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

Sneaky tactics: Ingenious immune evasion mechanisms of Bartonella

Gram-negative Bartonella species are facultative intracellular bacteria that can survive in the harsh intracellular milieu of host cells. They have evolved strategies to evade detection and degradation by the host immune system, which ensures their proliferation in the host. Following infection, Bartonella alters the initial immunogenic surface-exposed proteins to evade immune recognition via antigen or phase variation. The diverse lipopolysaccharide structures of certain Bartonella species allow them to escape recognition by the host pattern recognition receptors. Additionally, the survival of mature erythrocytes and their resistance to lysosomal fusion further complicate the immune clearance of this species. Certain Bartonella species also evade immune attacks by producing biofilms and anti-inflammatory cytokines and decreasing endothelial cell apoptosis. Overall, these factors create a challenging landscape for the host immune system to rapidly and effectively eradicate the Bartonella species, thereby facilitating the persistence of Bartonella infections and creating a substantial obstacle for therapeutic interventions. This review focuses on the effects of three human-specific Bartonella species, particularly their mechanisms of host invasion and immune escape, to gain new perspectives in the development of effective diagnostic tools, prophylactic measures, and treatment options for Bartonella infections.

Dog ectoparasites as sentinels for pathogenic Rickettsia and Bartonella in rural Guatemala

Fleas and ticks serve as vectors of multiple pathogens in the genera Rickettsia and Bartonella that cause diseases in humans and other animals. Although human rickettsiosis and bartonellosis have been reported in all countries in Central America, limited research has been conducted to investigate the natural cycles of flea- and tick-borne rickettsiosis and bartonellosis, especially in Guatemala. We evaluated dog parasites as sentinels for zoonotic disease risk in rural Guatemala by sampling ticks and fleas from dogs, which were then identified and individually screened for Rickettsia and Bartonella. A total of 77 households were surveyed and 80.5 % of them had dogs. Overall, 133 dogs were examined for fleas and ticks, of which 68.4 % had fleas and 35.3 % had ticks. A total of 433 fleas and 181 ticks were collected from the infested dogs, with an additional 33 ticks collected from house walls. Three flea species were identified: Ctenocephalides felis (70.0 %), Echidnophaga gallinacea (11.8 %), and Pulex sp. (17.8 %). Among the collected ticks, 97 % were identified as Rhipicephalus sanguineus sensu lato with the rest being Amblyomma cajennense, A. auricularium, and A. ovale. Rickettsia felis were detected in six C. felis, in one Pulex sp., and in two R. sanguineus sensu lato, while Candidatus R. senegalensis was detected in one C. felis. Bartonella was detected only in fleas, including three Pulex sp. infected with B. vinsonii subsp. berkhoffii, B. henselae, and Bartonella sp., respectively, and 11 C. felis infected with B. henselae. This study reports Candidatus R. senegalensis and B. vinsonii subsp. berkhoffii in Guatemala for the first time, and indicates the potential risk of human and dog exposure to Rickettsia and Bartonella species. These results show that dogs provide critical information relevant to managing human potential exposure to flea- and tick-borne pathogens in rural Guatemala. This approach can potentially be expanded to other regions in Central America where domestic dogs are abundant and suffer from ectoparasite infestation.

Genome sequences of three Bartonella schoenbuchensis strains from Czechia

Bartonella schoenbuchensis causes bacteremia in ruminants and is transmitted by deer keds. Here, we report the complete genome sequences of three B. schoenbuchensis strains (L2, L19, and L24) recently isolated from deer keds (Lipoptena fortisetosa) in Czechia.

Bartonella species in dromedaries and ruminants from Lower Shabelle and Benadir regions, Somalia

BACKGROUND

Bartonellosis, caused by bacteria of the genus Bartonella, is a zoonotic disease with several mammalian reservoir hosts. In Somalia, a country heavily reliant on livestock, zoonotic diseases pose significant public health and economic challenges. To the best of our knowledge, no study has been performed aiming to verify the occurrence of Bartonella spp. in Somalia. This study investigated the occurrence and molecular characterization of Bartonella in dromedary (Camelus dromedarius, Linnaeus, 1758), cattle, sheep, and goats from Somalia.

MATERIALS AND METHODS

530 blood samples were collected from various animals (155 dromedary, 199 goat, 131 cattle, and 45 sheep) in Benadir and Lower Shabelle regions. DNA was extracted for molecular analysis, and a qPCR assay targeting the NADH dehydrogenase gamma subunit (nuoG) gene was used for Bartonella screening. Positive samples were also subjected to PCR assays targeting seven molecular markers including: nuoG, citrate synthase gene (gltA), RNA polymerase beta-subunit gene (rpoB), riboflavin synthase gene (ribC), 60 kDa heat-shock protein gene (groEL), cell division protein gene (ftsZ), and pap31 and qPCR targeting the 16-23S rRNA internal transcribed spacer (ITS) followed by Sanger sequencing, BLASTn and phylogenetic analysis.

RESULTS

Out of 530 tested animals, 5.1% were positive for Bartonella spp. by the nuoG qPCR assay. Goats showed the highest Bartonella occurrence (17/199, 8.5%), followed by sheep (6/44, 6.8%), cattle (4/131, 3.1%), and dromedary (1/155, 1.9%). Goats, sheep, and cattle had higher odds of infection compared to dromedary. Among nuoG qPCR-positive samples, 11.1%, 14.8%, 11.1%, and 25.9% were positive in PCR assays based on nuoG, gltA, and pap31 genes, and in the qPCR based on the ITS region, respectively. On the other hand, nuoG qPCR-positive samples were negative in the PCR assays targeting the ribC, rpoB, ftsZ, and groEL genes. While Bartonella bovis sequences were detected in cattle (nuoG and ITS) and goats (gltA), Bartonella henselae ITS sequences were detected in dromedary, goat, and sheep. Phylogenetic analysis placed gltA Bartonella sequence from a goat in the same clade of B. bovis.

CONCLUSION

The present study showed, for the first time, molecular evidence of Bartonella spp. in dromedary and ruminants from Somalia and B. henselae in sheep and goats globally. These findings contribute valuable insights into Bartonella spp. occurrence in Somali livestock, highlighting the need for comprehensive surveillance and control measures under the One Health approach.

Dog ectoparasites as sentinels for pathogenic Rickettsia and Bartonella in rural Guatemala

Background

Fleas and ticks serve as vectors of multiple pathogens in the genera Rickettsia and Bartonellathat cause diseases in humans and other animals. Although human rickettsiosis and bartonellosis have been reported in all countries in Central America, limited research has been conducted to investigate the natural cycles of flea- and tick-borne rickettsiosis and bartonellosis, especially in Guatemala.

Methods

We evaluated dog parasites as sentinels for zoonotic disease risk in rural Guatemala by sampling ticks and fleas from dogs, which were then identified and individually screened for Rickettsia and Bartonella.

