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Background   Rattus  spp. are frequently implicated as key reservoir hosts for leptospirosis, one of the most common, but neglected, bacterial zoonoses in the world. Although leptospirosis is predicted to be a significant public health threat in Africa, studies from the continent are limited.    Methods   Rattus  spp. ( n  = 171) were sampled (January–May 2016) across the City of Johannesburg, South Africa’s largest inland metropole.  Rattus  spp. genetic diversity was evaluated by full length (1140 bp) cyt  b  sequencing of 42 samples. For comparison, a further 12  Rattus norvegicus  samples collected in Cape Town, South Africa’s largest coastal metropole, were also genotyped.  Leptospira  infections were identified and genotyped using real-time PCR and multi-locus ( lfb1 ,  secY  and  lipL41 ) DNA sequencing.    Results  Five  R. norvegicus  haplotypes were identified across Johannesburg, four of which have not previously been detected in South Africa, and one in Cape Town. Across Johannesburg we identified a  Leptospira  spp. infection prevalence of 44% (75/171) and noted significant differences in the prevalence between administrative regions within the metropole. Multi-locus sequence analyses identified a clonal genotype consistent with  L. borgpetersenii  serogroup Javanica (serovar Ceylonica).    Discussion  The prevalence of infection identified in this study is amongst the highest detected in  Rattus  spp .  in similar contexts across Africa. Despite the complex invasion history suggested by the heterogeneity in  R. norvegicus  haplotypes identified in Johannesburg, a single  L. borgpetersenii  genotype was identified in all infected rodents. The lack of  L. interrogans  in a rodent community dominated by  R. norvegicus  is notable, given the widely recognised host-pathogen association between these species and evidence for  L. interrogans  infection in  R. norvegicus  in Cape Town. It is likely that environmental conditions (cold, dry winters) in Johannesburg may limit the transmission of  L. interrogans . Spatial heterogeneity in prevalence suggest that local factors, such as land use, influence disease risk in the metropole.    Conclusions  In South Africa, as in other African countries, leptospirosis is likely underdiagnosed. The high prevalence of infection in urban rodents in Johannesburg suggest that further work is urgently needed to understand the potential public health risk posed by this neglected zoonotic pathogen.

parasites and vectors

Multi-locus sequence analyses reveal a clonal L. borgpetersenii genotype in a heterogeneous invasive Rattus spp. community across the City of Johannesburg, South Africa