Abstract
Antimicrobial-resistant Escherichia coli strains have been circulating in various sectors and can be cross-transferred between them. Among pathogenic E. coli strains, Shiga toxin-producing E. coli (STEC) and hybrid pathogenic E. coli (HyPEC) emerged as responsible for outbreaks worldwide. As bovine are reservoir of STEC strains, these pathogens primarily spread to food products, exposing humans to risk. Therefore, this study aimed to characterize antimicrobial-resistant and potentially pathogenic E. coli strains from fecal samples of dairy cattle. In this regard, most E. coli strains (phylogenetic groups A, B1, B2, and E) were resistant to β-lactams and non-β-lactams and were classified as multidrug-resistant (MDR). Antimicrobial resistance genes (ARGs) related to multidrug resistance profiles were detected. Furthermore, mutations in fluoroquinolone and colistin resistance determinants were also identified, highlighting the deleterious mutation His152Gln in PmrB that may have contributed to the high level (> 64 mg/L) of colistin resistance. Virulence genes of diarrheagenic and extraintestinal pathogenic E. coli (ExPEC) pathotypes were shared among strains and even within the same strain, evidencing the presence of HyPEC (i.e., ExPEC/STEC), which were assigned as unusual B2-ST126-H3 and B1-ST3695-H31. These findings provide phenotypic and molecular data of MDR, ARGs-producing, and potentially pathogenic E. coli strains in dairy cattle, contributing to the monitoring of antimicrobial resistance and pathogens in healthy animals and alerting to potential bovine-associated zoonotic infections.
Similar content being viewed by others
Data Availability
All data generated or analyzed during this study are included in this published article.
References
Amos GCA, Ploumakis S, Zhang L, Hawkey PM, Gaze WH, Wellington EMH (2018) The widespread dissemination of integrons throughout bacterial communities in a riverine system. ISME J 12(3):681–691. https://doi.org/10.1038/s41396-017-0030-8
Anes J, Nguyen SV, Eshwar AK, McCabe E, Macori G, Hurley D, Lehner A, Fanning S (2020) Molecular characterisation of multi-drug resistant Escherichia coli of bovine origin. Vet Microbiol 242:108566. https://doi.org/10.1016/j.vetmic.2019.108566
Aranda KR, Fabbricotti SH, Fagundes-Neto U, Scaletsky IC (2007) Single multiplex assay to identify simultaneously enteropathogenic, enteroaggregative, enterotoxigenic, enteroinvasive and Shiga toxin-producing Escherichia coli strains in brazilian children. FEMS Microbiol Lett 267(2):145–150. https://doi.org/10.1111/j.1574-6968.2006.00580.x
Binsker U, Käsbohrer A, Hammerl JA (2022) Global colistin use: a review of the emergence of resistant Enterobacterales and the impact on their genetic basis. FEMS Microbiol Rev 46(1):fuab049. https://doi.org/10.1093/femsre/fuab049
Boyd E, Trmcic A, Taylor M, Shyng S, Hasselback P, Man S, Tchao C, Stone J, Janz L, Hoang L, Galanis E (2021) Escherichia coli O121 outbreak associated with raw milk gouda-like cheese in British Columbia, Canada, 2018. Can Commun Dis Rep 47(2):11–16. https://doi.org/10.14745/ccdr.v47i01a03
Braz VS, Melchior K, Moreira CG (2020) Escherichia coli as a multifaceted pathogenic and versatile bacterium. Front Cell Infect Microbiol 10:548492. https://doi.org/10.3389/fcimb.2020.548492
Brennan E, Martins M, McCusker MP, Wang J, Alves BM, Hurley D, El Garch F, Woehrlé F, Miossec C, McGrath L, Srikumar S, Wall P, Fanning S (2016) Multidrug-resistant Escherichia coli in bovine animals, Europe. Emerg Infect Dis 22(9):1650–1652. https://doi.org/10.3201/eid2209.160140
