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Microbial Genomics logo Microbial Genomics

Volume 11, Issue 1

recovered from hospital patients, livestock and dogs in Nigeria share near-identical genome sequences Open Access

Abstract

Genomic data on from the African continent are currently lacking, resulting in the region being under-represented in global analyses of infection (CDI) epidemiology. For the first time in Nigeria, we utilized whole-genome sequencing and phylogenetic tools to compare isolates from diarrhoeic human patients (=142), livestock (=38), poultry manure (=5) and dogs (=9) in the same geographic area (Makurdi, north-central Nigeria) and relate them to the global population. In addition, selected isolates were tested for antimicrobial susceptibility (=33) and characterized by PCR ribotyping (=53). Hierarchical clustering of core-genome multilocus sequence typing (cgMLST) allelic profiles revealed large diversity at the level HC150 (i.e. clusters of related genomes with maximally 150 pairwise allelic differences), which was previously shown to correlate with PCR ribotypes (RT). While several globally disseminated strains were detected, including HC150_1 (associated with RT078), HC150_3 (RT001) and HC150_3622 (RT014), 42 HC150 clusters (79%) represented unique genotypes that were new to the public genomic record, and 16 (30%) of these were novel PCR ribotypes. Considerable proportions of the isolates displayed resistance to fluoroquinolones, macrolides and linezolid, potentially reflecting human and animal antibiotic consumption patterns in the region. Notably, our comparative phylogenomic analyses revealed human–human, human–livestock and farm–farm sharing of near-identical genomes (≤2 core-genome allelic differences), suggesting the continued spread of multiple strains across human and animal (pig, poultry, cattle and dog) host populations. Our findings highlight the interconnectivity between livestock production and the epidemiology of human CDI and inform the need for increased CDI awareness among clinicians in this region. A large proportion of strains appeared to be unique to the region, reflecting both the significant geographic patterning present in the population and a general need for additional pathogen sequencing data from Africa.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Africa , Clostridioides difficile , epidemiology , One Health , phylogenomics and zoonosis
Funding
This study was supported by the:
  • Bundesministerium für Bildung und Forschung (Award DZIF - German Center for Infection Research)
    • Principal Award Recipient: UlrichNübel
  • Leibniz-Gemeinschaft (Award Leibniz Research Alliance INFECTIONS)
    • Principal Award Recipient: UlrichNübel
  • Alexander von Humboldt-Stiftung
    • Principal Award Recipient: EmmanuelO. Ngbede
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2026-03-16

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References

  1. Bouza E. Consequences of Clostridium difficile infection: understanding the healthcare burden. Clin Microbiol Infect 2012; 18:5–12 [View Article]
     [Google Scholar]
  2. Bouza E, Muñoz P, Alonso R. Clinical manifestations, treatment and control of infections caused by Clostridium difficile. Clin Microbiol Infect 2005; 11:57–64 [View Article]
     [Google Scholar]
  3. Kullin B, Abratt VR, Reid SJ, Riley TV. Clostridioides difficile infection in Africa: a narrative review. Anaerobe 2022; 74:102549 [View Article]
     [Google Scholar]
  4. Troeger C, Blacker BF, Khalil IA, Rao PC, Cao S. Estimates of the global, regional, and national morbidity, mortality, and aetiologies of diarrhoea in 195 countries: a systematic analysis for the Global Burden of disease Study 2016. Lancet Infect Dis 2018; 18:1211–1228 [View Article] [PubMed]
     [Google Scholar]
  5. Forrester JD, Cai LZ, Mbanje C, Rinderknecht TN, Wren SM. Clostridium difficile infection in low‐ and middle‐human development index countries: a systematic review. Tropical Med Int Health 2017; 22:1223–1232 [View Article]
