Thai_bats_supplement.bib

@article{Kosoy1997,
abstract = {A number of Bartonella isolates were obtained from seven species of rodents sampled from 12 geographic sites representing the major biotic communities of the southeastern United States. Bartonella were isolated from the blood of 42.2{\%} of 279 tested rodents. The highest prevalence of infection typically occurred among the most commonly captured species in the rodent community. Four phylogenetic groups, uniting 14 genotypic variants of Bartonella, were identified by sequence analysis of the citrate synthase gene. The level of sequence homology between genotypic groups varied from 88.8{\%} to 96.4{\%}, and the degree of homology among variants within groups was {\textgreater} or = 97{\%}. Cotton rats (Sigmodon hispidus) harbored up to three phylogenetic groups of Bartonella at a single site, and Bartonella of two phylogenetic groups were isolated from a single rodent. All the Bartonella isolated from three species of Peromyscus clustered in a single distinct phylogenetic group, suggesting some host specificity may occur. Mouse ascitic fluids produced in BALB/c mice inoculated with Bartonella of three phylogenetic groups demonstrated high indirect fluorescent antibody (IFA) titers to homologous antigens. However, use of eight Bartonella antigens in an IFA test with sera from 394 wild-caught rodents resulted in either little or extremely low titers of antibody.},
author = {Kosoy, Michael Y and Regnery, Russell L and Tzianabos, Theodore and Marston, Eric L and Jones, Dana C and Green, Douglas and Maupin, Gary O and Olson, James G and Childs, James E},
isbn = {0002-9637},
issn = {0002-9637},
journal = {American Journal of Tropical Medicine and Hygiene},
mendeley-groups = {Bartonella},
month = {nov},
number = {5},
pages = {578--588},
pmid = {9392599},
title = {{Distribution, diversity, and host specificity of Bartonella in rodents from the Southeastern United States}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9392599},
volume = {57},
year = {1997}
}
@article{Stamatakis2014,
abstract = {MOTIVATION: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.$\backslash$n$\backslash$nRESULTS: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available.},
archivePrefix = {arXiv},
arxivId = {10.1093/bioinformatics/btu033},
author = {Stamatakis, Alexandros},
doi = {10.1093/bioinformatics/btu033},
eprint = {bioinformatics/btu033},
isbn = {1367-4811},
issn = {1367-4803},
journal = {Bioinformatics},
mendeley-groups = {Phylogenetics},
month = {may},
number = {9},
pages = {1312--1313},
pmid = {24451623},
primaryClass = {10.1093},
title = {{RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies}},
url = {http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btu033},
volume = {30},
year = {2014}
}
@article{Davoust2016,
annote = {1 star},
author = {Davoust, Bernard and Mari{\'{e}}, Jean-Lou and Dahmani, Mustapha and Berenger, Jean-Michel and Bompar, Jean-Michel and Blanchet, Denis and Cheuret, Marie and Raoult, Didier and Mediannikov, Oleg},
doi = {10.1089/vbz.2015.1918},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Davoust et al. - 2016 - Evidence of Bartonella spp. in blood and ticks (Ornithodoros hasei) of bats, in French Guiana.pdf:pdf},
issn = {1530-3667},
journal = {Vector-Borne and Zoonotic Diseases},
keywords = {1 star,bartonella,bartonellosis,bat,french guiana,ornithodoros hasei,reservoir,unchecked},
mendeley-groups = {Bartonella/Barcoding review,Bartonella,Bat parasites/Bat vector-borne parasites review/Bacteria/Bartonella,Bat parasites/Guatemala bats},
mendeley-tags = {1 star,unchecked},
month = {aug},
number = {8},
pages = {516--519},
title = {{Evidence of Bartonella spp. in blood and ticks (Ornithodoros hasei) of bats, in French Guiana}},
url = {http://online.liebertpub.com/doi/10.1089/vbz.2015.1918},
volume = {16},
year = {2016}
}
@article{Lin2010,
abstract = {We describe a new Bartonella species for which we propose the name Candidatus Bartonella mayotimonensis. It was isolated from native aortic valve tissue of a person with infective endocarditis. The new species was identified by using PCR amplification and sequencing of 5 genes (16S rRNA gene, ftsZ, rpoB, gltA, and internal transcribed spacer region).},
author = {Lin, Eleanor Y and Tsigrelis, Constantine and Baddour, Larry M and Lepidi, Hubert and Rolain, Jean-Marc and Patel, Robin and Raoult, Didier},
doi = {10.3201/eid1603.081673},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Lin et al. - 2010 - Candidatus Bartonella mayotimonensis and endocarditis.pdf:pdf},
issn = {10806040},
journal = {Emerging Infectious Diseases},
mendeley-groups = {Bartonella/Barcoding review,Bartonella,Bat parasites/Guatemala bats,Bat parasites/Bat vector-borne parasites review/Bacteria/Bartonella},
number = {3},
pages = {500--503},
pmid = {20202430},
title = {{Candidatus Bartonella mayotimonensis and endocarditis}},
