Review of Escherichia coli O157:H7 Prevalence, Pathogenicity, Heavy Metal and Antimicrobial Resistance, African Perspective

References

• Lim JY, Yoon JW, Hovide CJ. A BRIEF overview of Escherichia coli O157:H7 and Its Plasmid O157. J Microbiol Biotechnol. 2010;20(1):5–14. doi:10.4014/jmb.0908.08007
   PubMed Web of Science ®Google Scholar
• Clermont O, Christenson JK, Denamur E, Gordon DM. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep. 2013;5(1):58–65. doi:10.1111/1758-2229.12019
   PubMed Web of Science ®Google Scholar
• Kaper JB, Nataro JP, Mobley HL. Pathogenic Escherichia coli. Nat Rev Microbiol. 2004;2(2):123–140. doi:10.1038/nrmicro818
   PubMed Web of Science ®Google Scholar
• Eckburg PB, Bik EM, Bernstein CN, et al. Diversity of the human intestinal microbial flora. Science. 2005;308(5728):1635–1638.
   PubMed Web of Science ®Google Scholar
• Bergeron CR, Prussing C, Boerlin P, et al. Chicken as reservoir for extraintestinal pathogenic Escherichia coli in humans, Canada. Emerg Infect Dis. 2012;18(3):415–421. doi:10.3201/eid1803.111099
   Web of Science ®Google Scholar
• Schroeder CM, Zhao C, DebRoy C, et al. Antimicrobial resistance of Escherichia coli O157 isolated from humans, cattle, swine, and food. Appl Environ Microbiol. 2002;68(2):576–581. doi:10.1128/AEM.68.2.576-581.2002
   PubMed Web of Science ®Google Scholar
• Arshad R, Farooq S, Ali SS. Manipulation of different media and methods for cost-effective characterization of E. coli strains collected from different habitats. Pak. J Bot. 2006;38:779–781.
   Google Scholar
• Garrine M, Matambisso G, Nobela N, et al. Low frequency of enterohemorrhagic, enteroinvasive and diffusely adherent Escherichia coli in children under 5 years in rural Mozambique: a case-control study. BMC Infect Dis. 2020;20(1):1–6. doi:10.1186/s12879-020-05380-1
   Web of Science ®Google Scholar
• Jianga L, Yanga W, Jiangb X, Yaoa T, Wanga L, Yang B. Virulence-related O islands in enterohemorrhagic Escherichia coli O157:H7. Gut Microbes. 2021;13(1):e1992237. doi:10.1080/19490976.2021.1992237
   Web of Science ®Google Scholar
• Ateba CN, Mbewe M. Detection of Escherichia coli O157:H7 virulence genes in isolates from beef, pork, water, human and animal species in the northwest province, South Africa: public health implications. Res Microbiol. 2011;162(3):240–248. doi:10.1016/j.resmic.2010.11.008
   Web of Science ®Google Scholar
• Casey TA, Bosworth BT. Design, and evaluation of a multiplex polymerase chain reaction assay for the simultaneous identification of genes for nine different virulence factors associated with Escherichia coli that cause diarrhea and edema disease in swine. J Vet Diagn Investig. 2009;21:25–30. doi:10.1177/104063870902100104
   Web of Science ®Google Scholar
• Zhang W, Zhao M, Ruesch L, Omot A, Francis D. Prevalence of virulence genes in Escherichia coli strains recently isolated from young pigs with diarrhea in the US. Vet Microbiol. 2007;123(1–3):145–152. doi:10.1016/j.vetmic.2007.02.018
   Web of Science ®Google Scholar
• Conway T, Cohen PS. Commensal and pathogenic Escherichia coli metabolism in the gut. Microbiol Spect. 2015;3:3. doi:10.1128/microbiolspec.MBP-0006-2014
   Google Scholar
• Scheutz F, Teel LD, Beutin L, et al. Multicenter evaluation of a sequence-based protocol for subtyping Shiga toxins and standardizing Stx nomenclature. J Clin Microbiol. 2012;50(9):2951–2963. doi:10.1128/JCM.00860-12
   PubMed Web of Science ®Google Scholar
• Chase-Topping M, Gally D, Low C, Matthews L, Woolhouse M. Super-shedding and the link between human infection and livestock carriage of Escherichia coli O157. Nat Rev Microbiol. 2008;6(12):904–912. doi:10.1038/nrmicro2029
   Web of Science ®Google Scholar
• Anjum MF, Mafura M, Slickers P, et al. Pathotyping Escherichia coli by using miniaturized DNA microarrays. Appl Environ Microbiol. 2007;73(17):5692–5697. doi:10.1128/AEM.00419-07
   Web of Science ®Google Scholar
• Ewers C, Li G, Wilking H, et al. Avian pathogenic, uropathogenic, and newborn meningitis-causing Escherichia coli: how closely related are they? Int J Med Microbiol. 2007;297(3):163–176. doi:10.1016/j.ijmm.2007.01.003
   PubMed Web of Science ®Google Scholar
• Ewers C, Bethe A, Semmler T, Guenther S, Wieler LH. Extended-spectrum β-lactamase-producing and AmpC-producing Escherichia coli from livestock and companion animals, and their putative impact on public health: a global perspective. Clin Microbiol Infect. 2012;18(7):646–655. doi:10.1111/j.1469-0691.2012.03850.x
   PubMed Web of Science ®Google Scholar
• Bujnáková D, Karahutová L, Kmet’ V. Escherichia coli specific virulence-gene markers analysis for quality control of ovine cheese in Slovakia. Microorganisms. 2021;9(9):2–11. doi:10.3390/microorganisms9091808
   Web of Science ®Google Scholar
• Mccollum JT, Williams NJ, Beam SW, et al. Multistate outbreak of Escherichia coli O157:H7 Infections associated with in-store sampling of an aged raw-milk gouda cheese, 2010†. J Food Prot. 2012;75(10):1759–1765. doi:10.4315/0362-028X.JFP-12-136
   Web of Science ®Google Scholar
• Bielaszewska M, Mellmann A, Zhang W, et al. Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study. Lancet Infect Dis. 2011;11(9):671–676. doi:10.1016/S1473-3099(11)70165-7
   PubMed Web of Science ®Google Scholar
• Panel EB, Koutsoumanis K, Allende A, et al. Pathogenicity assessment of Shiga toxin-producing Escherichia coli (STEC) and the public health risk posed by contamination of food with STEC. EFSA J. 2020;18:13.
   Web of Science ®Google Scholar
• Frenzen PD, Drake A, Angulo FJ. Economic cost of illness due to Escherichia coli O157 infections in the United States. J Food Prot. 2005;68(12):2623–2630. doi:10.4315/0362-028X-68.12.2623
   PubMed Web of Science ®Google Scholar
• Michino H, Araki K, Minami S, et al. Massive outbreak of Escherichia coli O157: H7 Infection in School children in Sakai City, Japan, associated with consumption of white radish sprouts. Am J Epidemiol. 1999;150(8):787–796. doi:10.1093/oxfordjournals.aje.a010082
   PubMed Web of Science ®Google Scholar
• Varma JK, Greene KD, Reller ME, et al. An outbreak of Escherichia coli O157 infection following exposure to a contaminated building. JAMA. 2003;290:2709–2712.