     [Google Scholar]
  6. Roldan GA, Cui AX, Pollock NR. Assessing the burden of Clostridium difficile infection in low- and middle-income countries. J Clin Microbiol 2018; 56:e01747-17 [View Article] [PubMed]
     [Google Scholar]
  7. Abdel-Glil MY, Thomas P, Schmoock G, Abou-El-Azm K, Wieler LH et al. Presence of Clostridium difficile in poultry and poultry meat in Egypt. Anaerobe 2018; 51:21–25 [View Article] [PubMed]
     [Google Scholar]
  8. Berger FK, Mellmann A, Bischoff M, von Müller L, Becker SL et al. Molecular epidemiology and antimicrobial resistance of Clostridioides difficile detected in chicken, soil and human samples from Zimbabwe. Int J Infect Dis 2020; 96:82–87 [View Article] [PubMed]
     [Google Scholar]
  9. de Jager P, Smith O, Bolon S, Thomas J, Richards GA. Epidemiology of Clostridioides difficile in South Africa. PLoS One 2021; 16:e0259771 [View Article] [PubMed]
     [Google Scholar]
  10. Janssen I, Cooper P, Gunka K, Rupnik M, Wetzel D et al. High prevalence of nontoxigenic Clostridium difficile isolated from hospitalized and non-hospitalized individuals in rural Ghana. Int J Med Microbiol 2016; 306:652–656 [View Article] [PubMed]
     [Google Scholar]
  11. Kullin B, Wojno J, Abratt V, Reid SJ. Toxin A-negative toxin B-positive ribotype 017 Clostridium difficile is the dominant strain type in patients with diarrhoea attending tuberculosis hospitals in Cape Town, South Africa. Eur J Clin Microbiol Infect Dis 2017; 36:163–175 [View Article] [PubMed]
     [Google Scholar]
  12. Kullin BR, Reid S, Abratt V. Clostridium difficile in patients attending tuberculosis hospitals in Cape Town, South Africa, 2014-2015. Afr J Lab Med 2018; 7:846 [View Article] [PubMed]
     [Google Scholar]
  13. Mutai WC, Mureithi MW, Anzala O, Revathi G, Kullin B et al. High prevalence of multidrug-resistant Clostridioides difficile following extensive use of antimicrobials in hospitalized patients in Kenya. Front Cell Infect Microbiol 2020; 10:604986 [View Article] [PubMed]
     [Google Scholar]
  14. Seugendo M, Janssen I, Lang V, Hasibuan I, Bohne W et al. Prevalence and strain characterization of Clostridioides (Clostridium) difficile in representative regions of Germany, Ghana, Tanzania, and Indonesia – a comparative multi-center cross-sectional study. Front Microbiol 2018; 9:1843 [View Article] [PubMed]
     [Google Scholar]
  15. Becker SL, Chatigre JK, Coulibaly JT, Mertens P, Bonfoh B et al. Molecular and culture-based diagnosis of Clostridium difficile isolates from Côte d’Ivoire after prolonged storage at disrupted cold chain conditions. Trans R Soc Trop Med Hyg 2015; 109:660–668 [View Article] [PubMed]
     [Google Scholar]
  16. Adesoji AT, Mgbere O, Darkoh C. Pediatric diarrhea patients living in urban areas have a higher incidence of Clostridioides difficile infection. PLoS Glob Public Health 2023; 3:e0000477 [View Article] [PubMed]
     [Google Scholar]
  17. Onwueme K, Fadairo Y, Idoko L, Onuh J, Alao O et al. High prevalence of toxinogenic Clostridium difficile in Nigerian adult HIV patients. Trans R Soc Trop Med Hyg 2011; 105:667–669 [View Article]
     [Google Scholar]
  18. Weese JS, Mshelbwala PP, Lohr F. Clostridium difficile shedding by healthy dogs in Nigeria and Malawi. Zoonoses Public Health 2019; 66:618–621 [View Article] [PubMed]
     [Google Scholar]
  19. Eyre DW, Fawley WN, Rajgopal A, Settle C, Mortimer K et al. Comparison of control of Clostridium difficile infection in six English hospitals using whole-genome sequencing. Clin Infect Dis 2017; 65:433–441 [View Article] [PubMed]
     [Google Scholar]
  20. Eyre DW, Davies KA, Davis G, Fawley WN, Dingle KE et al. Two distinct patterns of Clostridium difficile diversity across Europe indicating contrasting routes of spread. Clin Infect Dis 2018; 67:1035–1044 [View Article] [PubMed]
     [Google Scholar]
