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LA\u2010MRSA has been reported as a zoonotic agent that has the potential to spread to humans and may cause infections in at\u2010risk groups. In this study, whole genome sequencing was used to describe the genetic environment (resistance mechanisms, virulence factors and mobile genetic elements) and investigate the genetic lineages of MRSA isolates from pigs in Cameroonian and South African abattoirs. During March\u2013October 2016, 288 nasal and rectal pooled samples from 432 pigs as well as nasal and hand swabs from 82 humans were collected. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were de novo\u2010assembled using the Qiagen CLC Genomics Workbench and SPAdes. The assembled contigs were annotated, and antibiotic resistance genes, virulence factors, plasmids, SCC<jats:italic>mec<\/jats:italic> and phage elements were identified with ResFinder, Virulence Finder, PlasmidFinder, SCC<jats:italic>mec<\/jats:italic> Finder and PHAST, respectively. Core genome single nucleotide analysis was undertaken to assess clonal relatedness among isolates. A lower MRSA prevalence was observed in pigs in Cameroon (<jats:italic>n<\/jats:italic>\u00a0=\u00a01\/13; 0.07%) compared with South Africa (<jats:italic>n<\/jats:italic>\u00a0=\u00a04\/22; 18.18%), and none of the workers were colonized by MRSA. Genome analysis identified various antibiotic resistance genes along with six virulence factors in all isolates. All MRSA isolates belonged to the clonal lineage ST398 (<jats:italic>spa<\/jats:italic>\u2010type t011) and harboured the type Vc SCC<jats:italic>mec<\/jats:italic> and several plasmids. Our study shows that the livestock\u2010associated MRSA clonal lineage ST398 is already present in both Cameroon and South Africa and is probably underestimated in the absence of molecular epidemiological studies. It reveals the serious food safety and public health threat associated with this animal strain and underscores the need for interventions to contain this resistant clone.<\/jats:p>","DOI":"10.1111\/zph.12586","type":"journal-article","created":{"date-parts":[[2019,5,24]],"date-time":"2019-05-24T07:43:03Z","timestamp":1558683783000},"page":"512-525","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Genome analysis of methicillin\u2010resistant <i>Staphylococcus aureus<\/i> isolated from pigs: Detection of the clonal lineage ST398 in Cameroon and South Africa"],"prefix":"10.1111","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3874-8175","authenticated-orcid":false,"given":"Luria Leslie","family":"Founou","sequence":"first","affiliation":[{"name":"Antimicrobial Research Unit, College of Health Sciences University of KwaZulu\u2010Natal Durban South Africa"},{"name":"Department of Food Safety and Environmental Microbiology Centre of Expertise and Biological Diagnostic of Cameroon Yaound\u00e9 Cameroon"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raspail Carrel","family":"Founou","sequence":"additional","affiliation":[{"name":"Antimicrobial Research Unit, College of Health Sciences University of KwaZulu\u2010Natal Durban South Africa"},{"name":"Department of Clinical Microbiology Centre of Expertise and Biological Diagnostic of Cameroon Yaound\u00e9 Cameroon"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mushal","family":"Allam","sequence":"additional","affiliation":[{"name":"Sequencing Core Facility National Health Laboratory Service Johannesburg South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arshad","family":"Ismail","sequence":"additional","affiliation":[{"name":"Sequencing Core Facility National Health Laboratory Service Johannesburg South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cyrille","family":"Finyom Djoko","sequence":"additional","affiliation":[{"name":"Metabiota Inc. Yaound\u00e9 Cameroon"},{"name":"Centre for Research and Doctoral Training in Life Science, Health and Environment The Biotechnology Centre University of Yaound\u00e9 I Yaound\u00e9 Cameroon"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabiha Yusuf","family":"Essack","sequence":"additional","affiliation":[{"name":"Antimicrobial Research Unit, College of Health Sciences University of KwaZulu\u2010Natal Durban South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2019,5,24]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0088083"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.3201\/eid1105.040866"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0028529"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.4102\/sajs.v106i11\/12.243"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-9-75"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2014.06.006"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01979-14"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1089\/fpd.2015.1958"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.000119"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajic.2012.06.013"},{"key":"e_1_2_10_14_1","volume-title":"Performance Standards for Antimicrobial Susceptibility Testing; Twenty\u2010Fourth Informational Supplement. 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