   PubMed Web of Science ®Google Scholar
• Karmali MA, Mascarenhas M, Shen S, et al. Association of genomic O island 122 of Escherichia coli EDL 933 with verocytotoxin-producing Escherichia coli seropathotypes that are linked to epidemic and/or serious disease. J Clin Microbiol. 2003;41(11):4930–4940. doi:10.1128/JCM.41.11.4930-4940.2003
   PubMed Web of Science ®Google Scholar
• Karch H, Denamur E, Dobrindt U, et al. The enemy within us: lessons from the 2011 European Escherichia coli O104:H4 outbreak. EMBO Mol Med. 2012;4(9):841–848. doi:10.1002/emmm.201201662
   PubMed Web of Science ®Google Scholar
• Caprioli A, Maugliani A, Michelacci V, Morabito S. Molecular typing of Verocytotoxin-producing E. coli (VTEC) strains isolated from food, feed, and animals: state of play and standard operating procedures for pulsed field gel electrophoresis (PFGE) typing, profiles interpretation and curation. EFSA. 2014;1:1–55.
   Google Scholar
• Blanco Crivelli X, Rumi MV, Carfagnini JC, Degregorio O, Bentancor AB. Synanthropic rodents as possible reservoirs of Shiga toxigenic Escherichia coli strains. Front Cell Infect Microbiol. 2012;2:134. doi:10.3389/fcimb.2012.00134
   Web of Science ®Google Scholar
• Karch H, Sorbitol-fermenting BM. Shiga toxin-producing Escherichia coli O157: H(-) strains: epidemiology, phenotypic and molecular characteristics, and microbiological diagnosis. J Clin Microbiol. 2001;39(6):2043–2049. doi:10.1128/JCM.39.6.2043-2049.2001
   Web of Science ®Google Scholar
• Eagar H, Swan G, Van Vuuren M. A survey of antimicrobial usage in South Africa with specific reference to food animals. J S Afr Vet Assoc. 2012;83(1):1–8. doi:10.4102/jsava.v83i1.16
   Web of Science ®Google Scholar
• Clements A, Young JC, Constantinou N, Frankel G. Infection strategies of enteric pathogenic Escherichia coli. Gut Microbes. 2012;3(2):71–87. doi:10.4161/gmic.19182
   PubMed Web of Science ®Google Scholar
• Byun JW, Jung BY, Kim HY, Fairbrother JM, Lee MH, Lee WK. Real-time PCR for differentiation of F18 variants among enterotoxigenic and Shiga toxin-producing Escherichia coli from piglets with diarrhoea and oedema disease. Vet J. 2013;198(2):538–540. doi:10.1016/j.tvjl.2013.07.021
   Web of Science ®Google Scholar
• Paletta AC, Castro VS, Conte-Junior CA. Shiga toxin-producing and enteroaggregative Escherichia coli in animal, foods, and humans: pathogenicity mechanisms, detection methods, and epidemiology. Curr Microbiol. 2020;77(4):612–620. doi:10.1007/s00284-019-01842-1
   PubMed Web of Science ®Google Scholar
• Panel EB, Koutsoumanis K, Allende A, et al. Pathogenicity assessment of Shiga toxin-producing Escherichia coli (STEC) and the public health risk posed by contamination of food with STEC. EFSA J. 2020;18:e05967.
   Web of Science ®Google Scholar
• Nataro JP, Kaper JB. Diarrheagenic Escherichia coli. Clin Microbiol Rev. 1998;11(1):142–201. doi:10.1128/CMR.11.1.142
   PubMed Web of Science ®Google Scholar
• Caprioli A, Morabito S, Brugere H, Oswald E. Enterohaemorrhagic Escherichia coli: emerging issues on virulence and modes of transmission. Vet Res. 2005;36(3):289–311. doi:10.1051/vetres:2005002
   Web of Science ®Google Scholar
• Cho S, Bender JB, Diez-Gonzalez F, et al. Prevalence and characterization of Escherichia coli O157 isolates from Minnesota dairy farms and county fairs. J Food Prot. 2006;69(2):252–259. doi:10.4315/0362-028X-69.2.252
   Web of Science ®Google Scholar
• Jores J, Rumer L, Wieler LH. Impact of the locus of enterocyte effacement Pathogenicity Island on the evolution of pathogenic Escherichia coli. Int J Med Microbiol. 2004;294(2–3):103–113. doi:10.1016/j.ijmm.2004.06.024
   PubMed Web of Science ®Google Scholar
• Beata S, Michał T, Mateusz O, et al. Norepinephrine affects the interaction of adherent-invasive Escherichia coli with intestinal epithelial cells. Virulence. 2021;12:630–637. doi:10.1080/21505594.2021.1882780
   PubMed Web of Science ®Google Scholar
• Ogura Y, Ooka T, Iguchi A, et al. Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci U S A. 2009;106(42):17939–17944. doi:10.1073/pnas.0903585106
   Web of Science ®Google Scholar
• Boerlin P, McEwen SA, Boerlin-Petzold F, Wilson JB, Johnson RP, Gyles CL. Associations between virulence factors of Shiga toxin-producing Escherichia coli and disease in humans. J Clin Microbiol. 1999;37:497–503. doi:10.1128/JCM.37.3.497-503.1999
   PubMed Web of Science ®Google Scholar
• Ostroff SM, Tarr PI, Neill MA, Lewis JH, Hargrett-Bean N, Kobayashi JM. Toxin genotypes and plasmid profiles as determinants of systemic sequelae in Escherichia coli O157:H7 infections. J Infect Dis. 1989;160:994–998. doi:10.1093/infdis/160.6.994
   PubMed Web of Science ®Google Scholar
• Shaheen BW, Nayak R, Boothe DM. Emergence of a New Delhi Metallo-β-Lactamase (NDM-1)-Encoding Gene in Clinical Escherichia coli Isolates Recovered from Companion Animals in the United States. Antimicrob Agents Chemother. 2013;57(6):2902–2903. doi:10.1128/AAC.02028-12
   PubMed Web of Science ®Google Scholar
• Serna A, Boedeker EC. Pathogenesis and treatment of Shiga toxin producing Escherichia coli infections. Curr Opin Gastroenterol. 2008;24(1):38–47. doi:10.1097/MOG.0b013e3282f2dfb8
   Web of Science ®Google Scholar
• Wong AR, Pearson JS, Bright MD, et al. Enteropathogenic and enterohaemorrhagic Escherichia coli: even more subversive elements. Mol Microbiol. 2011;80(6):1420–1438. doi:10.1111/j.1365-2958.2011.07661.x
   PubMed Web of Science ®Google Scholar
• Bardiau M, Szalo M, Mainil JG. Initial adherence of EPEC, EHEC and VTEC to host cells. Vet Res. 2010;41;57. doi:10.1051/vetres/2010029.
