Assessment of animal hosts of pathogenic Leptospira in northern Tanzania

Funding: This work was supported by the Wellcome Trust (grant number 096400/Z/11/Z; https://wellcome.ac.uk/). JEBH, VPM, JAC, and SC received support from the Research Councils UK, UK Department for International Development, and UK Biotechnology and Biological Sciences Research Council (BBSRC) (grant numbers BB/J010367/1, BB/L018926, BB/L017679, BB/L018845; http://www.bbsrc.ac.uk/). JAC and VPM also received support from the US National Institutes of Health (NIH)-National Science Foundation (NSF) Ecology and Evolution of Infectious Disease program (R01TW009237; https://www.fic.nih.gov/programs/pages/ecology-infectious-diseases.aspx). MM received support from the BBSRC East of Scotland Bioscience Doctoral Training Partnership (http://www.eastscotbiodtp.ac.uk/). MJM received support from a University of Otago Frances G. Cotter Scholarship and a University of Otago MacGibbon PhD Travel Fellowship (http://www.otago.ac.nz/). VPM and JAC received support from the US National Institutes of Health National Institute for Allergy and Infectious (grant number R01 AI121378; https://www.niaid.nih.gov/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Data Availability: Datasets supporting this manuscript are available through: http://dx.doi.org/10.5525/gla.researchdata.582. Unique sequences generated through this study are available through GenBank (accession numbers MF955862 to MF955882).Peer reviewedPublisher PD

Molecular detection and genetic characterization of Bartonella species from rodents and their associated ectoparasites from northern Tanzania

Three excel files that include rodent, flea and genotype level data (as indicated in file names). These together provide the source data for the work presented in the paper

Summary of rodent trapping effort and success by village.

<p>Summary of rodent trapping effort and success by village.</p

Map of Tanzania showing the administrative regions of Tanzania (main map) and the location of the Moshi Municipal and Moshi Rural Districts within the Kilimanjaro Region (inset).

<p>Maps were made using Quantum Geographic Information System (QGIS) open access software [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006444#pntd.0006444.ref019" target="_blank">19</a>]. Shapefiles were obtained from Tanzania National Bureau of Statistics [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006444#pntd.0006444.ref020" target="_blank">20</a>].</p

Map of Moshi Municipal and Moshi Rural Districts showing representative locations of rodent study villages and study slaughterhouses in relation to the two study hospitals (Kilimanjaro Christian Medical Centre (KCMC) and Mawenzi Regional Referral Hospital (MRRH).

<p>Maps were made using Quantum Geographic Information System (QGIS) open access software [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006444#pntd.0006444.ref019" target="_blank">19</a>]. Districts shapefiles were obtained from Tanzania National Bureau of Statistics [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006444#pntd.0006444.ref020" target="_blank">20</a>].</p

Results of <i>Leptospira lip</i>L32 qPCR testing of kidneys from peri-domestic rodents and ruminant livestock (cattle, goats and sheep).

<p>Results of <i>Leptospira lip</i>L32 qPCR testing of kidneys from peri-domestic rodents and ruminant livestock (cattle, goats and sheep).</p

Infecting <i>Leptospira</i> species based on <i>sec</i>Y sequencing from qPCR positive samples from cattle, goats and sheep.

<p>Infecting <i>Leptospira</i> species based on <i>sec</i>Y sequencing from qPCR positive samples from cattle, goats and sheep.</p

Phylogenetic tree showing the relatedness of the <i>Leptospira sec</i>Y gene (434-bp fragment) derived from qPCR-positive livestock samples.

<p>The phylogenetic tree was constructed using the maximum likelihood method based on the Tamura-Nei nucleotide substitution model [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006444#pntd.0006444.ref073" target="_blank">73</a>]. The tree with the highest log likelihood is shown and drawn to scale with branch lengths measured in the number of substitutions per site. Sequences from this study are labelled with unique identifiers (C0025-C0658); host species; and GenBank accession numbers (MF955862 to MF955882). Sequence from reference <i>Leptospira</i> serovars are also shown [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006444#pntd.0006444.ref034" target="_blank">34</a>]. Expanded clades show reference serovars closely related to study genotypes. More distantly related species clades are collapsed and shown with species labels only. Host and country locations shown for Africa isolates are show in parentheses. Sequences from this study that show 100% identity with <i>L</i>. <i>borgpetersenii</i> serovar Hardjo are highlighted in blue; non-Hardjo <i>L</i>. <i>borgpetersenii</i> sequences are highlighted in pink; <i>L</i>. <i>kirschneri</i> sequences are highlighted in green and sequences without an attributed species are highlighted in orange. Abbreviations: (sv) serovar; DRC (Democratic Republic of Congo).</p