  21. Frentrup M, Zhou Z, Steglich M, Meier-Kolthoff JP, Göker M et al. A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics. Microb Genom 2020; 6:mgen000410 [View Article] [PubMed]
     [Google Scholar]
  22. Frentrup M, Thiel N, Junker V, Behrens W, Münch S et al. Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile. Environ Microbiol 2021; 23:7591–7602 [View Article] [PubMed]
     [Google Scholar]
  23. Wen X, Shen C, Xia J, Zhong L-L, Wu Z et al. Whole-genome sequencing reveals the high nosocomial transmission and antimicrobial resistance of Clostridioides difficile in a single center in China: a four-year retrospective study. Microbiol Spectr 2022; 10:e0132221 [View Article] [PubMed]
     [Google Scholar]
  24. Miles-Jay A, Snitkin ES, Lin MY, Shimasaki T, Schoeny M et al. Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit. Nat Med 2023; 29:2526–2534 [View Article] [PubMed]
     [Google Scholar]
  25. Knetsch CW, Kumar N, Forster SC, Connor TR, Browne HP et al. Zoonotic transfer of Clostridium difficile harboring antimicrobial resistance between farm animals and humans. J Clin Microbiol 2018; 56:e01384-17 [View Article] [PubMed]
     [Google Scholar]
  26. Knetsch CW, Connor TR, Mutreja A, van Dorp SM, Sanders IM et al. Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011. Euro Surveill 2014; 19:20954 [View Article] [PubMed]
     [Google Scholar]
  27. Knight DR, Squire MM, Collins DA, Riley TV. Genome analysis of Clostridium difficile PCR ribotype 014 lineage in Australian pigs and humans reveals a diverse genetic repertoire and signatures of long-range interspecies transmission. Front Microbiol 2016; 7:2138 [View Article] [PubMed]
     [Google Scholar]
  28. Cairns MD, Preston MD, Hall CL, Gerding DN, Hawkey PM et al. Comparative genome analysis and global phylogeny of the toxin variant Clostridium difficile PCR ribotype 017 reveals the evolution of two independent sublineages. J Clin Microbiol 2017; 55:865–876 [View Article]
     [Google Scholar]
  29. Williamson CHD, Stone NE, Nunnally AE, Roe CC, Vazquez AJ et al. Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations. Microb Genom 2022; 8:000742 [View Article] [PubMed]
     [Google Scholar]
  30. Akinyemi KO, Fakorede CO, Linde J, Methner U, Wareth G et al. Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria. BMC Microbiol 2023; 23:164 [View Article] [PubMed]
     [Google Scholar]
  31. Happi AN, Ayinla AO, Ogunsanya OA, Sijuwola AE, Saibu FM et al. Detection of SARS-CoV-2 in terrestrial animals in Southern Nigeria: potential cases of reverse zoonosis. Viruses 2023; 15:1187 [View Article] [PubMed]
     [Google Scholar]
  32. Adeyemo AdebayoJ, Akingbola OO, Ojeniyi SO. Effects of poultry manure on soil infiltration, organic matter contents and maize performance on two contrasting degraded alfisols in southwestern Nigeria. Int J Recycl Org Waste Agricult 2019; 8:73–80 [View Article]
     [Google Scholar]
  33. Alhaji NB, Haruna AE, Muhammad B, Lawan MK, Isola TO. Antimicrobials usage assessments in commercial poultry and local birds in North-central Nigeria: associated pathways and factors for resistance emergence and spread. Prev Vet Med 2018; 154:139–147 [View Article] [PubMed]
     [Google Scholar]
  34. Chukwu VA, Smith JU, Strachan NJC, Avery LM, Obiekezie SO. Impacts of different treatment methods for cattle manure on the spread of faecal indicator organisms from soil to lettuce in Nigeria. J Appl Microbiol 2022; 132:618–632 [View Article] [PubMed]
     [Google Scholar]
  35. Masembe C, Adedeji AJ, Jambol AR, Weka R, Muwanika V et al. Diversity and emergence of new variants of African swine fever virus Genotype I circulating in domestic pigs in Nigeria (2016–2018). Vet Med Sci 2023; 9:819–828 [View Article]
     [Google Scholar]
  36. Kelly CR, Fischer M, Allegretti JR, LaPlante K, Stewart DB et al. ACG clinical guidelines: prevention, diagnosis, and treatment of Clostridioides difficile Infections. Am J Gastroenterol 2021; 116:1124–1147 [View Article]