volume = {16},
year = {2010}
}
@article{Kosoy2010b,
abstract = {We report the presence and diversity of Bartonella spp. in bats of 13 insectivorous and frugivorous species collected from various locations across Kenya. Bartonella isolates were obtained from 23 Eidolon helvum, 22 Rousettus aegyptiacus, 4 Coleura afra, 7 Triaenops persicus, 1 Hipposideros commersoni, and 49 Miniopterus spp. bats. Sequence analysis of the citrate synthase gene from the obtained isolates showed a wide assortment of Bartonella strains. Phylogenetically, isolates clustered in specific host bat species. All isolates from R. aegyptiacus, C. afra, and T. persicus bats clustered in separate monophyletic groups. In contrast, E. helvum and Miniopterus spp. bats harbored strains that clustered in several groups. Further investigation is needed to determine whether these agents are responsible for human illnesses in the region.},
annote = {- Cited 11 times},
author = {Kosoy, Michael Y and Bai, Ying and Lynch, Tarah and Kuzmin, Ivan V and Niezgoda, Michael and Franka, Richard and Agwanda, Bernard and Breiman, Robert F and Rupprecht, Charles E},
doi = {10.3201/eid1612.100601},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Kosoy et al. - 2010 - Bartonella spp. in bats, Kenya.pdf:pdf},
institution = {Centers for Disease Control and Prevention, Fort Collins, Colorado 80521, USA. mck3@cdc.gov},
journal = {Emerging Infectious Diseases},
mendeley-groups = {Bartonella/Barcoding review,Bartonella,Bat parasites/Bat vector-borne parasites review/Bacteria/Bartonella},
number = {12},
pages = {1875--1881},
pmid = {21122216},
title = {{Bartonella spp. in bats, Kenya}},
url = {http://www.cdc.gov/eid/content/16/12/1875.htm},
volume = {16},
year = {2010}
}
@article{Morse2012,
abstract = {Recently, a growing number Bartonella spp. have been identified as causative agents for a broadening spectrum of zoonotic diseases, emphasizing their medical importance. Many mammalian reservoirs and vectors however are still unknown, hindering our understanding of pathogen ecology and obscuring epidemiological connections. New Bartonella genotypes were detected in a global sampling of 19 species of blood-feeding bat flies (Diptera, Hippoboscoidea, Nycteribiidae, Streblidae) from 20 host bat species, suggesting an important role of bat flies in harboring bartonellae. Evolutionary relationships were explored in the context of currently known Bartonella species and genotypes. Phylogenetic and gene network analyses point to an early evolutionary association and subsequent radiation of bartonellae with bat flies and their hosts. The recovery of unique clades, uniting Bartonella genotypes from bat flies and bats, supports previous ideas of these flies potentially being vectors for Bartonella. Presence of bartonellae in some female bat flies and their pupae suggests vertical transmission across developmental stages. The specific function of bartonellae in bats and bat flies remains a subject of debate, but in addition to pathogenic interactions, parasitic, mutualistic, or reservoir functions need to be considered.},
author = {Morse, Solon F and Olival, Kevin J and Kosoy, Michael Y and Billeter, Sarah A and Patterson, Bruce D and Dick, Carl W and Dittmar, Katharina},
doi = {10.1016/j.meegid.2012.06.009},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Morse et al. - 2012 - Global distribution and genetic diversity of Bartonella in bat flies (Hippoboscoidea, Streblidae, Nycteribiidae).pdf:pdf},
issn = {1567-7257},
journal = {Infection, Genetics and Evolution},
keywords = {Animals,Bacterial,Bartonella,Bartonella Infections,Bartonella Infections: epidemiology,Bartonella Infections: microbiology,Bartonella Infections: transmission,Bartonella Infections: veterinary,Bartonella: classification,Bartonella: genetics,Bartonella: isolation {\&} purification,Chiroptera,Chiroptera: parasitology,Cluster Analysis,DNA,Diptera,Diptera: microbiology,Female,Genes,Genetic Variation,Male,Phylogeny,Sequence Analysis,checked for bartonella prevalence,checked for bat species,checked for ectoparasite species},
mendeley-groups = {Bartonella/Barcoding review,Bartonella,Bat parasites/Eurobats review,Bat parasites/Guatemala bats,Bat parasites/Bat vector-borne parasites review/Bacteria/Bartonella},
mendeley-tags = {checked for bartonella prevalence,checked for bat species,checked for ectoparasite species},
month = {dec},
number = {8},
pages = {1717--23},
pmid = {22771358},
publisher = {Elsevier B.V.},
title = {{Global distribution and genetic diversity of Bartonella in bat flies (Hippoboscoidea, Streblidae, Nycteribiidae)}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22771358},
volume = {12},
year = {2012}
}
@article{Bai2010,
