1887

Access Microbiology open research platform logo

Volume 5, Issue 7

Genetic characterization of and spp. from humans and poultry in Nigeria Open Access

Abstract

The emergence of antibiotic resistance in livestock, especially food-producing animals, is of major public health importance as a result of the possibility of these bacteria entering the food chain. In this study, the genetic characteristics of antibiotic-resistant and spp. isolates from humans and poultry in Edo state, Nigeria, were investigated. In April 2017, 45 spp. and 46 isolates were obtained from urine, clinical wounds, nasal and chicken faecal samples. Isolates were recovered and identified as previously described. Species identification was achieved by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing. Antimicrobial susceptibility testing was carried out using the Kirby–Bauer method for 12 antibiotics. A double disc synergy test was used to screen for extended-spectrum beta-lactamse (ESBL) production. Whole genome sequencing was performed for strain characterization of the isolates. Thirteen spp. isolates yielded positive results by the ESBL phenotypic test and harboured ESBL genes. Of the 46 isolates, 21 human and 13 poultry isolates were resistant to at least one of the tested antibiotics. Four human isolates harboured ESBL genes and revealed positive results when applying ESBL double disc synergy tests. ESBL genes in the spp. and isolates include and . Whole genome-based core gene multilocus sequence typing of the spp. and isolates revealed a close relatedness among the isolates. An integrated ‘One Health’ surveillance system is required to monitor transmission of antimicrobial resistance in Nigeria.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antibiotic resistance , Escherichia coli , human , Klebsiella spp. , poultry and whole genome sequencing
Funding
This study was supported by the:
  • Austrian Agency for Health and Food Safety
    • Principle Award Recipient: NotApplicable
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/acmi/10.1099/acmi.0.000509.v4
2023-07-12
2024-05-15
Loading full text...

Full text loading...

/deliver/fulltext/acmi/5/7/acmi000509.v4.html?itemId=/content/journal/acmi/10.1099/acmi.0.000509.v4&mimeType=html&fmt=ahah

