governs Susceptibility to Colistin in Salmonella enterica. mBio 2020, 11, e02831-19. [Google Scholar] [CrossRef]
- Fortini, D.; Owczarek, S.; Dionisi, A.M.; Lucarelli, C.; Arena, S.; Carattoli, A.; Villa, L.; Gárcia-Fernández, A. Colistin Resistance Mechanisms in Human Salmonella enterica Strains Isolated by the National Surveillance Enter-Net Italia (2016–2018). Antibiotics 2022, 11, 102. [Google Scholar] [CrossRef] [PubMed]
- Grimont, P.A.D.; Weil, F.X. Antigenic formulae of the Salmonella serovars, 9th ed.; Institut Pasteur: Paris, France, 2007; 166p, Centre Collaborateur OMS de Référence et de Recherche pour les Salmonella. [Google Scholar]
- EUCAST/BrCAST Guidelines. Available online: https://www.eucast.org/ (accessed on 10 July 2023).
- Rebelo, A.R.; Bortolaia, V.; Kjedldgaard, J.S.; Pedersen, S.K.; Leekitchaeroenphon, P.; Hansen, I.M.; Guerra, B.; Malorny, B.; Borowiak, M.; Hammerrl, J.A.; et al. Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes. Euro Surveill. 2018, 23, 17-00672. [Google Scholar] [CrossRef] [PubMed]
- Borowiak, M.; Baumann, B.; Fischer, J.; Thomas, K.; Deneke, C.; Hammerl, J.A.; Szabo, I.; Malorny, B. Development of a Novel mcr-6 to mcr-9 Multiplex PCR and Assessment of mcr-1 to mcr-9 Occurrence in Colistin-Resistant Salmonella enterica Isolates From Environment, Feed, Animals and Food (2011–2018) in Germany. Front. Microbiol. 2020, 11, 80. [Google Scholar] [CrossRef] [PubMed]
- Galaxy Europe. Available online: https://usegalaxy.eu/ (accessed on 10 July 2023).
- Zhang, S.; Yin, Y.; Jones, M.; Zhang, Z.; Kaiser, B.L.D.; Dinsmore, B.A.; Fitzgerald, C.; Fields, P.I.; Deng, X. Salmonella Serotype Determination Utilizing High-throughput Genome Sequencing Data. J. Clin. Microbiol. 2015, 53, 1685–1692. [Google Scholar] [CrossRef]
Serotype | Number of Isolates Resistant to Colistin (Drop Test) | ||||||
---|---|---|---|---|---|---|---|
2016 | 2017 | 2018 | 2019 | 2020 | 2021 | Total | |
Agona | 0 | 0 | 0 | 1 | 0 | 1 | 2 |
Brandenburg | 0 | 5 | 0 | 0 | 0 | 0 | 5 |
Dublin | 3 | 0 | 0 | 0 | 0 | 1 | 4 |
Enteritidis | 43 | 3 | 1 | 0 | 1 | 34 | 82 |
Gallinarum | 0 | 2 | 0 | 1 | 2 | 4 | 9 |
Grumpensis | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
Heidelberg | 0 | 1 | 11 | 0 | 3 | 5 | 20 |
Infantis | 0 | 0 | 1 | 0 | 0 | 0 | 1 |
Javiana | 3 | 0 | 0 | 0 | 0 | 0 | 3 |
Madelia | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
Mbandaka | 1 | 0 | 0 | 0 | 0 | 0 | 1 |
Miami | 4 | 0 | 0 | 0 | 0 | 1 | 5 |
Minnesota | 0 | 1 | 6 | 0 | 8 | 0 | 15 |
Newport | 0 | 1 | 0 | 0 | 0 | 0 | 1 |
Ohio | 0 | 0 | 0 | 0 | 0 | 2 | 2 |
Panama | 0 | 0 | 1 | 0 | 1 | 0 | 2 |
Poona | 0 | 0 | 0 | 2 | 9 | 2 | 13 |
Pullorum | 0 | 1 | 0 | 0 | 1 | 3 | 5 |
Rubislaw | 0 | 0 | 1 | 0 | 0 | 0 | 1 |
S.enterica subsp.enterica | 0 | 0 | 1 | 0 | 1 | 2 | 4 |
S. I. 4,[5],12:i:- | 12 | 0 | 1 | 0 | 1 | 1 | 15 |
Sandiego | 0 | 1 | 0 | 0 | 0 | 0 | 1 |
Schwarzengrund | 1 | 0 | 3 | 0 | 0 | 0 | 4 |
Typhimurium | 0 | 0 | 2 | 0 | 0 | 10 | 12 |