Results

A total of 77 households were surveyed and 80.52% of them had dogs. Overall, 133 dogs were examined for fleas and ticks, of which 68.42% had fleas and 35.34% had ticks. A total of 433 fleas and 181 ticks were collected from the infested dogs, with an additional 33 ticks collected from house walls. Three flea species were identified: Ctenocephalides felis (70%), Echidnophaga gallinacea(11.8%), and Pulex sp. (17.8%). Among the collected ticks, 97% were Rhipicephalus sanguineus with the rest being Amyblyomma cajennense, A. auricularium, and A. ovale. Rickettsia felis were detected in six C. felis, in one Pulex sp., and in two R. sanguineus, while Candidatus R. senegalensis was detected in one C. felis. Bartonella was detected only in fleas, including three Pulexsp. infected with B. vinsonii subsp. Berkhoffii, B. henselae, and Bartonella sp., respectively, and 11 C. felis infected with B. henselae.

Conclusions

This study reports Candidatus R. senegalensis and B. vinsonii subsp. Berkhoffiiin Guatemala for the first time, and indicates the potential risk of human and dog exposure to Rickettsia and Bartonella species. These results show that dogs provide critical information relevant to managing human potential exposure to flea- and tick-borne pathogens in rural Guatemala.

Co-opting bacterial viruses for DNA exchange: structure and regulation of gene transfer agents

Horizontal gene transfer occurs via a range of mechanisms, including transformation, conjugation and bacteriophage transduction. Gene transfer agents (GTAs) are an alternative, less-studied route for interbacterial DNA exchange. Encoded within bacterial or archaeal genomes, GTAs assemble into phage-like particles that selflessly package and transmit host DNA to recipient bacteria. Several unique features distinguish GTAs from canonical phages such as an inability to self-replicate, thus producing non-infectious particles. GTAs are also deeply integrated into the physiology of the host cell and are maintained under tight host-regulatory control. Recent advances in understanding the structure and regulation of GTAs have provided further insights into a DNA transfer mechanism that is proving increasingly widespread across the bacterial tree of life.

Gene transfer agents: The ambiguous role of selfless viruses in genetic exchange and bacterial evolution

Gene transfer agents (GTAs) are genetic elements derived from ancestral bacteriophages that have become domesticated by the host. GTAs are present in diverse prokaryotic organisms, where they can facilitate horizontal gene transfer under certain conditions. Unlike typical bacteriophages, GTAs do not exhibit any preference for the replication or transfer of the genes encoding them; instead, they exhibit a remarkable capacity to package chromosomal, and sometimes extrachromosomal, DNA into virus-like capsids and disseminate it to neighboring cells. Because GTAs resemble defective prophages, identification of novel GTAs is not trivial. The detection of candidates relies on the genetic similarity to known GTAs, which has been fruitful in α-proteobacterial lineages but challenging in more distant bacteria. Here we consider several fundamental questions: What is the true prevalence of GTAs in prokaryote genomes? Given there are high costs for GTA production, what advantage do GTAs provide to the bacterial host to justify their maintenance? How is the bacterial chromosome recognized and processed for inclusion in GTA particles? This article highlights the challenges in comprehensively understanding GTAs' prevalence, function and DNA packaging method. Going forward, broad study of atypical GTAs and use of ecologically relevant conditions are required to uncover their true impact on bacterial chromosome evolution.

With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities

IMPORTANCE

The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.

Adaptive radiations in natural populations of prokaryotes: innovation is key

Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process by which macrobiological diversity is generated. Here, we discuss whether ecological opportunity could lead to similar bursts of diversification in bacteria. We explore how adaptive radiations in prokaryotes can be kickstarted by horizontally acquired key innovations allowing lineages to invade new niche space that subsequently is partitioned among diversifying specialist descendants. We discuss how novel adaptive zones are colonized and exploited after the evolution of a key innovation and whether certain types of are more prone to adaptive radiation. Radiation into niche specialists does not necessarily lead to speciation in bacteria when barriers to recombination are absent. We propose that in this scenario, niche-specific genes could accumulate within a single lineage, leading to the evolution of an open pangenome.

The evolution of intramitochondriality in Midichloria bacteria

Midichloria spp. are intracellular bacterial symbionts of ticks. Representatives of this genus colonise mitochondria in the cells of their hosts. To shed light on this unique interaction we evaluated the presence of an intramitochondrial localization for three Midichloria in the respective tick host species and generated eight high-quality draft genomes and one closed genome, showing that this trait is non-monophyletic, either due to losses or multiple acquisitions. Comparative genomics supports the first hypothesis, as the genomes of non-mitochondrial symbionts are reduced subsets of those capable of colonising the organelles. We detect genomic signatures of mitochondrial tropism, including the differential presence of type IV secretion system and flagellum, which could allow the secretion of unique effectors and/or direct interaction with mitochondria. Other genes, including adhesion molecules, proteins involved in actin polymerisation, cell wall and outer membrane proteins, are only present in mitochondrial symbionts. The bacteria could use these to manipulate host structures, including mitochondrial membranes, to fuse with the organelles or manipulate the mitochondrial network.

Virus-like Particles from Wolbachia-Infected Cells May Include a Gene Transfer Agent

Wolbachia are obligate intracellular bacteria that occur in insects and filarial worms. Strains that infect insects have genomes that encode mobile genetic elements, including diverse lambda-like prophages called Phage WO. Phage WO packages an approximately 65 kb viral genome that includes a unique eukaryotic association module, or EAM, that encodes unusually large proteins thought to mediate interactions between the bacterium, its virus, and the eukaryotic host cell. The Wolbachia supergroup B strain, wStri from the planthopper Laodelphax striatellus, produces phage-like particles that can be recovered from persistently infected mosquito cells by ultracentrifugation. Illumina sequencing, assembly, and manual curation of DNA from two independent preparations converged on an identical 15,638 bp sequence that encoded packaging, assembly, and structural proteins. The absence of an EAM and regulatory genes defined for Phage WO from the wasp, Nasonia vitripennis, was consistent with the possibility that the 15,638 bp sequence represents an element related to a gene transfer agent (GTA), characterized by a signature head-tail region encoding structural proteins that package host chromosomal DNA. Future investigation of GTA function will be supported by the improved recovery of physical particles, electron microscopic examination of potential diversity among particles, and rigorous examination of DNA content by methods independent of sequence assembly.

Molecular pathogen screening of louse flies (Diptera: Hippoboscidae) from domestic and wild ruminants in Austria

BACKGROUND

Hippoboscid flies (Diptera: Hippoboscidae), also known as louse flies or keds, are obligate blood-sucking ectoparasites of animals, and accidentally of humans. The potential role of hippoboscids as vectors of human and veterinary pathogens is being increasingly investigated, but the presence and distribution of infectious agents in louse flies is still unknown in parts of Europe. Here, we report the use of molecular genetics to detect and characterize vector-borne pathogens in hippoboscid flies infesting domestic and wild animals in Austria.

METHODS

Louse flies were collected from naturally infested cattle (n = 25), sheep (n = 3), and red deer (n = 12) across Austria between 2015 and 2019. Individual insects were morphologically identified to species level and subjected to DNA extraction for molecular pathogen screening and barcoding. Genomic DNA from each louse fly was screened for Borrelia spp., Bartonella spp., Trypanosomatida, Anaplasmataceae, Filarioidea and Piroplasmida. Obtained sequences of Trypanosomatida and Bartonella spp. were further characterized by phylogenetic and haplotype networking analyses.