References

  1. Jesumirhewe C, Springer B, Allerberger F, Ruppitsch W. Genetic characterization of antibiotic resistant Enterobacteriaceae isolates from bovine animals and the environment in Nigeria. Front Microbiol 2022; 13:793541 [View Article] [PubMed]
     [Google Scholar]
  2. Reygaert WC. An overview of the antimicrobial resistance mechanisms of bacteria. AIMS Microbiol 2018; 4:482–501 [View Article] [PubMed]
     [Google Scholar]
  3. Alekshun MN, Levy SB. Molecular mechanisms of antibacterial multidrug resistance. Cell 2007; 128:1037–1050 [View Article] [PubMed]
     [Google Scholar]
  4. Ayandiran TO, Falgenhauer L, Schmiedel J, Chakraborty T, Ayeni FA. High resistance to tetracycline and ciprofloxacin in bacteria isolated from poultry farms in Ibadan, Nigeria. J Infect Dev Ctries 2018; 12:462–470 [View Article] [PubMed]
     [Google Scholar]
  5. Boamah VE, Agyare C, Odoi H, Dalsgaard A. Antibiotic practices and factors influencing the use of antibiotics in selected poultry farms in Ghana. J Antimicrob Agents 2016; 2:120 [View Article]
     [Google Scholar]
  6. Fatokun EN, Fakorede CN, Atobatele KZ. Antibiotic susceptibility profile of bacterial isolates from commercial poultry farms in Ile-Ife, Nigeria. Chem Biomol Eng 2021; 6:59–67 [View Article]
     [Google Scholar]
  7. Mensah GI, Adjei VY, Vicar EK, Atsu PS, Blavo DL et al. Safety of retailed poultry: analysis of antibiotic resistance in Escherichia coli from raw chicken and poultry fecal matter from selected farms and retail outlets in Accra, Ghana. Microbiol Insights 2022; 15:11786361221093278 [View Article] [PubMed]
     [Google Scholar]
  8. Jibril AH, Okeke IN, Dalsgaard A, Olsen JE. Association between antimicrobial usage and resistance in Salmonella from poultry farms in Nigeria. BMC Vet Res 2021; 17:234 [View Article] [PubMed]
     [Google Scholar]
  9. Jesumirhewe C, Springer B, Allerberger F, Ruppitsch W. Whole genome sequencing of extended-spectrum β-lactamase genes in Enterobacteriaceae isolates from Nigeria. PLoS One 2020; 15:e0231146 [View Article] [PubMed]
     [Google Scholar]
  10. Kimera ZI, Mgaya FX, Misinzo G, Mshana SE, Moremi N et al. Multidrug-resistant, including extended-spectrum beta lactamase-producing and quinolone-resistant, Escherichia coli isolated from poultry and domestic pigs in Dar es Salaam, Tanzania. Antibiotics 2021; 10:406 [View Article] [PubMed]
     [Google Scholar]
  11. Adebowale O, Makanjuola M, Bankole N, Olasoju M, Alamu A et al. Multi-drug resistant Escherichia coli, biosecurity and anti-microbial use in live bird markets, Abeokuta, Nigeria. Antibiotics 2022; 11:253 [View Article] [PubMed]
     [Google Scholar]
  12. Sharma P, Gupta SK, Adenipekun EO, Barrett JB, Hiott LM et al. Draft genome sequence analysis of multidrug-resistant Escherichia coli strains isolated in 2013 from humans and chickens in Nigeria. Genome Announc 2017; 5:e01073-17 [View Article] [PubMed]
     [Google Scholar]
  13. Grundmann H, Gelband H. Antimicrobial resistance surveillance with whole genome sequencing in Africa: It’s (about) time. Afr J Lab Med 2018; 7:761 [View Article] [PubMed]
     [Google Scholar]
  14. Cheesbrough M. District Laboratory Practice in Tropical Countries. 2nd edn Cambridge: Cambridge University Press; 2006 pp 178–187 [View Article]
     [Google Scholar]
  15. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [View Article] [PubMed]
     [Google Scholar]
  16. European Committee On Antimicrobial Susceptibility Testing Breakpoint tables for interpretation of MICs and zone diameters. Version 8.0.växjö: European committee on antimicrobial susceptibility testing; 2018
  17. Bradford PA. Extended-spectrum beta-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat. Clin Microbiol Rev 2001; 14:933–951 [View Article] [PubMed]
     [Google Scholar]
  18. CLSI Performance Standards for Antimicrobial Susceptibility Testing. 28th edition Wayne, USA: Clinical and Laboratory Standards Institute; 2018
     [Google Scholar]
  19. Zerbino DR. Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics 2010; Chapter 11:Unit [View Article] [PubMed]
     [Google Scholar]
  20. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [View Article] [PubMed]
     [Google Scholar]
  21. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 2017; 45:D566–D573 [View Article] [PubMed]
     [Google Scholar]
  22. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol 2014; 52:1501–1510 [View Article] [PubMed]
     [Google Scholar]