   Web of Science ®Google Scholar
• Dallman TJ, Byrne L, Ashton PM, et al. Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157. Clin Infect Dis. 2015;61(3):305–312. doi:10.1093/cid/civ318
   PubMed Web of Science ®Google Scholar
• Brandal LT, Wester AL, Lange H, et al. Shiga toxin-producing Escherichia coli infections in Norway, 1992–2012: characterization of isolates and identification of risk factors for haemolytic uremic syndrome. BMC Infect Dis. 2015;15(1):324. doi:10.1186/s12879-015-1017-6
   Web of Science ®Google Scholar
• Hancock DD, Besser TE, Rice DH, Herriott DE, Tarr PI. A. longitudinal study of Escherichia coli O157 in fourteen cattle herds. Epidemiol Infect. 1997;118:193–195. doi:10.1017/S0950268896007212
   PubMed Web of Science ®Google Scholar
• Bennett PM. Integrons and gene cassettes: a genetic construction kit for bacteria. J Antimicrob Chemother. 1999;43(1):1–4. doi:10.1093/jac/43.1.1
   PubMed Web of Science ®Google Scholar
• LeJeune JT, Besser TE, Hancock DD. Cattle water troughs as reservoirs of Escherichia coli O157. Appl Environ Microbiol. 2001;67:3053–3057. doi:10.1128/AEM.67.7.3053-3057.2001
   PubMed Web of Science ®Google Scholar
• Barker J, Humphrey TJ, Brown MW. Survival of Escherichia coli O157 in a soil protozoan: implications for disease. FEMS Microbiol Lett. 1999;173:291–295. doi:10.1111/j.1574-6968.1999.tb13516.x
   PubMed Web of Science ®Google Scholar
• Maule A. Survival of verocytotoxigenic Escherichia coli O157 in soil, water and on surfaces. Symp Ser Soc Appl Microbiol. 2000;29:71S–78S. doi:10.1111/j.1365-2672.2000.tb05334.x
   Google Scholar
• Mead PS, Slutsker L, Dietz V, et al. Food related illness and death in the United States. Emerg Infect Dis. 1999;5(5):607–625. doi:10.3201/eid0505.990502
   PubMed Web of Science ®Google Scholar
• Banatvala N, Griffin PM, Greene KD, et al. The United States national prospective haemolytic uremic syndrome study: microbiologic, serologic, clinical, and epidemiologic findings. J Infect Dis. 2001;183:1063–1070. doi:10.1086/319269
   Web of Science ®Google Scholar
• Thompson JS, Hodge DS, Borczyk AA. Rapid biochemical test to identify verocytotoxin-positive strains of Escherichia coli serotype O157. J Clin Microbiol. 1990;28(10):2165–2168. doi:10.1128/jcm.28.10.2165-2168.1990
   Web of Science ®Google Scholar
• Dahmen S, Haenni M, Madec JY. IncI1/ST3 plasmids contribute to the dissemination of the blaCTX-M-1 gene in Escherichia coli from several animal species in France. J Antimicrob Chemother. 2012;67(12):3011–3012. doi:10.1093/jac/dks308
   Web of Science ®Google Scholar
• Dobrindt U, Agerer F, Michaelis K, et al. Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J Bacteriol. 2003;185:1831–1840. doi:10.1128/JB.185.6.1831-1840.2003
   PubMed Web of Science ®Google Scholar
• Perna NT, Plunkett G, Burland V, et al. Genome sequence of enterohaemorrhagic Escherichia coli O157: H7. Nature. 2001;409:529–533. . doi:10.1038/35054089
   PubMed Web of Science ®Google Scholar
• Wick LM, Qi W, Lacher DW, Whittam TS. Evolution of genomic content in the stepwise emergence of Escherichia coli O157:H7. J Bacteriol. 2005;187(5):1783–1791. doi:10.1128/JB.187.5.1783-1791.2005
   PubMed Web of Science ®Google Scholar
• Noller AC, McEllistrem MC, Stine OC, et al. Multilocus sequence typing reveals a lack of diversity among Escherichia coli O157:H7 isolates that are distinct by pulsed-field gel electrophoresis. J Clin Microbiol. 2003;41(2):675–679. doi:10.1128/JCM.41.2.675-679.2003
   Web of Science ®Google Scholar
• Kudva IT, Evans PS, Perna NT, et al. Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms. J Bacteriol. 2002;184(7):1873–1879. doi:10.1128/JB.184.7.1873-1879.2002
   Web of Science ®Google Scholar
• Zhou Z, Li X, Liu B, et al. Derivation of Escherichia coli O157:H7 from its O55:H7 precursor. PLoS One. 2010;5(1):e8700. doi:10.1371/journal.pone.0008700
   Web of Science ®Google Scholar
• Feng P, Lampel KA, Karch H, Whittam TS. Genotypic and phenotypic changes in the emergence of Escherichia coli O157:H7. J Infect Dis. 1998;177(6):1750–1753. doi:10.1086/517438
   PubMed Web of Science ®Google Scholar
• Bilge SS, Vary JC, Dowell SF, Tarr PI. Role of the Escherichia coli O157: H7O side chain in adherence and analysis of a rfb locus. Infect Immun. 1996;64(11):4795–4801. doi:10.1128/iai.64.11.4795-4801.1996
   Web of Science ®Google Scholar
• Whittam TS, Wolfe ML, Wachsmuth IK, Orskov F, Orskov I, Wilson RA. Clonal relationships among Escherichia coli strains that cause hemorrhagic colitis and infantile diarrhea. Infect Immun. 1993;61(5):1619–1629. doi:10.1128/iai.61.5.1619-1629.1993
   Web of Science ®Google Scholar
• Karch H, Bielaszewska M. Sorbitol-fermenting Shiga toxin-producing Escherichia coli O157: H(-) strains: epidemiology, phenotypic and molecular characteristics, and microbiological diagnosis. J Clin Microbiol. 2001;39(6):2043–2049.
   Web of Science ®Google Scholar
• Kim YJ, Kim JH, Hur J, Lee JH. Isolation of Escherichia coli from piglets in South Korea with diarrhea and characteristics of the virulence genes. Can J Vet Res. 2010;74:59–64.