Cattoir V, Poirel L, Rotimi V, Soussy CJ, Nordmann P (2007) Multiplex PCR for detection of plasmid-mediated quinolone resistance qnr genes in ESBL-producing enterobacterial isolates. J Antimicrob Chemother 60(2):394–397. https://doi.org/10.1093/jac/dkm204
Choi Y, Chan AP (2015) PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 31(16):2745–2747. https://doi.org/10.1093/bioinformatics/btv195
Clermont O, Christenson JK, Denamur E, Gordon DM (2013) The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep 5(1):58–65. https://doi.org/10.1111/1758-2229.12019
Crémet L, Broquet A, Brulin B, Jacqueline C, Dauvergne S, Brion R, Asehnoune K, Corvec S, Heymann D, Caroff N (2015) Pathogenic potential of Escherichia coli clinical strains from orthopedic implant infections towards human osteoblastic cells. Pathog Dis 73(8):ftv065. https://doi.org/10.1093/femspd/ftv065
Dallenne C, Da Costa A, Decré D, Favier C, Arlet G (2010) Development of a set of multiplex PCR assays for the detection of genes encoding important beta-lactamases in Enterobacteriaceae. J Antimicrob Chemother 65(3):490–495. https://doi.org/10.1093/jac/dkp498
De La Cadena E, Mojica MF, Castillo N, Correa A, Appel TM, García-Betancur JC, Pallares CJ, Villegas MV (2020) Genomic analysis of CTX-M-Group-1-Producing Extraintestinal Pathogenic E. coli (ExPEC) from patients with urinary tract infections (UTI) from Colombia. Antibiotics 9(12):899. https://doi.org/10.3390/antibiotics9120899
de Silva KC, Knobl T, Moreno AM (2013) Antimicrobial resistance in veterinary medicine: mechanisms and bacterial agents with the greatest impact on human health. Braz J Vet Res Anim Sci 50:171–183. https://doi.org/10.11606/issn.1678-4456.v50i3p171-183
Furlan JPR, Stehling EG (2021) Multiple sequence types, virulence determinants and antimicrobial resistance genes in multidrug- and colistin-resistant Escherichia coli from agricultural and non-agricultural soils. Environ Pollut 288:117804. https://doi.org/10.1016/j.envpol.2021.117804
Gogry FA, Siddiqui MT, Sultan I, Haq QMR (2021) Current update on intrinsic and acquired Colistin Resistance Mechanisms in Bacteria. Front Med 8:677720. https://doi.org/10.3389/fmed.2021.677720
Gomes TA, Elias WP, Scaletsky IC, Guth BE, Rodrigues JF, Piazza RM, Ferreira LC, Martinez MB (2016) Diarrheagenic Escherichia coli. Braz J Microbiol 47(Suppl 1):3–30. https://doi.org/10.1016/j.bjm.2016.10.015
Ikeda M, Kobayashi T, Fujimoto F, Okada Y, Higurashi Y, Tatsuno K, Okugawa S, Moriya K (2021) The prevalence of the iutA and ibeA genes in Escherichia coli isolates from severe and non-severe patients with bacteremic acute biliary tract infection is significantly different. Gut Pathog 13(1):32. https://doi.org/10.1186/s13099-021-00429-1
Irrgang A, Roschanski N, Tenhagen BA, Grobbel M, Skladnikiewicz-Ziemer T, Thomas K, Roesler U, Käsbohrer A (2016) Prevalence of mcr-1 in E. coli from Livestock and Food in Germany, 2010–2015. PLoS One 11(7):e0159863. https://doi.org/10.1371/journal.pone.0159863
Jesumirhewe C, Springer B, Allerberger F, Ruppitsch W (2022) Genetic characterization of antibiotic resistant Enterobacteriaceae isolates from bovine animals and the Environment in Nigeria. Front Microbiol 13:793541. https://doi.org/10.3389/fmicb.2022.793541
Johnson JR, Stell AL (2000) Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise. J Infect Dis 181(1):261–272. https://doi.org/10.1086/315217