  23. Chen L, Yang J, Yu J, Yao Z, Sun L et al. VFDB: A reference database for bacterial virulence factors. Nucleic Acids Res 2005; 33:D325–D328 [View Article] [PubMed]
     [Google Scholar]
  24. Joensen KG, Tetzschner AMM, Iguchi A, Aarestrup FM, Scheutz F. Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data. J Clin Microbiol 2015; 53:2410–2426 [View Article] [PubMed]
     [Google Scholar]
  25. Johansson MHK, Bortolaia V, Tansirichaiya S, Aarestrup FM, Roberts AP et al. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother 2021; 76:101–109 [View Article] [PubMed]
     [Google Scholar]
  26. Diancourt L, Passet V, Verhoef J, Grimont PAD, Brisse S. Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol 2005; 43:4178–4182 [View Article] [PubMed]
     [Google Scholar]
  27. Ruppitsch W, Pietzka A, Prior K, Bletz S, Fernandez HL et al. Defining and evaluating a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of Listeria monocytogenes. J Clin Microbiol 2015; 53:2869–2876 [View Article] [PubMed]
     [Google Scholar]
  28. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using plasmid finder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article] [PubMed]
     [Google Scholar]
  29. Ngbede EO, Adekanmbi F, Poudel A, Kalalah A, Kelly P et al. Concurrent resistance to carbapenem and colistin among Enterobacteriaceae recovered from human and animal sources in Nigeria is associated with multiple genetic mechanisms. Front Microbiol 2021; 12:740348 [View Article] [PubMed]
     [Google Scholar]
  30. Falgenhauer L, Imirzalioglu C, Oppong K, Akenten CW, Hogan B et al. Detection and characterization of ESBL-producing Escherichia coli from humans and poultry in Ghana. Front Microbiol 2019; 9:3358 [View Article] [PubMed]
     [Google Scholar]
  31. García-Vello P, González-Zorn B, Setsoafia Saba CK. Antibiotic resistance patterns in human, animal, food and environmental isolates in Ghana: a review. Pan Afr Med J 2020; 35:37 [View Article] [PubMed]
     [Google Scholar]
  32. Shawa M, Furuta Y, Paudel A, Kabunda O, Mulenga E et al. Clonal relationship between multidrug-resistant Escherichia coli ST69 from poultry and humans in Lusaka, Zambia. FEMS Microbiol Lett 2022; 368:1–11 [View Article] [PubMed]
     [Google Scholar]
  33. Musawa AI, Bashiru G, Al-Rasheed A, Yakubu Y, Jibril AH et al. Prevalence and Antimicrobial Susceptibility Profiling of Salmonella Isolated from Poultry Products Sold in Sokoto Metropolis, Nigeria. J Anim Health Prod 2021; 9: [View Article]
     [Google Scholar]
  34. García-Béjar B, García de Blas Martín I, Arévalo-Villena M, Briones Pérez A. High prevalence of antibiotic-resistant Escherichia coli isolates from retail poultry products in Spain. Animals 2021; 11:3197 [View Article] [PubMed]
     [Google Scholar]
  35. Badr H, Reda RM, Hagag NM, Kamel E, Elnomrosy SM et al. Multidrug-resistant and genetic characterization of extended-spectrum beta-lactamase-producing E. coli recovered from chickens and humans in Egypt. Animals 2022; 12:346 [View Article] [PubMed]
     [Google Scholar]
  36. Ilyas S, Rasool MH, Arshed MJ, Qamar MU, Aslam B et al. The Escherichia coli sequence type 131 harboring extended-spectrum beta-lactamases and carbapenemases genes from poultry birds. Infect Drug Resist 2021; 14:805–813 [View Article] [PubMed]
     [Google Scholar]
  37. Castellanos LR, Donado-Godoy P, León M, Clavijo V, Arevalo A et al. High heterogeneity of Escherichia coli sequence types harbouring ESBL/AmpC genes on IncI1 plasmids in the Colombian poultry chain. PLoS One 2017; 12:e0170777 [View Article] [PubMed]
     [Google Scholar]
  38. Skurnik D, Clermont O, Guillard T, Launay A, Danilchanka O et al. Emergence of antimicrobial-resistant Escherichia coli of animal origin spreading in humans. Mol Biol Evol 2016; 33:898–914 [View Article] [PubMed]
     [Google Scholar]
  39. Baquero F, Tedim AP, Coque TM. Antibiotic resistance shaping multi-level population biology of bacteria. Front Microbiol 2013; 4:15 [View Article] [PubMed]
     [Google Scholar]
  40. Mathers AJ, Peirano G, Pitout JDD. The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin Microbiol Rev 2015; 28:565–591 [View Article] [PubMed]
     [Google Scholar]
  41. Aworh MK, Kwaga J, Okolocha E, Harden L, Hull D et al. Extended-spectrum ß-lactamase-producing Escherichia coli among humans, chickens and poultry environments in Abuja, Nigeria. One Health Outlook 2020; 2:8 [View Article] [PubMed]
     [Google Scholar]
