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