RESULTS

A total of 282 hippoboscid flies corresponding to three species were identified: Hippobosca equina (n = 62) collected from cattle, Melophagus ovinus (n = 100) from sheep and Lipoptena cervi (n = 120) from red deer (Cervus elaphus). Molecular screening revealed pathogen DNA in 54.3% of hippoboscids, including infections with single (63.39%), two (30.71%) and up to three (5.90%) distinct pathogens in the same individual. Bartonella DNA was detected in 36.9% of the louse flies. Lipoptena cervi were infected with 10 distinct and previously unreported Bartonella sp. haplotypes, some closely associated with strains of zoonotic potential. DNA of trypanosomatids was identified in 34% of hippoboscids, including the first description of Trypanosoma sp. in H. equina. Anaplasmataceae DNA (Wolbachia spp.) was detected only in M. ovinus (16%), while < 1% of the louse flies were positive for Borrelia spp. and Filarioidea. All hippoboscids were negative for Piroplasmida.

CONCLUSIONS

Molecular genetic screening confirmed the presence of several pathogens in hippoboscids infesting domestic and wild ruminants in Austria, including novel pathogen haplotypes of zoonotic potential (e.g. Bartonella spp.) and the first report of Trypanosoma sp. in H. equina, suggesting a potential role of this louse fly as vector of animal trypanosomatids. Experimental transmission studies and expanded monitoring of hippoboscid flies and hippoboscid-associated pathogens are warranted to clarify the competence of these ectoparasites as vectors of infectious agents in a One-Health context.

Viriforms-A New Category of Classifiable Virus-Derived Genetic Elements

The International Committee on Taxonomy of Viruses (ICTV) recently accepted viriforms as a new polyphyletic category of classifiable virus-derived genetic elements, juxtaposed to the polyphyletic virus, viroid, and satellite nucleic acid categories. Viriforms are endogenized former viruses that have been exapted by their cellular hosts to fulfill functions important for the host's life cycle. While morphologically resembling virions, particles made by viriforms do not package the viriform genomes but instead transport host genetic material. Known viriforms are highly diverse: members of family Polydnaviriformidae (former Polydnaviridae) have thus far been found exclusively in the genomes of braconid and ichneumonid parasitoid wasps, whereas the completely unrelated gene transfer agents (GTAs) are widely distributed among prokaryotes. In addition, recent discoveries likely extend viriforms to mammalian genomes. Here, we briefly outline the properties of these viriform groups and the first accepted and proposed ICTV frameworks for viriform classification.

Formal recognition and classification of gene transfer agents as viriforms

Morphological and genetic features strongly suggest that gene transfer agents (GTAs) are caudoviricete-derived entities that have evolved in concert with cellular genomes to such a degree that they should not be considered viruses. Indeed, GTA particles resemble caudoviricete virions, but, in contrast to caudoviricetes (or any viruses), GTAs can encapsidate at best only part of their own genomes, are induced solely in small subpopulations of prokaryotic host cells, and are transmitted vertically as part of cellular genomes during replication and division. Therefore, the lifecycles of GTAs are analogous to virus-derived entities found in the parasitoid wasps, which have recently been recognized as non-virus entities and therefore reclassified as viriforms. We evaluated three distinct, independently exapted GTA groups, for which the genetic basis for GTA particle production has been established. Based on the evidence, we outline a classification scheme for these viriforms.

The Impact of Bartonella VirB/VirD4 Type IV Secretion System Effectors on Eukaryotic Host Cells

Bartonella spp. are facultative intracellular pathogens that infect a wide range of mammalian hosts including humans. The VirB/VirD4 type IV secretion system (T4SS) is a key virulence factor utilized to translocate Bartonella effector proteins (Beps) into host cells in order to subvert their functions. Crucial for effector translocation is the C-terminal Bep intracellular delivery (BID) domain that together with a positively charged tail sequence forms a bipartite translocation signal. Multiple BID domains also evolved secondary effector functions within host cells. The majority of Beps possess an N-terminal filamentation induced by cAMP (FIC) domain and a central connecting oligonucleotide binding (OB) fold. FIC domains typically mediate AMPylation or related post-translational modifications of target proteins. Some Beps harbor other functional modules, such as tandem-repeated tyrosine-phosphorylation (EPIYA-related) motifs. Within host cells the EPIYA-related motifs are phosphorylated, which facilitates the interaction with host signaling proteins. In this review, we will summarize our current knowledge on the molecular functions of the different domains present in Beps and highlight examples of Bep-dependent host cell modulation.

Antibiotic resistance genes in bacteria: Occurrence, spread, and control

The production and use of antibiotics are becoming increasingly common worldwide, and the problem of antibiotic resistance is increasing alarmingly. Drug-resistant infections threaten human life and health and impose a heavy burden on the global economy. The origin and molecular basis of bacterial resistance is the presence of antibiotic resistance genes (ARGs). Investigations on ARGs mostly focus on the environments in which antibiotics are frequently used, such as hospitals and farms. This literature review summarizes the current knowledge of the occurrence of antibiotic-resistant bacteria in nonclinical environments, such as air, aircraft wastewater, migratory bird feces, and sea areas in-depth, which have rarely been involved in previous studies. Furthermore, the mechanism of action of plasmid and phage during horizontal gene transfer was analyzed, and the transmission mechanism of ARGs was summarized. This review highlights the new mechanisms that enhance antibiotic resistance and the evolutionary background of multidrug resistance; in addition, some promising points for controlling or reducing the occurrence and spread of antimicrobial resistance are also proposed.

Evolutionary Diversification of Host-Targeted Bartonella Effectors Proteins Derived from a Conserved FicTA Toxin-Antitoxin Module

Proteins containing a FIC domain catalyze AMPylation and other post-translational modifications (PTMs). In bacteria, they are typically part of FicTA toxin-antitoxin modules that control conserved biochemical processes such as topoisomerase activity, but they have also repeatedly diversified into host-targeted virulence factors. Among these, Bartonella effector proteins (Beps) comprise a particularly diverse ensemble of FIC domains that subvert various host cellular functions. However, no comprehensive comparative analysis has been performed to infer molecular mechanisms underlying the biochemical and functional diversification of FIC domains in the vast Bep family. Here, we used X-ray crystallography, structural modelling, and phylogenetic analyses to unravel the expansion and diversification of Bep repertoires that evolved in parallel in three Bartonella lineages from a single ancestral FicTA toxin-antitoxin module. Our analysis is based on 99 non-redundant Bep sequences and nine crystal structures. Inferred from the conservation of the FIC signature motif that comprises the catalytic histidine and residues involved in substrate binding, about half of them represent AMP transferases. A quarter of Beps show a glutamate in a strategic position in the putative substrate binding pocket that would interfere with triphosphate-nucleotide binding but may allow binding of an AMPylated target for deAMPylation or another substrate to catalyze a distinct PTM. The β-hairpin flap that registers the modifiable target segment to the active site exhibits remarkable structural variability. The corresponding sequences form few well-defined groups that may recognize distinct target proteins. The binding of Beps to promiscuous FicA antitoxins is well conserved, indicating a role of the antitoxin to inhibit enzymatic activity or to serve as a chaperone for the FIC domain before translocation of the Bep into host cells. Taken together, our analysis indicates a remarkable functional plasticity of Beps that is mostly brought about by structural changes in the substrate pocket and the target dock. These findings may guide future structure–function analyses of the highly versatile FIC domains.

