Detection ofBartonella tamiaeDNA in Ectoparasites from Rodents in Thailand and Their Sequence Similarity with Bacterial Cultures from Thai Patients

Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia

BACKGROUND

Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear.

RESULTS

Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin.

CONCLUSIONS

P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.

The chigger microbiome: big questions in a tiny world

'Chiggers' (trombiculid mite larvae) are best known as vectors of rickettsial pathogens, Orientia spp., which cause a zoonosis, scrub typhus. However, several other pathogens (e.g., Hantaan orthohantavirus, Dabie bandavirus, Anaplasma spp., Bartonella spp., Borrelia spp., and Rickettsia spp.) and bacterial symbionts (e.g., Cardinium, Rickettsiella, and Wolbachia) are being reported from chiggers with increasing frequency. Here, we explore the surprisingly diverse chigger microbiota and potential interactions within this microcosm. Key conclusions include a possible role for chiggers as vectors of viral diseases; the dominance in some chigger populations of unidentified symbionts in several bacterial families; and increasing evidence for vertical transmission of potential pathogens and symbiotic bacteria in chiggers, suggesting intimate interactions and not simply incidental acquisition of bacteria from the environment or host.

Bacterial pathogens' screening in Brazilian chigger mites (Trombidiformes: Trombiculidae), with the first report of 'Candidatus Rickettsia colombianensi'-like in avian-associated chiggers

Chiggers are larval ectoparasites of the Trombiculidae that can transmit pathogens to their hosts. In this study, chiggers collected from birds in Brazil were morphologically identified as Blankaartia sinnamaryi, Eutrombicula batatas, Eutrombicula daemoni, Eutrombicula goeldii, Eutrombicula tinami, and Parasecia gilbertoi. For these specimens, a beginning attempt at molecular identification were also provided, as well as, were genetically screened to detect bacterial pathogens. The species B. sinnamaryi and E. tinami were positive for Rickettsia felis-like and 'Candidatus Rickettsia colombianensi'-like, respectively. For the other agents (Anaplasmataceae, Borrelia spp. and Orientia tsutsugamushi), the tests were negative. This is the first report of 'Ca. R. colombianensi'-like and the second record of R. felis-like in chigger collected on birds from Brazil.

Bartonella spp. detection in laelapid (Mesostigmata: Laelapidae) mites collected from small rodents in Lithuania

The genus Bartonella contains facultative Gram-negative intracellular bacteria from the family Bartonellaceae that can cause diseases in humans and animals. Various Bartonella species have been detected in rodents' ectoparasites, such as fleas, ticks, mites, and lice. However, the role of laelapid mites (Mesostigmata: Laelapidae) as carriers of Bartonella spp. needs to be confirmed. We aimed to investigate the presence of Bartonella spp. in laelapid mites collected from small rodents in Lithuania using real-time PCR targeting the transfer-messenger RNA/tmRNA (ssrA) gene and to characterize Bartonella strains using nested PCR and sequence analysis of the 16S-23S rRNA intergenic transcribed spacer region (ITS). A total of 271 laelapid mites of five species (Laelaps agilis, Haemogamasus nidi, Eulaelaps stabularis, Myonyssus gigas, and Hyperlaelaps microti) were collected from five rodent species (Apodemus flavicollis, Apodemus agrarius, Clethrionomys glareolus, Micromys minutus, and Microtus oeconomus) during 2015-2016. Bartonella DNA was detected in three mite species L. agilis, M. gigas, and Hg. nidi with an overall prevalence of 11.4%. Sequence analysis of the 16S-23S rRNA ITS region revealed the presence of Bartonella taylorii in L. agilis, Hg. nidi, and M. gigas, and Bartonella grahamii in L. agilis. Our results suggest that laelapid mites are involved in the maintenance of rodent-associated Bartonella spp. in nature. To the best of the authors' knowledge, this is the first study to demonstrate the presence of Bartonella spp. DNA in laelapid mites from small rodents.

Biology, Systematics, Microbiome, Pathogen Transmission and Control of Chiggers (Acari: Trombiculidae, Leeuwenhoekiidae) with Emphasis on the United States

Chiggers are the larval stage of Trombiculidae and Leeuwenhoekiidae mites of medical and veterinary importance. Some species in the genus Leptotrombidium and Herpetacarus vector Orientia species, the bacteria that causes scrub typhus disease in humans. Scrub typhus is a life-threatening, febrile disease. Chigger bites can also cause dermatitis. There were 248 chigger species reported from the US from almost every state. However, there are large gaps in our knowledge of the life history of other stages of development. North American wide morphological keys are needed for better species identification, and molecular sequence data for identification are minimal and not clearly matched with morphological data. The role of chiggers in disease transmission in the US is especially understudied, and the role of endosymbionts in Orientia infection are suggested in the scientific literature but not confirmed. The most common chiggers in the eastern United States were identified as Eutrombicula alfreddugesi but were likely misidentified and should be replaced with Eutrombicula cinnabaris. Scrub typhus was originally believed to be limited to the Tsutsugamushi Triangle and the chigger genus, Leptotrombidium, but there is increasing evidence this is not the case. The potential of Orientia species establishing in the US is high. In addition, several other recognized pathogens to infect humans, namely Hantavirus, Bartonella, Borrelia, and Rickettsia, were also detected in chiggers. The role that chiggers play in these disease transmissions in the US needs further investigation. It is possible some of the tick-borne diseases and red meat allergies are caused by chiggers.

Host specificity and genetic diversity of Bartonella in rodents and shrews from Eastern China

Bartonella are vector-borne gram-negative facultative intracellular bacteria causing emerging infectious diseases worldwide, and two thirds of known Bartonella species are carried by rodents. We captured rodents, shrews and rodent ectoparasitic mites in rural areas of Qingdao City, Shandong Province, China from 2012 to 2021 and used the animal spleen tissues for the PCR amplification of Bartonella gltA and rpoB genes. PCR showed 9.4% (40/425) rodents, and 5.1% (12/235) shrews were positive for Bartonella. Seven Bartonella species including three novel species were identified in five rodent species and one shrew species, indicating the abundance and genetic diversity of Bartonella in rodents and shrews. The infection rate of each Bartonella species in the animal species was as below: novel Candidatus Bartonella crocidura in shrews Crocidura lasiura (5.1%, 12/235); novel Candidatus Bartonella cricetuli in hamsters Tscherskia triton (20%, 9/45); novel Candidatus Bartonella muris in striped field mice Apodemus agrarius (4.2%, 7/168) and house mice Mus musculus (1.5%, 2/135); Bartonella fuyuanensis in striped field mice (8.9%, 15/168) and house mice (0.7%, 1/135); Bartonella rattimassiliensis and Bartonella tribocorum in brown rats Rattus norvegicus (6.7%, 3/45 and 4.2%, 2/45, respectively); Bartonella queenslandensis in Chinese white-bellied rat Niviventer confucianus (12.5%, 1/8). These results suggest that Bartonella infected a variety of rodent and shrew species with high infection rate, but each Bartonella specie is restricted to infect only one or a few genetically closely related rodent species. In addition, Candidatus Bartonella cricetuli, Candidatus Bartonella muris and Bartonella coopersplainsensis were found in chigger Walchia micropelta (33.3%, 3/9), and B. fuyuanensis were found in chigger Leptotrombidium intermedium (4.1%, 1/24), indicating chiggers may be reservoirs of Bartonella. In conclusion, abundant genetic diversified Bartonella species are found to infect rodents, shrews and chiggers, but each Bartonella species has a strict rodent animal host specificity; and chigger mites may play a role in Bartonella transmission.