abstract = {Using pre-enrichment culture in Bartonella alpha- Proteobacteria growth medium (BAPGM) followed by PCR amplification and DNA sequence identification that targeted a fragment of the citrate synthase gene (gltA), we provide evidence of common bartonella infections and diverse Bartonella species in the blood of stray dogs from Bangkok and Khon Kaen, Thailand. The overall prevalence of all Bartonella species was 31.3{\%} (60/192), with 27.9{\%} (31/111) and 35.8{\%} (29/81) in the stray dogs from Bangkok and Khon Kaen, respectively. Phylogenetic analyzes of gltA identified eight species/genotypes of Bartonella in the blood of stray dogs, including B. vinsonii subsp. arupensis, B. elizabethae, B. grahamii, B. quintana, B. taylorii, and three novel genotypes (BK1, KK1 and KK2) possibly representing unique species with ???90.2{\%} similarities to any of the known Bartonella species B. vinsonii subsp. arupensis was the only species detected in dogs from both sites, B. quintana and BK1 were found in the dogs from Bangkok, B. elizabethae, B. taylorii, KK1 and KK2 were found in the dogs from Khon Kaen. We conclude that stray dogs in Thailand are frequently infected with Bartonella species that vary with geographic region. As some Bartonella species detected in the present study are considered pathogenic for humans, stray dogs in Thailand may serve as possible reservoirs for Bartonella causing human illnesses. Further work is needed to determine the role of those newly discovered Bartonella genotypes/species in human and veterinary medicine. ?? 2010.},
annote = {2 stars},
author = {Bai, Ying and Kosoy, Michael Y and Boonmar, Sumalee and Sawatwong, Pongpun and Sangmaneedet, Somboon and Peruski, Leonard F},
doi = {10.1016/j.vetmic.2010.05.017},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Bai et al. - 2010 - Enrichment culture and molecular identification of diverse Bartonella species in stray dogs.pdf:pdf},
isbn = {0378-1135},
issn = {03781135},
journal = {Veterinary Microbiology},
keywords = {2 stars,BAPGM,Bartonella,GltA,Pre-enrichment,Stray dogs},
mendeley-groups = {Bartonella/Barcoding review,Bartonella},
mendeley-tags = {2 stars},
month = {dec},
number = {3-4},
pages = {314--319},
pmid = {20570065},
publisher = {Elsevier B.V.},
title = {{Enrichment culture and molecular identification of diverse Bartonella species in stray dogs}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0378113510002440},
volume = {146},
year = {2010}
}
@article{Wilkinson2016,
abstract = {The Nycteribiidae are obligate blood-sucking Diptera (Hippoboscoidea) parasitizing bats. Depending on species, these wingless flies exhibit either high specialism or generalism towards their hosts, which may in turn have important consequences in terms of their associated microbial community structure. Bats have been hypothesized to be reservoirs of numerous infectious agents, some of which have recently emerged in human populations. Thus, bat flies may be important in the epidemiology and transmission of some of these bat-borne infectious diseases, acting either directly as arthropod vectors or indirectly by shaping pathogen communities among bats populations. In addition, bat flies commonly have associations with heritable bacterial endosymbionts that inhabit insect cells and depend on maternal transmission, through egg cytoplasm, to ensure their transmission. Some of these heritable bacteria are likely obligate mutualists required to support bat fly development but others are facultative symbionts with unknown effects. Here, we present bacterial community profiles obtained from seven bat fly species, representing five genera, parasitizing bats from the Malagasy region. The observed bacterial diversity includes Rickettsia , Wolbachia , several Arsenophonus -like-organisms, as well as other members of the Enterobacteriales, and a widespread association of Bartonella bacteria from bat flies of all five genera. Using the well-described host specificity of these flies and data on community structure from selected bacterial taxa with either vertical or horizontal transmission, we show that host/vector specificity and transmission mode are both important drivers of bacterial community structure.},
author = {Wilkinson, David A and Duron, Olivier and Cordonin, Colette and Gomard, Yann and Ramasindrazana, Beza and Mavingui, Patrick and Goodman, Steven M and Tortosa, Pablo},
doi = {10.1128/AEM.03505-15},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Wilkinson et al. - 2016 - The bacteriome of bat flies (Nycteribiidae) from the Malagasy region a community shaped by host ecology, bacte.pdf:pdf},
issn = {0099-2240},
journal = {Applied and Environmental Microbiology},
mendeley-groups = {Bartonella/Barcoding review,Bartonella,Bat parasites/Bat vector-borne parasites review/Bacteria/Rickettsia,Bat parasites/Bat vector-borne parasites review/Bacteria/Bartonella},
number = {6},
pages = {1778--1788},
pmid = {26746715},
title = {{The bacteriome of bat flies (Nycteribiidae) from the Malagasy region: a community shaped by host ecology, bacterial transmission mode, and host-vector specificity}},
