Genetic signature of reproductive manipulation in the phylogeography of the bat fly, Trichobius major

Trends in Bacterial Pathogens of Bats: Global Distribution and Knowledge Gaps

Bats have received considerable recent attention for infectious disease research because of their potential to host and transmit viruses, including Ebola, Hendra, Nipah, and multiple coronaviruses. These pathogens are occasionally transmitted from bats to wildlife, livestock, and to humans, directly or through other bridging (intermediate) hosts. Due to their public health relevance, zoonotic viruses are a primary focus of research attention. In contrast, other emerging pathogens of bats, such as bacteria, are vastly understudied despite their ubiquity and diversity. Here, we describe the currently known host ranges and geographic distributional patterns of potentially zoonotic bacterial genera in bats, using published presence-absence data of pathogen occurrence. We identify apparent gaps in our understanding of the distribution of these pathogens on a global scale. The most frequently detected bacterial genera in bats are Bartonella, Leptospira, and Mycoplasma. However, a wide variety of other potentially zoonotic bacterial genera are also occasionally found in bats, such as Anaplasma, Brucella, Borrelia, Coxiella, Ehrlichia, Francisella, Neorickettsia, and Rickettsia. The bat families Phyllostomidae, Vespertilionidae, and Pteropodidae are most frequently reported as hosts of bacterial pathogens; however, the presence of at least one bacterial genus was confirmed in all 15 bat families tested. On a spatial scale, molecular diagnostics of samples from 58 countries and four overseas departments and island states (French Guiana, Mayotte, New Caledonia, and Réunion Island) reported testing for at least one bacterial pathogen in bats. We also identified geographical areas that have been mostly neglected during bacterial pathogen research in bats, such as the Afrotropical region and Southern Asia. Current knowledge on the distribution of potentially zoonotic bacterial genera in bats is strongly biased by research effort towards certain taxonomic groups and geographic regions. Identifying these biases can guide future surveillance efforts, contributing to a better understanding of the ecoepidemiology of zoonotic pathogens in bats.

Parasitic fauna of bats from Costa Rica

Bats are important reservoirs and spreaders of pathogens, including those of zoonotic concern. Though Costa Rica hosts one of the highest bat species' diversity, no information is available about their parasites. In order to investigate the occurrence of vector-borne pathogens (VBPs) and gastrointestinal (GI) parasites of chiropterans from this neotropical area, ectoparasites (n = 231) and stools (n = 64) were collected from 113 bats sampled in Santa Cruz (site 1) and Talamanca (site 2). Mites, fleas and ticks were morphologically and molecularly identified, as well as pathogens transmitted by vectors (VBPs, i.e., Borrelia spp., Rickettsia spp., Bartonella spp.) and from feces, such as Giardia spp., Cryptosporidium spp. and Eimeria spp. were molecularly investigated. Overall, 21 bat species belonging to 15 genera and 5 families were identified of which 42.5% were infested by ectoparasites, with a higher percentage of mites (38.9%, i.e., Cameronieta sp. and Mitonyssoides sp.) followed by flies (2.6%, i.e., Joblingia sp.) and tick larvae (1.7%, i.e., Ornithodoros sp.). Rickettsia spp. was identified in one immature tick and phylogenetically clustered with two Rickettsia species of the Spotted Fever Group (i.e., R. massiliae and R. rhipicephali). The frequency of GI parasite infection was 14%, being 3.1% of bats infected by Giardia spp. (un-identified non-duodenalis species), 1.5% by Eimeria spp. and 9.4% by Cryptosporidium spp. (bat and rodent genotypes; one C. parvum-related human genotype). The wide range of ectoparasites collected coupled with the detection of Rickettsia sp., Giardia and Cryptosporidium in bats from Costa Rica highlight the role these mammals may play as spreaders of pathogens and the need to further investigate the pathogenic potential of these parasites.