Phlebotomine sand flies (Diptera: Psychodidae) and sand fly-borne pathogens in the Greater Mekong Subregion: a systematic review

Phlebotomine sand flies are proven or suspected vectors of several pathogens of importance, including leishmaniasis, bartonellosis and sand fly fevers. Although sand flies have a worldwide distribution, there has been limited research published on sand flies and sand fly-borne pathogens throughout the Greater Mekong Sub-region (GMS). This review followed the PRISMA guidelines to determine the biodiversity and presence of phlebotomine sand flies and their associated pathogens in the GMS, specifically Cambodia, Thailand, the Lao People’s Democratic Republic (Laos), Malaysia and Vietnam. A total of 1472 records were identified by searching electronic databases, scanning reference lists of articles and consulting experts in the field. After screening of title and abstracts, 178 records remained and were further screened for original data (n = 34), not having regional data (n = 14), duplication of data (n = 4), records not available (n = 4) and no language translation available (n = 2). A total of 120 studies were then included for full review, with 41 studies on sand fly-related disease in humans, 33 studies on sand fly-related disease in animals and 54 entomological studies focused on sand flies (5 papers contained data on > 1 category), with a majority of the overall data from Thailand. There were relatively few studies on each country, with the exception of Thailand, and the studies applied different methods to investigate sand flies and sand fly-borne diseases, impacting the ability to conduct meaningful meta-analysis. The findings suggest that leishmaniasis in humans and the presence of sand fly vectors have been reported across several GMS countries over the past 100 years, with local transmission in humans confirmed in Thailand and Vietnam. Additionally, local Mundinia species are likely transmitted by biting midges. Findings from this study provide a framework for future investigations to determine the geographic distribution and risk profiles of leishmaniasis and other associated sand fly-borne disease throughout the GMS. It is recommended that researchers expand surveillance efforts across the GMS, with an emphasis placed on entomological surveys, syndromic and asymptomatic monitoring in both humans and animals and molecular characterization of sand flies and sand fly-borne pathogens, particularly in the understudied countries of Cambodia, Vietnam and Laos.

Not Only Leptotrombidium spp. an Annotated Checklist of Chigger Mites (Actinotrichida: Trombiculidae) Associated with Bacterial Pathogens

Mites of the family Trombiculidae are known for playing a role in maintaining and spreading the scrub typhus etiologic agent, an intracellular Gram-negative bacterium, Orientia tsutsugamushi. Species of the genus Leptotrombidium are investigated most thoroughly, particularly in SE Asia, and a few are proven vectors for the pathogen. The mentioned association, however, is not the only one among trombiculids. Here, we present a list of chiggers indicated in the literature as positive for bacterial pathogens, tested throughout almost 100 years of research. Taxonomic identities of trombiculids follow recent revisions and checklists. Results point at 100 species, from 28 genera, evidenced for association with 31 bacterial taxa. Pathogen-positive mites constitute around 3.3% of the total number of species comprising the family. Discussed arachnids inhabit six biogeographic realms and represent free-living instars as well as external and internal parasites of rodents, soricomorphs, scadents, lagomorphs, peramelemorphs, bats, passerine birds, reptiles and humans. A variety of so far detected bacteria, including novel species, along with the mites’ vast geographical distribution and parasitism on differentiated hosts, indicate that revealing of more cases of Trombiculidae-pathogens association is highly probable, especially utilizing the newest techniques enabling a large-scale bacterial communities survey.

Mites, rodents, and pathogens: A global review for a multi-species interaction in disease ecology

More than ever, there is a need to understand how pathogens, vectors and hosts occur temporally and spatially to predict the occurrence of zoonotic outbreaks. Related to this, mites of the Mesostigmata and Trombidiformes orders have the potential to transmit several diseases, yet their information of occurrence, distribution and zoonotic accompanying agents have not been systematically organized. We conducted a systematic review using a combination of words through the Sysrev platform, as well as literature searches in specialised databases to identify global patterns of infections, trends in mite-rodent-pathogen research and existing knowledge gaps. The inclusion criterion was the detection of pathogens in mites, either by molecular or serological techniques or by direct observation under the microscope, which rendered 125 papers. Most works have been carried out in Asia, mainly around the transmission of Orientia tsutsugamushi. Interestingly, co-infections, i.e., the presence of more than one pathogen in an individual, are common in other Acari groups such as ticks. Moreover, this is not the case for Trombidiformes and Mesostigmata as only 4.7 percent of the articles reviewed detected more than one pathogen in these mites. It is important to include a multi-host, multi-vector and multi-pathogen approaches to understand complex systems in disease ecology. A synergy between mite taxonomists, physicians and veterinarians, decision-makers, governmental organisations, and society is needed to address the emergence of mite-borne new or neglected diseases.

The first report of the seroprevalence of antibodies against Bartonella spp. in water buffaloes (Bubalus bubalis) from South Thailand

Background and Aim:

Bartonellosis is an emerging worldwide zoonosis caused by bacteria belonging to the genus Bartonella. Several studies have been conducted on the prevalence of Bartonella infections from animals and humans, including reports from wild and domestic ruminants. However, there has been only one report of Bartonella infection in water buffaloes from the northeastern part of Thailand. Moreover, the seroprevalence of Bartonella spp. in water buffaloes still remains unknown. This study was conducted to explore the prevalence of Bartonella spp. among water buffaloes from South Thailand using molecular and serological techniques.

Materials and Methods:

A total of 312 samples (156 blood and 156 sera) of 156 water buffaloes from 29 farms in Phatthalung Province, South Thailand, were collected from January to March 2021. All samples were screened for Bartonella spp. using polymerase chain reaction and indirect immunofluorescence assay.

Results:

The seroprevalence of antibodies against three Bartonella spp. was 16.03% (25/156, 95% confidence interval: 10.65-22.74%), and among 25 water buffaloes with seroprevalence, 56%, 20%, and 24% were positive for antibodies against Bartonellahenselae, Bartonellavinsonii subspp. berkhoffii, and Bartonellatamiae, respectively. No significant difference was detected among seroprevalence, gender, age, and ectoparasite infestation.

Conclusion:

This is the first report of the seroprevalence of antibodies against B. henselae, B. vinsonii subspp. berkhoffii, and B. tamiae in water buffaloes from South Thailand. Further studies are required on the epidemiology of Bartonella infection among water buffaloes, related personnel, and ectoparasites.

A novel clade of bat-associated Bartonella detected in the bat fly Leptocyclopodia ferrari (Diptera: Nycteribiidae) parasitizing Cynopterus brachyotis (Chiroptera: Pteropodidae)

Bartonelloses are emerging infectious diseases that are common in humans and animals worldwide. Several Bartonella species associated with companion animals such as Bartonella henselae and Bartonella rochalimae are species with zoonotic implications and have become a global concern. Other Bartonella species associated with wild animals, however, remain underappreciated particularly in the developing regions of the world. To explore further on this neglected bacterial agent, Leptocyclopodia ferrari (Nycteribiidae) bat flies collected from Cynopterus brachyotis (Pteropodidae), an endemic fruit bat species in Southeast Asia, were molecularly examined for the presence of Bartonella. Both 16 S-23 S ribosomal RNA intergenic spacer region and citrate synthase gene sequences exhibited less than 95 % similarity to all previously reported Bartonella spp. Further phylogenetic analysis revealed a novel clade of this Bartonella sp. with high bootstrap support. The vectorial capacity of bat flies in transmitting this novel pathogen merits further investigation.

