Characterization of virulent Escherichia coli in healthy pet dog feces: Implications for public health

Year 2024, Volume: 8 Issue: 1, 5 - 12, 30.04.2024

Olutayo Israel Falodun , Akeem Ganiyu Rabiu , Abidemi Joseph Marcus , Rotimi Ayodeji Dada , Mobolaji Christianah Afolabi

https://doi.org/10.30704/http-www-jivs-net.1407165

Abstract

The characterization of Escherichia coli that colonizes pets is necessary to maintain animal health and to reduce the chance of transmission to owners. In this study, we investigated the incidence of potentially virulent E. coli inhabiting healthy pet dogs as a risk of infection to pet owners. Antibiotic-resistant E. coli isolated from freshly passed dog feces were whole-genome sequenced using Illumina chemistry and classified into pathogenic lineages using pathogen-specific markers. The antimicrobial resistance genes (ARGs), virulence-associated genes (VAGs), and plasmids were respectively predicted using the ResFinder, VirulenceFinder, and PlasmidFinder. Of the 32 isolates, 13 carried resistance genes such that four, six, and 11 contained β-lactam (blaTEM), aminoglycoside [aac-6(Ib7)/ant-3(Iia)/aph-3(Ib)/aph-6(Id)] and tetracycline (tet) resistance genes, respectively. The IncF plasmids were most prevalent (n=12, 38.71%) but the highly self-conjugative IncN plasmids occurred simultaneously with the plasmid-borne [quinolones (QnrS1/QnrB7) and sulfonamide (sul3)] ARGs in ≥ 2 E. coli. One E. coli each was classified as avian pathogenic E. coli, atypical enteropathogenic E. coli, enterotoxigenic E. coli, Shiga toxin-producing enteroaggregative E. coli, and enteroaggregative E. coli. Pet feces should be carefully handled because they contain virulent and drug-resistant E. coli.

Keywords

Escherichia coli, Escherichia coli, Antimicrobial resistance, Virulence genes, Diarrhoea