   PubMed Web of Science ®Google Scholar
• Leopold SR, Shaikh N, Tarr PI. Further evidence of constrained radiation in the evolution of pathogenic Escherichia coli O157:H7. Infect Genet Evol. 2010;10(8):1282–1285. doi:10.1016/j.meegid.2010.07.021
   Web of Science ®Google Scholar
• Eppinger M, Mammel MK, Leclerc JE, Ravel J, Cebula TA. Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir. Appl Environ Microbiol. 2011;77(9):2916–2925. doi:10.1128/AEM.02554-10
   Web of Science ®Google Scholar
• Ferdous M, Friedrich AW, Grundmann H, et al. Molecular characterization and phylogeny of Shiga toxin–producing Escherichia coli isolates obtained from two Dutch regions using whole genome sequencing. Clin Microbiol Infect. 2016;22(7):642e1–642.e9. doi:10.1016/j.cmi.2016.03.028
   Web of Science ®Google Scholar
• Manning SD, Motiwala AS, Springman AC, et al. Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc Natl Acad Sci U S A. 2008;105(12):4868–4873. doi:10.1073/pnas.0710834105
   PubMed Web of Science ®Google Scholar
• Eppinger M, Mammel MK, Leclerc JE, Ravel J, Cebula TA. Genomic anatomy of Escherichia coli O157:H7 outbreaks. Proc Natl Acad Sci U S A. 2011;108(50):20142–20147. doi:10.1073/pnas.1107176108
   PubMed Web of Science ®Google Scholar
• Liu W, Yuan C, Meng X, et al. Frequency of virulence factors in Escherichia coli isolated from suckling pigs with diarrhoea in China. Vet J. 2014;199(2):286–289. doi:10.1016/j.tvjl.2013.11.019
   Web of Science ®Google Scholar
• Iyoda S, Manning SD, Seto K, et al. Chromosomal and plasmid-encoded enzymes are Required for assembly of the R3-type core oligosaccharide in the Lipopolysaccharide of Escherichia coli O157:H7. J Biol Chem. 2004;279(30):31237–31250. doi:10.1074/jbc.M401879200
   Web of Science ®Google Scholar
• Soderlund R, Jernberg C, Ivarsson S, et al. Molecular typing of Escherichia coli O157:H7 isolates from Swedish cattle and human cases: population dynamics and virulence. J Clin Microbiol. 2014;52(11):3906–3912. doi:10.1128/JCM.01877-14
   PubMed Web of Science ®Google Scholar
• Bielaszewska M, Prager R, Kock R, et al. Shiga toxin gene loss and transfer in vitro and in vivo during enterohemorrhagic Escherichia coli O26 infection in humans. Appl Environ Microbiol. 2007;73(10):3144–3150. doi:10.1128/AEM.02937-06
   Web of Science ®Google Scholar
• Lim JY, Li J, Sheng H, Besser TE, Potter K, Hovde CJ. Escherichia coli O157:H7 colonization at the rectoanal junction of long duration culture-positive cattle. Appl Environ Microbiol. 2007;73(4):13802. doi:10.1128/AEM.02242-06
   Web of Science ®Google Scholar
• Sheng H, Lim JY, Knecht HJ, Li J, Hovde CJ. Role of Escherichia coli O157:H7 virulence factors in colonization at the bovine terminal rectal mucosa. Infect Immun. 2006;74(8):4685–4693. doi:10.1128/IAI.00406-06
   Web of Science ®Google Scholar
• Domingues S, Harms K, Fricke WF, Johnsen PJ, da Silva GJ, Nielsen KM. Natural transformation facilitates transfer of transposons, integrons and gene cassettes between bacterial species. PLoS Pathog. 2012;8:e1002837. doi:10.1371/journal.ppat.1002837
   PubMed Web of Science ®Google Scholar
• Bauer ME, Welch RA. Characterization of an RTX toxin from enterohemorrhagic Escherichia coli O157:H7. Infect Immun. 1996;64(1):167–175. doi:10.1128/iai.64.1.167-175.1996
   Web of Science ®Google Scholar
• Schmidt H, Beutin L, Karch H. Molecular analysis of the plasmid-encoded hemolysin of Escherichia coli O157:H7 strain EDL 933. Infect Immun. 1995;63(3):1055–1061. doi:10.1128/iai.63.3.1055-1061.1995
   PubMed Web of Science ®Google Scholar
• Schmidt H, Bielaszewska M, Karch H. Transduction of enteric Escherichia coli isolates with a derivative of Shiga toxin 2-encoding bacteriophage phi3538 isolated from Escherichia coli O157:H7. Appl Environ Microbiol. 1999;65(9):3855–3861. doi:10.1128/AEM.65.9.3855-3861.1999
   Web of Science ®Google Scholar
• Brunder W, Schmidt H, Karch H. KatP, a novel catalase-peroxidase encoded by the large plasmid of enterohaemorrhagic Escherichia coli O157:H7. Microbiology. 1996;142(11):3305–3315. doi:10.1099/13500872-142-11-3305
   Web of Science ®Google Scholar
• Brunder W, Schmidt H, Karch H. EspP, a novel extracellular serine protease of enterohaemorrhagic Escherichia coli O157:H7 cleaves human coagulation factor V. Mol Microbiol. 1997;24:767–778. doi:10.1046/j.1365-2958.1997.3871751.x
   PubMed Web of Science ®Google Scholar
• van Diemen PM, Dziva F, Stevens MP, Wallis TS. Identification of enterohemorrhagic Escherichia coli O26:H- genes required for intestinal colonization in calves. Infect Immun. 2005;73:1735–1743. [PubMed: 15731074]. doi:10.1128/IAI.73.3.1735-1743.2005
   PubMed Web of Science ®Google Scholar
• Lathem WW, Grys TE, Witowski SE, et al. StcE, a metalloprotease secreted by Escherichia coli O157:H7, specifically cleaves C1 esterase inhibitor. Mol Microbiol. 2002;45(2):277–288. doi:10.1046/j.1365-2958.2002.02997.x
   Web of Science ®Google Scholar
• Elliott SJ, Sperandio V, Giron JA, et al. The locus of enterocyte effacement (LEE)-encoded regulator controls expression of both LEE- and non-LEE-encoded virulence factors in enteropathogenic and enterohemorrhagic Escherichia coli. Infect Immun. 2000;68:6115–6126. doi:10.1128/IAI.68.11.6115-6126.2000
   PubMed Web of Science ®Google Scholar
• Klapproth JMA, Scaletsky CA, McNamara BP, et al. A large toxin from pathogenic Escherichia coli strains that inhibits lymphocyte activation. Infect Immun. 2000;68:2148–2155. doi:10.1128/IAI.68.4.2148-2155.2000
   PubMed Web of Science ®Google Scholar
• Stevens MP, Roe AJ, Vlisidou I, et al. Mutation of toxB and a truncated version of the efa-1 gene in Escherichia coli O157:H7 influences the expression and secretion of locus of enterocyte effacement-encoded proteins but not intestinal colonization in calves or sheep. Infect Immun. 2004;72:5402–5411. doi:10.1128/IAI.72.9.5402-5411.2004
   PubMed Web of Science ®Google Scholar
• Morabito S, Tozzoli R, Oswald E, Caprioli A. A mosaic pathogenicity island made up of the locus of enterocyte effacement and a pathogenicity island of Escherichia coli O157:H7 is frequently present in attaching and effacing E. coli. Infect Immun. 2003;71:3343–3348. doi:10.1128/IAI.71.6.3343-3348.2003
   Web of Science ®Google Scholar
• Yoon JW, Minnich SA, Ahn JS, Park YH, Paszczynski A, Hovde CJ. Thermoregulation of the Escherichia coli O157:H7 pO157 ecf operon and lipid A myristoyl transferase activity involves intrinsically curved DNA. Mol Microbiol. 2004;51(2):419–435. doi:10.1046/j.1365-2958.2003.03827.x
   Web of Science ®Google Scholar
• Schlech WF, Chase DP, Badley A. A model of food-borne Listeria monocytogenes infection in the Sprague–Dawley rat using gastric inoculation: development and effect of gastric acidity on infective dose. Int J Food Microbiol. 1993;18(1):15–24. doi:10.1016/0168-1605(93)90003-Y
   Web of Science ®Google Scholar
• Benjamin MM, Datta AR. Acid tolerance of enterohemorrhagic Escherichia coli. Appl Environ Microbiol. 1995;61(4):1669–1672. doi:10.1128/aem.61.4.1669-1672.1995
   PubMed Web of Science ®Google Scholar
• Castanie-Cornet MP, Penfound TA, Smith D, Elliott JF, Foster JW. Control of acid resistance in Escherichia coli. J Bacteriol. 1999;181:3525–3535. doi:10.1128/JB.181.11.3525-3535.1999
   PubMed Web of Science ®Google Scholar
• Heiman KE, Mody RK, Johnson SD, Griffin PM, Gould LH. Escherichia coli O157 outbreaks in the United States, 2003–2012. Emerg Infect Dis. 2015;21(8). doi:10.3201/eid2108.141364
   Web of Science ®Google Scholar
• Riley LW, Remis RS, Helgerson SD, et al. Hemorrhagic colitis associated with a rare Escherichia coli serotype. N Engl J Med. 1983;308(12):681. doi:10.1056/NEJM198303243081203
   PubMed Web of Science ®Google Scholar
• Gyles CL, Prescott JF, Songer G, Thoen CO. Pathogenomics of Bacterial Infection in Animals. 4th ed. USA: Wiley-Blackwell; 2010.