Detection of zoonotic Bartonella species in ticks and fleas parasitizing free-ranging cats and dogs residing in temples of Bangkok, Thailand

Bartonellosis is a vector-borne disease caused by intraerythrocytic bacteria known as Bartonella spp. The potential vectors that transmit Bartonella spp. are fleas, ticks, sand flies, and lice. Several Bartonella spp. cause diseases in humans; however, there is few molecular evidence of Bartonella spp. in vectors in Thailand. The objectives of this study were to investigate Bartonella spp. and to evaluate the spatial distribution of Bartonella spp. prevalence in the ectoparasites parasitizing free-ranging cats and dogs in temple clusters of Bangkok, Thailand. In total, 343 ectoparasites were studied to extract their genomic DNA. Species of all specimens were identified using an identification key and conventional polymerase chain reaction (cPCR) was applied to confirm flea and tick species. Extracted DNA samples were processed using primers that targeted the gltA, rpoB, ftsZ, and ribC genes of Bartonella spp. Then, PCR-positive amplicons were sequenced and a phylogenetic tree was constructed. Recorded data were statistically analyzed using descriptive statistics, the chi-square test, Fisher's exact test, and the odds ratio. Area data were analyzed and a prevalence distribution map was plotted. The major parasitizing ticks and fleas in this study were Rhipicephalus sanguineus and Ctenocephalides felis, respectively. Overall, the prevalence of Bartonella spp. in ectoparasites was 7.00%. The gltA amplicons revealed the presence of B. henselae (4.78%) and B. clarridgeiae (4.78%) in C. felis, and B. koehlerae (1.25%) and B. phoceensis (1.25%) in R. sanguineus. Bartonella DNA was encountered in 16/39 (41.03%) districts and 28.57% of the temple clusters. Bang Khun Thian district had the highest positive proportion and Bang Bon district showed co-evidence of different Bartonella species. In addition, the intervening zones were a risk factor of Bartonella (p < 0.05), and the distribution map showed a scattered pattern of Bartonella-positive clusters. Finally, fleas showed to be important vector reservoirs for Bartonella spp., especially zoonotic species, however, experimental studies are needed to prove the Bartonella transmission in ticks.

Ectoparasites of hedgehogs: From flea mite phoresy to their role as vectors of pathogens

Hedgehogs are synanthropic mammals, reservoirs of several vector-borne pathogens and hosts of ectoparasites. Arthropod-borne pathogens (i.e., Rickettsia spp., Borrelia spp., and Anaplasmataceae) were molecularly investigated in ectoparasites collected on hedgehogs (n = 213) from Iran (161 Hemiechinus auritus, 5 Erinaceus concolor) and Italy (47 Erinaceus europaeus). In Iran, most animals examined (n = 153; 92.2%) were infested by ticks (Rhipicephalus turanicus, Hyalomma dromedarii), and 7 (4.2%) by fleas (Archeopsylla erinacei, Ctenocephalides felis). Of the hedgehogs infested by arthropods in Italy (i.e., 44.7%), 18 (38.3%) were infested by fleas (Ar. erinacei), 7 (14.9%) by ticks (Haemaphysalis erinacei, Rh. turanicus, Rhipicephalus sanguineus sensu lato), and 6 (12.8%) by mites (Caparinia tripilis, Acarus nidicolous, Ornithonyssus spp.). Phoretic behavior of C. tripilis on Ar. erinacei was detected in two flea specimens from Italy. At the molecular analysis Rickettsia spp. was detected in 93.3% of the fleas of Italy. In Iran, Rickettsia spp. was detected in 8.0% out of 212 Rh. turanicus ticks, and in 85.7% of the Ar. erinacei fleas examined. The 16S rRNA gene for Ehrlichia/Anaplasma spp. was amplified in 4.2% of the 212 Rh. turanicus ticks. All sequences of Rickettsia spp. from fleas presented 100% nucleotide identity with Rickettsia asembonensis, whereas Rickettsia spp. from Rh. turanicus presented 99.84%–100% nucleotide identity with Rickettsia slovaca, except for one sequence, identical to Rickettsia massiliae. The sequences of the 16S rRNA gene revealed 99.57%–100% nucleotide identity with Anaplasma spp., except for one, identical to Ehrlichia spp. A new phoretic association between C. tripilis mites and Ar. erinacei fleas has been herein reported, which could be an important route for the spreading of this mite through hedgehog populations. Additionally, spotted fever group rickettsiae were herein detected in ticks and fleas, and Anaplasma/Ehrlichia spp. in ticks, suggesting that hedgehogs play a role as reservoirs for these vector-borne pathogens.

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New phoretic association of Caparinia tripilis mites on Archaeopsylla erinacei fleas.

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Occurrence of spotted fever group rickettsiae in Rhipicephalus turanicus from hedgehogs.

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Occurrence of Anaplasmataceae in Rhipicephalus turanicus from hedgehogs.

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High Prevalence of Rickettsia asembonensis in Archaeopsylla erinacei fleas from hedgehogs.

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Hedgehogs are suggested as reservoirs of vector-borne pathogens.

Chigger Mites (Acariformes: Trombiculidae) of Chiloé Island, Chile, With Descriptions of Two New Species and New Data on the Genus Herpetacarus

Three species of chigger mites are recorded in our collections from four species of cricetid rodents on Chiloé Island (southern Chile, Los Lagos Region), an area endemic to scrub typhus (Orientia sp.). Two species are described as new-Herpetacarus (Abonnencia) eloisae sp. nov. and Quadraseta chiloensis sp. nov. One species, Paratrombicula goffiStekolnikov and González-Acuña 2012, is for the first time recorded on a mammal host (one species of cricetid rodent), and its distribution is extended to the Los Lagos Region of Chile. The genus ProschoengastiaVercammen-Grandjean, 1967 is synonymized with the subgenus Herpetacarus (Abonnencia)Vercammen-Grandjean, 1960, and four new combinations are established: Herpetacarus (Abonnencia) herniosa (Brennan and Jones, 1961), comb. nov., Herpetacarus (Abonnencia) insolita (Brennan and Jones, 1961), comb. nov., Herpetacarus (Abonnencia) macrochaeta (Brennan and Jones, 1961), comb. nov., and Herpetacarus (Abonnencia) antarctica (Stekolnikov and Gonzalez-Acuña, 2015), comb. nov.

Bartonella species in medically important mosquitoes, Central Europe

Here, we provide the first mass molecular screening of medically important mosquitoes for Bartonella species using multiple genetic markers. We examined a total of 72,115 mosquito specimens, morphologically attributed to Aedes vexans (61,050 individuals), Culex pipiens (10,484 individuals) and species of the Anopheles maculipennis complex (581 individuals) for Bartonella spp. The initial screening yielded 63 Bartonella-positive A. vexans mosquitoes (mean prevalence 0.1%), 34 Bartonella-positive C. pipiens mosquitoes (mean prevalence 0.3%) and 158 Bartonella-positive A. maculipennis group mosquitoes (mean prevalence 27.2%). Several different Bartonella ITS sequences were recovered. This study highlights the need for molecular screening of mosquitoes, the most important vectors of arthropod-borne pathogens, for potential bacterial agents.

Bartonella spp. Prevalence (Serology, Culture, and PCR) in Sanitary Workers in La Rioja Spain

Bartonella spp. are increasingly implicated in association with a spectrum of zoonotic infectious diseases. One hundred sanitary workers in La Rioja, Spain completed a questionnaire and provided blood specimens for Bartonella spp. serology and Bartonella alpha-Proteobacteria growth medium (BAPGM) enrichment blood culture/PCR. Six immunofluorescence assays (IFA) were performed and aseptically obtained blood specimens were inoculated into liquid BAPGM and subcultured onto blood agar plates. Bartonella DNA was amplified using conventional and real-time PCR assays. The Bartonella spp., strain, or genotype was determined by DNA sequencing. Bartonella seroreactivity was documented in 83.1% and bloodstream infection in 21.6% of participants. Bartonella henselae, B. vinsonii subsp. berkhoffii genotypes I and III, and B. quintana were identified. IFA seroreactivity and PCR positivity were not statistically associated with self-reported symptoms. Our results suggest that exposure to and non-clinical infection with Bartonella spp. may occur more often than previously suspected in the La Rioja region.

Ecological and microbiological diversity of chigger mites, including vectors of scrub typhus, on small mammals across stratified habitats in Thailand

BACKGROUND

Scrub typhus, caused by a bacterial pathogen (Orientia spp.), is a potentially life-threatening febrile illness widely distributed in the Asia-Pacific region and is emerging elsewhere. The infection is transmitted by the larval stage of trombiculid mites ("chiggers") that often exhibit low host specificity. Here, we present an analysis of chigger ecology for 38 species sampled from 11 provinces of Thailand and microbiomes for eight widespread species.