url = {http://aem.asm.org/lookup/doi/10.1128/AEM.03505-15},
volume = {82},
year = {2016}
}
@article{Bai2015,
abstract = {Bartonellae are facultative intracellular bacteria and are highly adapted to their mammalian host cell niches. Straw-colored fruit bats (Eidolon helvum) are commonly infected with several bartonella strains. To elucidate the genetic diversity of these bartonella strains, we analyzed 79 bartonella isolates from straw-colored fruit bats in seven countries across Africa (Cameroon, Annobon island of Equatorial Guinea, Ghana, Kenya, Nigeria, Tanzania, and Uganda) using a multi-locus sequencing typing (MLST) approach based on nucleotide sequences of eight loci (ftsZ, gltA, nuoG, ribC, rpoB, ssrA, ITS, and 16S rRNA). The analysis of each locus but ribC demonstrated clustering of the isolates into six genogroups (E1 - E5 and Ew), while ribC was absent in the isolates belonging to the genogroup Ew. In general, grouping of all isolates by each locus was mutually supportive; however, nuoG, gltA, and rpoB showed some incongruity with other loci in several strains, suggesting a possibility of recombination events, which were confirmed by network analyses and recombination/mutation rate ratio (r/m) estimations. The MLST scheme revealed 45 unique sequence types (ST1 - 45) among the analyzed bartonella isolates. Phylogenetic analysis of concatenated sequences supported the discrimination of six phylogenetic lineages (E1 - E5 and Ew) corresponding to separate and unique Bartonella species. One of the defined lineages, Ew, consisted of only two STs (ST1 and ST2), and comprised more than one-quarter of the analyzed isolates, while other lineages contained higher numbers of STs with a smaller number of isolates belonging to each lineage. The low number of allelic polymorphisms of isolates belonging to Ew suggests a more recent origin for this species. Our findings suggest that at least six Bartonella species are associated with straw-colored fruit bats, and that distinct STs can be found across the distribution of this bat species, including in populations of bats which are genetically distinct.},
annote = {NULL},
author = {Bai, Ying and Hayman, David T S and McKee, Clifton D and Kosoy, Michael Y},
doi = {10.1371/journal.pntd.0003478},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Bai et al. - 2015 - Classification of Bartonella strains associated with straw-colored fruit bats (Eidolon helvum) across Africa using a.pdf:pdf},
issn = {1935-2735},
journal = {PLOS Neglected Tropical Diseases},
mendeley-groups = {Bartonella/Barcoding review,Bartonella,Phylogenetics,Phylogenetics/Barcoding review,Bat parasites/Bat vector-borne parasites review/Bacteria/Bartonella},
month = {jan},
number = {1},
pages = {e0003478},
pmid = {25635826},
title = {{Classification of Bartonella strains associated with straw-colored fruit bats (Eidolon helvum) across Africa using a multi-locus sequence typing platform}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25635826},
volume = {9},
year = {2015}
}
@article{Veikkolainen2014,
author = {Veikkolainen, Ville and Vesterinen, Eero J and Lilley, Thomas M and Pulliainen, Arto T},
doi = {10.3201/eid2006.130956},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Veikkolainen et al. - 2014 - Bats as reservoir hosts of human bacterial pathogen, Bartonella mayotimonensis.pdf:pdf},
issn = {1080-6040},
journal = {Emerging Infectious Diseases},
mendeley-groups = {Bartonella/Barcoding review,Bartonella,Bat parasites/Eurobats review,Phylogenetics/Barcoding review,Bat parasites/Bat vector-borne parasites review/Metagenomic studies/Reviews},
month = {jun},
number = {6},
pages = {960--967},
title = {{Bats as reservoir hosts of human bacterial pathogen, Bartonella mayotimonensis}},
url = {http://wwwnc.cdc.gov/eid/article/20/6/13-0956{\_}article.htm},
volume = {20},
year = {2014}
}
@article{Urushadze2017,
author = {Urushadze, Lela and Bai, Ying and Osikowicz, Lynn M and McKee, Clifton D and Kandaurov, Andrei and Kuzmin, Ivan V and Sidamonidze, Ketevan and Putkaradze, Davit and Imnadze, Paata and Kosoy, Michael Y},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Urushadze L et al [2017] PLOS NTD.pdf:pdf},
journal = {PLOS Neglected Tropical Diseases},
mendeley-groups = {Bartonella,Bat parasites/Bat vector-borne parasites review/Bacteria/Bartonella},
number = {4},
pages = {e0005428},
title = {{Prevalence, diversity, and host associations of Bartonella strains in bats from Georgia (Caucasus)}},
url = {https://doi.org/10.1371/journal.pntd.0005428{\%}0A},
volume = {11},
year = {2017}
}
@article{Anh2015,
annote = {Pretty basic report of Bartonella in bats from Vietnam, including a better sampling of Rhinolophus and Hipposideros spp. bats. I don't really trust their comparison of age groups since they didn't provide any evidence that tibial length is correlated with age.