Winslow | 0 | 0 | 0 | 0 | 0 | 1 | 1 |
Total | 67 | 15 | 28 | 6 | 27 | 67 | 210 |
Serotype | Colistin (mg/L) | ||||||
---|---|---|---|---|---|---|---|
0.5 | 1 | 2 | 4 | 8 | 16 | Total | |
Agona | 0 | 0 | 0 | 2 | 0 | 0 | 2 |
Anatum | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
Brandenburg | 0 | 0 | 0 | 3 | 2 | 0 | 5 |
Dublin | 0 | 0 | 0 | 3 | 1 | 0 | 4 |
Enteritidis | 0 | 0 | 0 | 41 | 32 | 12 | 85 |
Gallinarum | 0 | 0 | 0 | 1 | 3 | 2 | 6 |
Grumpensis | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
Heidelberg | 0 | 0 | 2 | 12 | 4 | 3 | 21 |
Infantis | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
Javiana | 1 | 1 | 0 | 0 | 1 | 0 | 3 |
Madelia | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
Mbandaka | 0 | 0 | 0 | 1 | 0 | 0 | 1 |
Miami | 0 | 0 | 0 | 5 | 0 | 0 | 5 |
Minnesota | 0 | 0 | 3 | 11 | 0 | 1 | 15 |
Newport | 0 | 0 | 0 | 1 | 0 | 1 | 2 |
Ohio | 0 | 0 | 0 | 1 | 1 | 0 | 2 |
Panama | 0 | 0 | 0 | 2 | 0 | 0 | 2 |
Poona | 0 | 0 | 3 | 11 | 0 | 0 | 14 |
Pullorum | 0 | 0 | 0 | 2 | 3 | 0 | 5 |
Rubislaw | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
S. I. 4,[5],12:i:- | 0 | 1 | 1 | 11 | 1 | 0 | 14 |
Sandiego | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
Schwarzengrund | 0 | 1 | 0 | 1 | 1 | 1 | 4 |
Typhimurium | 0 | 0 | 2 | 10 | 0 | 1 | 13 |
Winslow | 0 | 0 | 1 | 0 | 0 | 0 | 1 |
Total | 1 | 3 | 12 | 121 | 52 | 21 | 210 |
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Vieira, T.; Dos Santos, C.A.; de Jesus Bertani, A.M.; Costa, G.L.; Campos, K.R.; Sacchi, C.T.; Cunha, M.P.V.; Carvalho, E.; da Costa, A.J.; de Paiva, J.B.; et al. Polymyxin Resistance in Salmonella: Exploring Mutations and Genetic Determinants of Non-Human Isolates. Antibiotics 2024, 13, 110. https://doi.org/10.3390/antibiotics13020110
Vieira T, Dos Santos CA, de Jesus Bertani AM, Costa GL, Campos KR, Sacchi CT, Cunha MPV, Carvalho E, da Costa AJ, de Paiva JB, et al. Polymyxin Resistance in Salmonella: Exploring Mutations and Genetic Determinants of Non-Human Isolates. Antibiotics. 2024; 13(2):110. https://doi.org/10.3390/antibiotics13020110
Chicago/Turabian StyleVieira, Thais, Carla Adriana Dos Santos, Amanda Maria de Jesus Bertani, Gisele Lozano Costa, Karoline Rodrigues Campos, Cláudio Tavares Sacchi, Marcos Paulo Vieira Cunha, Eneas Carvalho, Alef Janguas da Costa, Jacqueline Boldrin de Paiva, and et al. 2024. "Polymyxin Resistance in Salmonella: Exploring Mutations and Genetic Determinants of Non-Human Isolates" Antibiotics 13, no. 2: 110. https://doi.org/10.3390/antibiotics13020110
APA StyleVieira, T., Dos Santos, C. A., de Jesus Bertani, A. M., Costa, G. L., Campos, K. R., Sacchi, C. T., Cunha, M. P. V., Carvalho, E., da Costa, A. J., de Paiva, J. B., Rubio, M. d. S., Camargo, C. H., & Tiba-Casas, M. R. (2024). Polymyxin Resistance in Salmonella: Exploring Mutations and Genetic Determinants of Non-Human Isolates. Antibiotics, 13(2), 110. https://doi.org/10.3390/antibiotics13020110