RESULTS

In total, > 16,000 individual chiggers were collected from 1574 small mammal specimens belonging to 18 species across four horizontally-stratified habitat types. Chigger species richness was positively associated with higher latitudes, dry seasonal conditions, and host maturity; but negatively associated with increased human land use. Human scrub typhus incidence was found to be positively correlated with chigger species richness. The bacterial microbiome of chiggers was highly diverse, with Sphingobium, Mycobacterium, Neisseriaceae and various Bacillales representing the most abundant taxa. Only Leptotrombidium deliense was found to be infected with Orientia and another potential pathogen, Borrelia spp., was frequently detected in pools of this species. β-diversity, but not α-diversity, was significantly different between chigger species and geographic regions, although not between habitat types.

CONCLUSION

Our study identified several key environmental and host-derived correlates of chigger species richness across Thailand, which in turn impacted on human scrub typhus incidence. Moreover, this first extensive field survey of the chigger microbiome revealed species- and province-level variation in microbial β-diversity across the country, providing a framework for future studies on interactions between pathogens and other symbionts in these understudied vectors.

Human Exposure to Novel Bartonella Species from Contact with Fruit Bats

Twice a year in southwestern Nigeria, during a traditional bat festival, community participants enter designated caves to capture bats, which are then consumed for food or traded. We investigated the presence of Bartonella species in Egyptian fruit bats (Rousettus aegyptiacus) and bat flies (Eucampsipoda africana) from these caves and assessed whether Bartonella infections had occurred in persons from the surrounding communities. Our results indicate that these bats and flies harbor Bartonella strains, which multilocus sequence typing indicated probably represent a novel Bartonella species, proposed as Bartonella rousetti. In serum from 8 of 204 persons, we detected antibodies to B. rousetti without cross-reactivity to other Bartonella species. This work suggests that bat-associated Bartonella strains might be capable of infecting humans.

Human Bartonellosis: An Underappreciated Public Health Problem?

Bartonella spp. bacteria can be found around the globe and are the causative agents of multiple human diseases. The most well-known infection is called cat-scratch disease, which causes mild lymphadenopathy and fever. As our knowledge of these bacteria grows, new presentations of the disease have been recognized, with serious manifestations. Not only has more severe disease been associated with these bacteria but also Bartonella species have been discovered in a wide range of mammals, and the pathogens’ DNA can be found in multiple vectors. This review will focus on some common mammalian reservoirs as well as the suspected vectors in relation to the disease transmission and prevalence. Understanding the complex interactions between these bacteria, their vectors, and their reservoirs, as well as the breadth of infection by Bartonella around the world will help to assess the impact of Bartonellosis on public health.

Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism

Background

Trombidid mites have a unique life cycle in which only the larval stage is ectoparasitic. In the superfamily Trombiculoidea ("chiggers"), the larvae feed preferentially on vertebrates, including humans. Species in the genus Leptotrombidium are vectors of a potentially fatal bacterial infection, scrub typhus, that affects 1 million people annually. Moreover, chiggers can cause pruritic dermatitis (trombiculiasis) in humans and domesticated animals. In the Trombidioidea (velvet mites), the larvae feed on other arthropods and are potential biological control agents for agricultural pests. Here, we present the first trombidid mites genomes, obtained both for a chigger, Leptotrombidium deliense, and for a velvet mite, Dinothrombium tinctorium.

Results

Sequencing was performed using Illumina technology. A 180 Mb draft assembly for D. tinctorium was generated from two paired-end and one mate-pair library using a single adult specimen. For L. deliense, a lower-coverage draft assembly (117 Mb) was obtained using pooled, engorged larvae with a single paired-end library. Remarkably, both genomes exhibited evidence of ancient lateral gene transfer from soil-derived bacteria or fungi. The transferred genes confer functions that are rare in animals, including terpene and carotenoid synthesis. Thirty-seven allergenic protein families were predicted in the L. deliense genome, of which nine were unique. Preliminary proteomic analyses identified several of these putative allergens in larvae.

Conclusions

Trombidid mite genomes appear to be more dynamic than those of other acariform mites. A priority for future research is to determine the biological function of terpene synthesis in this taxon and its potential for exploitation in disease control.

Global fingerprint of humans on the distribution of Bartonella bacteria in mammals

As humans move and alter habitats, they change the disease risk for themselves, their commensal animals and wildlife. Bartonella bacteria are prevalent in mammals and cause numerous human infections. Understanding how this genus has evolved and switched hosts in the past can reveal how current patterns were established and identify potential mechanisms for future cross-species transmission. We analyzed patterns of Bartonella transmission and likely sources of spillover using the largest collection of Bartonella gltA genotypes assembled, including 67 new genotypes. This pathogenic genus likely originated as an environmental bacterium and insect commensal before infecting mammals. Rodents and domestic animals serve as the reservoirs or at least key proximate host for most Bartonella genotypes in humans. We also find evidence of exchange of Bartonella between phylogenetically distant domestic animals and wildlife, likely due to increased contact. Care should be taken to avoid contact between humans, domestic animals and wildlife to protect the health of all.

As humans move around the globe they contact new environments, potentially introducing novel diseases to wildlife, domestic animals and humans. Understanding how current infection patterns were established and how humans have likely altered them can help protect human, animal and environmental health. We traced the evolution of and distribution of globally distributed, pathogenic Bartonella, a common and well-studied bacterial genus in wildlife and humans that can cause cat scratch disease, trench fever and other diseases. We showed that humans are likely changing disease risk for themselves and the animals in their environment by moving themselves and domestic animals, as evidenced by large geographic movements of infections or shared infections in distantly related species. Not only does this increase our knowledge about Bartonella, an important emerging pathogen, but our investigation can serve as a model for elucidating the driving role of humans in changing disease landscapes.

Dietary specialization in mutualistic acacia-ants affects relative abundance but not identity of host-associated bacteria

Acacia-ant mutualists in the genus Pseudomyrmex nest obligately in acacia plants and, as we show through stable isotope analysis, feed at a remarkably low trophic level. Insects with diets such as these sometimes depend on bacterial symbionts for nutritional enrichment. We, therefore, examine the bacterial communities associated with acacia-ants in order to determine whether they host bacterial partners likely to contribute to their nutrition. Despite large differences in trophic position, acacia-ants and related species with generalized diets do not host distinct bacterial taxa. However, we find that a small number of previously undescribed bacterial taxa do differ in relative abundance between acacia-ants and generalists, including several Acetobacteraceae and Nocardiaceae lineages related to common insect associates. Comparisons with an herbivorous generalist, a parasite that feeds on acacias and a mutualistic species with a generalized diet show that trophic level is likely responsible for these small differences in bacterial community structure. While we did not experimentally test for a nutritional benefit to hosts of these bacterial lineages, metagenomic analysis reveals a Bartonella relative with an intact nitrogen-recycling pathway widespread across Pseudomyrmex mutualists and generalists. This taxon may be contributing to nitrogen enrichment of its ant hosts through urease activity and, concordant with an obligately host-associated lifestyle, appears to be experiencing genomewide relaxed selection. The lack of distinctiveness in bacterial communities across trophic level in this group of ants shows a remarkable ability to adjust to varied diets, possibly with assistance from these diverse ant-specific bacterial lineages.