Molecular Survey and Genetic Diversity of Bartonella spp. in Small Indian Mongooses (Urva auropunctata) and Their Fleas on Saint Kitts, West Indies

This study aimed to molecularly survey and evaluate the genetic diversity of Bartonella spp. in mongooses and their fleas from St. Kitts. Spleen (n = 54), blood (n = 71), and pooled flea samples, all identified as Ctenocephalides felis (n = 53), were submitted to TaqMan real-time quantitative PCR (qPCR) targeting Bartonella-nuoG fragment (84 bp). Positive samples underwent further conventional PCR assays targeting five loci (gltA, rpoB, fstZ, nuoG, and ITS), subsequent sequencing, and phylogenetic and haplotype analyses. The overall occurrence of Bartonella spp. in mongooses and fleas was 51.2% (64/125 [95% CI (42.1–60.2%)]) and 62.3% (33/53) [95% CI (47.9–75.2%)]), respectively. From samples sequenced across the five loci, 50.8% (33/65) were identified as Bartonella henselae, 26.2% (17/65) were 96.74–99.01% similar by BLAST analysis to an unidentified Bartonella sp. previously reported in Japanese badgers (Meles anakuma), and 23.1% (15/65) were co-infected with both species. Nucleotide polymorphism analysis showed low diversity amongst haplotypes but did concur with phylogenetic analysis, placing the unidentified species in a separate clade from B. henselae by multiple mutational events. Our data confirms that mongooses and Ctenocephalides felis fleas collected from them are not only potential reservoirs for B. henselae but also a novel Bartonella sp. which we propose be called ‘Candidatus Bartonella kittensis’.

Molecular survey of Bartonella spp. in rodents and fleas from Chile

The aim of this study was to molecularly survey Bartonella spp. in rodents from the Valdivia Province, Southern Chile and from wild black rat-fleas in Guafo Island, Chilean Patagonia. Thrity-three spleens from synanthropic (Mus musculus, Rattus novergicus and Rattus rattus) and wild (Abrothrix longipilis, Oligoryzomys longicaudatus, Abrothrix sp.) rodents from Valdivia and 39 fleas/flea-pools (Plocopsylla sp. and Nosopsyllus sp.) from R. rattus in Guafo Island were obtained. All samples were screened by high-resolution melting (HRM) real-time PCR for Bartonella ITS locus (190 bp). ITS-Positive samples were further analyzed for two HRM real-time PCR assays targeting Bartonella rpoB (191 bp) and gltA (340 bp) gene fragments. All positive ITS, gltA and rpoB real-time PCR products were purified and sequenced. Bayesian inference trees were built for the gltA and rpoB gene fragments. Bartonella-ITS DNA was detected in 36.3% (12/33) [95% CI (22-53%)] of the tested rodents from Valdivia, being identified in all but O. longicaudatus rodent species captured in this study. ITS DNA was detected in 28% (11/39) [95% CI (16-43%)] of fleas/flea-pools from Guafo Island and identified in both Plocopsylla and Nosopsyllus genera. Sequencing and phylogenic analyses targeting three loci of Bartonella spp. allowed the identification of five genotypes in rodents from Southern Chile, potentially belonging to three different Bartonella spp. Those included Bartonella tribocorum identified from R. rattus, Bartonella rochalimae detected from Abrothix sp., and one novel genotype from uncharacterized Bartonella sp. identified in M. musculus, R. norvegicus, A. longipilis, and Abothrix sp., related to strains previously isolated in Phyllotis sp. from Peru. Additionally, two genotypes of B. tribocorum were identified in fleas from Guafo. In a nutshell, highly diverse and potentially zoonotic Bartonella spp. are described for the first time in wild and synanthropic rodents from Chile, and B. tribocorum was detected in wild back rat fleas from Guafo Island.

Bartonella spp. detection in ticks, Culicoides biting midges and wild cervids from Norway

Bartonella spp. are fastidious, gram-negative, aerobic, facultative intracellular bacteria that infect humans, and domestic and wild animals. In Norway, Bartonella spp. have been detected in cervids, mainly within the distribution area of the arthropod vector deer ked (Lipoptena cervi). We used PCR to survey the prevalence of Bartonella spp. in blood samples from 141 cervids living outside the deer ked distribution area (moose [Alces alces, n = 65], red deer [Cervus elaphus, n = 41] and reindeer [Rangifer tarandus, n = 35]), in 44 pool samples of sheep tick (Ixodes ricinus, 27 pools collected from 74 red deer and 17 from 45 moose) and in biting midges of the genus Culicoides (Diptera: Ceratopogonidae, 120 pools of 6,710 specimens). Bartonella DNA was amplified in moose (75.4%, 49/65) and in red deer (4.9%, 2/41) blood samples. All reindeer were negative. There were significant differences in Bartonella prevalence among the cervid species. Additionally, Bartonella was amplified in two of 17 tick pools collected from moose and in 3 of 120 biting midge pool samples. The Bartonella sequences amplified in moose, red deer and ticks were highly similar to B. bovis, previously identified in cervids. The sequence obtained from biting midges was only 81.7% similar to the closest Bartonella spp. We demonstrate that Bartonella is present in moose across Norway and present the first data on northern Norway specimens. The high prevalence of Bartonella infection suggests that moose could be the reservoir for this bacterium. This is the first report of bacteria from the Bartonella genus in ticks from Fennoscandia and in Culicoides biting midges worldwide.

Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in Rhizobiales

Bacteria form diverse interactions with eukaryotic hosts. This is well represented by the Rhizobiales, a clade of Alphaproteobacteria strategically important for their large diversity of lifestyles with implications for agricultural and medical research. To investigate their lifestyle evolution, we compiled a comprehensive data set of genomes and lifestyle information for over 1,000 Rhizobiales genomes. We show that the origins of major host-associated lineages in Rhizobiales broadly coincided with the emergences of their host plants/animals, suggesting bacterium-host interactions as a driving force in the evolution of Rhizobiales. We further found that, in addition to gene gains, preexisting traits and recurrent losses of specific genomic traits may have played underrecognized roles in the origin of host-associated lineages, providing clues to genetic engineering of microbial agricultural inoculants and prevention of the emergence of potential plant/animal pathogens.

Members of the order Rhizobiales include those capable of nitrogen fixation in nodules as well as pathogens of animals and plants. This lifestyle diversity has important implications for agricultural and medical research. Leveraging large-scale genomic data, we infer that Rhizobiales originated as a free-living ancestor ∼1,500 million years ago (Mya) and that the later emergence of host-associated lifestyles broadly coincided with the rise of their eukaryotic hosts. In particular, the first nodulating lineage arose from either Azorhizobium or Bradyrhizobium 150 to 80 Mya, a time range in general concurrent with the emergence of legumes. The rates of lifestyle transitions are highly variable; nodule association is more likely to be lost than gained, whereas animal association likely represents an evolutionary dead end. We searched for statistical correlations between gene presence and lifestyle and identified genes likely contributing to the transition and adaptation to the same lifestyle in divergent lineages. Among the genes potentially promoting successful transitions to major nodulation lineages, the nod and nif clusters for nodulation and nitrogen fixation, respectively, were repeatedly acquired during each transition; the fix, dct, and phb clusters involved in energy conservation under micro-oxic conditions were present in the nonnodulating ancestors; and the secretion systems were acquired in lineage-specific patterns. Our study data suggest that increased eukaryote diversity drives lifestyle diversification of bacteria and highlight both acquired and preexisting traits facilitating the origin of host association.

