Unveiling the High Diversity of Clones and Antimicrobial Resistance Genes in Originating from ST10 Across Different Ecological Niches

Overview

Journal Antibiotics (Basel)

Specialty Pharmacology

Date 2024 Aug 29

PMID 39200037

Authors

Maxsueli Aparecida Moura Machado

Pedro Panzenhagen

Cesar Lazaro

Miguel Rojas

Eduardo Eustaquio de Souza Figueiredo

Carlos Adam Conte-Junior

Affiliations

Soon will be listed here.

Abstract

In this pioneering in silico study in Peru, we aimed to analyze () genomes for antimicrobial resistance genes (ARGs) diversity and virulence and for its mobilome. For this purpose, 469 assemblies from human, domestic, and wild animal hosts were investigated. Of these genomes, three were strains (pv05, pv06, and sf25) isolated from chickens in our previous study, characterized for antimicrobial susceptibility profile, and sequenced in this study. Three other genomes were included in our repertoire for having rare cgMLSTs. The phenotypic analysis for antimicrobial resistance revealed that pv05, pv06, and sf25 strains presented multidrug resistance to antibiotics belonging to at least three classes. Our in silico analysis indicated that many Peruvian genomes included resistance genes, mainly to the aminoglycoside class, ESBL-producing , sulfonamides, and tetracyclines. In addition, through Multi-locus Sequence Typing, we found more than 180 different STs, with ST10 being the most prevalent among the genomes. Pan-genome mapping revealed that, with new lineages, the repertoire of accessory genes in increased, especially genes related to resistance and persistence, which may be carried by plasmids. The results also demonstrated several genes related to adhesion, virulence, and pathogenesis, especially genes belonging to the high pathogenicity island (HPI) from , with a prevalence of 42.2% among the genomes. The complexity of the genetic profiles of resistance and virulence in our study highlights the adaptability of the pathogen to different environments and hosts. Therefore, our in silico analysis through genome sequencing enables tracking the epidemiology of from Peru and the future development of strategies to mitigate its survival.

Citing Articles

Evolution of pathogenic Escherichia coli harboring the transmissible locus of stress tolerance: from food sources to clinical environments.

Machado M, Panzenhagen P, Aburjaile F, Brenig B, da Costa M, Azevedo V Sci Rep. 2025; 15(1):5014.

PMID: 39934272 PMC: 11814101. DOI: 10.1038/s41598-025-89066-1.

Antibiotic resistance gene pollution in poultry farming environments and approaches for mitigation: A system review.

Chen Y, Liu Y, Zhao C, Ma J, Guo J Poult Sci. 2025; 104(3):104858.

PMID: 39874786 PMC: 11808494. DOI: 10.1016/j.psj.2025.104858.

References

Ross B, Rojas-Lopez M, Cieza R, McWilliams B, Torres A . The Role of Long Polar Fimbriae in Escherichia coli O104:H4 Adhesion and Colonization. PLoS One. 2015; 10(10):e0141845. PMC: 4636846. DOI: 10.1371/journal.pone.0141845. View

. Global mortality associated with 33 bacterial pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet. 2022; 400(10369):2221-2248. PMC: 9763654. DOI: 10.1016/S0140-6736(22)02185-7. View

Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O . Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012; 67(11):2640-4. PMC: 3468078. DOI: 10.1093/jac/dks261. View

Dozois C, Curtiss 3rd R . Pathogenic diversity of Escherichia coli and the emergence of 'exotic' islands in the gene stream. Vet Res. 1999; 30(2-3):157-79. View

Chapman T, Wu X, Barchia I, Bettelheim K, Driesen S, Trott D . Comparison of virulence gene profiles of Escherichia coli strains isolated from healthy and diarrheic swine. Appl Environ Microbiol. 2006; 72(7):4782-95. PMC: 1489375. DOI: 10.1128/AEM.02885-05. View

Carattoli A, Zankari E, Garcia-Fernandez A, Larsen M, Lund O, Villa L . In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014; 58(7):3895-903. PMC: 4068535. DOI: 10.1128/AAC.02412-14. View