Molecular assessment of Bartonella in Gerbillus nanus from Saudi Arabia reveals high levels of prevalence, diversity and co-infection

Bartonellae bacteria are associated with several re-emerging human diseases. These vector-borne pathogens have a global distribution, yet data on Bartonella prevalence and diversity in the Arabian Peninsula are limited. In this study we assessed the Bartonella infection status of the Baluchistan gerbil (Gerbillus nanus), a species associated with pastoral communities throughout the Middle East region, using a multi-gene PCR screening approach. The results demonstrated that 94 (68.1%) of the 138 gerbils trapped on a monthly basis, over a period of one year, were PCR-positive. Sequencing of the gltA gene region confirmed the presence of four discrete Bartonella lineages (I-IV) and high levels of co-infection (33.0%). Each of the four lineages, varied in overall abundance (7.5%-47.9%) and had discernible seasonal peaks. Bartonella status was significantly correlated with ectoparasite presence, but not with sex, nor with season. Statistical analyses further revealed that co-infected individuals had a significantly higher relative body condition. Multi-locus sequence analysis (MLSA) performed with a concatenated dataset of three genetic loci (gltA, nuoG, and rpoB), 1452 nucleotides (nt) in length confirmed that lineage IV, which occurred in 24 PCR-positive animals (25.5%), is most closely related to zoonotic B. elizabethae. The remaining three lineages (I-III) formed a monophyletic clade which, on the basis of gltA was shown to contain bartonellae from diverse Gerbillinae species from the Middle East, suggestive of a gerbil-associated species complex in this region. Lineage I was identical to a Candidatus B. sanaae strain identified previously in Bushy-tailed jirds (Sekeetamys calurus) from Egypt, wherease MLSA indicate that lineages II and III are novel. The high levels of infection and co-infection, together with the presence of multiple Bartonella lineages indicate that Gerbillus nanus is likely a natural reservoir of Bartonella in the Arabian Peninsula.

Bartonella Species, an Emerging Cause of Blood-Culture-Negative Endocarditis

Since the reclassification of the genus Bartonella in 1993, the number of species has grown from 1 to 45 currently designated members. Likewise, the association of different Bartonella species with human disease continues to grow, as does the range of clinical presentations associated with these bacteria. Among these, blood-culture-negative endocarditis stands out as a common, often undiagnosed, clinical presentation of infection with several different Bartonella species. The limitations of laboratory tests resulting in this underdiagnosis of Bartonella endocarditis are discussed. The varied clinical picture of Bartonella infection and a review of clinical aspects of endocarditis caused by Bartonella are presented. We also summarize the current knowledge of the molecular basis of Bartonella pathogenesis, focusing on surface adhesins in the two Bartonella species that most commonly cause endocarditis, B. henselae and B. quintana. We discuss evidence that surface adhesins are important factors for autoaggregation and biofilm formation by Bartonella species. Finally, we propose that biofilm formation is a critical step in the formation of vegetative masses during Bartonella-mediated endocarditis and represents a potential reservoir for persistence by these bacteria.

Genotyping ofBartonellabacteria and their animal hosts: current status and perspectives

Growing evidence demonstrates that bacterial species diversity is substantial, and many of these species are pathogenic in some contexts or hosts. At the same time, laboratories and museums have collected valuable animal tissue and ectoparasite samples that may contain substantial novel information on bacterial prevalence and diversity. However, the identification of bacterial species is challenging, partly due to the difficulty in culturing many microbes and the reliance on molecular data. Although the genomics revolution will surely add to our knowledge of bacterial systematics, these approaches are not accessible to all researchers and rely predominantly on cultured isolates. Thus, there is a need for comprehensive molecular analyses capable of accurately genotyping bacteria from animal tissues or ectoparasites using common methods that will facilitate large-scale comparisons of species diversity and prevalence. To illustrate the challenges of genotyping bacteria, we focus on the genusBartonella, vector-borne bacteria common in mammals. We highlight the value and limitations of commonly used techniques for genotyping bartonellae and make recommendations for researchers interested in studying the diversity of these bacteria in various samples. Our recommendations could be applicable to many bacterial taxa (with some modifications) and could lead to a more complete understanding of bacterial species diversity.

Genomic changes associated with the evolutionary transition of an insect gut symbiont into a blood-borne pathogen

The genus Bartonella comprises facultative intracellular bacteria with a unique lifestyle. After transmission by blood-sucking arthropods they colonize the erythrocytes of mammalian hosts causing acute and chronic infectious diseases. Although the pathogen–host interaction is well understood, little is known about the evolutionary origin of the infection strategy manifested by Bartonella species. Here we analyzed six genomes of Bartonella apis, a honey bee gut symbiont that to date represents the closest relative of pathogenic Bartonella species. Comparative genomics revealed that B. apis encodes a large set of vertically inherited genes for amino acid and cofactor biosynthesis and nitrogen metabolism. Most pathogenic bartonellae have lost these ancestral functions, but acquired specific virulence factors and expanded a vertically inherited gene family for harvesting cofactors from the blood. However, the deeply rooted pathogen Bartonella tamiae has retained many of the ancestral genome characteristics reflecting an evolutionary intermediate state toward a host-restricted intraerythrocytic lifestyle. Our findings suggest that the ancestor of the pathogen Bartonella was a gut symbiont of insects and that the adaptation to blood-feeding insects facilitated colonization of the mammalian bloodstream. This study highlights the importance of comparative genomics among pathogens and non-pathogenic relatives to understand disease emergence within an evolutionary-ecological framework.

The genome of Rhizobiales bacteria in predatory ants reveals urease gene functions but no genes for nitrogen fixation

Gut-associated microbiota of ants include Rhizobiales bacteria with affiliation to the genus Bartonella. These bacteria may enable the ants to fix atmospheric nitrogen, but no genomes have been sequenced yet to test the hypothesis. Sequence reads from a member of the Rhizobiales were identified in the data collected in a genome project of the ant Harpegnathos saltator. We present an analysis of the closed 1.86 Mb genome of the ant-associated bacterium, for which we suggest the species name Candidatus Tokpelaia hoelldoblerii. A phylogenetic analysis reveals a relationship to Bartonella and Brucella, which infect mammals. Novel gene acquisitions include a gene for a putative extracellular protein of more than 6,000 amino acids secreted by the type I secretion system, which may be involved in attachment to the gut epithelium. No genes for nitrogen fixation could be identified, but genes for a multi-subunit urease protein complex are present in the genome. The urease genes are also present in Brucella, which has a fecal-oral transmission pathway, but not in Bartonella, which use blood-borne transmission pathways. We hypothesize that the gain and loss of the urease function is related to transmission strategies and lifestyle changes in the host-associated members of the Rhizobiales.

Detection of Bartonella tamiae, Coxiella burnetii and rickettsiae in arthropods and tissues from wild and domestic animals in northeastern Algeria

Background

In recent years, the scope and importance of emergent vector-borne diseases has increased dramatically. In Algeria, only limited information is currently available concerning the presence and prevalence of these zoonotic diseases. For this reason, we conducted a survey of hematophagous ectoparasites of domestic mammals and/or spleens of wild animals in El Tarf and Souk Ahras, Algeria.

Methods

Using real-time PCR, standard PCR and sequencing, the presence of Bartonella spp., Rickettsia spp., Borrelia spp. and Coxiella burnetii was evaluated in 268/1626 ticks, 136 fleas, 11 Nycteribiidae flies and 16 spleens of domestic and/or wild animals from the El Tarf and Souk Ahras areas.

Results

For the first time in Algeria, Bartonella tamiae was detected in 12/19 (63.2 %) Ixodes vespertilionis ticks, 8/11 (72.7 %) Nycteribiidae spp. flies and in 6/10 (60 %) bat spleens (Chiroptera spp.). DNA from Coxiella burnetii, the agent of Q fever, was also identified in 3/19 (15.8 %) I. vespertilionis from bats. Rickettsia slovaca, the agent of tick-borne lymphadenopathy, was detected in 1/1 (100 %) Haemaphysalis punctata and 2/3 (66.7 %) Dermacentor marginatus ticks collected from two boars (Sus scrofa algira) respectively. Ri. massiliae, an agent of spotted fever, was detected in 38/94 (40.4 %) Rhipicephalus sanguineus sensu lato collected from cattle, sheep, dogs, boars and jackals. DNA of Ri. aeschlimannii was detected in 6/20 (30 %) Hyalomma anatolicum excavatum and 6/20 (30 %) Hy. scupense from cattle. Finally, Ri. felis, an emerging rickettsial pathogen, was detected in 80/110 (72.7 %) Archaeopsylla erinacei and 2/2 (100 %) Ctenocephalides felis of hedgehogs (Atelerix algirus).

Conclusion

In this study, we expanded knowledge about the repertoire of ticks and flea-borne bacteria present in ectoparasites and/or tissues of domestic and wild animals in Algeria.