   Google Scholar
• Van TTH, Yidana Z, Smooker PM, Coloe PJ. Antibiotic use in food animals worldwide, with a focus on Africa: pluses and minuses. J Glob Antimicrob Resist. 2020;20:170–177. doi:10.1016/j.jgar.2019.07.031
   PubMed Web of Science ®Google Scholar
• Lim JM, Singh SR, Duong MC, Legido-Quigley H, Hsu LY, Tam CC. Impact of national interventions to promote responsible antibiotic use: a systematic review. J Antimicrob Chemother. 2020;75(1):14–29. doi:10.1093/jac/dkz348
   PubMed Web of Science ®Google Scholar
• Ateb CN, Mbewe M. Determination of the genetic similarities of fingerprints from Escherichia coli O157:H7 isolated from different sources in the North West Province, South Africa using ISR, BOXAIR and REP-PCR analysis. Microbiol Res. 2013;168(7):438–446. doi:10.1016/j.micres.2013.02.003
   Web of Science ®Google Scholar
• Willshaw GA, Smith HR, Cheasty T, Wall PG, Rowe B. Vero cytotoxin-producing Escherichia coli O157 outbreaks in England and Wales, 1995: phenotypic methods and genotypic subtyping. Emerg Infect Dis. 1997;3(4):561–565. doi:10.3201/eid0304.970422
   Web of Science ®Google Scholar
• Riley LW, Remis RS, Helgerson SD, et al. Haemorrhagic colitis associated with a rare Escherichia coli serotype. N Engl J Med. 1983;308:681–685.
   PubMed Web of Science ®Google Scholar
• Johnson TJ, Nolan LK. Pathogenomics of the virulence plasmids of Escherichia coli. Microbiol Mol Biol Rev. 2009;73:750–774. doi:10.1128/MMBR.00015-09
   PubMed Web of Science ®Google Scholar
• Ooka T, Ogura Y, Asadulghani M, et al. Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes. Genome Res. 2009;19(10):1809–1816. doi:10.1101/gr.089615.108
   Web of Science ®Google Scholar
• Kusumoto M, Fukamizu D, Ogura Y, et al. Lineage-specific distribution of insertion sequence excision enhancer in enterotoxigenic Escherichia coli isolated from swine. Appl Environ Microbiol. 2014;80(4):394–402. doi:10.1128/AEM.03696-13
   Web of Science ®Google Scholar
• Clement M, Olabisi M, David E, Issa M. Veterinary Pharmaceuticals and Antimicrobial Resistance in Developing Countries. In: Bekoe S, Saravanan M, Adosraku K, Ramkumar P, editors. Veterinary Medicine and Pharmaceuticals. Intechopen Limited; 2020.
   Google Scholar
• Leonard SR, Mammel MK, Lacher DW, Elkins CA. Application of metagenomic sequencing to food safety: detection of Shiga toxin-producing Escherichia coli on fresh bagged spinach. Appl Environ Microbiol. 2015;81(23):8183–8191. doi:10.1128/AEM.02601-15
   Web of Science ®Google Scholar
• Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods. 2012;9(8):811–814. doi:10.1038/nmeth.2066
   PubMed Web of Science ®Google Scholar
• Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15(3):46. doi:10.1186/gb-2014-15-3-r46
   PubMed Web of Science ®Google Scholar
• Ounit R, Wanamaker S, Close TJ, Lonardi S. CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics. 2015;16(1):236. doi:10.1186/s12864-015-1419-2
   PubMed Web of Science ®Google Scholar
• Feng P, Weagant SD, Jinneman K. Diarrheagenic Escherichia coli. In: Bacteriological Analytical Manual (BAM). Silver Spring, MD: US Food and Drug Administration; 2013. Availabe at: https://www.fda.gov/food/laboratory-methods-food/bam-chapter-4a-diarrheagenic-escherichia-coli.
   Google Scholar
• Akindolire MA, Aremu BR, Ateba CN. Complete genome sequence of Escherichia coli O157: h7Phage PhiG17. Am Soc Microbiol. 2019;8(3):e01296–18.
   Google Scholar
• Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–3402. doi:10.1093/nar/25.17.3389
   PubMed Web of Science ®Google Scholar
• Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 2004;32(1):11–16. doi:10.1093/nar/gkh152
   PubMed Web of Science ®Google Scholar
• Lowe TM, Chan PP. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 2016;44(W1):54–57. doi:10.1093/nar/gkw413
   PubMed Web of Science ®Google Scholar
• Kulikov E, Kropinski AM, Golomidova A, et al. Isolation, and characterization of a novel indigenous intestinal N4-related coliphage vB_EcoP_G7C. Virology. 2012;426(2):93–99. doi:10.1016/j.virol.2012.01.027
   Web of Science ®Google Scholar
• Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–2644. doi:10.1093/jac/dks261
   PubMed Web of Science ®Google Scholar
• Tsonos J, Oosterik LH, Tuntufye HN, et al. A cocktail of in vitro efficient phages is not a guarantee for in vivo therapeutic results against avian colibacillosis. Vet Microbiol. 2014;171(3–4):470–479. doi:10.1016/j.vetmic.2013.10.021
   Web of Science ®Google Scholar
• Carattol A, Zankari E, García-Fernández A, et al. In silico detection and typing of plasmids using 92 PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(3):895–903.
   Google Scholar
• Beyi AF, Fite AT, Tora E, et al. Prevalence, and antimicrobial susceptibility of Escherichia coli O157 in beef at butcher shops and restaurants in central Ethiopia. BMC Microbiol. 2017;17(49):1–6. doi:10.1186/s12866-017-0964-z
   Web of Science ®Google Scholar
• Havelaar AH, Kirk MD, Torgerson PR, Gibb HJ, Hald T, Lake RJ. World Health Organization Global Estimates and regional comparisons of the burden of foodborne disease in 2010. PLoS Med. 2010;12(12):e1001923.
   Web of Science ®Google Scholar
• Lupindu AM. Epidemiology of Shiga toxin-producing Escherichia coli O157:H7 in Africa in review. S Afr J Infect Dis. 2018;33(1):24–30. doi:10.1080/23120053.2017.1376558
   Web of Science ®Google Scholar
• Lupindu AM, Olsen JE, Ngowi HA, et al. Occurrence and characterization of Shiga Toxin-producing Escherichia coli O157:H7 and other nonsorbitol–fermenting E. coli in cattle and humans in urban areas of Morogoro, Tanzania. Vector-Borne Zoonotic Dis. 2014;14(7):503–510. doi:10.1089/vbz.2013.1502
   Web of Science ®Google Scholar
• Dahmen S, Bettaieb D, Mansour W, Boujaafar N, Boualleque O, Arlet G. Characterization, and molecular epidemiology of extended-spectrum beta-lactamases in clinical isolates of Enterobacteriaceae in a Tunisian University Hospital. Microb Drug Resist. 2010;16(2):163–170. doi:10.1089/mdr.2009.0108
   Web of Science ®Google Scholar
• Browning NG, Botha JR, Sacho H, et al. Escherichia coli O157: H7 haemorrhagic colitis. Report of the first South African case. S Afr J Surg. 1990;28(1):28.