     [Google Scholar]
  37. Zaiss NH, Rupnik M, Kuijper EJ, Harmanus C, Michielsen D et al. Typing Clostridium difficile strains based on tandem repeat sequences. BMC Microbiol 2009; 9:6 [View Article] [PubMed]
     [Google Scholar]
  38. Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM et al. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS One 2015; 10:e0128036 [View Article] [PubMed]
     [Google Scholar]
  39. Zhou Z, Charlesworth J, Achtman M. HierCC: a multi-level clustering scheme for population assignments based on core genome MLST. Bioinformatics 2021; 37:3645–3646 [View Article] [PubMed]
     [Google Scholar]
  40. Zhou Z, Alikhan N-F, Sergeant MJ, Luhmann N, Vaz C et al. GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res 2018; 28:1395–1404 [View Article] [PubMed]
     [Google Scholar]
  41. Zhou Z, Alikhan N-F, Mohamed K, Fan Y et al.Agama Study Group The enterobase user’s guide, with case studies on salmonella transmissions, yersinia pestis phylogeny, and escherichia core genomic diversity. Genome Res 2020; 30:138–152 [View Article]
     [Google Scholar]
  42. Letunic I, Bork P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res 2024; 52:W78–W82 [View Article] [PubMed]
     [Google Scholar]
  43. Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol 2020; 38:276–278 [View Article] [PubMed]
     [Google Scholar]
  44. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  45. Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J et al. AMRFinderPlus and the reference Gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 2021; 11:12728 [View Article] [PubMed]
     [Google Scholar]
  46. Kolte B, Nübel U. Genetic determinants of resistance to antimicrobial therapeutics are rare in publicly available Clostridioides difficile genome sequences. J Antimicrob Chemother 2024; 79:1320–1328 [View Article] [PubMed]
     [Google Scholar]
  47. Gonzales-Luna AJ, Dureja C, Eubank TA, Garey KW, Hurdle JG. Surveillance of Clostridioides difficile antimicrobial resistance in the United States. Clin Infect Dis 2023; 76:2038–2039 [View Article] [PubMed]
     [Google Scholar]
  48. CLSI Clinical and Laboratory Standards Institute Performance Standards for Antimicrobial Susceptibility Testing, 33rd Edn CLSI;
     [Google Scholar]
  49. Fawley WN, Knetsch CW, MacCannell DR, Harmanus C, Du T et al. Development and validation of an internationally-standardized, high-resolution capillary gel-based electrophoresis PCR-ribotyping protocol for Clostridium difficile. PLoS One 2015; 10:e0118150 [View Article] [PubMed]
     [Google Scholar]
  50. Oyaro MO, Plants-Paris K, Bishoff D, Malonza P, Gontier CS et al. High rate of Clostridium difficile among young adults presenting with diarrhea at two hospitals in Kenya. Int J Infect Dis 2018; 74:24–28 [View Article] [PubMed]
     [Google Scholar]
  51. Legenza L, Barnett S, Rose W, Bianchini M, Safdar N et al. Epidemiology and outcomes of Clostridium difficile infection among hospitalised patients: results of a multicentre retrospective study in South Africa. BMJ Glob Health 2018; 3:e000889 [View Article] [PubMed]
     [Google Scholar]
  52. Djebbar A, Sebaihia M, Kuijper E, Harmanus C, Sanders I et al. First molecular characterisation and PCR ribotyping of Clostridium difficile strains isolated in two Algerian Hospitals. J Infect Dev Ctries 2018; 12:15–21 [View Article] [PubMed]
     [Google Scholar]
  53. Knight DR, Imwattana K, Kullin B, Guerrero-Araya E, Paredes-Sabja D et al. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. Elife 2021; 10:e64325 [View Article]
     [Google Scholar]
  54. Knight DR, Imwattana K, Collins DA, Lim S-C, Hong S et al. Genomic epidemiology and transmission dynamics of recurrent Clostridioides difficile infection in Western Australia. Eur J Clin Microbiol Infect Dis 2023; 42:607–619 [View Article]
     [Google Scholar]