IMPORTANCE Bacteria form diverse interactions with eukaryotic hosts. This is well represented by the Rhizobiales, a clade of Alphaproteobacteria strategically important for their large diversity of lifestyles with implications for agricultural and medical research. To investigate their lifestyle evolution, we compiled a comprehensive data set of genomes and lifestyle information for over 1,000 Rhizobiales genomes. We show that the origins of major host-associated lineages in Rhizobiales broadly coincided with the emergences of their host plants/animals, suggesting bacterium-host interactions as a driving force in the evolution of Rhizobiales. We further found that, in addition to gene gains, preexisting traits and recurrent losses of specific genomic traits may have played underrecognized roles in the origin of host-associated lineages, providing clues to genetic engineering of microbial agricultural inoculants and prevention of the emergence of potential plant/animal pathogens.

Bartonella kosoyi sp. nov. and Bartonella krasnovii sp. nov., two novel species closely related to the zoonotic Bartonella elizabethae, isolated from black rats and wild desert rodent-fleas

The genus Bartonella (Family: Bartonellaceae; Order: Rhizobiales; Class: Alphaproteobacteria) comprises facultative intracellular Gram-negative, haemotropic, slow-growing, vector-borne bacteria. Wild rodents and their fleas harbor a great diversity of species and strains of the genus Bartonella, including several zoonotic ones. This genetic diversity coupled with a fastidious nature of the organism results in a taxonomic challenge that has led to a massive collection of uncharacterized strains. Here, we report the genomic and phenotypic characterization of two strains, members of the genus Bartonella (namely Tel Aviv and OE 1-1), isolated from Rattus rattus rats and Synosternus cleopatrae fleas, respectively. Scanning electron microscopy revealed rod-shaped bacteria with polar pili, lengths ranging from 1.0 to 2.0 µm and widths ranging from 0.3 to 0.6 µm. OE 1-1 and Tel Aviv strains contained one single chromosome of 2.16 and 2.23 Mbp and one plasmid of 29.0 and 41.5 Kbp, with average DNA G+C contents of 38.16 and 38.47 mol%, respectively. These strains presented an average nucleotide identity (ANI) of 89.9 %. Bartonella elizabethae was found to be the closest phylogenetic relative of both strains (ANI=90.9-93.6 %). The major fatty acids identified in both strains were C_18:1ω7c, C_18 : 0 and C_16 : 0. They differ from B. elizabethae in their C_17 : 0 and C_15 : 0 compositions. Both strains are strictly capnophilic and their biochemical profiles resembled those of species of the genus Bartonella with validly published names, whereas differences in arylamidase activities partially assisted in their speciation. Genomic and phenotypic differences demonstrate that OE 1-1 and Tel Aviv strains represent novel individual species, closely related to B. elizabethae, for which we propose the names Bartonella kosoyi sp. nov. and Bartonella krasnovii sp. nov.

Gene Transfer Agents in Symbiotic Microbes

Prokaryotes commonly undergo genome reduction, particularly in the case of symbiotic bacteria. Genome reductions tend toward the energetically favorable removal of unnecessary, redundant, or nonfunctional genes. However, without mechanisms to compensate for these losses, deleterious mutation and genetic drift might otherwise overwhelm a population. Among the mechanisms employed to counter gene loss and share evolutionary success within a population, gene transfer agents (GTAs) are increasingly becoming recognized as important contributors. Although viral in origin, GTA particles package fragments of their "host" genome for distribution within a population of cells, often in a synchronized manner, rather than selfishly packaging genes necessary for their spread. Microbes as diverse as archaea and alpha-proteobacteria have been known to produce GTA particles, which are capable of transferring selective advantages such as virulence factors and antibiotic resistance. In this review, we discuss the various types of GTAs identified thus far, focusing on a defined set of symbiotic alpha-proteobacteria known to carry them. Drawing attention to the predicted presence of these genes, we discuss their potential within the selective marine and terrestrial environments occupied by mutualistic, parasitic, and endosymbiotic microbes.

Small extracellular particles with big potential for horizontal gene transfer: membrane vesicles and gene transfer agents

Bacteria are known to release different types of particles that serve various purposes such as the processing of metabolites, communication, and the transfer of genetic material. One of the most interesting aspects of the production of such particles is the biogenesis and trafficking of complex particles that can carry DNA, RNA, proteins or toxins into the surrounding environment to aid in bacterial survival or lead to gene transfer. Two important bacterial extracellular complexes are membrane vesicles and gene transfer agents. In this review, we will discuss the production, contents and functions of these two types of particles as related to their abilities to facilitate horizontal gene transfer.

Bartonella gene transfer agent: Evolution, function, and proposed role in host adaptation

The processes underlying host adaptation by bacterial pathogens remain a fundamental question with relevant clinical, ecological, and evolutionary implications. Zoonotic pathogens of the genus Bartonella constitute an exceptional model to study these aspects. Bartonellae have undergone a spectacular diversification into multiple species resulting from adaptive radiation. Specific adaptations of a complex facultative intracellular lifestyle have enabled the colonisation of distinct mammalian reservoir hosts. This remarkable host adaptability has a multifactorial basis and is thought to be driven by horizontal gene transfer (HGT) and recombination among a limited genus‐specific pan genome. Recent functional and evolutionary studies revealed that the conserved Bartonella gene transfer agent (BaGTA) mediates highly efficient HGT and could thus drive this evolution. Here, we review the recent progress made towards understanding BaGTA evolution, function, and its role in the evolution and pathogenesis of Bartonella spp. We notably discuss how BaGTA could have contributed to genome diversification through recombination of beneficial traits that underlie host adaptability. We further address how BaGTA may counter the accumulation of deleterious mutations in clonal populations (Muller's ratchet), which are expected to occur through the recurrent transmission bottlenecks during the complex infection cycle of these pathogens in their mammalian reservoir hosts and arthropod vectors.

Origin and Evolution of the Bartonella Gene Transfer Agent

Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transfer of bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forces that drive the emergence of GTAs are still poorly understood. Two GTAs have been identified in the Alphaproteobacteria: the RcGTA, which is widely distributed in a broad range of species; and the BaGTA, which has a restricted host range that includes vector-borne intracellular bacteria of the genus Bartonella. The RcGTA packages chromosomal DNA randomly, whereas the BaGTA particles contain a relatively higher fraction of genes for host interaction factors that are amplified from a nearby phage-derived origin of replication. In this study, we compare the BaGTA genes with homologous bacteriophage genes identified in the genomes of Bartonella species and close relatives. Unlike the BaGTA, the prophage genes are neither present in all species, nor inserted into homologous genomic sites. Phylogenetic inferences and substitution frequency analyses confirm codivergence of the BaGTA with the host genome, as opposed to multiple integration and recombination events in the prophages. Furthermore, the organization of segments flanking the BaGTA differs from that of the prophages by a few rearrangement events, which have abolished the normal coordination between phage genome replication and phage gene expression. Based on the results of our comparative analysis, we propose a model for how a prophage may be transformed into a GTA that transfers amplified bacterial DNA segments.