Review of studies about bat-fly interactions inside roosts, with observations on partnership patterns for publications

Pressures from anthropogenic disturbances have triggered a wealth of studies focusing on the assessment and mitigation of the negative impacts of these disturbances on inter and intraspecific ecological interactions, including bats and bat flies in their roosts. The heterogeneity of research methods employed for these studies and the scientific imbalance between countries may constrain advances and the consolidation of the knowledge on this subject. We reviewed the literature regarding bat and bat-ectoparasite interactions in roosts assessing global research trends and patterns of author collaborative work to be able to identify key questions for future studies and potential initiatives to improve the knowledge on this subject. Current information available has mostly come from the Americas and is predominantly focused on the recognition and description of parasite-host interactions between bats and bat flies. Our findings suggest the value of increasing collaboration for future research, as several countries with largely diverse environments and high organismal richness are disconnected from the countries that produce the most publications in this area, and/or have low records of publications. These regions are in the Global South, mostly in South American and African countries. We suggest that more collaborative networks may increase scientific production in the area, and that investing in local research development and enhancing partnerships for publications may strengthen the field. These research programs and collaborations are key for the development of conservation strategies for bats and bat flies, for their roosts, and for understanding bat and bat-ectoparasite interactions.

Cascading effects of habitat loss on ectoparasite-associated bacterial microbiomes

Suitable habitat fragment size, isolation, and distance from a source are important variables influencing community composition of plants and animals, but the role of these environmental factors in determining composition and variation of host-associated microbial communities is poorly known. In parasite-associated microbial communities, it is hypothesized that evolution and ecology of an arthropod parasite will influence its microbiome more than broader environmental factors, but this hypothesis has not been extensively tested. To examine the influence of the broader environment on the parasite microbiome, we applied high-throughput sequencing of the V4 region of 16S rRNA to characterize the microbiome of 222 obligate ectoparasitic bat flies (Streblidae and Nycteribiidae) collected from 155 bats (representing six species) from ten habitat fragments in the Atlantic Forest of Brazil. Parasite species identity is the strongest driver of microbiome composition. To a lesser extent, reduction in habitat fragment area, but not isolation, is associated with an increase in connectance and betweenness centrality of bacterial association networks driven by changes in the diversity of the parasite community. Controlling for the parasite community, bacterial network topology covaries with habitat patch area and exhibits parasite-species specific responses to environmental change. Taken together, habitat loss may have cascading consequences for communities of interacting macro- and microorgansims.

Bat Flies and Their Microparasites: Current Knowledge and Distribution

Bats are the second most diverse mammalian group, playing keystone roles in ecosystems but also act as reservoir hosts for numerous pathogens. Due to their colonial habits which implies close contacts between individuals, bats are often parasitized by multiple species of micro- and macroparasites. The particular ecology, behavior, and environment of bat species may shape patterns of intra- and interspecific pathogen transmission, as well as the presence of specific vectorial organisms. This review synthetizes information on a multi-level parasitic system: bats, bat flies and their microparasites. Bat flies (Diptera: Nycteribiidae and Streblidae) are obligate, hematophagous ectoparasites of bats consisting of ~500 described species. Diverse parasitic organisms have been detected in bat flies including bacteria, blood parasites, fungi, and viruses, which suggest their vectorial potential. We discuss the ecological epidemiology of microparasites, their potential physiological effects on both bats and bat flies, and potential research perspectives in the domain of bat pathogens. For simplicity, we use the term microparasite throughout this review, yet it remains unclear whether some bacteria are parasites or symbionts of their bat fly hosts.

Molecular detection of Bartonella spp. and Rickettsia spp. in bat ectoparasites in Brazil

