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

Mark Moseley*, Kovashnee Naidoo, Armanda Bastos, Liezl Retief, John Frean, Sandra Telfer, Jennifer Rossouw

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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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.[Figure not available: see fulltext.].

Original languageEnglish
Article number570
Number of pages9
JournalParasites & Vectors
Publication statusPublished - 11 Nov 2020

Bibliographical note

Funding Information:
This study was made possible by a Royal Society for Tropical Medicine and Hygiene small grant (MM, Grant Number GR000556), by a Biotechnology and Biological Sciences Research Council (BBSRC) PhD studentship (MM, Grant Number BB/M010996/1) and by support from the Wellcome Trust (MM, Grant Number 216634/Z/19/Z) . Rodent genotyping was funded through the Centers for Disease Control and Prevention (CDC) Cooperative Agreement (AB, Grant Number 5 NU2GGH001874-02-00) and a Facility Grant (UID78566) from the National Research Foundation of South Africa.


  • Disease ecology
  • Leptospirosis
  • lfb1
  • Molecular epidemiology
  • Public health
  • Rats
  • Urbanisation
  • Zoonosis


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