1 star},
author = {Anh, Pham Hong and {Van Cuong}, Nguyen and Son, Nguyen Truong and Tue, Ngo Tri and Kosoy, Michael Y and Woolhouse, Mark E J and Baker, Stephen and Bryant, Juliet E and Thwaites, Guy and Carrique-Mas, Juan J and Rabaa, Maia A},
doi = {10.3201/eid2107.141760},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Anh et al. - 2015 - Diversity of Bartonella spp. in bats, southern Vietnam.pdf:pdf},
isbn = {0031182011},
issn = {1080-6040},
journal = {Emerging Infectious Diseases},
keywords = {1 star},
mendeley-groups = {Bartonella/Barcoding review,Bartonella,Bat parasites/Guatemala bats,Bat parasites/Bat vector-borne parasites review/Bacteria/Bartonella},
mendeley-tags = {1 star},
month = {jul},
number = {7},
pages = {1266--1267},
title = {{Diversity of Bartonella spp. in bats, southern Vietnam}},
url = {http://wwwnc.cdc.gov/eid/article/21/7/14-1760{\_}article.htm},
volume = {21},
year = {2015}
}
@article{Podsiadly2010,
abstract = {Abstract The presence of antibodies to Rickettsia conorii, R. helvetica, R. felis, R. slovaca, R. sibirica, and R. massiliae in sera of 129 forest workers from northeastern and southern Poland was assayed by indirect immunofluorescence. Previous environmental studies revealed presence of spotted fever group (SFG) rickettsiae in ticks collected from these areas. Additionally, the workers were examinated for the presence of antibodies specific to other tick-borne bacteria: Anaplasma phagocytophilum, Bartonella spp., and B. burgdorferi. The results of the studies have shown the presence of specific SFG rickettsiae antibodies in 14.7{\%} of tested forest workers, among them 78.9{\%} had species-specific antibodies to R. massiliae. Contrary to previous detection R. helvetica and R. slovaca in ticks collected in the environment of the examined area, no species-specific antibodies to these species were detected in studied workers. Antibodies to B. burgdorferi (44{\%}) were found in forest workers more often than antibodies to other tested pathogens. B. burgdorferi was also the main component of coinfections. The most frequent confirmed serologically coinfections were simultaneous infections with B. burgdorferi and Bartonella spp. found in 10{\%} of tested individuals. So far, SFG rickettsiae infections have not been diagnosed in Poland; however, the presence of the bacteria in ticks and presence of specific antibodies in humans exposed to arthropods show the need for monitoring the situation. The list of tick-borne pathogens is increasing, but knowledge about the possibility of humans acquiring multipathogens infections after tick bite still needs evaluation.},
annote = {1 star},
author = {Podsiadly, E and Chmielewski, T and Karbowiak, G and Kedra, E and Tylewska-Wierzbanowska, S},
doi = {10.1089/vbz.2010.0080},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Podsiadly et al. - 2010 - The occurrence of spotted fever rickettsioses and other tick-borne infections in forest workers in Poland.pdf:pdf},
isbn = {1557-7759 (Electronic) 1530-3667 (Linking)},
issn = {1530-3667},
journal = {Vector-Borne and Zoonotic Diseases},
keywords = {1 star,bacterial tick-borne coinfections,spotted fever group rickettsiae,tick-borne infections},
mendeley-groups = {Bartonella/Barcoding review,Bartonella},
mendeley-tags = {1 star},
number = {7},
pages = {985--989},
pmid = {21083370},
title = {{The occurrence of spotted fever rickettsioses and other tick-borne infections in forest workers in Poland}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/21083370},
volume = {11},
year = {2010}
}
@article{Malania2016,
abstract = {Bartonella infections are widespread and highly prevalent in rodents. Several rodent-associated Bartonella species have been related to human diseases. Recently, Bartonella species was reported as the etiology of a human case in the country of Georgia (Caucasus). However, information on Bartonella in rodents in Georgia is absent. Rodent hearts were collected from Georgia to investigate the presence and diversity of Bartonella species. Bartonella bacteria were cultured from 37.2{\%} (16/43) of rodents examined, while Bartonella DNA was detected in 41.2{\%} (28/68) of rodents by polymerase chain reaction targeting citrate synthase (gltA) gene. Sequences of gltA showed that rodents in this region harbored multiple Bartonella strains, including Bartonella elizabethae, Bartonella tribocorum, Bartonella grahamii, and an unknown genogroup. The first three Bartonella species, known to be rat-associated and human cases linked, were com-monly observed in wood mice (Apodemus [Sylvaemus] uralensis) (5/8 positive with B. elizabethae and B. tribocorum) and social voles (Microtus socialis) (4/6 positive with B. grahamii and B. elizabethae) in this study. The frequent distribution of these Bartonella species suggests that they may contribute to unidentified clinical infections. The unknown genogroup was observed in 24 Bartonella isolates and/or DNA extracts from heart tissues, all of which were obtained from Libyan jirds (Meriones libycus). Further characterization of the bacterial cultures based on sequence analysis of four additional genes (ftsZ, nuoG, rpoB, and ssrA) supported that the jird-associated Bartonella strains comprise a distinct monophyletic clade. The impact of this bacterium on wildlife and human health needs to be determined.},