Bartonella species and trombiculid mites of rats from the Mekong Delta of Vietnam

A survey of Bartonella spp. from 275 rats purchased in food markets (n=150) and trapped in different ecosystems (rice field, forest, and animal farms) (n=125) was carried out during October, 2012–March, 2013, in the Mekong Delta of Vietnam. The overall Bartonella spp. prevalence detected by culture and PCR in blood was 14.9% (10.7–19.1%), the highest corresponding to Rattus tanezumi (49.2%), followed by Rattus norvegicus (20.7%). Trapped rats were also investigated for the presence and type of chiggers (larvae of trombiculid mites), and Bartonella spp. were investigated on chigger pools collected from each rat by RT-PCR. A total of five Bartonella spp. were identified in rats, three of which (B. elizabethae, B. rattimassiliensis, and B. tribocorum) are known zoonotic pathogens. Among trapped rats, factors independently associated with increased prevalence of Bartonella spp. included: (1) Rat species (R. tanezumi); (2) the number of Trombiculini–Blankaartia and Schoengastiini–Ascoschoengastia mites found on rats; and (3) the habitat of the rat (i.e., forest/fields vs. animal farms). The prevalence of Bartonella infection among chiggers from Bartonella spp.–positive R. tanezumi rats was 5/25 (25%), compared with 1/27 (3.7%) among Bartonella spp.–negative R. tanezumi rats (relative risk [RR]=5.4, 95% confidence interval [CI] 0.68–43.09). The finding of Bartonella spp.–positive chiggers on Bartonella spp.–negative rats is strongly suggestive of a transovarial transmission cycle. Rats are ubiquitous in areas of human activity and farms in the Mekong Delta; in addition, trapping and trading of rats for food is common. To correctly assess the human risks due to rat trapping, marketing, and carcass dressing, further studies are needed to establish the routes of transmission and cycle of infection. The widespread presence of these zoonotic pathogens in rats and the abundance of human—rat interactions suggest that surveillance efforts should be enhanced to detect any human cases of Bartonella infection that may arise.

Bartonella spp. infections in rodents of Cambodia, Lao PDR, and Thailand: identifying risky habitats

This study investigated the type of environmental habitat that may explain the infection of 1176 individuals from 17 rodent species by Bartonella species in seven sites in Cambodia, Lao PDR, and Thailand. No effects of host sex and host maturity on the level of individual infection by all Bartonella spp., but significant effects of locality, season, and host species were observed. The patterns differed when investigating the three more prevalent Bartonella species. For B. rattimassiliensis, season and habitat appeared to be significant factors explaining host infection, with higher levels of infection in wet season and lower levels of infection in rain-fed field, dry field, and human settlement habitats compared to forest habitat. The infection by B. queenslandensis was found to vary, although not significantly, with season and locality, and Bartonella n. sp. (a species mostly associated with Mus spp.) was found to be more prevalent in the wet season and dry field habitat compared to forest habitat. We discuss these results in relation to rodent habitat specificity.

The Distribution and Diversity of Bartonella Species in Rodents and Their Ectoparasites across Thailand

Our study highlights the surveillance of Bartonella species among rodents and their associated ectoparasites (ticks, fleas, lice, and mites) in several regions across Thailand. A total of 619 rodents and 554 pooled ectoparasites (287 mite pools, 62 flea pools, 35 louse pools, and 170 tick pools) were collected from 8 provinces within 4 regions of Thailand. Bandicota indica (279), Rattus rattus (163), and R. exulans (96) were the most prevalent species of rats collected in this study. Real-time PCR assay targeting Bartonella-specific ssrA gene was used for screening and each positive sample was confirmed by PCR using nuoG gene. The prevalence of Bartonella DNA in rodent (around 17%) was recorded in all regions. The highest prevalence of Bartonella species was found in B. savilei and R. rattus with the rate of 35.7% (5/14) and 32.5% (53/163), respectively. High prevalence of Bartonella-positive rodent was also found in B. indica (15.1%, 42/279), and R. norvegicus (12.5%, 5/40). In contrast, the prevalence of Bartonella species in ectoparasites collected from the rats varied significantly according to types of ectoparasites. A high prevalence of Bartonella DNA was found in louse pools (Polyplax spp. and Hoplopleura spp., 57.1%) and flea pools (Xenopsylla cheopis, 25.8%), while a low prevalence was found in pools of mites (Leptotrombidium spp. and Ascoschoengastia spp., 1.7%) and ticks (Haemaphysalis spp., 3.5%). Prevalence of Bartonella DNA in ectoparasites collected from Bartonella-positive rodents (19.4%) was significantly higher comparing to ectoparasites from Bartonella-negative rodents (8.7%). The phylogenetic analysis of 41 gltA sequences of 16 Bartonella isolates from rodent blood and 25 Bartonella-positive ectoparasites revealed a wide range of diversity among Bartonella species with a majority of sequences (61.0%) belonging to Bartonella elizabethae complex (11 rodents, 1 mite pool, and 5 louse pools), while the remaining sequences were identical to B. phoceensis (17.1%, 1 mite pool, 5 louse pools, and 1 tick pool), B. coopersplainensis (19.5%, 5 rodents, 1 louse pool, and 2 tick pools), and one previously unidentified Bartonella species (2.4%, 1 louse pool).

Symbiosis in an overlooked microcosm: a systematic review of the bacterial flora of mites

A dataset of bacterial diversity found in mites was compiled from 193 publications (from 1964 to January 2015). A total of 143 mite species belonging to the 3 orders (Mesostigmata, Sarcoptiformes and Trombidiformes) were recorded and found to be associated with approximately 150 bacteria species (in 85 genera, 51 families, 25 orders and 7 phyla). From the literature, the intracellular symbiont Cardinium, the scrub typhus agent Orientia, and Wolbachia (the most prevalent symbiont of arthropods) were the dominant mite-associated bacteria, with approximately 30 mite species infected each. Moreover, a number of bacteria of medical and veterinary importance were also reported from mites, including species from the genera Rickettsia, Anaplasma, Bartonella, Francisella, Coxiella, Borrelia, Salmonella, Erysipelothrix and Serratia. Significant differences in bacterial infection patterns among mite taxa were identified. These data will not only be useful for raising awareness of the potential for mites to transmit disease, but also enable a deeper understanding of the relationship of symbionts with their arthropod hosts, and may facilitate the development of intervention tools for disease vector control. This review provides a comprehensive overview of mite-associated bacteria and is a valuable reference database for future research on mites of agricultural, veterinary and/or medical importance.

Parasitic mites of medical and veterinary importance--is there a common research agenda?

There are an estimated 0.5-1 million mite species on earth. Among the many mites that are known to affect humans and animals, only a subset are parasitic but these can cause significant disease. We aim here to provide an overview of the most recent work in this field in order to identify common biological features of these parasites and to inform common strategies for future research. There is a critical need for diagnostic tools to allow for better surveillance and for drugs tailored specifically to the respective parasites. Multi-'omics' approaches represent a logical and timely strategy to identify the appropriate mite molecules. Recent advances in sequencing technology enable us to generate de novo genome sequence data, even from limited DNA resources. Consequently, the field of mite genomics has recently emerged and will now rapidly expand, which is a particular advantage for parasitic mites that cannot be cultured in vitro. Investigations of the microbiota associated with mites will elucidate the link between parasites and pathogens, and define the role of the mite in transmission and pathogenesis. The databases generated will provide the crucial knowledge essential to design novel diagnostic tools, control measures, prophylaxes, drugs and immunotherapies against the mites and associated secondary infections.

Estimation of the genome sizes of the chigger mites Leptotrombidium pallidum and Leptotrombidium scutellare based on quantitative PCR and k-mer analysis

BACKGROUND

Leptotrombidium pallidum and Leptotrombidium scutellare are the major vector mites for Orientia tsutsugamushi, the causative agent of scrub typhus. Before these organisms can be subjected to whole-genome sequencing, it is necessary to estimate their genome sizes to obtain basic information for establishing the strategies that should be used for genome sequencing and assembly.