The family Streblidae comprises a monophyletic group of Hippoboscoidea, hematophagous dipterans that parasitize bats. Bartonella spp. and Rickettsia spp. have been reported in bats sampled in Europe, Africa, Asia, North, Central and South America. However, there are few reports on the Bartonella and Rickettsia bacteria infecting Hippoboscoidea flies and mites. While Spinturnicidae mites are ectoparasites found only in bats, those belonging to the family Macronyssidae comprise mites that also parasitize other mammal species. This study investigates the occurrence and assesses the phylogenetic positioning of Bartonella spp. and Rickettsia spp. found in Streblidae flies and Spinturnicidae and Macronyssidae mites collected from bats captured in Brazil. From May 2011 to April 2012 and September 2013 to December 2014, 400 Streblidae flies, 100 Macronyssidaes, and 100 Spinturnicidae mites were collected from bats captured in two sites in northeastern Nova Iguaçu, Rio de Janeiro, southeastern Brazil. Forty (19.8%) out of 202 Streblidae flies were positive for Bartonella spp. in qPCR assays based on the nuoG gene. Among the flies positive for the bacterium, six (18%) were Paratrichobius longicrus, seven (29%) Strebla guajiro, two (40%) Aspidoptera phyllostomatis, five (11%) Aspidoptera falcata, one (10%) Trichobius anducei, one (25%) Megistopoda aranea, and 18 (32%) Trichobius joblingi, and collected from bats of the following species: Artibeus lituratus, Carollia perspicillata, Artibeus planirostris, Sturnira lilium, and Artibeus obscurus. Six sequences were obtained for Bartonella (nuoG [n = 2], gltA [n = 2], rpoB [n = 1], ribC = 1]). The phylogenetic analysis based on gltA (750pb) gene showed that the Bartonella sequences clustered with Bartonella genotypes detected in bats and ectoparasites previously sampled in Latin America, including Brazil. Only one sample (0.49%) of the species Trichobius joblingi collected from a specimen of Carollia perspicillata was positive for Rickettsia sp. in cPCR based on the gltA gene (401bp). This sequence was clustered with a 'Candidatus Rickettsia andaenae" genotype detected in an Amblyomma parvum tick collected from a rodent in the southern region of Brazilian Pantanal. The sampled Macronyssidae and Spinturnicidae mites were negative for Bartonella spp. and Rickettsia spp. This study demonstrated the first occurrence of Bartonella spp. and Rickettsia spp. DNA in Streblidae flies collected from bats in Brazil.

Origin, acquisition and diversification of heritable bacterial endosymbionts in louse flies and bat flies

The γ-proteobacterium Arsenophonus and its close relatives (Arsenophonus and like organisms, ALOs) are emerging as a novel clade of endosymbionts, which are exceptionally widespread in insects. The biology of ALOs is, however, in most cases entirely unknown, and it is unclear how these endosymbionts spread across insect populations. Here, we investigate this aspect through the examination of the presence, the diversity and the evolutionary history of ALOs in 25 related species of blood-feeding flies: tsetse flies (Glossinidae), louse flies (Hippoboscidae) and bat flies (Nycteribiidae and Streblidae). While these endosymbionts were not found in tsetse flies, we identify louse flies and bat flies as harbouring the highest diversity of ALO strains reported to date, including a novel ALO clade, as well as Arsenophonus and the recently described Candidatus Aschnera chinzeii. We further show that the origin of ALO endosymbioses extends deep into the evolutionary past of louse flies and bat flies, and that it probably played a major role in the ecological specialization of their hosts. The evolutionary history of ALOs is notably complex and was shaped by both vertical transmission and horizontal transfers with frequent host turnover and apparent symbiont replacement in host lineages. In particular, ALOs have evolved repeatedly and independently close relationships with diverse groups of louse flies and bat flies, as well as phylogenetically more distant insect families, suggesting that ALO endosymbioses are exceptionally dynamic systems.

Lack of population genetic structure and host specificity in the bat fly, Cyclopodia horsfieldi, across species of Pteropus bats in Southeast Asia

Background

Population-level studies of parasites have the potential to elucidate patterns of host movement and cross-species interactions that are not evident from host genealogy alone. Bat flies are obligate and generally host-specific blood-feeding parasites of bats. Old-World flies in the family Nycteribiidae are entirely wingless and depend on their hosts for long-distance dispersal; their population genetics has been unstudied to date.

Methods

We collected a total of 125 bat flies from three Pteropus species (Pteropus vampyrus, P. hypomelanus, and P. lylei) from eight localities in Malaysia, Cambodia, and Vietnam. We identified specimens morphologically and then sequenced three mitochondrial DNA gene fragments (CoI, CoII, cytB; 1744 basepairs total) from a subset of 45 bat flies. We measured genetic diversity, molecular variance, and population genetic subdivision (F_ST), and used phylogenetic and haplotype network analyses to quantify parasite genetic structure across host species and localities.

