Whole genome sequencing analysis of non-O157 Shiga toxin-producing Escherichia coli in milk in Kwara State, Nigeria

Document Type : Full paper (Original article)

Authors

1 Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Ilorin, Ilorin, Nigeria

2 Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Ilorin, Ilorin, Nigeria

3 Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria

Abstract

Background: Escherichia coli is a major cause of poor microbial quality of milk, often resulting from unhygienic milk handling. Milk contamination poses public health concerns. Shiga toxin-producing Escherichia coli (STEC) strains in food products, particularly milk, is a critical concern for public health. Limited information exists on the detection of non-O157 E. coli pathotypes in milk sold by local processors in Nigeria. Aims: This study aimed to explore the diversity of non-O157 STEC isolates found in commercially available milk in Kwara State, Nigeria, to find the genetic diversity and potential risks associated with these strains. Methods: A subgroup of 18 representative non-O157 STEC isolated from milk samples (n=1225) was selected for whole genome sequencing (WGS) analysis. Results: Four novel sequence types (ST): ST398, ST540, ST1727, and ST9891 of non-O157 E. coli involving five serotypes: O176:H30, O176:H20, O8:H20, O21:H45, and O22:H7, carrying variable proportions of virulence factors, antimicrobial resistance genes, and plasmids, were identified. Conclusion: This investigation contributes valuable data to the ongoing efforts to ensure food safety and prevent the transmission of E. coli strains through dairy products. The findings have implications for public health policies and food quality standards in Kwara State, Nigeria. Improved hygienic practices during milk handling are recommended.