References

• Afolayan, A. O., Aboderin, A. O., Oaikhena, A. O., Odih, E. E., Ogunleye, V. O., Adeyemo, A. T., Adeyemo, A. T., Bejide, O. S., Underwood, A., Argimón, S., Abrudan, M., Egwuenu, A., Ihekweazu, C., Aanensen, D. M., & Okeke, I. N. (2022). An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals. Microbial Genomics 8(12), mgen000863.
• Aibinu, I., Odugbemi, T., Koenig, W., & Ghebremedhin, B. (2012). Sequence type ST131 and ST10 complex (ST617) is predominant among CTX-M-15-producing Escherichia coli isolates from Nigeria. Clinical Microbiology and Infection: the official publication of the European Society of Clinical Microbiology and Infectious Diseases 18(3), E49–E51.
• Ashbolt, N., Pruden, A., Miller, J., Riquelme, M.V., & Maile-Moskowitz, A. (2018). Antimicrobial resistance: fecal sanitation strategies for combatting a global public health threat. Rose, J.B., Jiménez-Cisneros, B., eds, Glob Water Pathogen Project.
• Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., & Pevzner, P. A. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 19(5), 455–477.
• Beghain, J., Bridier-Nahmias, A., Le Nagard, H., Denamur, E., & Clermont, O. (2018). Clermont Typing: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microbes 4:e000192.
• Carattoli, A., & Hasman, H. (2020). PlasmidFinder and in silico pMLST: Identification and typing of plasmid replicons in whole-genome sequencing (wgs). Methods in Molecular Biology (Clifton, N.J.) 2075, 285–294.
• Clausen, P.T.L.C., Aarestrup, F. M., & Lund, O. (2018). Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 19(1), 307.
• Clermont, O., Christenson, J. K., Denamur, E., & Gordon, D. M. (2013). The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environmental Microbiology Reports 5(1), 58–65.
• Clermont, O., Olier, M., Hoede, C., Diancourt, L., Brisse, S., Clermont, O., Olier, M., Hoede, C., Diancourt, L., Brisse, S., Keroudean, M., Glodt, J., Picard, B., Oswald, E., & Denamur, E. (2011). Animal and human pathogenic Escherichia coli strains share common genetic backgrounds. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases 11(3), 654–662.
• Doumith, M., Dhanji, H., Ellington, M.J., Hawkey, P., & Woodford, N. (2012). Characterization of plasmids encoding extended-spectrum-lactamases and their addiction systems circulating among Escherichia coli clinical isolates in the UK. Journal of Antimicrobial Chemotherapy 67(4), 878-885.
• Ewels, P., Måns, M., Sverker, L., & Max, K. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19), 3047-3048.
• Falodun, O. I., Afolabi, M. C., & Rabiu, A. G. (2022). Detection of extended Spectrum β-lactamase (ESBL) genes in Escherichia coli isolated from fecal samples of apparently healthy dogs in Ibadan. Animal Gene 26, 2352-4065.
• Feng, P., Lampel, K. A., Karch, H., & Whittam, T. S. (1998). Genotypic and phenotypic changes in the emergence of Escherichia coli O157:H7. The Journal of Infectious Diseases, 177(6), 1750–1753.
• Hua, P., Badat, M., Hanssen, L. L. P., Hentges, L. D., Crump, N., Downes, D. J., Jeziorska, D. M., Oudelaar, A. M., Schwessinger, R., Taylor, S., Milne, T. A., Hughes, J. R., Higgs, D. R., & Davies, J. O. J. (2021). Defining genome architecture at base-pair resolution. Nature 595(7865), 125–129. https://doi.org/10.1038/s41586-021-03639-4
• Ikhimiukor, O. O., Odih, E. E., Donado-Godoy, P., & Okeke, I. N. (2022). A bottom-up view of antimicrobial resistance transmission in developing countries. Nature Microbiology 7(6), 757–765. https://doi.org/10.1038/s41564-022-01124-w
• Jacob, J., & Lorber, B. (2015). Diseases transmitted by man's best friend: The Dog. Microbiology Spectrum 3(4), 10.1128/microbiolspec.IOL5-0002-2015.
• Kjaergaard, A.B., Carr, A.P., & Gaunt, M.C. (2016). Enteropathogenic Escherichia coli (EPEC) infection in association with acute gastroenteritis in 7 dogs from Saskatchewan. Canadian Veterinary Journal 57.
• LeCuyer, T. E., Byrne, B. A., Daniels, J. B., Diaz-Campos, D. V., Hammac, G. K., Miller, C. B., Besser, T. E., & Davis, M. A. (2018). Population structure and antimicrobial resistance of canine uropathogenic Escherichia coli. Journal of Clinical Microbiology 56(9), e00788-18.
• Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science 3: e104.
• Majowicz, S. E., Scallan, E., Jones-Bitton, A., Sargeant, J. M., Stapleton, J., Angulo, F. J., Yeung, D. H., & Kirk, M. D. (2014). Global incidence of human Shiga toxin-producing Escherichia coli infections and deaths: a systematic review and knowledge synthesis. Foodborne Pathogens and Disease 11(6), 447–455.
• Malberg Tetzschner, A. M., Johnson, J. R., Johnston, B. D., Lund, O., & Scheutz, F. (2020). In silico genotyping of Escherichia coli isolates for extraintestinal virulence genes by use of whole-genome sequencing data. Journal of Clinical Microbiology 58(10), e01269-20.