   Web of Science ®Google Scholar
• Magwira CA, Gashe BA, Collison EK. Prevalence and antibiotic resistance profiles of Escherichia coli O157:H7 in beef products from retail outlets in Gaborone, Botswana. J Food Prot. 2005;68(2):403–406. doi:10.4315/0362-028X-68.2.403
   PubMed Web of Science ®Google Scholar
• Abong’o BO, Momba MNB. Prevalence and potential link between E. coli O157: H7 isolated from drinking water, meat and vegetables and stools of diarrheic confirmed and non-confirmed HIV/AIDS patients in the Amathole District - South Africa. J Appl Microbiol. 2008;105(2):424–431. doi:10.1111/j.1365-2672.2008.03756.x
   Web of Science ®Google Scholar
• Addo KK, Mensah GI, Aning KG, et al. Microbiological quality, and antibiotic residues in informally marketed raw cow milk within the coastal Savannah zone of Ghana. Trop Med Int Health. 2011;16(2):227–232. doi:10.1111/j.1365-3156.2010.02666.x
   Web of Science ®Google Scholar
• Siwila J, Phiri IGK, Vercruysse J, et al. Asymptomatic cryptosporidiosis in Zambian dairy farm workers and their household members. Trans R Soc Trop Med Hyg. 2007;101(7):733–734. doi:10.1016/j.trstmh.2007.01.006
   Web of Science ®Google Scholar
• Liu T. Custom, taste, and science: raising chickens in the Pearl River Delta region, South China, Anthropol. Med. 2008;15:7–18.
   Google Scholar
• Lohiniva AL, Dueger E, Talaat M, et al. Poultry rearing and slaughtering practices in rural Egypt: an exploration of risk factors for H5N1 virus human transmission, Influenza Other Respir. Viruses. 2013;7:1251–1259.
   Google Scholar
• Wang W, Owen H, Traub EJ, et al. Molecular epidemiology of Blastocystis in pigs and their in-contact humans in Southeast Queensland, Australia, and Cambodia. Vet Parasitol. 2014;203(3–4):264–269. doi:10.1016/j.vetpar.2014.04.006
   Web of Science ®Google Scholar
• Huo X, Zu R, Qi X, et al. Seroprevalence of avian influenza A (H5N1) virus among poultry workers in Jiangsu Province, China: an observational study. BMC Infect. 2012;10:12–93.
   Google Scholar
• Ming PX, Ti YLX, Bulmer GS. Outbreak of Trichophyton verrucosum in China transmitted from cows to humans. Mycopathologia. 2006;161(4):225–228. doi:10.1007/s11046-005-0223-y
   Web of Science ®Google Scholar
• Wang J, Stanford K, McAllister TA, et al. Biofilm formation, virulence gene profiles, and antimicrobial resistance of nine serogroups of non-O157 Shiga toxin–producing Escherichia coli. Foodborne Pathog Dis. 2016;13(6):316–324. doi:10.1089/fpd.2015.2099
   Web of Science ®Google Scholar
• Amézquita-López BA, Quiñones B, Soto-Beltrán M, et al. Antimicrobial resistance profiles of Shiga toxin-producing Escherichia coli O157 and non-O157 recovered from domestic farm animals in rural communities in Northwestern Mexico. Antimicrob Resist Infect Control. 2016;5(1):1. doi:10.1186/s13756-015-0100-5
   Web of Science ®Google Scholar
• Mashak Z. Prevalence and antibiotic resistance of Escherichia coli O157: h7Isolated from raw meat samples of ruminants and poultry. J Food Nutr Res. 2018;6(2):96–102. doi:10.12691/jfnr-6-2-5
   Google Scholar
• Abdi S, Ranjbar R, Vala MH, Jonaidi N, Bejestany OB, Bejestany FB. Frequency of bla TEM, bla SHV, bla CTX-M, and qnrA among Escherichia coli isolated from urinary tract infection. Arch Clin Infect Dis. 2014;9(1). doi:10.5812/archcid.18690
   Google Scholar
• Momtaz H, Karimian A, Madani M, et al. Uropathogenic Escherichia coli in Iran: serogroup distributions, virulence factors and antimicrobial resistance properties. Ann Clin Microbiol Antimicrob. 2013;12(1):1. doi:10.1186/1476-0711-12-8
   Web of Science ®Google Scholar
• Founou LL, Founou RC, Essack SY. Antibiotic resistance in the food chain: a developing country-perspective. Front Microbiol. 2016;7:1881. doi:10.3389/fmicb.2016.01881
   PubMed Web of Science ®Google Scholar
• Magiorakos AP, Srinivasan A, Carey RB, et al. Multidrug-resistant, extensively drug-resistant and pan drug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect. 2012;18(3):268–281. doi:10.1111/j.1469-0691.2011.03570.x
   PubMed Web of Science ®Google Scholar
• Van Boeckel TP, Brower C, Gilbert M, et al. Global trends in antimicrobial use in food animals. Proc Natl Acad Sci USA. 2015;112(18):5649–5654. doi:10.1073/pnas.1503141112
   PubMed Web of Science ®Google Scholar
• Corona F, Martinez JL. Phenotypic resistance to antibiotics. Antibiotics. 2013;2(2):237–255. doi:10.3390/antibiotics2020237
   Google Scholar
• Literak I, Dolejska M, Janoszowska D, et al. Antibiotic-resistant Escherichia coli bacteria, including strains with genes encoding the extended spectrum beta-lactamase and QnrS, in waterbirds on the Baltic Sea Coast of Poland. Appl Environ Microbiol. 2010;76:8126–8134. doi:10.1128/AEM.01446-10
   PubMed Web of Science ®Google Scholar
• Henton MM, Eagar HA, Swan GE, van Vuuren M. Part VI. Antibiotic management and resistance in livestock production. S Afr Med J. 2011;101:583–586.
   Web of Science ®Google Scholar
• Carattoli A. Resistance plasmid families in Enterobacteriaceae. Antimicrob Agents Chemother. 2009;53(22):27–38. doi:10.1128/AAC.01707-08
   Web of Science ®Google Scholar
• El-Halfway OM, Valvano MA. Non-genetic mechanisms communicating antibiotic resistance: rethinking strategies for antimicrobial drug design. Expert Opin Drug Discov. 2012;7(10):923–933. doi:10.1517/17460441.2012.712512
   Web of Science ®Google Scholar
• Ojala V, Laitalainen J, Jalasvuori M. Fight evolution with evolution: plasmid dependent phages with a wide host range prevent the spread of antibiotic resistance. Evol Appl. 2013;3:925–32.
   Web of Science ®Google Scholar
• Dale JW, Park SF. Molecular Genetics of Bacteria. United Kingdom: Wiley-Blackwell; 2010.
   Google Scholar
• Masood F, Malik A. Current aspects of metal resistant bacteria in bioremediation: from genes to ecosystem. In: Management of Microbial Resources in the Environment. New York: Springer; 2013.