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Adzitey, F; Asante, J; Kumalo, HM; Khan, RB; Somboro, AM and Amoako, DG (2020). Genomic investigation into the virulome, pathogenicity, stress response factors, clonal lineages, and phylogenetic relationship of Escherichia coli strains isolated from meat sources in Ghana. Genes (Basel), 11: 1504.
Alhaji, NB; Aliyu, MB; Ghali-Mohammed, I and Odetokun, IA (2019). Survey on antimicrobial usage in local dairy cows in North-central Nigeria: Drivers for misuse and public health threats. PLoS One. 4: e0224949.
Allard, MW; Strain, E; Melka, D; Bunning, K; Musser, SM; Brown, EW and Timme, R (2016). Practical value of food pathogen traceability through building a whole-genome sequencing network and database. J. Clin. Microbiol., 54: 1975-1983.
Anes, J; Nguyen, SV; Eshwar, AK; McCabe, E; Macori, G; Hurley, D; Lehner, A and Fanning, S (2020). Molecular characterisation of multi-drug resistant Escherichia coli of bovine origin. Vet. Microbiol., 242: 108566.
Aworh, MK; Kwaga, JKP; Hendriksen, RS; Okolocha, EC and Thakur, S (2021). Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environments. Antimicrob. Resist. Infect. Control. 10: 58.
Ayoade, F; Oguzie, J; Eromon, P; Omotosho, OE; Ogunbiyi, T; Olumade, T; Akano, K; Folarin, O and Happi, C (2021). Molecular surveillance of shiga toxigenic Escherichia coli in selected beef abattoirs in Osun State Nigeria. Sci. Rep., 11: 13966.
Bankevich, A; Nurk, S; Antipov, D; Gurevich, AA; Dvorkin, M; Kulikov, AS; Lesin, VM; Nikolenko, SI; Pham, S; Prjibelski, AD; Pyshkin, AV; Sirotkin, AV; Vyahhi, N; Tesler, G; Alekseyev, MA and Pevzner, PA (2012). SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comp. Biol., 19: 455-477.
Bergholz, TM; Tarr, CL; Christensen, LM; Betting, DJ and Whittam, TS (2007). Recent gene conversions between duplicated glutamate decarboxylase genes (gadA and gadB) in pathogenic Escherichia coli. Mol. Biol. Evol., 24: 2323-2333.
Bonvegna, M; Tomassone, L; Christensen, H and Olsen, JE (2022). Whole Genome Sequencing (WGS) analysis of virulence and AMR genes in extended-spectrum β-lactamase (ESBL)-producing Escherichia coli from animal and environmental samples in four Italian swine farms. Antibiotics. 11: 1774.
Chen, L; Wang, L; Yassin, AK; Zhang, J; Gong, J; Qi, K; Ganta, RR; Zhang, Y; Yang, Y; Han, X and Wang, C (2018). Genetic characterization of extraintestinal Escherichia coli isolates from chicken, cow and swine. AMB Express. 17: 117.
Dos Santos Alves, T; Rosa, VS; da Silva Leite, D; Guerra, ST; Joaquim, SF; Guimarães, FF; de Figueiredo Pantoja, JC; Lucheis, SB; Rall, VLM; Hernandes, RT; Langoni, H and Ribeiro, MG (2023). Genome-based characterization of multidrug-resistant Escherichia coli isolated from clinical bovine mastitis. Curr. Microbiol., 80: 89.
Enabulele, SA and Nwankiti, OO (2016). Shiga toxin (stx) gene detection and verotoxigenic potentials of non-O157 Escherichia coli isolated from fermented fresh cow milk (nono) sold in selected cities in Nigeria. Nig. J. Basic Appl. Sci., 24: 98-105.
Fayemi, OE; Akanni, GB; Elegbeleye, JA; Aboaba, OO and Njage, PM (2021). Prevalence, characterization and antibiotic resistance of Shiga toxigenic Escherichia coli serogroups isolated from fresh beef and locally processed ready-to-eat meat products in Lagos, Nigeria. Int. J. Food Microbiol., 347: 109191.
Findlay, J; Mounsey, O; Lee, WWY; Newbold, N; Morley, K; Schubert, H; Gould, VC; Cogan, TA; Reyher, KK and Avison, MB (2020). Molecular epidemiology of Escherichia coli producing CTX-M and pAmpC-Lactamases from dairy farms identifies a dominant plasmid encoding CTX-M-32 but no evidence for transmission to humans in the same geographical region. Appl. Environ. Microbiol., 87: e01842-20.
Ghali-Mohammed, I; Odetokun, IA; Raufu, IA and Adetunji, VO (2022). Handling practices and contamination of raw milk sold for consumption in markets of Kwara State, Nigeria. Sokoto J. Vet. Sci., 20: 50-58.
Ghali-Mohammed, I; Odetokun, IA; Raufu, IA; Alhaji, NB and Adetunji, VO (2023). Prevalence of Escherichia coli O157 isolated from marketed raw cow milk in Kwara State, Nigeria. Sci. Afr., 19: e01469.
Grace, D (2015). Food safety in low and middle income countries. Int. J. Environ. Res. Public Health. 12:10490-10507.
Hadler, JL; Clogher, P; Hurd, S; Phan, Q; Mandour, M; Bemis, K and Marcus, R (2011). Ten-year trends and risk factors for non-O157 shiga toxin-producing Escherichia coli found through Shiga toxin testing, Connecticut, 2000-2009. Clin. Infect. Dis., 53: 269-276.
Hale, CR; Scallan, E; Cronquist, AB; Dunn, J; Smith, K; Robinson, T; Lathrop, S; Tobin-D’Angelo, M and Clogher, P (2012). Estimates of enteric illness attributable to contact with animals and their environments in the United States. Clin. Infect. Dis., 54: S472-479.