Johnson JR, Murray AC, Gajewski A, Sullivan M, Snippes P, Kuskowski MA, Smith KE (2003) Isolation and molecular characterization of nalidixic acid-resistant extraintestinal pathogenic Escherichia coli from retail chicken products. Antimicrob Agents Chemother 47(7):2161–2168. https://doi.org/10.1128/AAC.47.7.2161-2168.2003
Jolley KA, Bray JE, Maiden MCJ (2018) Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 3:124. https://doi.org/10.12688/wellcomeopenres.14826.1
Jones G, Lefèvre S, Donguy MP, Nisavanh A, Terpant G, Fougère E, Vaissière E, Guinard A, Mailles A, de Valk H, Fila M, Tanné C, Le Borgne C, Weill FX, Bonacorsi S, Jourdan-Da Silva N, Mariani-Kurkdjian P (2019) Outbreak of Shiga toxin-producing Escherichia coli (STEC) O26 paediatric haemolytic uraemic syndrome (HUS) cases associated with the consumption of soft raw cow’s milk cheeses, France, March to May 2019. Euro Surveill 24(22):1900305. https://doi.org/10.2807/1560-7917.ES.2019.24.22.1900305
Karczmarczyk M, Walsh C, Slowey R, Leonard N, Fanning S (2011) Molecular characterization of multidrug-resistant Escherichia coli isolates from irish cattle farms. Appl Environ Microbiol 77(20):7121–7127. https://doi.org/10.1128/AEM.00601-11
Khan A, Miller WR, Arias CA (2018) Mechanisms of antimicrobial resistance among hospital-associated pathogens. Expert Rev Anti Infect Ther 16(4):269–287. https://doi.org/10.1080/14787210.2018.1456919
Lagarde M, Vanier G, Arsenault J, Fairbrother JMM (2021) High risk clone: a proposal of Criteria adapted to the One Health Context with Application to Enterotoxigenic Escherichia coli in the Pig Population. Antibiotics 10(3):244. https://doi.org/10.3390/antibiotics10030244
Lima T, Domingues S, Da Silva GJ (2020) Manure as a potential hotspot for Antibiotic Resistance dissemination by horizontal gene transfer events. Vet Sci 7(3):110. https://doi.org/10.3390/vetsci7030110
Liu YY, Wang Y, Walsh TR, Yi LX, Zhang R, Spencer J, Doi Y, Tian G, Dong B, Huang X, Yu LF, Gu D, Ren H, Chen X, Lv L, He D, Zhou H, Liang Z, Liu JH, Shen J (2016) 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 16(2):161–168. https://doi.org/10.1016/S1473-3099(15)00424-7
Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, Harbarth S, Hindler JF, Kahlmeter G, Olsson-Liljequist B, Paterson DL, Rice LB, Stelling J, Struelens MJ, Vatopoulos A, Weber JT, Monnet DL (2012) Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 18(3):268–281. https://doi.org/10.1111/j.1469-0691.2011.03570.x
Manges AR, Geum HM, Guo A, Edens TJ, Fibke CD, Pitout JDD (2019) Global Extraintestinal Pathogenic Escherichia coli (ExPEC) lineages. Clin Microbiol Rev 32(3):e00135–e00118. https://doi.org/10.1128/CMR.00135-18
Martínez-Vázquez AV, Vázquez-Villanueva J, Leyva-Zapata LM, Barrios-García H, Rivera G, Bocanegra-García V (2021) Multidrug Resistance of Escherichia coli strains isolated from bovine feces and carcasses in Northeast Mexico. Front Vet Sci 8:643802. https://doi.org/10.3389/fvets.2021.643802
McEwen SA, Collignon PJ (2018) Antimicrobial Resistance: a one health perspective. Microbiol Spectr 6(2). https://doi.org/10.1128/microbiolspec.ARBA-0009-2017
Mughini-Gras L, van Pelt W, van der Voort M, Heck M, Friesema I, Franz E (2018) Attribution of human infections with Shiga toxin-producing Escherichia coli (STEC) to livestock sources and identification of source-specific risk factors, the Netherlands (2010–2014). Zoonoses Public Health 65(1):e8–e22. https://doi.org/10.1111/zph.12403