author = {Malania, Lile and Bai, Ying and Osikowicz, Lynn M and Tsertsvadze, Nikoloz and Katsitadze, Guram and Imnadze, Paata and Kosoy, Michael},
doi = {10.4269/ajtmh.16-0041},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Malania L et al [2016] AJTMH.pdf:pdf},
issn = {0002-9637},
journal = {American Journal of Tropical Medicine and Hygiene},
mendeley-groups = {Bartonella},
month = {aug},
number = {2},
pages = {466--471},
pmid = {27162268},
title = {{Prevalence and diversity of Bartonella species in rodents from Georgia (Caucasus)}},
url = {http://www.ajtmh.org/content/journals/10.4269/ajtmh.16-0041},
volume = {95},
year = {2016}
}
@article{Lin2012,
abstract = {Many studies indicated that small mammals are important reservoirs for Bartonella species. Using molecular methods, several studies have documented that bats could harbor Bartonella. This study was conducted to investigate the relationship of Bartonella spp. identified in bats and small mammals living in the same ecological environment. During May 2009 and March 2010, a total of 102 blood specimens were collected. By whole blood culture and molecular identification, a total of 6 bats, 1 rodent and 9 shrews were shown to be infected by Bartonella species. After sequencing and phylogenetic analyses of the sequences of gltA, ftsZ, rpoB and ribC genes, these specific isolates from bats were not similar to the known Bartonella species (the similarity values were less than 91.2{\%}, 90.5{\%}, 88.8{\%}, and 82.2{\%}, respectively); these isolates formed an independent clade away from other known Bartonella type strains. The Bartonella spp. isolated from small mammals, which were closely related to Bartonella tribocorum, Bartonella elizabethae, Bartonella grahamii, Bartonella rattimassiliensis and Bartonella queenslandensis, were similar to the findings in previous studies worldwide. Therefore, the results implied that the species of Bartonella strains isolated from small mammals were different from those identified in bats. Our results strongly suggested that the bat isolate could be a new Bartonella species. This study is also the first one to isolate Bartonella organisms from Asian gray shrews, Crocidura attenuata tanakae.},
author = {Lin, Jen-Wei and Hsu, Yuan-Man and Chomel, Bruno B and Lin, Liang-Kong and Pei, Jai-Chyi and Wu, Sheng-Hai and Chang, Chao-Chin},
doi = {10.1016/j.vetmic.2011.09.031},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Lin et al. - 2012 - Identification of novel Bartonella spp. in bats and evidence of Asian gray shrew as a new potential reservoir of Bar.pdf:pdf},
issn = {1873-2542},
journal = {Veterinary Microbiology},
keywords = {Animals,Bartonella,Bartonella Infections,Bartonella Infections: transmission,Bartonella Infections: veterinary,Bartonella: classification,Bartonella: genetics,Bartonella: isolation {\&} purification,Chiroptera,Disease Reservoirs,Phylogeny,Rodentia,Rodentia: microbiology,Shrews,Shrews: microbiology,Taiwan},
mendeley-groups = {Bartonella/Barcoding review,Bartonella,Bat parasites/Bat vector-borne parasites review/Bacteria/Bartonella},
month = {apr},
number = {1-2},
pages = {119--126},
pmid = {22005177},
publisher = {Elsevier B.V.},
title = {{Identification of novel Bartonella spp. in bats and evidence of Asian gray shrew as a new potential reservoir of Bartonella}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22005177},
volume = {156},
year = {2012}
}
@article{Lilley2015,
annote = {1 star},
author = {Lilley, Thomas M and Veikkolainen, Ville and Pulliainen, Arto T},
doi = {10.1089/vbz.2015.1783},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Lilley, Veikkolainen, Pulliainen - 2015 - Molecular detection of Candidatus Bartonella hemsundetiensis in bats.pdf:pdf},
issn = {1530-3667},
journal = {Vector-Borne and Zoonotic Diseases},
keywords = {1 star,Bats,Zoonosis,bartonella,bats,zoonosis},
mendeley-groups = {Bartonella/Barcoding review,Bartonella,Bat parasites/Bat vector-borne parasites review/Bacteria/Bartonella},
mendeley-tags = {1 star},
number = {11},
pages = {706--708},
title = {{Molecular detection of Candidatus Bartonella hemsundetiensis in bats}},
url = {http://online.liebertpub.com/doi/10.1089/vbz.2015.1783},
volume = {15},
year = {2015}
}
@article{Concannon2005,
abstract = {The presence of haemoparasites from the Order Piroplasmida and the genera Bartonella and Trypanosoma was assessed in the blood of 60 bats, belonging to 7 species, inhabiting sites across Cornwall in southwest England. DNA extracted from macerated heart tissue was incorporated into taxon-specific polymerase chain reactions (PCRs) and amplification products were sequenced as a means of identifying, or assigning an identity, to detected haemoparasites. A Piroplasmida species was detected in 6 Pipistrellus spp., whereas Bartonella infections were detected in 5 bats belonging to 4 different species. Trypanosoma dionisii was detected in 1 Pipistrellus spp. Phylogenetic inference from alignment of a partial 18S rRNA-encoding gene sequence of the pipistrelle-associated Piroplasmida species with homologous sequences available for other members of the Order indicated that this organism was unique but specifically related to members of the genus Babesia, a phylogeny that would be in keeping with the organism being Babesia vesperuginis. Alignment of partial citrate synthase gene sequences from the bat-associated bartonellae revealed 5 distinct genotypes that were probably derived from 2 distinct Bartonella species. The study demonstrates the utility of molecular methods for detecting haemoparasites in dead bats and provides, for the first time, tangible identities for bat-associated Babesia and Bartonella species.},