  55. Spigaglia P, Barbanti F, Faccini S, Vescovi M, Criscuolo EM et al. Clostridioides difficile in pigs and dairy cattle in Northern Italy: prevalence, characterization, and comparison between animal and human strains. Microorganisms 2023; 11:1738 [View Article]
     [Google Scholar]
  56. Lv T, Zheng L, Wu T, Shen P, Chen Y. Molecular characterization and antibiotic resistance of Clostridioides difficile in patients with inflammatory bowel disease from two hospitals in China. J Glob Antimicrob Resist 2022; 30:252–258 [View Article] [PubMed]
     [Google Scholar]
  57. Behra-Miellet J, Calvet L, Dubreuil L. Activity of linezolid against anaerobic bacteria. Int J Antimicrob Agents 2003; 22:28–34 [View Article] [PubMed]
     [Google Scholar]
  58. He M, Miyajima F, Roberts P, Ellison L, Pickard DJ et al. Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet 2013; 45:109–113 [View Article] [PubMed]
     [Google Scholar]
  59. McDonald LC, Gerding DN, Johnson S, Bakken JS, Carroll KC et al. Clinical practice guidelines for Clostridium difficile infection in adults and children: 2017 update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin Infect Dis 2018; 66:e1–e48 [View Article] [PubMed]
     [Google Scholar]
  60. Turner NA, Grambow SC, Woods CW, Fowler VG Jr, Moehring RW et al. Epidemiologic trends in Clostridioides difficile infections in a regional community hospital network. JAMA Netw Open 2019; 2:e1914149 [View Article] [PubMed]
     [Google Scholar]
  61. Vintila BI, Arseniu AM, Morgovan C, Butuca A, Bîrluțiu V et al. A real-world study on the clinical characteristics, outcomes, and relationship between antibiotic exposure and Clostridioides difficile infection. Antibiotics 2024; 13:144 [View Article] [PubMed]
     [Google Scholar]
  62. Pechal A, Lin K, Allen S, Reveles K. National age group trends in Clostridium difficile infection incidence and health outcomes in United States Community Hospitals. BMC Infect Dis 2016; 16:682 [View Article] [PubMed]
     [Google Scholar]
  63. Boven A, Vlieghe E, Engstrand L, Andersson FL, Callens S et al. Clostridioides difficile infection-associated cause-specific and all-cause mortality: a population-based cohort study. Clin Microbiol Infect 2023; 29:1424–1430 [View Article] [PubMed]
     [Google Scholar]
  64. Lessa FC, Mu Y, Bamberg WM, Beldavs ZG, Dumyati GK et al. Burden of Clostridium difficile infection in the United States. N Engl J Med 2015; 372:825–834 [View Article] [PubMed]
     [Google Scholar]
  65. Mizusawa M, Doron S, Gorbach S. Clostridium difficile diarrhea in the elderly: current issues and management options. Drugs Aging 2015; 32:639–647 [View Article] [PubMed]
     [Google Scholar]
  66. Tijerina-Rodríguez L, Garza-González E, Martínez-Meléndez A, Morfín-Otero R, Camacho-Ortiz A et al. Clinical characteristics associated with the severity of Clostridium [Clostridioides] difficile infection in a tertiary teaching hospital from Mexico. Biomed J 2022; 45:200–205 [View Article] [PubMed]
     [Google Scholar]
  67. Birczyńska M, Czepiel J, Pejka K, Biesiada G, Jędrychowski M et al. Clostridium difficile infection in young people - 2 case reports. Pol Merkur Lekarski 2018; 44:284–286 [PubMed]
     [Google Scholar]
  68. Yang TJ, Patel AA, Singh J, Jahagirdar V, Solanki D et al. Increasing trends of Clostridium difficile infection in hospitalized young patients: a study of the National Inpatient Sample from 2007 to 2017. Cureus 2022; 14:e29497 [View Article] [PubMed]
     [Google Scholar]
  69. Gupta A, Pardi DS, Baddour LM, Khanna S. Outcomes in children with Clostridium difficile infection: results from a nationwide survey. Gastroenterol Rep 2016; 4:293–298 [View Article] [PubMed]
     [Google Scholar]
  70. Olsen MA, Stwalley D, Demont C, Dubberke ER. Increasing age has limited impact on the risk of Clostridium difficile infection in an elderly population. Open Forum Infect Dis 2018; 5:fy160 [View Article] [PubMed]
     [Google Scholar]