Munhoz DD, Santos FF, Mitsunari T, Schüroff PA, Elias WP, Carvalho E, Piazza RMF (2021) Hybrid atypical enteropathogenic and Extraintestinal Escherichia coli (aEPEC/ExPEC) BA1250 strain: a draft genome. Pathogens 10(4):475. https://doi.org/10.3390/pathogens10040475
Nagy Á, Székelyhidi R, Hanczné Lakatos E, Kapcsándi V (2021) Review on the occurrence of the mcr-1 gene causing colistin resistance in cow’s milk and dairy products. Heliyon 7(4):e06800. https://doi.org/10.1016/j.heliyon.2021.e06800
Nascimento JAS, Santos FF, Valiatti TB, Santos-Neto JF, M Santos AC, Cayô R, Gales AC, Gomes AT T (2021) Frequency and diversity of Hybrid Escherichia coli strains isolated from urinary tract infections. Microorganisms 9(4):693. https://doi.org/10.3390/microorganisms9040693
Obaidat MM, Bani Salman AE, Davis MA, Roess AA (2018) Major diseases, extensive misuse, and high antimicrobial resistance of Escherichia coli in large- and small-scale dairy cattle farms in Jordan. J Dairy Sci 101(3):2324–2334. https://doi.org/10.3168/jds.2017-13665
Odonkor ST, Ampofo JK (2013) Escherichia coli as an Indicator of Bacteriological Quality of Water: an overview. Microbiol Res 4(1):e2. https://doi.org/10.4081/mr.2013.e2
Oporto B, Ocejo M, Alkorta M, Marimón JM, Montes M, Hurtado A (2019) Zoonotic approach to Shiga toxin-producing Escherichia coli: integrated analysis of virulence and antimicrobial resistance in ruminants and humans. Epidemiol Infect 147:e164. https://doi.org/10.1017/S0950268819000566
Palmeira JD, Ferreira H, Madec JY, Haenni M (2018) Draft genome of a ST443 mcr-1- and blaCTX–M–2-carrying Escherichia coli from cattle in Brazil. J Glob Antimicrob Resist 13:269–270. https://doi.org/10.1016/j.jgar.2018.05.010
Poirel L, Jayol A, Nordmann P (2017) Polymyxins: antibacterial activity, susceptibility testing, and Resistance Mechanisms encoded by plasmids or chromosomes. Clin Microbiol Rev 30(2):557–596. https://doi.org/10.1128/CMR.00064-16
Pokharel S, Shrestha P, Adhikari B (2020) Antimicrobial use in food animals and human health: time to implement ‘one health’ approach. Antimicrob Resist Infect Control 9(1):181. https://doi.org/10.1186/s13756-020-00847-x
Quesnell RR, Klaessig S, Watts JL, Schukken YH (2012) Bovine intramammary Escherichia coli challenge infections in late gestation demonstrate a dominant antiinflammatory immunological response. J Dairy Sci 95(1):117–126. https://doi.org/10.3168/jds.2011-4289
Robins-Browne RM, Holt KE, Ingle DJ, Hocking DM, Yang J, Tauschek M (2016) Are Escherichia coli Pathotypes still relevant in the era of whole-genome sequencing? Front Cell Infect Microbiol 6:141. https://doi.org/10.3389/fcimb.2016.00141
Roer L, Tchesnokova V, Allesøe R, Muradova M, Chattopadhyay S, Ahrenfeldt J, Thomsen MCF, Lund O, Hansen F, Hammerum AM, Sokurenko E, Hasman H (2017) Development of a web Tool for Escherichia coli Subtyping based on fimH alleles. J Clin Microbiol 55(8):2538–2543. https://doi.org/10.1128/JCM.00737-17
Santos ACM, Santos FF, Silva RM, Gomes TAT (2020) Diversity of hybrid- and hetero-pathogenic Escherichia coli and their potential implication in more severe Diseases. Front Cell Infect Microbiol 10:339. https://doi.org/10.3389/fcimb.2020.00339
Shanmugakani RK, Akeda Y, Sugawara Y, Laolerd W, Chaihongsa N, Sirichot S, Yamamoto N, Hagiya H, Morii D, Fujiya Y, Nishi I, Yoshida H, Takeuchi D, Sakamoto N, Malathum K, Santanirand P, Tomono K, Hamada S (2019) PCR-Dipstick-oriented surveillance and characterization of mcr-1- and carbapenemase-carrying Enterobacteriaceae in a Thai Hospital. Front Microbiol 10:149. https://doi.org/10.3389/fmicb.2019.00149