Havelaar, AH; Kirk, MD; Torgerson, PR; Gibb, HJ; Hald, T; Lake, RJ; Praet, N; Bellinger, DC; de Silva, NR; Gargouri, N; Speybroeck, N; Cawthorne, A; Mathers, C; Stein, C; Angulo, FJ; Devleesschauwer, B and World Health Organization Foodborne Disease Burden Epidemiology Reference Group (2015). World Health Organization global estimates and regional comparisons of the burden of foodborne disease in 2010. PLoS Med., 12: e1001923.
Hughes, JM; Wilson, ME; Johnson, KE; Thorpe, CM and Sears, CL (2006). The emerging clinical importance of non-O157 Shiga toxin-producing Escherichia coli. 43: 1587-1595.
Ikumapayi, UN; Boisen, N; Hossain, MJ; Betts, M; Lamin, M; Saha, D; Kwambana-Adams, B; Dione, M; Adegbola, RA; Roca, A; Nataro, JP and Antonio, M (2017). Identification of subsets of enteroaggregative Escherichia coli associated with diarrheal disease among under 5 years of age children from Rural Gambia. Am. J. Trop. Med. Hyg., 97: 997-1004.
Labar, AS; Millman, JS; Ruebush, E; Opintan, JA; Bishar, RA; Aboderin, AO; Newman, MJ; Lamikanra, A and Okeke, IN (2012). Regional dissemination of a trimethoprim-resistance gene cassette via a successful transposable element. PLoS One. 7: e38142.
Li, Q; Chang, W; Zhang, H; Hu, D and Wang, X (2019). The role of plasmids in the multiple antibiotic resistance transfer in ESBLs-producing Escherichia coli isolated from wastewater treatment plants. Front. Microbiol., 10: 633.
Madoshi, BP; Kudirkiene, E; Mtambo, MMA; Muhairwa, AP; Lupindu, AM and Olsen, JE (2016). Characterisation of commensal Escherichia coli isolated from apparently healthy cattle and their attendants in Tanzania. PLoS One. 11: e0168160.
Malik, A; Nagy, B; Kugler, R and Szmolka, A (2017). Pathogenic potential and virulence genotypes of intestinal and faecal isolates of porcine post-weaning enteropathogenic Escherichia coli. Res. Vet. Sci., 115: 102-108.
Manyahi, J; Moyo, SJ; Tellevik, MG; Ndugulile, F; Urassa, W; Blomberg, B and Langeland, N (2017). Detection of CTX-M-15 beta-lactamases in Enterobacteriaceae causing hospital- and community-acquired urinary tract infections as early as 2004, in Dar es Salaam, Tanzania. BMC Infect. Dis., 17: 282.
Mathusa, EC; Chen, Y; Enache, E and Hontz, L (2010). Non-O157 Shiga toxin-producing Escherichia coli in Foods. J. Food Prot., 73: 1721-1736.
Mohammadi, P; Abiri, R; Rezaei, M and Salmanzadeh-Ahrabi, S (2013). Isolation of Shiga toxin-producing Escherichia coli from raw milk in Kermanshah, Iran. Iran J. Microbiol., 5: 233-238.
Monaghan, ÁI; Byrne, B; Fanning, S; Sweeney, T; McDowell, D and Bolton, DJ (2011). Serotypes and virulence profiles of non-O157 Shiga toxin-producing Escherichia coli isolates from bovine farms. Appl. Environ. Microbiol., 77: 8662-8668.
NCBI Resource Coordinators (2018). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 4: D8-D13.
Nüesch-Inderbinen, M; Hänni, C; Zurfluh, K; Hartnack, S and Stephan, R (2022). Antimicrobial resistance profiles of Escherichia coli and prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae in calves from organic and conventional dairy farms in Switzerland. Microbiol. Open., 11: e1269.
Odetokun, IA; Adetona, MA; Ade-Yusuf, RO; Adewoye, AO; Ahmed, AA; Ghali-Mohammed, I; Al-Mustapha, AI and Fetsch, A (2023). Staphylococcus aureus contamination of animal-derived foods in Nigeria: a systematic review, 2002-2022. Food Saf. Risk. 10: 6.
Odetokun, IA; Afolaranmi, ZM; Nuhu, AA; Borokinni, BO; Ghali-Mohammed, I; Cisse, H and Alhaji, NB (2022). Knowledge and self-reported food safety practices among meat consumers in Ilorin, Nigeria. Dialog. Health. 1: 100039.
Odetokun, IA; Ballhausen, B; Adetunji, VO; Ghali-Mohammed, I; Adelowo, MT; Adetunji, SA and Fetsch, A (2018). Staphylococcus aureus in two municipal abattoirs in Nigeria: Risk perception, spread and public health implications. Vet. Microbiol., 216: 52-59.
Odetokun, IA; Borokinni, BO; Bakare, SD; Ghali-Mohammed, I and Alhaji, NB (2021). A cross-sectional survey of consumers’ risk perception and hygiene of retail meat: A Nigerian study. Food Prot. Trends. 41: 274-283.
Olowe, OA; Aboderin, BW; Idris, OO; Mabayoje, VO; Opaleye, OO; Adekunle, OC; Olowe, RA; Akinduti, PA and Ojurongbe, O (2014). Genotypes and phenotypes of Shiga toxin-producing Escherichia coli (STEC) in Abeokuta, Southwestern Nigeria. Infect. Drug Resist., 7: 253-259.
Prendergast, DM; Slowey, R; Burgess, CM; Murphy, D; Johnston, D; Morris, D; O’ Doherty, Á; Moriarty, J and Gutierrez, M (2023). Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing. Front. Microbiol., 14: 1118264.
Raufu, IA; Ahmed, OA; Aremu, A; Ameh, JA; Timme, RE; Hendriksen, RS and Ambali, AG (2021). Occurrence, antimicrobial resistance and whole genome sequence analysis of Salmonella serovars from pig farms in Ilorin, North-central Nigeria. Int. J. Food Microbiol., 350: 109245.
 