  71. Rajabally NM, Pentecost M, Pretorius G, Whitelaw A, Mendelson M et al. The Clostridium difficile problem: a South African tertiary institution’s prospective perspective. S Afr Med J 2013; 103:168–172 [View Article] [PubMed]
     [Google Scholar]
  72. Moloney G, Eyre DW, Mac Aogáin M, McElroy MC, Vaughan A et al. Human and porcine transmission of Clostridioides difficile ribotype 078, Europe. Emerg Infect Dis 2021; 27:2294–2300 [View Article] [PubMed]
     [Google Scholar]
  73. Moore MP, Wilcox MH, Walker AS, Eyre DW. K-mer based prediction of Clostridioides difficile relatedness and ribotypes. Microb Genom 2022; 8:000804 [View Article] [PubMed]
     [Google Scholar]
  74. Baktash A, Corver J, Harmanus C, Smits WK, Fawley W et al. Comparison of whole-genome sequence-based methods and PCR ribotyping for subtyping of Clostridium difficile. J Clin Microbiol 2022; 60:e0173721 [View Article] [PubMed]
     [Google Scholar]
  75. Seth-Smith HMB, Biggel M, Roloff T, Hinic V, Bodmer T et al. Transition from PCR-ribotyping to whole genome sequencing based typing of Clostridioides difficile. Front Cell Infect Microbiol 2021; 11:681518 [View Article] [PubMed]
     [Google Scholar]
  76. Lim S-C, Hain-Saunders NMR, Imwattana K, Putsathit P, Collins DA et al. Genetically related Clostridium difficile from water sources and human CDI cases revealed by whole-genome sequencing. Environ Microbiol 2022; 24:1221–1230 [View Article]
     [Google Scholar]
  77. Tkalec V, Viprey V, Davis G, Janezic S, Sente B et al. Clostridioides difficile positivity rate and PCR ribotype distribution on retail potatoes in 12 European countries, January to June 2018. Euro Surveill 2022; 27:2100417 [View Article] [PubMed]
     [Google Scholar]
  78. Lim SC, Foster NF, Elliott B, Riley TV. High prevalence of Clostridium difficile on retail root vegetables. Western Australia J Appl Microbiol 2018; 124:585–590 [View Article]
     [Google Scholar]
  79. Adedeji AJ, Atai RB, Gyang HE, Gambo P, Habib MA et al. Live pig markets are hotspots for spread of African swine fever virus in Nigeria. Transbounding Emerging Dis 2022; 69:e1526–e1540 [View Article]
     [Google Scholar]
  80. Chieloka OS. Descriptive epidemiology of the outbreak of avian influenza in Nigeria: a retrospective review, 2015-2017. PAMJ-OH 2021; 6: [View Article]
     [Google Scholar]
  81. Jibril AH, Okeke IN, Dalsgaard A, Olsen JE. Prevalence and whole genome phylogenetic analysis reveal genetic relatedness between antibiotic resistance Salmonella in hatchlings and older chickens from farms in Nigeria. Poult Sci 2023; 102:102427 [View Article] [PubMed]
     [Google Scholar]
  82. Meseko C, Milani A, Inuwa B, Chinyere C, Shittu I et al. The evolution of highly pathogenic avian influenza A (H5) in poultry in Nigeria, 2021-2022. Viruses 2023; 15:1387 [View Article] [PubMed]
     [Google Scholar]
  83. Loo VG, Bourgault A-M, Poirier L, Lamothe F, Michaud S et al. Host and pathogen factors for Clostridium difficile infection and colonization. N Engl J Med 2011; 365:1693–1703 [View Article] [PubMed]
     [Google Scholar]
  84. O’Grady K, Knight DR, Riley TV. Antimicrobial resistance in Clostridioides difficile. Eur J Clin Microbiol Infect Dis 2021; 40:2459–2478 [View Article]
     [Google Scholar]
  85. Darkoh C, Keita K, Odo C, Oyaro M, Brown EL et al. Emergence of clinical Clostridioides difficile isolates with decreased susceptibility to vancomycin. Clin Infect Dis 2022; 74:120–126 [View Article] [PubMed]
     [Google Scholar]
  86. Greentree DH, Rice LB, Donskey CJ. Houston, we have a problem: reports of Clostridioides difficile isolates with reduced vancomycin susceptibility. Clin Infect Dis 2022; 75:1661–1664 [View Article] [PubMed]
     [Google Scholar]
  87. Lutgring JD, McKay SL, Gargis AS, Halpin AL, McDonald LC. Are vancomycin non-susceptible Clostridioides difficile strains emerging?. Clin Infect Dis 2022; 75:1677–1678 [View Article] [PubMed]
     [Google Scholar]
  88. Iwu CD, Korsten L, Okoh AI. The incidence of antibiotic resistance within and beyond the agricultural ecosystem: a concern for public health. Microbiol Open 2020; 9:e1035 [View Article] [PubMed]