METHOD

The genome sizes of L. pallidum and L. scutellare were estimated by a method based on quantitative real-time PCR. In addition, a k-mer analysis of the whole-genome sequences obtained through Illumina sequencing was conducted to verify the mutual compatibility and reliability of the results.

RESULTS

The genome sizes estimated using qPCR were 191 ± 7 Mb for L. pallidum and 262 ± 13 Mb for L. scutellare. The k-mer analysis-based genome lengths were estimated to be 175 Mb for L. pallidum and 286 Mb for L. scutellare. The estimates from these two independent methods were mutually complementary and within a similar range to those of other Acariform mites.

CONCLUSIONS

The estimation method based on qPCR appears to be a useful alternative when the standard methods, such as flow cytometry, are impractical. The relatively small estimated genome sizes should facilitate whole-genome analysis, which could contribute to our understanding of Arachnida genome evolution and provide key information for scrub typhus prevention and mite vector competence.

Contrasting patterns in mammal-bacteria coevolution: bartonella and leptospira in bats and rodents

BACKGROUND

Emerging bacterial zoonoses in bats and rodents remain relatively understudied. We conduct the first comparative host-pathogen coevolutionary analyses of bacterial pathogens in these hosts, using Bartonella spp. and Leptospira spp. as a model.

METHODOLOGY/PRINCIPAL FINDINGS

We used published genetic data for 51 Bartonella genotypes from 24 bat species, 129 Bartonella from 38 rodents, and 26 Leptospira from 20 bats. We generated maximum likelihood and Bayesian phylogenies for hosts and bacteria, and tested for coevoutionary congruence using programs ParaFit, PACO, and Jane. Bartonella spp. and their bat hosts had a significant coevolutionary fit (ParaFitGlobal = 1.9703, P≤0.001; m2 global value = 7.3320, P≤0.0001). Bartonella spp. and rodent hosts also indicated strong overall patterns of cospeciation (ParaFitGlobal = 102.4409, P≤0.001; m2 global value = 86.532, P≤0.0001). In contrast, we were unable to reject independence of speciation events in Leptospira and bats (ParaFitGlobal = 0.0042, P = 0.84; m2 global value = 4.6310, P = 0.5629). Separate analyses of New World and Old World data subsets yielded results congruent with analysis from entire datasets. We also conducted event-based cophylogeny analyses to reconstruct likely evolutionary histories for each group of pathogens and hosts. Leptospira and bats had the greatest number of host switches per parasite (0.731), while Bartonella and rodents had the fewest (0.264).

CONCLUSIONS/SIGNIFICANCE

In both bat and rodent hosts, Bartonella exhibits significant coevolution with minimal host switching, while Leptospira in bats lacks evolutionary congruence with its host and has high number of host switches. Reasons underlying these variable coevolutionary patterns in host range are likely due to differences in disease-specific transmission and host ecology. Understanding the coevolutionary patterns and frequency of host-switching events between bacterial pathogens and their hosts will allow better prediction of spillover between mammal reservoirs, and ultimately to humans.

Bartonella-like bacteria carried by domestic mite species

Bacteria of the genus Bartonella are carried by haematophagous mites, ticks, fleas and flies, and attack the erythrocytes of mammals. Here we describe a Bartonella-like clade, a distinct group related to Bartonellaceae, in stored-product mites (Acari: Astigmata) and a predatory mite Cheyletus eruditus (Acari: Prostigmata) based on the analysis of cloned 16S rRNA gene sequences. By using the clade-specific primers, closely related Bartonella-like 16S rRNA sequences were amplified from both laboratory colonies and field strains of three synanthropic mite species (Acarus siro, Lepidoglyphus destructor and Tyrophagus putrescentiae) and a predatory mite. Altogether, sequences of Bartonella-like bacteria were found in 11 strains, but were not detected in Dermatophagoides farinae and D. pteronyssinus and two strains of L. destructor. All obtained sequences formed a separate cluster branching as a sister group to Bartonellaceae and related to other separate clusters comprising uncultured bacterial clones from human skin and hemipteran insects (Nysius plebeius and Nysius sp.). The classification of sequences into operational taxonomic units (OTUs) showed a difference between A. siro and T. putrescentiae suggesting that the Bartonella-like bacteria are different in these two mite species. However, species specific sequences in separate OTUs were observed also for C. eruditus. Possible symbiotic interactions between Bartonella-like bacteria and their mite hosts are discussed.

Natural history of Bartonella-infecting rodents in light of new knowledge on genomics, diversity and evolution

Among the 33 confirmed Bartonella species to date, more than half are hosted by rodent species, and at least five of them have been involved in human illness causing diverse symptoms including fever, myocarditis, endocarditis, lymphadenitis and hepatitis. In almost all countries, wild rodents are infected by extremely diverse Bartonella strains with a high prevalence. In the present paper, in light of new knowledge on rodent-adapted Bartonella species genomics, we bring together knowledge gained in recent years to have an overview of the impact of rodent-adapted Bartonella infection on humans and to determine how diversity of Bartonella helps to understand their mechanisms of adaptation to rodents and the consequences on human health.

Molecular detection and identification of Bartonella species in rat fleas from northeastern Thailand

The presence of Bartonella species in Xenopsylla cheopis fleas collected from Rattus spp. (R. exulans, R. norvegicus, and R. rattus) in Khon Kaen Province, Thailand was investigated. One hundred ninety-three fleas obtained from 62 rats, were screened by polymerase chain reaction using primers specific for the 16S-23S intergenic spacer region, and the presence of Bartonella DNA was confirmed by using the citrate synthase gene. Bartonella DNA was detected in 59.1% (114 of 193) of fleas examined. Sequencing demonstrated the presence of Bartonella spp. similar to B. elizabethae, B. rattimassiliensis, B. rochalimae, and B. tribocorum in the samples tested with a cutoff for sequence similarity ≥ 96% and 4 clustered together with the closest match with B. grahamii (95.5% identity). If X. cheopis proves to be a competent vector of these species, our results suggest that humans and animals residing in this area may be at risk for infection by several zoonotic Bartonella species.

Prevalence and diversity of Bartonella species in commensal rodents and ectoparasites from Nigeria, West Africa

Background

Bartonellae are fastidious bacteria causing persistent bacteremia in humans and a wide variety of animals. In recent years there is an increasing interest in mammalian bartonelloses in general and in rodent bartonelloses in particular. To date, no studies investigating the presence of Bartonella spp. in rodents and ectoparasites from Nigeria were carried out.

Methodology/Principal Findings

The aim of the current study was to investigate the presence of Bartonella spp. in commensal rodents and their ectoparasites in Nigeria. We report, for the first time, the molecular detection of Bartonella in 26% (46/177) of commensal rodents (Rattus rattus, R. norvegicus and Cricetomys gambianus) and 28% (9/32) of ectoparasite pools (Xenopsylla cheopis, Haemolaelaps spp., Ctenophthalmus spp., Hemimerus talpoides, and Rhipicephalus sanguineus) from Nigeria. Sequence analysis of the citrate synthase gene (gltA) revealed diversity of Bartonella spp. and genotypes in Nigerian rodents and their ectoparasites. Bartonella spp. identical or closely related to Bartonella elizabethae, Bartonella tribocorum and Bartonella grahamii were detected.

Conclusions/Significance

High prevalence of infection with Bartonella spp. was detected in commensal rodents and ectoparasites from Nigeria. The Bartonella spp. identified were previously associated with human diseases highlighting their importance to public health. Further studies need to be conducted to determine whether the identified Bartonella species could be responsible for human cases of febrile illness in Nigeria.

Bartonella species are zoonotic vector-borne bacteria that typically parasitize the erythrocytes of mammalian hosts, resulting in long lasting infections. They are responsible for a wide range of clinical manifestations in both immunocompetent and immunocompromised hosts.