• Manges, A. R., Geum, H. M., Guo, A., Edens, T. J., Fibke, C. D., & Pitout, J. D. D. (2019). Global extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Clinical Microbiology Reviews 32(3), e00135-18.
• Mercado, E. H., Piscoche, C., Contreras, C., Durand, D., Riveros, M., Ruiz, J., & Ochoa, T. J. (2016). Pathogenicity Island O-122 in enteropathogenic Escherichia coli strains is associated with diarrhea severity in children from Lima Peru. International Journal of Medical Microbiology 306(4), 231–236.
• Mounsey, O., Wareham, K., Hammond, A., Findlay, J., Gould, V. C., Morley, K., Cogan, T. A., Turner, K. M. E., Avison, M. B., & Reyher, K. K., 2022, Evidence that fecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding. One Health (Amsterdam, Netherlands) 14, 100370.
• National Health Research Ethics Committee of Nigeria, NHREC, 2007, Federal Ministry of Health. Available at http://www.nhrec.net (Accessed on 15 September, 2020).
• Ogbolu, D. O., Piddock, L. J. V., & Webber, M. A. (2020). Opening Pandora's box: High-level resistance to antibiotics of last resort in Gram-negative bacteria from Nigeria. Journal of Global Antimicrobial Resistance, 21, 211–217.
• Olowe, O. A., Adewumi, O., Odewale, G., Ojurongbe, O., & Adefioye, O. J. (2015). Phenotypic and molecular characterization of extended-spectrum beta-lactamase-producing Escherichia coli obtained from animal fecal samples in Ado Ekiti, Nigeria. Journal of Environmental and Public Health 497980.
• Ovi, F., Zhang, L., Nabors, H., Jia, L., & Adhikari, P. (2023). A compilation of virulence-associated genes that are frequently reported in avian pathogenic Escherichia coli (APEC) compared to other E. coli. Journal of Applied Microbiology 134 (3), lxad014.
• Penakalapati, G., Swarthout, J., Delahoy, M. J., McAliley, L., Wodnik, B., Levy, K., & Freeman, M. C. (2017). Exposure to animal feces and human health: a systematic review and proposed research priorities. Environmental Science and Technology 51(20), 11537–11552.
• Puño-Sarmiento, J., Medeiros, L., Chiconi, C., Martins, F., Pelayo, J., Rocha, S., Blanco, J., Blanco, M., Zanutto, M., Kobayashi, R., & Nakazato, G. (2013). Detection of diarrheagenic Escherichia coli strains isolated from dogs and cats in Brazil. Veterinary Microbiology 166(3-4), 676–680.
• Robins-Browne, R. M., Holt, K. E., Ingle, D. J., Hocking, D. M., Yang, J., and Tauschek, M. (2016). Are Escherichia coli pathotypes still relevant in the era of whole-genome sequencing? Frontiers in Cellular and Infection Microbiology 6, 141.
• Salgado-Caxito, M., Benavides, J. A., Adell, A. D., Paes, A. C., and Moreno-Switt, A. I. (2021). Global prevalence and molecular characterization of extended-spectrum β-lactamase producing-Escherichia coli in dogs and cats - A scoping review and meta-analysis. One Health (Amsterdam, Netherlands), 12, 100236.
• Seemann, T. (2014). Prokka: rapid prokaryotic genome annotation. Bioinformatics (Oxford, England) 30(14), 2068–2069.
• Sheikh, J., Dudley, J.E.G., Sui, B., Tamboura, B., Suleman, A., & Nataro, J.P. (2006). EilA, a HilA-like regulator in enteroaggregative Escherichia coli. Molecular Microbiology 61, 338-350.
• Sherwin, C. M., Christiansen, S. B., Duncan, I. J., Erhard, H. W., Lay, D. C., Mench, J. A., O’Connor, C. E., & Petherick, J. C. (2003). Guidelines for the ethical use of animals in applied ethology studies. Applied Animal Behaviour Science 81, 291–305.
• Sumrall, E. T., Gallo, E. B., Aboderin, A. O., Lamikanra, A., & Okeke, I. N. (2014). Dissemination of the transmissible quinolone-resistance gene qnrS1 by IncX plasmids in Nigeria. PloS One 9(10), e110279. https://doi.org/10.1371/journal.pone.0110279.
• Trifinopoulos, J., Nguyen, L. T., von Haeseler, A., & Minh, B. Q. (2016). W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research, 44(W1), W232–W235.
• Tudu, R., Banerjee, J., Habib, M., Bandyopadhyay, S., Biswas, S., Kesh, S. S., Maity, A., Batabyal, S., & Polley, S. (2022). Prevalence and molecular characterization of extended-spectrum β-lactamase (ESBL) producing Escherichia coli isolated from dogs suffering from diarrhea in and around Kolkata. Iranian Journal of Veterinary Research 23(3), 237–246.
• Vega-Manriquez, X. D., Ubiarco-López, A., Verdugo-Rodríguez, A., Hernández-Chiñas, U., Navarro-Ocaña, A., Ahumada-Cota, R. E., Ramírez-Badillo, D., Hernández-Díaz de León, N., & Eslava, C. A. (2020). Pet dogs potential transmitters of pathogenic Escherichia coli with resistance to antimicrobials. Archives of Microbiology 202(5), 1173–1179.
• Wood, D. E., & Salzberg, S. L. (2014). Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 15: R46.