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Bartonella species are recognized globally as emerging zoonotic pathogens. Small mammals such as rodents and shrews are implicated as major natural reservoirs for these microbial agents. Nevertheless, in several tropical countries, like India, the diversity of Bartonella in small mammals remain unexplored and limited information exists on the natural transmission cycles (reservoirs and vectors) of these bacteria. Using a multi-locus sequencing approach, we investigated the prevalence, haplotype diversity, and phylogenetic affinities of Bartonella in small mammals and their associated mites in a mixed-use landscape in the biodiverse Western Ghats in southern India. We sampled 141 individual small mammals belonging to eight species. Bartonella was detected in five of the eight species, including three previously unknown hosts. We observed high interspecies variability of Bartonella prevalence in the host community. However, the overall prevalence (52.5%) and haplotype diversity (0.9) was high for the individuals tested. Of the seven lineages of Bartonella identified in our samples, five lineages were phylogenetically related to putative zoonotic species– B . tribocorum , B . queenslandensis , and B . elizabethae . Haplotypes identified from mites were identical to those identified from their host species. This indicates that these Bartonella species may be zoonotic, but further work is necessary to confirm whether these are pathogenic and pose a threat to humans. Taken together, these results emphasize the presence of hitherto unexplored diversity of Bartonella in wild and synanthropic small mammals in mixed-use landscapes. The study also highlights the necessity to assess the risk of spillover to humans and other incidental hosts.

Bats are reservoirs for several zoonotic pathogens, including filoviruses. Recent work highlights the diversity of bat borne filoviruses in Asia. High risk activities at the bat-human interface pose the threat of zoonotic virus transmission. We present evidence for prior exposure of bat harvesters and two resident fruit bat species to filovirus surface glycoproteins by screening sera in a multiplexed serological assay. Antibodies reactive to two antigenically distinct filoviruses were detected in human sera and to three individual filoviruses in bats in remote Northeast India. Sera obtained from Eonycteris spelaea bats showed similar patterns of cross-reactivity as human samples, suggesting them as the species responsible for the spillover. In contrast, sera from Rousettus leschenaultii bats reacted to two different virus glycoproteins. Our results indicate circulation of several filoviruses in bats and the possibility for filovirus transmission from bats to humans.

Bacterial infections account for a large proportion of zoonoses. Our current understanding of zoonotic spillover, however, is largely based on studies from viral systems. Small mammals such as rodents and their ectoparasites present a unique system for studying several bacterial pathogens and mapping their spillover pathways. Using Bartonella spp. (a Gram‐negative bacteria) as a model system within a rainforest human‐use landscape, we investigated (1) ecological correlates of Bartonella prevalence in small mammal hosts and (2) evolutionary relationships between Bartonella spp. and various hosts and ectoparasites to gain insight into pathogen movement pathways within ecological communities. We detected Bartonella in five out of eight small mammal species and in 86 (40.56%) out of 212 individuals, but prevalence varied widely among species (0%–75.8%). Seven of the ten ectoparasite species found on these small mammals were positive for Bartonella. Interestingly, while Bartonella genotypes (15) in small mammals were host‐specific, ectoparasites had nonspecific associations, suggesting the possibility for vector‐mediated cross‐species transmission. We also found that Bartonella prevalence in hosts was positively correlated with their aggregated ectoparasite loads, further emphasizing the crucial role that ectoparasites may play in these transmission pathways. Our cophylogenetic analysis and ancestral trait (host) reconstruction revealed incongruence between small mammal and Bartonella phylogenies, indicating historic host shifts and validating the potential for contemporary spillover events. We found that small mammal hosts in this fragmented landscape often move across habitat boundaries, creating a transmission pathway (via shared ectoparasites) to novel hosts, which may include synanthropic species like Rattus rattus. Our results highlight the necessity to disentangle the complex relationship among hosts, ectoparasites, and bacterial pathogens to understand the implications of undetected spillover events. This study focuses on Bartonella spp. (a Gram‐negative bacteria) in small mammals and their ectoparasites within a rainforest human‐use landscape. We found that a high proportion (40.56%) of the tested small mammals across five species and two sites carry Bartonella, with prevalence being positively correlated with aggregated ectoparasite load. Despite the occurrence of host‐specific genotypes, we observed incongruence in small mammal and Bartonella phylogenies, indicating historic host shifts within the community, and the potential for cross‐species transmissions in the future mediated by ectoparasites.

[This corrects the article DOI: 10.1371/journal.pntd.0007733.].[This corrects the article DOI: 10.1371/journal.pntd.0007733.].

[This corrects the article DOI: 10.1371/journal.pntd.0007733.].