Role of distinct type-IV-secretion systems and secreted effector sets in host adaptation by pathogenic Bartonella species

The α‐proteobacterial genus Bartonella comprises a large number of facultative intracellular pathogens that share a common lifestyle hallmarked by hemotrophic infection and arthropod transmission. Speciation in the four deep‐branching lineages (L1–L4) occurred by host adaptation facilitating the establishment of long lasting bacteraemia in specific mammalian reservoir host(s). Two distinct type‐IV‐secretion systems (T4SSs) acquired horizontally by different Bartonella lineages mediate essential host interactions during infection and represent key innovations for host adaptation. The Trw‐T4SS confined to the species‐rich L4 mediates host‐specific erythrocyte infection and likely has functionally replaced flagella as ancestral virulence factors implicated in erythrocyte colonisation by bartonellae of the other lineages. The VirB/VirD4‐T4SS translocates Bartonella effector proteins (Bep) into various host cell types to modulate diverse cellular and innate immune functions involved in systemic spreading of bacteria following intradermal inoculation. Independent acquisition of the virB/virD4/bep locus by L1, L3, and L4 was likely driven by arthropod vectors associated with intradermal inoculation of bacteria rather than facilitating direct access to blood. Subsequently, adaptation to colonise specific niches in the new host has shaped the evolution of complex species‐specific Bep repertoires. This diversification of the virulence factor repertoire of Bartonella spp. represents a remarkable example for parallel evolution of host adaptation.

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.

Genome Evolution of Bartonellaceae Symbionts of Ants at the Opposite Ends of the Trophic Scale

Many insects rely on bacterial symbionts to supply essential amino acids and vitamins that are deficient in their diets, but metabolic comparisons of closely related gut bacteria in insects with different dietary preferences have not been performed. Here, we demonstrate that herbivorous ants of the genus Dolichoderus from the Peruvian Amazon host bacteria of the family Bartonellaceae, known for establishing chronic or pathogenic infections in mammals. We detected these bacteria in all studied Dolichoderus species, and found that they reside in the midgut wall, that is, the same location as many previously described nutritional endosymbionts of insects. The genomic analysis of four divergent strains infecting different Dolichoderus species revealed genes encoding pathways for nitrogen recycling and biosynthesis of several vitamins and all essential amino acids. In contrast, several biosynthetic pathways have been lost, whereas genes for the import and conversion of histidine and arginine to glutamine have been retained in the genome of a closely related gut bacterium of the carnivorous ant Harpegnathos saltator. The broad biosynthetic repertoire in Bartonellaceae of herbivorous ants resembled that of gut bacteria of honeybees that likewise feed on carbohydrate-rich diets. Taken together, the broad distribution of Bartonellaceae across Dolichoderus ants, their small genome sizes, the specific location within hosts, and the broad biosynthetic capability suggest that these bacteria are nutritional symbionts in herbivorous ants. The results highlight the important role of the host nutritional biology for the genomic evolution of the gut microbiota-and conversely, the importance of the microbiota for the nutrition of hosts.

Prophage-Driven Genomic Structural Changes Promote Bartonella Vertical Evolution

Bartonella is a genetically diverse group of vector-borne bacteria. Over 40 species have been characterized to date, mainly from mammalian reservoirs and arthropod vectors. Rodent reservoirs harbor one of the largest Bartonella diversity described to date, and novel species and genetic variants are continuously identified from these hosts. Yet, it is still unknown if this significant genetic diversity stems from adaptation to different niches or from intrinsic high mutation rates. Here, we explored the vertical occurrence of spontaneous genomic alterations in 18 lines derived from two rodent-associated Bartonella elizabethae-like strains, evolved in nonselective agar plates under conditions mimicking their vector- and mammalian-associated temperatures, and the transmission cycles between them (i.e., 26 °C, 37 °C, and alterations between the two), using mutation accumulation experiments. After ∼1,000 generations, evolved genomes revealed few point mutations (average of one-point mutation per line), evidencing conserved single-nucleotide mutation rates. Interestingly, three large structural genomic changes (two large deletions and an inversion) were identified over all lines, associated with prophages and surface adhesin genes. Particularly, a prophage, deleted during constant propagation at 37 °C, was associated with an increased autonomous replication at 26 °C (the flea-associated temperature). Complementary molecular analyses of wild strains, isolated from desert rodents and their fleas, further supported the occurrence of structural genomic variations and prophage-associated deletions in nature. Our findings suggest that structural genomic changes represent an effective intrinsic mechanism to generate diversity in slow-growing bacteria and emphasize the role of prophages as promoters of diversity in nature.

Evolution of Bacterial Gene Transfer Agents

Bacterial gene transfer agents (GTAs) are small virus-like particles that package DNA fragments and inject them into cells. They are encoded by gene clusters resembling defective prophages, with genes for capsid head and tail components. These gene clusters are usually assumed to be maintained by selection for the benefits of GTA-mediated recombination, but this has never been tested. We rigorously examined the potential benefits of GTA-mediated recombination, considering separately transmission of GTA-encoding genes and recombination of all chromosomal genes. In principle GTA genes could be directly maintained if GTA particles spread them to GTA^- cells often enough to compensate for the loss of GTA-producing cells. However, careful bookkeeping showed that losses inevitably exceed gains for two reasons. First, cells must lyse to release particles to the environment. Second, GTA genes are not preferentially replicated before DNA is packaged. A simulation model was then used to search for conditions where recombination of chromosomal genes makes GTA⁺ populations fitter than GTA^- populations. Although the model showed that both synergistic epistasis and some modes of regulation could generate fitness benefits large enough to overcome the cost of lysis, these benefits neither allowed GTA⁺ cells to invade GTA^- populations, nor allowed GTA⁺ populations to resist invasion by GTA^- cells. Importantly, the benefits depended on highly improbable assumptions about the efficiencies of GTA production and recombination. Thus, the selective benefits that maintain GTA gene clusters over many millions of years must arise from consequences other than transfer of GTA genes or recombination of chromosomal genes.

The depths of virus exaptation

Viruses are ubiquitous parasites of cellular life forms and the most abundant biological entities on earth. The relationships between viruses and their hosts involve the continuous arms race but are by no account limited to it. Growing evidence shows that, in the course of evolution, viruses and their components are repeatedly recruited (exapted) for host functions. The functions of exapted viruses typically involve either defense from other viruses or cellular competitors or transfer of nucleic acids between cells, or storage functions. Virus exaptation can reach different depths, from recruitment of a fully functional virus to exploitation of defective, partially degraded viruses, to utilization of individual virus proteins.

Phylogeny and putative virulence gene analysis of Bartonella bovis

Bartonella bovis is a small Gram-negative bacterium recognized as an etiological agent for bacteremia and endocarditis in cattle. As few reports are available on the taxonomic position of B. bovis and its mechanism of virulence, this study aims to resolve the phylogeny of B. bovis and investigate putative virulence genes based on whole genome sequence analysis. Genome-wide comparisons based on single nucleotide polymorphisms (SNP) and orthologous genes were performed in this study for phylogenetic inference of 27 Bartonella species. Rapid Annotation using Subsystem Technology (RAST) analysis was used for annotation of putative virulence genes. The phylogenetic tree generated from the genome-wide comparison of orthologous genes exhibited a topology almost similar to that of the tree generated from SNP-based comparison, indicating a high concordance in the nucleotide and amino acid sequences of Bartonella spp. The analyses show consistent grouping of B. bovis in a cluster related to ruminant-associated species, including Bartonella australis, Bartonella melophagi and Bartonella schoenbuchensis. RAST analysis revealed genes encoding flagellar components, in corroboration with the observation of flagella-like structure of BbUM strain under negative straining. Genes associated with virulence, disease and defence, prophages, membrane transport, iron acquisition, motility and chemotaxis are annotated in B. bovis genome. The flagellin (flaA) gene of B. bovis is closely related to Bartonella bacilliformis and Bartonella clarridgeiae but distinct from other Gram-negative bacteria. The absence of type IV secretion systems, the bona fide pathogenicity factors of bartonellae, in B. bovis suggests that it may have a different mechanism of pathogenicity.

