Comparative Pathogenomics of <i>Aeromonas Veronii</i> from Pigs in South Africa: Dominance of the Novel ST657 Clone

• Main Authors: Yogandree Ramsamy, Koleka P. Mlisana, Daniel G. Amoako, Akebe Luther King Abia, Mushal Allam, Arshad Ismail, Ravesh Singh, Sabiha Y. Essack
• Format: Article
• Language: English
• Published: MDPI AG 2020-12-01
• Series: Microorganisms
• Subjects: genomics; <i>Aeromonas veronii</i>; intensive pig farming; abattoir; antibiotics; mobile genetic elements
• Online Access: https://www.mdpi.com/2076-2607/8/12/2008

The pathogenomics of carbapenem-resistant <i>Aeromonas veronii (A. veronii)</i> 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 (bla<i>_CPHA</i>₃ and bla<i>_OXA-</i>₁₂) and belonged to a novel sequence type, ST657 (a satellite clone). Isolates in the same sub-clades clustered according to their clonal lineages and host. Mobilome analysis revealed the presence of chromosome-borne insertion sequence families. The estimated pathogenicity score (P_score ≈ 0.60) indicated their potential pathogenicity in humans. Furthermore, these isolates carried several virulence factors (adherence factors, toxins, and immune evasion), in different permutations and combinations, indicating a differential ability to establish infection. Phylogenomic and metadata analyses revealed a predilection for water environments and aquatic animals, with more recent reports in humans and food animals across geographies, making <i>A. veronii</i> a potential One Health indicator bacterium.