Kamal S, Cimdins-Ahne A, Lee C, Li F, Martin-Rodriguez A, Seferbekova Z . A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid. Mol Microbiol. 2020; 115(2):255-271. PMC: 7984374. DOI: 10.1111/mmi.14614. View

Van Boeckel T, Brower C, Gilbert M, Grenfell B, Levin S, Robinson T . Global trends in antimicrobial use in food animals. Proc Natl Acad Sci U S A. 2015; 112(18):5649-54. PMC: 4426470. DOI: 10.1073/pnas.1503141112. View

Da Silva R, Arenas N, Luiza V, Bermudez J, Clarke S . Regulations on the Use of Antibiotics in Livestock Production in South America: A Comparative Literature Analysis. Antibiotics (Basel). 2023; 12(8). PMC: 10451520. DOI: 10.3390/antibiotics12081303. View

10.

Seemann T . Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014; 30(14):2068-9. DOI: 10.1093/bioinformatics/btu153. View

11.

Baschera M, Cernela N, Stevens M, Liljander A, Jores J, Corman V . Shiga toxin-producing (STEC) isolated from fecal samples of African dromedary camels. One Health. 2019; 7:100087. PMC: 6416407. DOI: 10.1016/j.onehlt.2019.100087. View

12.

Mikheenko A, Prjibelski A, Saveliev V, Antipov D, Gurevich A . Versatile genome assembly evaluation with QUAST-LG. Bioinformatics. 2018; 34(13):i142-i150. PMC: 6022658. DOI: 10.1093/bioinformatics/bty266. View

13.

Magalhaes R, Vieira T, Fernandes H, Melo A, Simoes M, Sousa S . The Biofilms Structural Database. Trends Biotechnol. 2020; 38(9):937-940. DOI: 10.1016/j.tibtech.2020.04.002. View

14.

Raymond F, Boissinot M, Ouameur A, Deraspe M, Plante P, Kpanou S . Culture-enriched human gut microbiomes reveal core and accessory resistance genes. Microbiome. 2019; 7(1):56. PMC: 6451232. DOI: 10.1186/s40168-019-0669-7. View

15.

Fuga B, Sellera F, Cerdeira L, Esposito F, Cardoso B, Fontana H . WHO Critical Priority Escherichia coli as One Health Challenge for a Post-Pandemic Scenario: Genomic Surveillance and Analysis of Current Trends in Brazil. Microbiol Spectr. 2022; 10(2):e0125621. PMC: 8941879. DOI: 10.1128/spectrum.01256-21. View

16.

Pitta J, Bezerra M, Fernandes D, de Block T, de Souza Novaes A, de Almeida A . Genomic Analysis of Strains from Brazil: Search for Virulence Factors and Association with Epidemiological Data. Pathogens. 2023; 12(8). PMC: 10459997. DOI: 10.3390/pathogens12080991. View

17.

Machado M, Chapartegui-Gonzalez I, Castro V, Figueiredo E, Conte-Junior C, Torres A . Biofilm-producing Escherichia coli O104:H4 overcomes bile salts toxicity by expressing virulence and resistance proteins. Lett Appl Microbiol. 2024; 77(4). DOI: 10.1093/lambio/ovae032. View

18.

Villa L, Garcia-Fernandez A, Fortini D, Carattoli A . Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants. J Antimicrob Chemother. 2010; 65(12):2518-29. DOI: 10.1093/jac/dkq347. View

19.

Ju W, Shen J, Toro M, Zhao S, Meng J . Distribution of pathogenicity islands OI-122, OI-43/48, and OI-57 and a high-pathogenicity island in Shiga toxin-producing Escherichia coli. Appl Environ Microbiol. 2013; 79(11):3406-12. PMC: 3648051. DOI: 10.1128/AEM.03661-12. View

20.

Hadfield J, Croucher N, Goater R, Abudahab K, Aanensen D, Harris S . Phandango: an interactive viewer for bacterial population genomics. Bioinformatics. 2017; 34(2):292-293. PMC: 5860215. DOI: 10.1093/bioinformatics/btx610. View