annote = {NULL},
author = {Concannon, R and Wynn-Owen, K and Simpson, V R and Birtles, Richard J},
doi = {10.1017/S0031182005008097},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Concannon et al. - 2005 - Molecular characterization of haemoparasites infecting bats (Microchiroptera) in Cornwall, UK.pdf:pdf},
issn = {0031-1820},
journal = {Parasitology},
keywords = {18S,18S: analysis,Animal,Animal: diagnosis,Animal: parasitology,Animals,Babesia,Babesia: classification,Babesia: genetics,Bartonella,Bartonella: classification,Bartonella: genetics,Chiroptera,Chiroptera: blood,Chiroptera: microbiology,Chiroptera: parasitology,DNA,England,Gene Amplification,Phylogeny,Piroplasmida,Piroplasmida: classification,Piroplasmida: genetics,Polymerase Chain Reaction,Protozoan,Protozoan Infections,Protozoan: analysis,RNA,Ribosomal,Sequence Alignment,Species Specificity,Theileria,Theileria: classification,Theileria: genetics},
mendeley-groups = {Bartonella/Barcoding review,Bartonella,Bat parasites/Eurobats review,Bat parasites/Bat vector-borne parasites review/Bacteria/Bartonella,Bat parasites/Bat vector-borne parasites review/Hemoparasites/Babesia},
month = {jun},
number = {04},
pages = {489--496},
pmid = {16174413},
title = {{Molecular characterization of haemoparasites infecting bats (Microchiroptera) in Cornwall, UK}},
url = {http://www.journals.cambridge.org/abstract{\_}S0031182005008097},
volume = {131},
year = {2005}
}
@article{Han2017,
annote = {5 stars},
author = {Han, Hui-Ju and Wen, Hong-ling and Zhao, Li and Liu, Jian-Wei and Luo, Li-Mei and Zhou, Chuan-Min and Qin, Xiang-Rong and Zhu, Ye-Lei and Zheng, Xue-Xing and Yu, Xue-Jie},
doi = {10.1371/journal.pone.0167915},
editor = {Munderloh, Ulrike Gertrud},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Han et al. - 2017 - Novel Bartonella species in insectivorous bats, northern China.pdf:pdf},
isbn = {1111111111},
issn = {1932-6203},
journal = {PLOS ONE},
keywords = {2 stars},
mendeley-tags = {2 stars},
month = {jan},
number = {1},
pages = {e0167915},
title = {{Novel Bartonella species in insectivorous bats, northern China}},
url = {http://dx.plos.org/10.1371/journal.pone.0167915},
volume = {12},
year = {2017}
}
@article{Lilley2017,
annote = {2 stars},
author = {Lilley, Thomas M and Wilson, Cali A and Bernard, Riley F and Willcox, Emma V and Vesterinen, Eero J and Webber, Quinn M R and Kurpiers, Laura and Prokkola, Jenni M and Ejotre, Imran and Kurta, Allen and Field, Kenneth A and Reeder, DeeAnn M and Pulliainen, Arto T},
doi = {10.1089/vbz.2016.2080},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Lilley et al. - 2017 - Molecular detection of Candidatus Bartonella mayotimonensis in North American bats.pdf:pdf},
issn = {1530-3667},
journal = {Vector-Borne and Zoonotic Diseases},
keywords = {2 stars,Chiroptera,bartonella,bats,chiroptera,endocarditis,unchecked},
mendeley-tags = {2 stars,unchecked},
month = {feb},
number = {Xx},
pages = {vbz.2016.2080},
title = {{Molecular detection of Candidatus Bartonella mayotimonensis in North American bats}},
url = {http://online.liebertpub.com/doi/10.1089/vbz.2016.2080},
volume = {XX},
year = {2017}
}
@article{Judson2015,
annote = {Informative for its findings that bats and the bat flies parasitizing the same individual can have the same Bartonella genotype. Doesn't add much more to our knowledge of these bacteria in their hosts. The phylogeny may be improved by only looking at bat-borne genotypes, which may show that all isolates from phyllostomid bats cluster together. The connections to other disease-causing species (B. washoensis) are spurious because of low similarity ({\textless}95{\%}).
2 stars (but 3 stars for its data).},
author = {Judson, S D and Frank, H K and Hadly, E A},
doi = {10.1111/zph.12188},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Judson, Frank, Hadly - 2015 - Bartonellae are prevalent and diverse in Costa Rican bats and bat flies.pdf:pdf},
issn = {18631959},
journal = {Zoonoses and Public Health},
keywords = {2 stars,arthropod,bacteria,blood-borne pathogens,checked for bartonella prevalence,checked for bat species,checked for ectoparasite species,chiroptera,parasites,vectors,zoonosis},
mendeley-tags = {2 stars,checked for bartonella prevalence,checked for bat species,checked for ectoparasite species},
number = {8},
pages = {609--617},
title = {{Bartonellae are prevalent and diverse in Costa Rican bats and bat flies}},
url = {http://doi.wiley.com/10.1111/zph.12188},
volume = {62},
year = {2015}
}
@article{Bai2012a,
abstract = {Bartonella infections were investigated in bats in the Amazon part of Peru. A total of 112 bats belonging to 19 species were surveyed. Bartonella bacteria were cultured from 24.1{\%} of the bats (27/112). Infection rates ranged from 0{\%} to 100{\%} per bat species. Phylogenetic analyses of gltA of the Bartonella isolates revealed 21 genetic variants clustering into 13 divergent phylogroups. Some Bartonella strains were shared by bats of multiple species, and bats of some species were infected with multiple Bartonella strains, showing no evident specific Bartonella sp.-bat relationships. Rarely found in other bat species, the Bartonella strains of phylogroups I and III discovered from the common vampire bats (Desmodus rotundus) were more specific to the host bat species, suggesting some level of host specificity.},