Sobur MA, Sabuj AAM, Sarker R, Rahman AMMT, Kabir SML, Rahman MT (2019) Antibiotic-resistant Escherichia coli and Salmonella spp. associated with dairy cattle and farm environment having public health significance. Vet World 12(7):984–993. https://doi.org/10.14202/vetworld.2019.984-993
Tark DS, Moon DC, Kang HY, Kim SR, Nam HM, Lee HS, Jung SC, Lim SK (2017) Antimicrobial susceptibility and characterization of extended-spectrum β-lactamases in Escherichia coli isolated from bovine mastitic milk in South Korea from 2012 to 2015. J Dairy Sci 100(5):3463–3469. https://doi.org/10.3168/jds.2016-12276
Valiatti TB, Santos FF, Santos ACM, Nascimento JAS, Silva RM, Carvalho E, Sinigaglia R, Gomes TAT (2020) Genetic and virulence characteristics of a hybrid atypical enteropathogenic and uropathogenic Escherichia coli (aEPEC/UPEC) strain. Front Cell Infect Microbiol 10:492. https://doi.org/10.3389/fcimb.2020.00492
Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173(2):697–703. https://doi.org/10.1128/jb.173.2.697-703
Zalewska M, Błażejewska A, Czapko A, Popowska M (2021) Antibiotics and antibiotic resistance genes in animal manure - consequences of its application in Agriculture. Front Microbiol 12:610656. https://doi.org/10.3389/fmicb.2021.610656
Zhang X, Payne M, Kaur S, Lan R (2022) Improved genomic identification, clustering, and Serotyping of Shiga Toxin-Producing Escherichia coli using Cluster/Serotype-Specific gene markers. Front Cell Infect Microbiol 11:772574. https://doi.org/10.3389/fcimb.2021.772574
Zheng B, Huang C, Xu H, Guo L, Zhang J, Wang X, Jiang X, Yu X, Jin L, Li X, Feng Y, Xiao Y, Li L (2017) Occurrence and genomic characterization of ESBL-Producing, MCR-1-Harboring Escherichia coli in Farming Soil. Front Microbiol 8:2510. https://doi.org/10.3389/fmicb.2017.02510
Acknowledgements
The authors thank the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [grant no. 2018/01890-3], the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior [88882.180855/2018-01, 88887.519091/2020-00, and Finance code 001], and the Conselho Nacional de Desenvolvimento Científico e Tecnológico [grant no. 308914/2019-8, 304905/2022-4, 130086/2021-5, 141016/2021-3, and 150712/2022-7].
Funding
This study was supported by FAPESP [grant no. 2021/01655-7].
Author information
Authors and Affiliations
Contributions
J.P.R.F.: Conceptualization, Resources, Investigation, Methodology, Validation, Formal analysis, Data Curation, Writing — Original Draft, Writing — Review & Editing. M.S.R., L.D.R.S. and R.S.R.: Investigation, Methodology. E.G.S.: Conceptualization, Funding acquisition, Supervision, Investigation, Project administration, Data Curation, Writing — Original Draft, Writing — Review & Editing; Visualization. All authors reviewed the manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Ethics approval
Not applicable.
Consent to participate
Not applicable.
Consent to publish
Not applicable.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Furlan, J.P.R., Ramos, M.S., dos Santos, L.D.R. et al. Multidrug-resistant Shiga toxin-producing Escherichia coli and hybrid pathogenic strains of bovine origin. Vet Res Commun 47, 1907–1913 (2023). https://doi.org/10.1007/s11259-023-10141-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11259-023-10141-x