Host-symbiont-pathogen interactions in blood-feeding parasites: nutrition, immune cross-talk and gene exchange

Animals are common hosts of mutualistic, commensal and pathogenic microorganisms. Blood-feeding parasites feed on a diet that is nutritionally unbalanced and thus often rely on symbionts to supplement essential nutrients. However, they are also of medical importance as they can be infected by pathogens such as bacteria, protists or viruses that take advantage of the blood-feeding nutritional strategy for own transmission. Since blood-feeding evolved multiple times independently in diverse animals, it showcases a gradient of host-microbe interactions. While some parasitic lineages are possibly asymbiotic and manage to supplement their diet from other food sources, other lineages are either loosely associated with extracellular gut symbionts or harbour intracellular obligate symbionts that are essential for the host development and reproduction. What is perhaps even more diverse are the pathogenic lineages that infect blood-feeding parasites. This microbial diversity not only puts the host into a complicated situation - distinguishing between microorganisms that can greatly decrease or increase its fitness - but also increases opportunity for horizontal gene transfer to occur in this environment. In this review, I first introduce this diversity of mutualistic and pathogenic microorganisms associated with blood-feeding animals and then focus on patterns in their interactions, particularly nutrition, immune cross-talk and gene exchange.

Whole-Genome Analysis of Bartonella ancashensis, a Novel Pathogen Causing Verruga Peruana, Rural Ancash Region, Peru

The genus Bartonella contains >40 species, and an increasing number of these Bartonella species are being implicated in human disease. One such pathogen is Bartonella ancashensis, which was isolated in blood samples from 2 patients living in Caraz, Peru, during a clinical trial of treatment for bartonellosis. Three B. ancashensis strains were analyzed by using whole-genome restriction mapping and high-throughput pyrosequencing. Genome-wide comparative analysis of Bartonella species showed that B. ancashensis has features seen in modern and ancient lineages of Bartonella species and is more related to B. bacilliformis. The divergence between B. ancashensis and B. bacilliformis is much greater than what is seen between known Bartonella genetic lineages. In addition, B. ancashensis contains type IV secretion system proteins, which are not present in B. bacilliformis. Whole-genome analysis indicates that B. ancashensis might represent a distinct Bartonella lineage phylogenetically related to B. bacilliformis.

A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes

Mobile genetic elements (MGEs) are an important feature of prokaryote genomes but are seldom well annotated and, consequently, are often underestimated. MGEs include transposons (Tn), insertion sequences (ISs), prophages, genomic islands (GEIs), integrons, and integrative and conjugative elements (ICEs). They are intimately involved in genome evolution and promote phenomena such as genomic expansion and rearrangement, emergence of virulence and pathogenicity, and symbiosis. In spite of the annotation bottleneck, there are so far at least 75 different programs and databases dedicated to prokaryotic MGE analysis and annotation, and this number is rapidly growing. Here, we present a practical guide to explore, compare, and visualize prokaryote MGEs using a combination of available software and databases tailored to small scale genome analyses. This protocol can be coupled with expert MGE annotation and exploited for evolutionary and comparative genomic analyses.

Carrion's Disease: the Sound of Silence

Carrion's disease (CD) is a neglected biphasic vector-borne illness related to Bartonella bacilliformis. It is found in the Andean valleys and is transmitted mainly by members of the Lutzomyia genus but also by blood transfusions and from mother to child. The acute phase, Oroya fever, presents severe anemia and fever. The lethality is high in the absence of adequate treatment, despite the organism being susceptible to most antibiotics. Partial immunity is developed after infection by B. bacilliformis, resulting in high numbers of asymptomatic carriers. Following infection there is the chronic phase, Peruvian warts, involving abnormal proliferation of the endothelial cells. Despite potentially being eradicable, CD has been expanded due to human migration and geographical expansion of the vector. Moreover, in vitro studies have demonstrated the risk of the development of antimicrobial resistance. These findings, together with the description of new Bartonella species producing CD-like infections, the presence of undescribed potential vectors in new areas, the lack of adequate diagnostic tools and knowledge of the immunology and bacterial pathogenesis of CD, and poor international visibility, have led to the risk of increasing the potential expansion of resistant strains which will challenge current treatment schemes as well as the possible appearance of CD in areas where it is not endemic.

Insights into origin and evolution of α-proteobacterial gene transfer agents

Several bacterial and archaeal lineages produce nanostructures that morphologically resemble small tailed viruses, but, unlike most viruses, contain apparently random pieces of the host genome. Since these elements can deliver the packaged DNA to other cells, they were dubbed gene transfer agents (GTAs). Because many genes involved in GTA production have viral homologs, it has been hypothesized that the GTA ancestor was a virus. Whether GTAs represent an atypical virus, a defective virus, or a virus co-opted by the prokaryotes for some function, remains to be elucidated. To evaluate these possibilities, we examined the distribution and evolutionary histories of genes that encode a GTA in the α-proteobacterium Rhodobacter capsulatus (RcGTA). We report that although homologs of many individual RcGTA genes are abundant across bacteria and their viruses, RcGTA-like genomes are mainly found in one subclade of α-proteobacteria. When compared with the viral homologs, genes of the RcGTA-like genomes evolve significantly slower, and do not have higher %A+T nucleotides than their host chromosomes. Moreover, they appear to reside in stable regions of the bacterial chromosomes that are generally conserved across taxonomic orders. These findings argue against RcGTA being an atypical or a defective virus. Our phylogenetic analyses suggest that RcGTA ancestor likely originated in the lineage that gave rise to contemporary α-proteobacterial orders Rhizobiales, Rhodobacterales, Caulobacterales, Parvularculales, and Sphingomonadales, and since that time the RcGTA-like element has co-evolved with its host chromosomes. Such evolutionary history is compatible with maintenance of these elements by bacteria due to some selective advantage. As for many other prokaryotic traits, horizontal gene transfer played a substantial role in the evolution of RcGTA-like elements, not only in shaping its genome components within the orders, but also in occasional dissemination of RcGTA-like regions across the orders and even to different bacterial phyla.

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.