  42. Lowe M, Kock MM, Coetzee J, Hoosien E, Peirano G et al. Klebsiella pneumoniae ST307 with blaOXA-181, South Africa, 2014-2016. Emerg Infect Dis 2019; 25:739–747 [View Article] [PubMed]
     [Google Scholar]
  43. Peirano G, Chen L, Kreiswirth BN, Pitout JDD. Emerging antimicrobial-resistant high-risk Klebsiella pneumoniae Clones ST307 and ST147. Antimicrob Agents Chemother 2020; 64:e01148-20 [View Article] [PubMed]
     [Google Scholar]
  44. Wyres KL, Hawkey J, Hetland MAK, Fostervold A, Wick RR et al. Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307. J Antimicrob Chemother 2019; 74:577–581 [View Article] [PubMed]
     [Google Scholar]
  45. Afolayan AO, Oaikhena AO, Aboderin AO, Olabisi OF, Amupitan AA et al. Clones and clusters of antimicrobial-resistant Klebsiella from southwestern Nigeria. Clin Infect Dis 2021; 73:S308–S315 [View Article] [PubMed]
     [Google Scholar]
  46. Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA et al. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci 2015; 112:E3574–E3581 [View Article] [PubMed]
     [Google Scholar]
  47. Liu Z, Gu Y, Li X, Liu Y, Ye Y et al. Identification and Characterization of NDM-1-producing hypervirulent (Hypermucoviscous) Klebsiella pneumoniae in China. Ann Lab Med 2019; 39:167–175 [View Article] [PubMed]
     [Google Scholar]
  48. Yang F, Deng B, Liao W, Wang P, Chen P et al. High rate of multiresistant Klebsiella pneumoniae from human and animal origin. Infect Drug Resist 2019; 12:2729–2737 [View Article] [PubMed]
     [Google Scholar]
  49. Zhan L, Wang S, Guo Y, Jin Y, Duan J et al. Outbreak by hypermucoviscous Klebsiella pneumoniae ST11 isolates with carbapenem resistance in a tertiary Hospital in China. Front Cell Infect Microbiol 2017; 7:182 [View Article] [PubMed]
     [Google Scholar]
  50. Spurbeck RR, Dinh PC, Walk ST, Stapleton AE, Hooton TM et al. Escherichia coli isolates that carry vat, fyuA, chuA, and yfcV efficiently colonize the urinary tract. Infect Immun 2012; 80:4115–4122 [View Article] [PubMed]
     [Google Scholar]
  51. Johnson JR, Murray AC, Gajewski A, Sullivan M, Snippes P et al. Isolation and molecular characterization of nalidixic acid-resistant extraintestinal pathogenic Escherichia coli from retail chicken products. Antimicrob Agents Chemother 2003; 47:2161–2168 [View Article] [PubMed]
     [Google Scholar]
  52. Galarce N, Sánchez F, Escobar B, Lapierre L, Cornejo J et al. Genomic epidemiology of Shiga toxin-producing Escherichia coli isolated from the livestock-food-human interface in South America. Animals 2021; 11:1845 [View Article] [PubMed]
     [Google Scholar]
  53. Malik A, Nagy B, Kugler R, Szmolka A. Pathogenic potential and virulence genotypes of intestinal and faecal isolates of porcine post-weaning enteropathogenic Escherichia coli. Res Vet Sci 2017; 115:102–108 [View Article] [PubMed]
     [Google Scholar]
  54. Varga C, Brash ML, Slavic D, Boerlin P, Ouckama R et al. Evaluating virulence-associated genes and antimicrobial resistance of avian pathogenic Escherichia coli isolates from broiler and broiler breeder chickens in Ontario, Canada. Avian Dis 2018; 62:291–299 [View Article] [PubMed]
     [Google Scholar]
  55. Hassan M, Moursi M, Abd El-Fattah R, Enany M. Molecular detection of some virulence genes of E. Coli isolated from broiler chickens and ducks at Ismailia governorate. SCVMJ 2020; 25:1–19 [View Article]
     [Google Scholar]
  56. Al-Mustapha AI, Raufu IA, Ogundijo OA, Odetokun IA, Tiwari A et al. Antibiotic resistance genes, mobile elements, virulence genes, and phages in cultivated ESBL-producing Escherichia coli of poultry origin in Kwara state, North Central Nigeria. Int J Food Microbiol 2023; 389:110086 [View Article] [PubMed]
     [Google Scholar]
  57. Udaondo Z, Abram KZ, Kothari A, Jun S-R. Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia. Microb Genom 2022; 8:mgen000855 [View Article] [PubMed]
     [Google Scholar]
  58. Ikhimiukor OO, Odih EE, Donado-Godoy P, Okeke IN. A bottom-up view of antimicrobial resistance transmission in developing countries. Nat Microbiol 2022; 7:757–765 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/acmi/10.1099/acmi.0.000509.v4
Loading
Genetic characterization of Escherichia coli and Klebsiella spp. from humans and poultry in Nigeria
Access Microbiology 5, 000509.v4 (2023); https://doi.org/10.1099/acmi.0.000509.v4
/content/journal/acmi/10.1099/acmi.0.000509.v4
/content/journal/acmi/10.1099/acmi.0.000509.v4
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error