Rodents and a wide range of small mammals serve as reservoirs of bartonellae, usually with no apparent clinical manifestations. Close association between rodents and humans especially in rural communities as well as in the overcrowded cities facilitates transmission of these bacteria.

There have been no studies investigating the presence of Bartonella spp. in rodents and ectoparasites from Nigeria. The aim of the current study was to investigate the presence of Bartonella spp. in commensal rodents and their ectoparasites in Nigeria and its public health implications. We report, for the first time, the molecular detection of Bartonella in 26% (46/177) of commensal rodents and 28% (9/32) of ectoparasite pools from Nigeria. Sequence analysis of the citrate synthase gene (gltA) revealed diversity of Bartonella spp. and genotypes in Nigerian commensal rodents and their ectoparasites. The Bartonella spp. detected in this study were identical or closely related to Bartonella elizabethae, Bartonella tribocorum and Bartonella grahamii previously associated with human diseases highlighting their importance to public health.

A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella

Gene transfer agents (GTAs) randomly transfer short fragments of a bacterial genome. A novel putative GTA was recently discovered in the mouse-infecting bacterium Bartonella grahamii. Although GTAs are widespread in phylogenetically diverse bacteria, their role in evolution is largely unknown. Here, we present a comparative analysis of 16 Bartonella genomes ranging from 1.4 to 2.6 Mb in size, including six novel genomes from Bartonella isolated from a cow, two moose, two dogs, and a kangaroo. A phylogenetic tree inferred from 428 orthologous core genes indicates that the deadly human pathogen B. bacilliformis is related to the ruminant-adapted clade, rather than being the earliest diverging species in the genus as previously thought. A gene flux analysis identified 12 genes for a GTA and a phage-derived origin of replication as the most conserved innovations. These are located in a region of a few hundred kb that also contains 8 insertions of gene clusters for type III, IV, and V secretion systems, and genes for putatively secreted molecules such as cholera-like toxins. The phylogenies indicate a recent transfer of seven genes in the virB gene cluster for a type IV secretion system from a cat-adapted B. henselae to a dog-adapted B. vinsonii strain. We show that the B. henselae GTA is functional and can transfer genes in vitro. We suggest that the maintenance of the GTA is driven by selection to increase the likelihood of horizontal gene transfer and argue that this process is beneficial at the population level, by facilitating adaptive evolution of the host-adaptation systems and thereby expansion of the host range size. The process counters gene loss and forces all cells to contribute to the production of the GTA and the secreted molecules. The results advance our understanding of the role that GTAs play for the evolution of bacterial genomes.

Viruses are selfish genetic elements that replicate and transfer their own DNA, often killing the host cell in the process. Unlike viruses, gene transfer agents (GTAs) transfer random pieces of the bacterial genome rather than their own DNA. GTAs are widespread in bacterial genomes, but it is not known whether they are beneficial to the bacterium. In this study, we have used the emerging pathogen Bartonella as our model to study the evolution of GTAs. We sequenced the genomes of six isolates of Bartonella, including two new strains isolated from wild moose in Sweden. Using a comparative genomics approach, we searched for innovations in the last common ancestor that could help explain the explosive radiation of the genus. Surprisingly, we found that a gene cluster for a GTA and a phage-derived origin of replication was the most conserved innovation, indicative of strong selective constraints. We argue that the reason for the remarkable stability of the GTA is that it provides a mechanism to duplicate and recombine genes for secretion systems. This leads to adaptability to a broad range of hosts.

Bartonella bacteria in nature: where does population variability end and a species start?

The application of new molecular approaches has permitted the differentiation of numerous strains belonging to the genus Bartonella and identification of new Bartonella species. However, the molecular typing of these organisms should be coupled with studies aimed at defining the biological properties of the newly described species. The long-history of co-adaptation between bartonella(1) bacteria and their mammalian hosts and possibly arthropod vectors provides a unique opportunity for applying this information for the sub-genus taxonomy. There can be a varying level of association between the bacteria and their hosts, ranging from animal species to animal genus to animal community. The commonality is that any level of association provides a certain degree of isolation for a given bartonella population that can mimic 'biological isolation'. Such an association defines a specific ecological niche and determines some specific characteristics, including sequence types that can be used as markers for demarcation of bacterial species. Usage of a combination of genetic markers and ecological information can delineate a number of species complexes that might combine several genospecies, named strains, and unique genotypes. The identification of such species complexes can be presented as (1) separate phylogenetic lineages distantly related to other species (e.g. Bartonella bacilliformis); (2) clusters of genetically similar strains associated with a specific mammalian group (e.g. Bartonella elizabethae species complex); and (3) clusters of genetically similar strains that combine a number of ecotypes (e.g. Bartonella vinsonii species complex).

Bartonella species and their ectoparasites: selective host adaptation or strain selection between the vector and the mammalian host?

A wide range of blood-sucking arthropods have either been confirmed or are suspected as important vectors in Bartonella transmission to mammals, including humans. Overall, it appears that the diversity of Bartonella species DNA identified in ectoparasites is much broader than the species detected in their mammalian hosts, suggesting a mechanism of adaptation of Bartonella species to their host-vector ecosystem. However, these mechanisms leading to the fitness between the vectors and their hosts still need to be investigated.

Combining culture techniques for Bartonella: the best of both worlds

In this study we compared some common Bartonella culturing methodologies using four diverse species causing human illnesses. Based on a review of the literature, we focused on three major inconsistencies between protocols: base medium, cell coculture, and temperature. Our data showed that Bartonella tamiae demonstrated temperature-dependent growth limitations between common culturing conditions only 2°C apart. Additionally, growth of B. quintana was significantly enhanced by the presence of mammalian cell coculture under mammalian cell culture conditions; however, when the medium was modified to incorporate insect cell culture-based medium, coculturing with mammalian cells was no longer needed. In this study, we were able to overcome these temperature- and cell-dependent limitations and accommodate all of the strains tested by combining mammalian cell culture-based medium with insect cell culture-based medium.

Human isolates of Bartonella tamiae induce pathology in experimentally inoculated immunocompetent mice

Background

Bartonella tamiae, a newly described bacterial species, was isolated from the blood of three hospitalized patients in Thailand. These patients presented with headache, myalgia, anemia, and mild liver function abnormalities. Since B. tamiae was presumed to be the cause of their illness, these isolates were inoculated into immunocompetent mice to determine their relative pathogenicity in inducing manifestations of disease and pathology similar to that observed in humans.

Methods

Three groups of four Swiss Webster female mice aged 15-18 months were each inoculated with 10^6-7 colony forming units of one of three B. tamiae isolates [Th239, Th307, and Th339]. A mouse from each experimental group was sampled at 3, 4, 5 and 6 weeks post-inoculation. Two saline inoculated age-matched controls were included in the study. Samples collected at necropsy were evaluated for the presence of B. tamiae DNA, and tissues were formalin-fixed, stained with hematoxylin and eosin, and examined for histopathology.

Results

Following inoculation with B. tamiae, mice developed ulcerative skin lesions and subcutaneous masses on the lateral thorax, as well as axillary and inguinal lymphadenopathy. B. tamiae DNA was found in subcutaneous masses, lymph node, and liver of inoculated mice. Histopathological changes were observed in tissues of inoculated mice, and severity of lesions correlated with the isolate inoculated, with the most severe pathology induced by B. tamiae Th239. Mice inoculated with Th239 and Th339 demonstrated myocarditis, lymphadenitis with associated vascular necrosis, and granulomatous hepatitis and nephritis with associated hepatocellular and renal necrosis. Mice inoculated with Th307 developed a deep dermatitis and granulomas within the kidneys.

Conclusions

The three isolates of B. tamiae evaluated in this study induce disease in immunocompetent Swiss Webster mice up to 6 weeks after inoculation. The human patients from whom these isolates were obtained had clinical presentations consistent with the multi-organ pathology observed in mice in this study. This mouse model for B. tamiae induced disease not only strengthens the causal link between this pathogen and clinical illness in humans, but provides a model to further study the pathological processes induced by these bacteria.