   Google Scholar
• Dionisio F, Matic I, Radman M, Rodrigues OR, Taddei F. Plasmids spread very fast in heterogeneous bacterial communities. Genetics. 2002;163(4):1525–1532. doi:10.1093/genetics/162.4.1525
   Google Scholar
• Uma B, Kesani P, Saddayappan R, Kannaiyan K, Yelavarthi LS. Antibiotic sensitivity and plasmid profiles of Escherichia coli isolated from pediatric diarrhea. J Glob Infect Dis. 2009;1:107–110. doi:10.4103/0974-777X.56255
   PubMedGoogle Scholar
• Nsofor CA, Iroegbu CU. Plasmid profile of antibiotic resistance of Escherichia coli isolated from domestic animals in South-East Nigeria. J Cell Animal Biol. 2013;7:1096–1115.
   Google Scholar
• Velappan N, Sblattero D, Chasteen L, Pavlik P, Bradbury ARM. Plasmid incompatibility: more compatible than previously thought? Protein Eng Des Sel. 2007;20(7):309–313. doi:10.1093/protein/gzm005
   Web of Science ®Google Scholar
• Gyles CL. Shiga toxin-producing Escherichia coli: an overview. J Anim Sci. 2007;85(suppl_13):45–62. doi:10.2527/jas.2006-508
   Web of Science ®Google Scholar
• Mazaitis AJ, Maas R, Maas WK. Structure of a naturally occurring plasmid with genes for enterotoxin production and drug resistance. J Bacteriol. 1981;145(1):97105. doi:10.1128/jb.145.1.97-105.1981
   Web of Science ®Google Scholar
• Fekete PZ, Brzuszkiewicz E, Blum-Oehler G, et al. DNA sequence analysis of the composite plasmid pTC conferring virulence and antimicrobial resistance for porcine enterotoxigenic Escherichia coli. Int J Med Microbiol. 2012;302(1):4–9. doi:10.1016/j.ijmm.2011.07.003
   Web of Science ®Google Scholar
• Cimermancic P, Medema MH, Claesen J, et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell. 2014;158(2):412–421. doi:10.1016/j.cell.2014.06.034
   PubMed Web of Science ®Google Scholar
• Doroghazi JR, Albright JC, Goering AW, et al. A roadmap for natural product discovery based on large-scale genomics and metabolomics. Nat Chem Biol. 2014;10(11):963–968. doi:10.1038/nchembio.1659
   PubMed Web of Science ®Google Scholar
• Dejong CA, Chen GM, Li H, et al. Polyketide and non-ribosomal peptide retro-biosynthesis and global gene cluster matching. Nat Chem Biol. 2016;12(12):1007–1014. doi:10.1038/nchembio.2188
   PubMed Web of Science ®Google Scholar
• Medema MH, Paalvast Y, Nguyen DD, et al. Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products. PLoS Comput Biol. 2014;10(9):e1003822. doi:10.1371/journal.pcbi.1003822
   PubMed Web of Science ®Google Scholar
• Mohimani H, Kersten RD, Liu WT, et al. Automated genome mining of ribosomal peptide natural products. ACS Chem Biol. 2014;9(7):1545–1551. doi:10.1021/cb500199h
   PubMed Web of Science ®Google Scholar
• Shao Z, Rao G, Li C, et al. Refactoring the silent sectionalizing gene cluster using a plug-and-play scaffold. ACS Synth Biol. 2013;2(11):662–669. doi:10.1021/sb400058n
   Web of Science ®Google Scholar
• Yamanaka K, Reynolds KA, Kersten RD, et al. Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A. Proc Natl Acad Sci USA. 2014;111(5):1957–1962. doi:10.1073/pnas.1319584111
   PubMed Web of Science ®Google Scholar
• Weber T, Blin K, Duddela S, et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 2015;43(W1):237–243. doi:10.1093/nar/gkv437
   PubMed Web of Science ®Google Scholar
• van Heel AJ, de Jong A, Montalban-Lopez M, et al. BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal post-translationally modified peptides. Nucleic Acids Res. 2013;41(W1):448–453. doi:10.1093/nar/gkt391
   PubMed Web of Science ®Google Scholar
• Boddy CN. Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides. J Ind Microbiol Biotechnol. 2014;41(2):443–450. doi:10.1007/s10295-013-1368-1
   Web of Science ®Google Scholar
• Medema MH, Fischbach MA. Computational approaches to natural product discovery. Nat Chem Biol. 2015;11(9):639–648. doi:10.1038/nchembio.1884
   Web of Science ®Google Scholar
• Pi B, Yu D, Dai F, et al. A Genomics Based discovery of secondary metabolite biosynthetic gene clusters in Aspergillus ustus. PLoS One. 2015;10(2):e0116089. doi:10.1371/journal.pone.0116089
   Web of Science ®Google Scholar
• Leikoski N, Liu L, Jokela J, et al. Genome mining expands the chemical diversity of the cyanobactin family to include highly modified linear peptides. Chem Biol. 2013;20(8):1033–1043. doi:10.1016/j.chembiol.2013.06.015
   Google Scholar
• Cox CL, Doroghazi JR, Mitchell DA. The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles. BMC Genomics. 2015;16(1):778. doi:10.1186/s12864-015-2008-0
   Web of Science ®Google Scholar
• Shen B, Yan X, Huang T, et al. Enediynes: exploration of microbial genomics to discover new anticancer drug leads. Bioorg Med Chem Lett. 2015;25:9–15. doi:10.1016/j.bmcl.2014.11.019
   Web of Science ®Google Scholar
• Ziemert N, Alanjary M, Weber T. The evolution of genome mining in microbes—a review. Nat Prod Rep. 2016;33:988–1005. doi:10.1039/C6NP00025H
   PubMed Web of Science ®Google Scholar
• Ogawara H. Self-resistance in Streptomyces, with special reference to ß-lactam. Antibiotic Mol. 2016;21:605.
   Google Scholar
• Tang X, Li J, Millan-Aguinaga N, et al. Identification of thiotetronic acid antibiotic biosynthetic pathways by target-directed genome mining. ACS Chem Biol. 2015;10(12):2841–2849. doi:10.1021/acschembio.5b00658
   PubMed Web of Science ®Google Scholar
• Yeh H, Ahuja M, Chiang Y, et al. Resistance gene-guided genome mining: serial promoter exchanges in Aspergillus nidulans reveal the biosynthetic pathway for fellutamide B, a proteasome inhibitor. ACS Chem Biol. 2016;11:22–75. doi:10.1021/acschembio.6b00213
   Web of Science ®Google Scholar
• Johnston CW, Skinnider MA, Dejong CA, et al. Assembly and clustering of natural antibiotics guides target identification. Nat Chem Biol. 2016;12(4):233–239. doi:10.1038/nchembio.2018
   PubMed Web of Science ®Google Scholar
• Clausen CA. Isolating metal-tolerant bacteria capable of removing copper, chromium, and arsenic from treated wood. Waste Manag Res. 2000;18(3):264–268. doi:10.1034/j.1399-3070.2000
   Web of Science ®Google Scholar
• Kumar S, Tripathi VR, Garg SK. Physicochemical and microbiological assessment of recreational and drinking waters. Environ Monit Assess. 2012;184(5):2691–2698. doi:10.1007/s10661-011-2144-1
   Web of Science ®Google Scholar
• Cui L, Zhang YJ, Hurang WE, et al. Surface-enhanced Raman spectroscopy for identification of heavy metal arsenic (V)-mediated enhancing effect on antibiotic resistance. Anal Chem. 2016;10:44–90.
