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Objective:To investigate the prevalence, species distribution and genetic diversity of zoonotic Arcobacter species. Design: Prospective study. Setting: Drainage system of a cosmopolitan chicken abattoir in Lagos, Nigeria. Methods : One hundred and fifity drainage water samples were enriched in a minimal antibiotics-containing medium at room temperature and bacteria then isolated by use of a membrane filtration method. Results: Twenty six (14%) of samples were positive for Arcobacter spp. Of these, 20 were examined by a comprehensive probabilistic identification scheme for Epsilobacteria and all strains identified as A. butzleri. AFLP analysis of these strains revealed considerable genetic diversity among the strains, with 12 genotypes defined at the 90% similarity level. Conclusion: The prevalence of A. butzleri in Nigerian poultry abattoir effluent indicates this species may constitute a public health problem in this country. AFLP profiling could be a useful tool for molecular epidemiological and population genetic studies of this organism. This is the first known report of A. butzleri in Nigeria, and first application of AFLP analysis for genotyping the species. (E Afr Med J:2003 80(4): 218-222)

<i>Arcobacter butzlieri </i>strains from poultry abattoir effluent in Nigeria