Results

All flies were identified as Cyclopodia horsfieldi with the exception of two individuals of Eucampsipoda sundaica. Low levels of population genetic structure were detected between populations of Cyclopodia horsfieldi from across a wide geographic range (~1000 km), and tests for isolation by distance were rejected. AMOVA results support a lack of geographic and host-specific population structure, with molecular variance primarily partitioned within populations. Pairwise F_ST values from flies collected from island populations of Pteropus hypomelanus in East and West Peninsular Malaysia supported predictions based on previous studies of host genetic structure.

Conclusions

The lack of population genetic structure and morphological variation observed in Cyclopodia horsfieldi is most likely due to frequent contact between flying fox species and subsequent high levels of parasite gene flow. Specifically, we suggest that Pteropus vampyrus may facilitate movement of bat flies between the three Pteropus species in the region. We demonstrate the utility of parasite genetics as an additional layer of information to measure host movement and interspecific host contact. These approaches may have wide implications for understanding zoonotic, epizootic, and enzootic disease dynamics. Bat flies may play a role as vectors of disease in bats, and their competence as vectors of bacterial and/or viral pathogens is in need of further investigation.

Evolution, multiple acquisition, and localization of endosymbionts in bat flies (Diptera: Hippoboscoidea: Streblidae and Nycteribiidae)

Bat flies are a diverse clade of obligate ectoparasites on bats. Like most blood-feeding insects, they harbor endosymbiotic prokaryotes, but the origins and nature of these symbioses are still poorly understood. To expand the knowledge of bacterial associates in bat flies, the diversity and evolution of the dominant endosymbionts in six of eight nominal subfamilies of bat flies (Streblidae and Nycteribiidae) were studied. Furthermore, the localization of endosymbionts and their transmission across developmental stages within the family Streblidae were explored. The results show diverse microbial associates in bat flies, with at least four ancestral invasions of distantly related microbial lineages throughout bat fly evolution. Phylogenetic relationships support the presence of at least two novel symbiont lineages (here clades B and D), and extend the geographic and taxonomic range of a previously documented lineage ("Candidatus Aschnera chinzeii"; here clade A). Although these lineages show reciprocally monophyletic clusters with several bat fly host clades, their phylogenetic relationships generally do not reflect current bat fly taxonomy or phylogeny. However, within some endosymbiont clades, congruent patterns of symbiont-host divergence are apparent. Other sequences identified in this study fall into the widely distributed, highly invasive, insect-associated Arsenophonus lineage and may be the result of symbiont replacements and/or transient infections (here clade C). Vertical transmission of endosymbionts of clades B and D is supported by fluorescent signal (fluorescent in situ hybridization [FISH]) and microbial DNA detection across developmental stages. The fluorescent bacterial signal is consistently localized within structures resembling bacteriomes, although their anatomical position differs by host fly clade. In summary, the results suggest an obligate host-endosymbiont relationship for three of the four known symbiont clades associated with bat flies (clades A, B, and D).

Some like it hot: evolution and ecology of novel endosymbionts in bat flies of cave-roosting bats (hippoboscoidea, nycterophiliinae)

We investigated previously unknown associations between bacterial endosymbionts and bat flies of the subfamily Nycterophiliinae (Diptera, Streblidae). Molecular analyses revealed a novel clade of Gammaproteobacteria in Nycterophilia bat flies. This clade was not closely related to Arsenophonus-like microbes found in its sister genus Phalconomus and other bat flies. High population infection rates in Nycterophilia across a wide geographic area, the presence of the symbionts in pupae, the general codivergence between hosts and symbionts, and high AT composition bias in symbiont genes together suggest that this host-symbiont association is obligate in nature and ancient in origin. Some Nycterophilia samples (14.8%) also contained Wolbachia supergroup F (Alphaproteobacteria), suggesting a facultative symbiosis. Likelihood-based ancestral character mapping revealed that, initially, obligate symbionts exhibited association with host-specific Nycterophilia bat flies that use a broad temperature range of cave environments for pupal development. As this mutualism evolved, the temperature range of bat flies narrowed to an exclusive use of hot caves, which was followed by a secondary broadening of the bat flies' host associations. These results suggest that the symbiosis has influenced the environmental tolerance of parasite life history stages. Furthermore, the contingent change to an expanded host range of Nycterophilia bat flies upon narrowing the ecological niche of their developmental stages suggests that altered environmental tolerance across life history stages may be a crucial factor in shaping parasite-host relationships.