   Google Scholar
• Jia B, Raphenya AR, Alcock B, et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 2016;45(D1):566–573. doi:10.1093/nar/gkw1004
   Web of Science ®Google Scholar
• Cruz-Morales P, Kopp JF, Martinez-Guerrero C, et al. Phylogenomic analysis of natural products biosynthetic gene clusters allow discovery of arseno-organic metabolites in model streptomycetes. Genome Biol Evol. 2016;8(6):1906–1916. doi:10.1093/gbe/evw125
   PubMed Web of Science ®Google Scholar
• Medema MH, Trefzer A, Kovalchuk A, et al. The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biol Evol. 2010;2:212–224. doi:10.1093/gbe/evq013
   Web of Science ®Google Scholar
• Suwa M, Sugino H, Sasaoka A, et al. Identification of two polyketide synthase gene clusters on the linear plasmid pSLA2-L in Streptomyces rochei. Gene. 2000;246(1–2):123–131. doi:10.1016/S0378-1119(00)00060-3
   Web of Science ®Google Scholar
• Belousoff MJ, Shapira T, Bashan A, et al. Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit. Proc Natl Acad Sci USA. 2011;108(7):2717. doi:10.1073/pnas.1019406108
   Web of Science ®Google Scholar
• Wolf T, Shelest V, Nath N, et al. CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes. Bioinformatics. 2016;32(8):1138–1143. doi:10.1093/bioinformatics/btv713
   Web of Science ®Google Scholar
• Tracanna V, de Jong A, Medema MH, Kuipers OP. Mining prokaryotes for antimicrobial compounds: from diversity to function. FEMS Microbiol Rev. 2017;41(3):417–429. doi:10.1093/femsre/fux014
   Web of Science ®Google Scholar
• Maron DF, Smith TJ, Nachman KE. Restrictions on antimicrobial use in food animal production: an international regulatory and economic survey. Global Health. 2013;9:48.
   PubMed Web of Science ®Google Scholar
• Zhang S, Abbas M, Rehman MU, et al. Dissemination of antibiotic resistance genes (ARGs) via integrons in Escherichia coli: a risk to human health. Environ Pollut. 2020;266:1152–1160. doi:10.1016/j.envpol.2020.115260
   Web of Science ®Google Scholar
• Adesokan HK, Akanbi IO, Akanbi IM, Obaweda RA. Pattern of antimicrobial usage in livestock animals in south-western Nigeria: the need for alternative plans. Onderstepoort J Vet Res. 2015;82(1):816. doi:10.4102/ojvr.v82i1.816
   Web of Science ®Google Scholar
• Mainda G, Bessell PR, Muma JB, et al. Prevalence and patterns of antimicrobial resistance among Escherichia coli isolated from Zambian dairy cattle across different production systems. Sci Rep. 2015;5:124–139.
   Web of Science ®Google Scholar
• Donkor ES, Newman MJ, Yeboah-Manu D. Epidemiological aspects of non-human antibiotic usage and resistance: implications for the control of antibiotic resistance in Ghana. Trop Med Int Health. 2012;17(4):462–468. doi:10.1111/j.1365-3156.2012.02955.x
   Web of Science ®Google Scholar
• Pakbin B, Brück WM, Rossen JWA. Virulence Factors of Enteric Pathogenic Escherichia coli: a Review. Int J Mol Sci. 2021;22(18):1–18. doi:10.3390/ijms22189922
   Web of Science ®Google Scholar
• Adenipekum EO, Jackson CR, Oluwadun A, et al. Prevalence and antimicrobial resistance in Escherichia coli from food animals in Lagos, Nigeria. Microb Drug Resist. 2015;21:358–365. doi:10.1089/mdr.2014.0222
   Web of Science ®Google Scholar
• Chantziaras I, Boyen F, Callens B, Dewulf J. Correlation between veterinary antimicrobial use and antimicrobial resistance in food-producing animals: a report on seven countries. J Antimicrob Chemother. 2014;69(3):827–834. doi:10.1093/jac/dkt443
   PubMed Web of Science ®Google Scholar
• Luanda CM, Buza J, Mwanyika G, et al. Bacterial contamination of pork carcasses from Arusha, Tanzania. GJAR. 2016;3:806–817.
   Google Scholar
• Odwar JA, Kikuvi G, Kariuki JN, Kariuki S. A cross-sectional study on the microbiological quality and safety of raw chicken meats sold in Nairobi, Kenya. BMC Res Notes. 2014;7(1):627. doi:10.1186/1756-0500-7-627
   PubMedGoogle Scholar
• Mrutu R, Luanda C, Rugumisa B, et al. Detection of microbial surface contamination and antibiotic resistant Escherichia coli on beef carcasses in Arusha, Tanzania. Afr J Microbiol Res. 2016;10:1148–1155.
   Google Scholar
• Tadesse DA, Zhao S, Tong E, et al. Antimicrobial drug resistance in Escherichia coli from humans and food animals, United States, 1950–2002. Emerg Infect Dis. 2012;18:741–749. doi:10.3201/eid1805.111153
   PubMed Web of Science ®Google Scholar
• Alonso CA, Zarazaga M, Sallem RB, Jouini A, Slama BK, Torres C. Antibiotic resistance in Escherichia coli in husbandry animals: the African perspective. Lett Appl Microbiol. 2017;64(5):318–334. doi:10.1111/lam.12724
   PubMed Web of Science ®Google Scholar
• Ben Sallem R, Ben Slama K, Saenz Y, et al. Prevalence and characterization of extended spectrum beta-lactamase (ESBL)- and CMY-2-producing Escherichia coli isolates from healthy food-producing animals in Tunisia. Foodborne Pathog Dis. 2012;9:1137–1142. doi:10.1089/fpd.2012.1267
   Web of Science ®Google Scholar
• Adelowo OO, Fagade OE, Agersø Y. Antibiotic resistance and resistance genes in Escherichia coli from poultry farms, southwest Nigeria. J Infect Dev Ctries. 2014;8:1103–1112
   Web of Science ®Google Scholar
• Grami R, Dahmen S, Mansour W, et al. blaCTX-M-15-carrying F2: a-: b- plasmid in Escherichia coli from cattle milk in Tunisia. Microb Drug Resist. 2014;20:344–349. doi:10.1089/mdr.2013.0160
   Web of Science ®Google Scholar
• Lebov J, Grieger K, Womack D, et al. A framework for One Health research. One Health. 2017;3:44–50. doi:10.1016/j.onehlt.2017.03.004
   PubMed Web of Science ®Google Scholar
• Wyrsch ER, Chowdhury PR, Jarocki VM, Brandis KJ, Djordjevic SP. Duplication and diversification of a unique chromosomal virulence island hosting the subtilase cytotoxin in Escherichia coli ST58. Microb Genom. 2020;6(6):e000387. doi:10.1099/mgen.0.000387
   Web of Science ®Google Scholar
• Al-Mustapha AI, Adetunji VO, Heikinheimo A. Risk perceptions of antibiotic usage and resistance: a cross-sectional survey of poultry farmers in Kwara State, Nigeria. Antibiotics. 2020;9(7):378. doi:10.3390/antibiotics9070378
   Web of Science ®Google Scholar
• Kumar S, Tripathi VR, Vikram S, Kumar B, Garg SK. Characterization of MAR and heavy metal-tolerant E. coli O157:H7 in water sources: a suggestion for behavioral intervention. Environ Dev Sustain. 2018;20(6):2447–2461. doi:10.1007/s10668-017-9998-5
   Web of Science ®Google Scholar