Prevalence and genetic diversity of <i>Bartonella</i> spp. in wild small mammals from South Africa

Abstract

<i>Bartonella</i> spp. are intracellular bacteria associated with several re-emerging human diseases. Small mammals play a significant role in the maintenance and spread of <i>Bartonella</i> spp. Despite the high small mammal biodiversity in South Africa, there is limited epidemiological information regarding <i>Bartonella</i> spp. in these mammals. The main aim of this study was to determine the prevalence and genetic diversity of <i>Bartonella</i> spp. from wild small mammals from 15 localities in 8 provinces of South Africa. Small mammals (<i>n</i> = 183) were trapped in the Eastern Cape, Free State, Gauteng, Limpopo, Mpumalanga, Northern Cape, North West, and Western Cape provinces of South Africa between 2010 and 2018. Heart, kidney, liver, lung, and spleen were harvested for <i>Bartonella</i> DNA screening, and prevalence was determined based on the PCR amplification of partial fragments of the 16S-23S rRNA intergenic spacer (ITS) region, <i>gltA,</i> and <i>rpoB</i> genes. <i>Bartonella</i> DNA was detected in <i>Aethomys chrysophilus</i>, <i>Aethomys ineptus</i>, <i>Gerbillurus</i> spp., <i>Lemniscomys rosalia</i>, <i>Mastomys coucha</i>, <i>Micaelamys namaquensis</i>, <i>Rhabdomys pumilio,</i> and <i>Thallomys paedulcus</i>. An overall prevalence of 16.9% (31/183, 95% CI: 12.2%-23%) was observed. <i>Bartonella elizabethae</i>, <i>Bartonella grahamii,</i> and <i>Bartonella tribocorum</i> were the zoonotic species identified, while the remaining sequences were aligned to uncultured <i>Bartonella</i> spp. with unknown zoonotic potential. Phylogenetic analyses confirmed five distinct <i>Bartonella</i> lineages (I-V), with lineage IV displaying strong <i>M. coucha</i> host specificity. Our results confirm that South African wild small mammals are natural reservoirs of a diverse assemblage of <i>Bartonella</i> spp., including some zoonotic species with high genetic diversity, although prevalence was relatively low.IMPORTANCESmall mammals play a significant role in the maintenance and spread of zoonotic pathogens such as <i>Bartonella</i> spp. Despite the high small mammal biodiversity in southern Africa including South Africa, there is limited epidemiological information regarding <i>Bartonella</i> spp. in these mammals across the country. Results from our study showed the liver and spleen had the highest positive cases for <i>Bartonella</i> spp. DNA among the tested organs. <i>Bartonella elizabethae</i>, <i>B. grahamii,</i> and <i>B. tribocorum</i> were the three zoonotic species identified and five distinct Bartonella lineages (I-V) were confirmed through phylogenetic analyses. To the best of our knowledge, this study presents the first extensive nuclear diversity investigation of <i>Bartonella</i> spp. in South African small mammals in South Africa.