     [Google Scholar]
  89. Skalet AH, Cevallos V, Ayele B, Gebre T, Zhou Z et al. Antibiotic selection pressure and macrolide resistance in nasopharyngeal Streptococcus pneumoniae: a cluster-randomized clinical trial. PLoS Med 2010; 7:e1000377 [View Article] [PubMed]
     [Google Scholar]
  90. Abubakar U. Antibiotic use among hospitalized patients in northern Nigeria: a multicenter point-prevalence survey. BMC Infect Dis 2020; 20:86 [View Article] [PubMed]
     [Google Scholar]
  91. Adebowale OO, Jimoh AB, Adebayo OO, Alamu AA, Adeleye AI et al. Evaluation of antimicrobial usage in companion animals at a veterinary teaching hospital in Nigeria. Sci Rep 2023; 13:18195 [View Article] [PubMed]
     [Google Scholar]
  92. Endacott IC, Galipo E, Ekiri AB, Alafiatayo R, Adebowale K et al. Baseline assessment of poultry production, pharmaceutical product use, and related challenges on commercial poultry flocks in kano and oyo states of Nigeria. Vet Sci 2021; 8:315 [View Article] [PubMed]
     [Google Scholar]
  93. Ogwuche A, Ekiri AB, Endacott I, Maikai B-V, Idoga ES et al. Antibiotic use practices of veterinarians and para-veterinarians and the implications for antibiotic stewardship in Nigeria. J S Afr Vet Assoc 2021; 92:e1–e14 [View Article] [PubMed]
     [Google Scholar]
  94. Popoola OO, Adepitan DS, Adeyemi AS, Oladeru OF, Yusuff SI. A national survey of the antibiotic use, self-medication practices, and knowledge of antibiotic resistance among graduates of tertiary institutions in Nigeria. Scientific African 2024; 23:e01978 [View Article]
     [Google Scholar]
  95. Sekoni KF, Oreagba IA, Oladoja FA. Antibiotic utilization study in a teaching hospital in Nigeria. JAC Antimicrob Resist 2022; 4:dlac093 [View Article] [PubMed]
     [Google Scholar]
  96. 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]
  97. Afolayan AO, Aboderin AO, Oaikhena AO, Odih EE, Ogunleye VO et al. 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. Microb Genom 2022; 8:mgen000863 [View Article] [PubMed]
     [Google Scholar]
  98. Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK et al. Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife 2023; 12:e85867 [View Article] [PubMed]
     [Google Scholar]
  99. Fagbamila IO, Ramon E, Lettini AA, Muhammad M, Longo A et al. Assessing the mechanisms of multi-drug resistant non-typhoidal Salmonella (NTS) serovars isolated from layer chicken farms in Nigeria. PLoS One 2023; 18:e0290754 [View Article] [PubMed]
     [Google Scholar]
  100. Akande-Sholabi W, Oyesiji E. Antimicrobial stewardship: knowledge, perceptions, and factors associated with antibiotics misuse among consumer’s visiting the community pharmacies in a Nigeria Southwestern State. J Pharm Policy Pract 2023; 16:120 [View Article] [PubMed]
     [Google Scholar]
  101. Alimi Y, Wabacha J. Strengthening coordination and collaboration of one health approach for zoonotic diseases in Africa. One Health Outlook 2023; 5:10 [View Article] [PubMed]
     [Google Scholar]
  102. Hayman DTS, Adisasmito WB, Almuhairi S, Behravesh CB, Bilivogui P et al. Developing one health surveillance systems. One Health 2023; 17:100617 [View Article] [PubMed]
     [Google Scholar]
  103. Shivaperumal N, Knight DR, Imwattana K, Androga GO, Chang BJ et al. Esculin hydrolysis negative and TcdA-only producing strains of Clostridium (Clostridioides) difficile from the environment in Western Australia. J Appl Microbiol 2022; 133:1183–1196 [View Article]
     [Google Scholar]
/content/journal/mgen/10.1099/mgen.0.001342
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Clostridioides difficile recovered from hospital patients, livestock and dogs in Nigeria share near-identical genome sequences
M Gen 11, 001342 (2025); https://doi.org/10.1099/mgen.0.001342
/content/journal/mgen/10.1099/mgen.0.001342
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