annote = {NULL},
author = {Bai, Ying and Recuenco, Sergio and Gilbert, Amy T and Osikowicz, Lynn M and Gomez, Jorge and Rupprecht, Charles E and Kosoy, Michael Y},
doi = {10.4269/ajtmh.2012.12-0097},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Bai et al. - 2012 - Prevalence and diversity of Bartonella spp. in bats in Peru.pdf:pdf},
issn = {0002-9637},
journal = {American Journal of Tropical Medicine and Hygiene},
keywords = {Animals,Bartonella,Bartonella Infections,Bartonella Infections: epidemiology,Bartonella Infections: microbiology,Bartonella Infections: veterinary,Bartonella: classification,Bartonella: genetics,Bartonella: isolation {\&} purification,Chiroptera,Chiroptera: microbiology,Citrate (si)-Synthase,Citrate (si)-Synthase: genetics,Erythrocytes,Genetic Variation,Peru,Peru: epidemiology,Phylogeny,Polymerase Chain Reaction,Prevalence,Species Specificity,checked for bartonella prevalence,checked for bat species},
mendeley-tags = {checked for bartonella prevalence,checked for bat species},
month = {sep},
number = {3},
pages = {518--523},
pmid = {22826480},
title = {{Prevalence and diversity of Bartonella spp. in bats in Peru}},
url = {http://www.ajtmh.org/cgi/doi/10.4269/ajtmh.2012.12-0097},
volume = {87},
year = {2012}
}
@article{Engel2011,
abstract = {Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the $\alpha$-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment.},
author = {Engel, Philipp and Salzburger, Walter and Liesch, Marius and Chang, Chao Chin and Maruyama, Soichi and Lanz, Christa and Calteau, Alexandra and Lajus, Aur{\'{e}}lie and M{\'{e}}digue, Claudine and Schuster, Stephan C and Dehio, Christoph},
doi = {10.1371/journal.pgen.1001296},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Engel P et al [2011] PLOS Genet.PDF:PDF},
isbn = {10.1371/journal.pgen.1001296},
issn = {15537390},
journal = {PLOS Genetics},
mendeley-groups = {Bartonella},
number = {2},
pages = {e1001296},
pmid = {21347280},
title = {{Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen bartonella}},
volume = {7},
year = {2011}
}
@article{Kuzmin2008,
abstract = {During lyssavirus surveillance, 1,221 bats of at least 30 species were collected from 25 locations in Kenya. One isolate of Lagos bat virus (LBV) was obtained from a dead Eidolon helvum fruit bat. The virus was most similar phylogenetically to LBV isolates from Senegal (1985) and from France (imported from Togo or Egypt; 1999), sharing with these viruses 100{\%} nucleoprotein identity and 99.8 to 100{\%} glycoprotein identity. This genome conservancy across space and time suggests that LBV is well adapted to its natural host species and that populations of reservoir hosts in eastern and western Africa have sufficient interactions to share pathogens. High virus concentrations, in addition to being detected in the brain, were detected in the salivary glands and tongue and in an oral swab, suggesting that LBV is transmitted in the saliva. In other extraneural organs, the virus was generally associated with innervations and ganglia. The presence of infectious virus in the reproductive tract and in a vaginal swab implies an alternative opportunity for transmission. The isolate was pathogenic for laboratory mice by the intracerebral and intramuscular routes. Serologic screening demonstrated the presence of LBV-neutralizing antibodies in E. helvum and Rousettus aegyptiacus fruit bats. In different colonies the seroprevalence ranged from 40 to 67{\%} and 29 to 46{\%} for E. helvum and R. aegyptiacus, respectively. Nested reverse transcription-PCR did not reveal the presence of viral RNA in oral swabs of bats in the absence of brain infection. Several large bat roosts were identified in areas of dense human populations, raising public health concerns for the potential of lyssavirus infection.},
annote = {- Cited by 41},
author = {Kuzmin, Ivan V and Niezgoda, Michael and Franka, Richard and Agwanda, Bernard and Markotter, Wanda and Beagley, Janet C and Urazova, Olga Y and Breiman, Robert F and Rupprecht, Charles E},
doi = {10.1128/JCM.00016-08},
file = {:Users/clifmckee/Documents/Mendeley Desktop/Kuzmin et al. - 2008 - Lagos bat virus in Kenya.pdf:pdf},
issn = {1098660X},
journal = {Journal of Clinical Microbiology},
keywords = {africa,animals,antibodies,antigens,bat,bats,brain,brain virology,chiroptera,chiroptera virology,colony,eidolon,eidolon helvum,female,fruit bat,fruit bats,genome,host species,inbred,kenya,kenya epidemiology,lyssavirus,lyssavirus classification,lyssavirus immunology,lyssavirus isolation {\&} purification,lyssavirus pathogenicity,male,mice,neutralization tests,population,populations,public health,rhabdoviridae infections,rhabdoviridae infections epidemiology,rhabdoviridae infections veterinary,rhabdoviridae infections virology,roost,roosts,rousettus,rousettus aegyptiacus,species,viral,viral analysis,viral blood},
number = {4},
pages = {1451--1461},
pmid = {18305130},
title = {{Lagos bat virus in Kenya}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2292963{\&}tool=pmcentrez{\&}rendertype=abstract},
volume = {46},
year = {2008}
}