microorganisms Article Comparative Pathogenomics of Aeromonas veronii from Pigs in South Africa: Dominance of the Novel ST657 Clone Yogandree Ramsamy 1,2,3,* , Koleka P. Mlisana 2, Daniel G. Amoako 3 , Akebe Luther King Abia 3 , Mushal Allam 4 , Arshad Ismail 4 , Ravesh Singh 1,2 and Sabiha Y. Essack 3 1 Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
[email protected] 2 National Health Laboratory Service, Durban 4001, South Africa;
[email protected] 3 Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
[email protected] (D.G.A.);
[email protected] (A.L.K.A.);
[email protected] (S.Y.E.) 4 Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa;
[email protected] (M.A.);
[email protected] (A.I.) * Correspondence:
[email protected] Received: 9 November 2020; Accepted: 15 December 2020; Published: 16 December 2020 Abstract: The pathogenomics of carbapenem-resistant Aeromonas veronii (A. veronii) isolates recovered from pigs in KwaZulu-Natal, South Africa, was explored by whole genome sequencing on the Illumina MiSeq platform. Genomic functional annotation revealed a vast array of similar central networks (metabolic, cellular, and biochemical). The pan-genome analysis showed that the isolates formed a total of 4349 orthologous gene clusters, 4296 of which were shared; no unique clusters were observed. All the isolates had similar resistance phenotypes, which corroborated their chromosomally mediated resistome (blaCPHA3 and blaOXA-12) and belonged to a novel sequence type, ST657 (a satellite clone).