A bacterial toxin-antitoxin module is the origin of inter-bacterial and inter-kingdom effectors of Bartonella

Host-targeting type IV secretion systems (T4SS) evolved from conjugative T4SS machineries that mediate interbacterial plasmid transfer. However, the origins of effectors secreted by these virulence devices have remained largely elusive. Previous work showed that some effectors exhibit homology to toxins of bacterial toxin-antitoxin modules, but the evolutionary trajectories underlying these ties had not been resolved. We previously reported that FicT toxins of FicTA toxin-antitoxin modules disrupt cellular DNA topology via their enzymatic FIC (filamentation induced by cAMP) domain. Intriguingly, the FIC domain of the FicT toxin VbhT of Bartonella schoenbuchensis is fused to a type IV secretion signal–the BID (Bep intracellular delivery) domain—similar to the Bartonella effector proteins (Beps) that are secreted into eukaryotic host cells via the host-targeting VirB T4SS. In this study, we show that the VbhT toxin is an interbacterial effector protein secreted via the conjugative Vbh T4SS that is closely related to the VirB T4SS and encoded by plasmid pVbh of B. schoenbuchensis. We therefore propose that the Vbh T4SS together with its effector VbhT represent an evolutionary missing link on a path that leads from a regular conjugation system and FicTA toxin-antitoxin modules to the VirB T4SS and the Beps. Intriguingly, phylogenetic analyses revealed that the fusion of FIC and BID domains has probably occurred independently in VbhT and the common ancestor of the Beps, suggesting parallel evolutionary paths. Moreover, several other examples of TA module toxins that are bona fide substrates of conjugative T4SS indicate that their recruitment as interbacterial effectors is prevalent and serves yet unknown biological functions in the context of bacterial conjugation. We propose that the adaptation for interbacterial transfer favors the exaptation of FicT and other TA module toxins as inter-kingdom effectors and may thus constitute an important stepping stone in the evolution of host-targeted effector proteins.

Many bacterial pathogens use secretion systems to translocate effector proteins into host cells where they manipulate cell functions in favor of the pathogen. It is well-known that these secretion systems evolved from ancestors with functions in genuine bacterial contexts, but the origins of their secreted effectors have largely remained elusive. In this article we studied the evolutionary history of a host-targeting effector secretion system of the mammalian pathogen Bartonella that belongs to a group of machineries descended from secretion systems originally mediating DNA transfer between bacterial cells. Intriguingly, we found that such a DNA transfer machinery closely related to the host-targeting secretion system of Bartonella has recruited a bacterial protein involved in modulating DNA topology as an interbacterial effector protein that is translocated together with the DNA into recipient cells. The overall setup of this interbacterial effector is remarkably similar to the host-targeted effectors of Bartonella, and we propose that it represents an evolutionary missing link on the path from a genuine bacterial protein to effectors that manipulates host cell functioning. Further analyses showed that interbacterial effectors in DNA transfer may be a more common phenomenon and represent an important reservoir for the evolution of new host-targeted effectors.

Evolutionary Dynamics of Pathoadaptation Revealed by Three Independent Acquisitions of the VirB/D4 Type IV Secretion System in Bartonella

The α-proteobacterial genus Bartonella comprises a group of ubiquitous mammalian pathogens that are studied as a model for the evolution of bacterial pathogenesis. Vast abundance of two particular phylogenetic lineages of Bartonella had been linked to enhanced host adaptability enabled by lineage-specific acquisition of a VirB/D4 type IV secretion system (T4SS) and parallel evolution of complex effector repertoires. However, the limited availability of genome sequences from one of those lineages as well as other, remote branches of Bartonella has so far hampered comprehensive understanding of how the VirB/D4 T4SS and its effectors called Beps have shaped Bartonella evolution. Here, we report the discovery of a third repertoire of Beps associated with the VirB/D4 T4SS of B. ancashensis, a novel human pathogen that lacks any signs of host adaptability and is only distantly related to the two species-rich lineages encoding a VirB/D4 T4SS. Furthermore, sequencing of ten new Bartonella isolates from under-sampled lineages enabled combined in silico analyses and wet lab experiments that suggest several parallel layers of functional diversification during evolution of the three Bep repertoires from a single ancestral effector. Our analyses show that the Beps of B. ancashensis share many features with the two other repertoires, but may represent a more ancestral state that has not yet unleashed the adaptive potential of such an effector set. We anticipate that the effectors of B. ancashensis will enable future studies to dissect the evolutionary history of Bartonella effectors and help unraveling the evolutionary forces underlying bacterial host adaptation.

Gene Transfer Agent Promotes Evolvability within the Fittest Subpopulation of a Bacterial Pathogen

The Bartonella gene transfer agent (BaGTA) is an archetypical example for domestication of a phage-derived element to permit high-frequency genetic exchange in bacterial populations. Here we used multiplexed transposon sequencing (TnSeq) and single-cell reporters to globally define the core components and transfer dynamics of BaGTA. Our systems-level analysis has identified inner- and outer-circle components of the BaGTA system, including 55 regulatory components, as well as an additional 74 and 107 components mediating donor transfer and recipient uptake functions. We show that the stringent response signal guanosine-tetraphosphate (ppGpp) restricts BaGTA induction to a subset of fast-growing cells, whereas BaGTA particle uptake depends on a functional Tol-Pal trans-envelope complex that mediates outer-membrane invagination upon cell division. Our findings suggest that Bartonella evolved an efficient strategy to promote genetic exchange within the fittest subpopulation while disfavoring exchange of deleterious genetic information, thereby facilitating genome integrity and rapid host adaptation.

Beyond the canonical strategies of horizontal gene transfer in prokaryotes

Efforts to identify and characterize strategies for horizontal gene transfer (HGT) in prokaryotes could have overlooked some mechanisms that do not entirely fit in with the canonical ones most often described (conjugation of plasmids, phage transduction and transformation). The difficulty in distinguishing the different HGT strategies could have contributed to underestimate their real extent. Here we review non classical HGT strategies: some that require mobile genetic elements (MGEs) and others independent of MGE. Among those strategies that require MGEs, there is a range of newly reported, hybrid and intermediate MGEs mobilizing only their own DNA, others that mobilize preferentially bacterial DNA, or both. Considering HGT strategies independent of MGE, a few are even not restricted to DNA transfer, but can also mobilize other molecules. This review considers those HGT strategies that are less commonly dealt with in the literature. The real impact of these elements could, in some conditions, be more relevant than previously thought.

Prevalence and Phylogenetic Analysis of Bartonella Species of Wild Carnivores and Their Fleas in Northwestern Mexico

The host-parasite-vector relationship of Bartonella spp. system in wild carnivores and their fleas from northwestern Mexico was investigated. Sixty-six carnivores belonging to eight species were sampled, and 285 fleas belonging to three species were collected during spring (April-May) and fall (October-November) seasons. We detected Bartonella species in 7 carnivores (10.6%) and 27 fleas (9.5%) through either blood culture or PCR. Of the 27 Bartonella-positive fleas, twenty-two were Pulex simulans, three were Pulex irritans and one was Echidnophaga gallinacea. The gltA gene and ITS region sequences alignment revealed six and eight genetic variants of Bartonella spp., respectively. These variants were clustered into Bartonella rochalimae, Bartonella vinsonii subsp. berkhoffii and another genotype, which likely represents a novel species of Bartonella spp. Although experimental infection studies are required to prove the vector role of P. simulans, our results suggest that this flea may play an important role in the Bartonella transmission. The results indicated possible host-specific relationships between Bartonella genotypes and the families of the carnivores, but further studies are needed to verify this finding. The presence of zoonotic species of Bartonella spp. in wild carnivores raises the issue of their potential risk for humans in fragmented ecosystems.

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.