Solà-Ginés, M; Cameron-Veas, K; Badiola, I; Dolz, R; Majó, N; Dahbi, G; Viso, S; Mora, A; Blanco, J; Piedra-Carrasco, N; González-López, JJ and Migura-Garcia, L (2015). Diversity of multi-drug resistant avian pathogenic Escherichia coli (APEC) causing outbreaks of colibacillosis in broilers during 2012 in Spain. PLoS One. 10: e0143191.
Sonda, T; Kumburu, H; van Zwetselaar, M; Alifrangis, M; Mmbaga, BT; Aarestrup, FM; Kibiki, G and Lund, O (2018). Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania. Antimicrob. Resist. Infect. Control. 7: 72.
Tate, H; Li, C; Nyirabahizi, E; Tyson, GH; Zhao, S; Rice-Trujillo, C; Jones, SB; Ayers, S; M’ikanatha, NM; Hanna, S; Ruesch, L; Cavanaugh, ME; Laksanalamai, P; Mingle, L; Matzinger, SR and McDermott, PF (2021). A national antimicrobial resistance monitoring system survey of antimicrobial-resistant foodborne bacteria isolated from Retail Veal in the United States. J. Food Prot., 84: 1749-1759.
Tofani, S; Albini, E; Blasi, F; Cucco, L; Lovito, C; Maresca, C; Pesciaroli, M; Orsini, S; Scoccia, E; Pezzotti, G; Magistrali, CF and Massacci, FR (2022). Assessing the load, virulence and antibiotic-resistant traits of ESBL/Ampc E. coli from broilers raised on conventional, antibiotic-free, and organic farms. Antibiotics. 11: 1484.
Unnevehr, L and Hirschhorn, N (2000). Food safety issues in the developing world. World Bank Technical Papers. Papers 469.
USDA/FSIS (2012). Risk profile for pathogenic non-O157 Shiga toxin-producing Escherichia coli (Non-O157 STEC). Office of Public Health Science Office of Policy and Program Development Food Safety and Inspection Service United States Department of Agriculture. https://www.fsis.usda.gov/sites/default/files/media_file/2020-07/Non_O157_STEC_Risk_Profile_May2012.pdf.
Valilis, E; Ramsey, A; Sidiq, S and DuPont, HL (2018). Non-O157 Shiga toxin-producing Escherichia coli—A poorly appreciated enteric pathogen: Systematic review. Int. J. Infect. Dis., 76: 82-87.
Zhang, S; Yin, Y; Jones, MB; Zhang, Z; Deatherage Kaiser, BL; Dinsmore, BA; Fitzgerald, C; Fields, PI and Deng, X (2015). Salmonella serotype determination utilizing high-throughput genome sequencing data. J. Clin. Microbiol., 53: 1685-1692.