Multi-locus sequence analysis reveals profound genetic diversity among isolates of the human pathogen Bartonella bacilliformis

Single-nucleotide polymorphisms in ialB, gltA and rpoB genes of Bartonella bacilliformis isolated from patients in endemic Peruvian regions

Bartonella bacilliformis is a Gram-negative, aerobic bacterium and the known causal agent of Carrion's disease, still considered a neglected disease. There is limited information about the nucleotide sequences of this bacterium in international databases, and few studies have addressed the genetic diversity of B. bacilliformis. We analyzed a total of 20 isolates of B. bacilliformis from the Peruvian regions of Ancash and Cajamarca. Three genes (ialB, gltA, and rpoB) were sequenced in each isolate and nucleotide sequences retrieved from GenBank (16 B. bacilliformis genomes) were also included in the study. All this information was merged in order to obtain clearer evidence of the phylogenetic relationships of B. bacilliformis. In the phylogenetic analysis conducted with the concatenated markers, four isolates (B.b-1, B. b-3, B. b- 7, B.b-8) from the Ancash region were observed to form a subgroup different from B. bacilliformis type strain KC583, showing dissimilarity levels of 5.96% (ialB), 3.69% (gltA) and 3.04% (rpoB). Our results suggest that B. bacilliformis consists of two different subgroups. Future investigations are needed to establish the taxonomic status of these subgroups.

In silico analysis of Pap31 from Bartonella bacilliformis and other Bartonella spp

Pap31 is an outer membrane protein of Bartonella bacilliformis which is considered to be a potential antigenic candidate for the development of diagnostic tools. The present study aimed to compare Pap31 from B. bacilliformis with that of other Bartonella spp. The results showed the presence of at least 5 different B. bacilliformis Pap31 alleles, with the strain Ver097 being the most divergent (89.7% of identity with the reference strain KC583). The most significant finding was the presence of a variable number (1 to 3) of 6 amino acid tandem repeats (GTEGGG) in the different B. bacilliformis Pap31 alleles, with no similar structure in other established Bartonella spp., except for Bartonella ancashensis, another Bartonella spp. isolated from chronic cases of Carrion's disease. In both B. bacilliformis and B. ancashensis this repetitive region was coincident with the most predicted immunogenic region of the protein. In other microorganisms, the presence of amino acid tandem repeats has been related to the development of poorly functional antibodies. The findings of this study also suggest a utility of Pap31 amino acid tandem repeats as potential contributors to the immune evasion of Carrion's disease-related Bartonella spp. and the establishment of asymptomatic B. bacilliformis / B. ancashensis infections.

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla

Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of speciation times the probability that two new species coexist long enough to reach a particular level of divergence. Here I have explored these two parameters of disparification in bacteria. Owing to low recombination rates, sexual isolation is not a necessary milestone of bacterial speciation. Rather, irreversible and indefinite divergence begins with ecological diversification, that is, transmission of a bacterial lineage to a new ecological niche, possibly to a new microhabitat but at least to new resources. Several algorithms use sequence data from a taxon of focus to identify phylogenetic groups likely to bear the dynamic properties of species. Identifying these newly divergent lineages allows us to characterize the genetic bases of speciation, as well as the ecological dimensions upon which new species diverge. Speciation appears to be least frequent when a given lineage has few new resources it can adopt, as exemplified by photoautotrophs, C1 heterotrophs, and obligately intracellular pathogens; speciation is likely most rapid for generalist heterotrophs. The genetic basis of ecological divergence may determine whether ecological divergence is irreversible and whether lineages will diverge indefinitely into the future. Long-term coexistence is most likely when newly divergent lineages utilize at least some resources not shared with the other and when the resources themselves will coexist into the remote future.

Revisiting Bartonella bacilliformis MLST

All the studies published including Bartonella bacilliformis MLST data, as well as all B. bacilliformis genomes present in GenBank were analyzed. Overall 64 isolates and their geographical distribution were analyzed, and 14 different MLST patterns were observed. The results highlight the need for expanding the MLST studies and adding a higher number of isolates from all endemic areas.

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.

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.

Genotyping ofBartonellabacteria and their animal hosts: current status and perspectives

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

Diversity and phylogenetic relationships among Bartonella strains from Thai bats

Bartonellae are phylogenetically diverse, intracellular bacteria commonly found in mammals. Previous studies have demonstrated that bats have a high prevalence and diversity of Bartonella infections globally. Isolates (n = 42) were obtained from five bat species in four provinces of Thailand and analyzed using sequences of the citrate synthase gene (gltA). Sequences clustered into seven distinct genogroups; four of these genogroups displayed similarity with Bartonella spp. sequences from other bats in Southeast Asia, Africa, and Eastern Europe. Thirty of the isolates representing these seven genogroups were further characterized by sequencing four additional loci (ftsZ, nuoG, rpoB, and ITS) to clarify their evolutionary relationships with other Bartonella species and to assess patterns of diversity among strains. Among the seven genogroups, there were differences in the number of sequence variants, ranging from 1-5, and the amount of nucleotide divergence, ranging from 0.035-3.9%. Overall, these seven genogroups meet the criteria for distinction as novel Bartonella species, with sequence divergence among genogroups ranging from 6.4-15.8%. Evidence of intra- and intercontinental phylogenetic relationships and instances of homologous recombination among Bartonella genogroups in related bat species were found in Thai bats.

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.

Mutation-Driven Divergence and Convergence Indicate Adaptive Evolution of the Intracellular Human-Restricted Pathogen, Bartonella bacilliformis

Among all species of Bartonella, human-restricted Bartonella bacilliformis is the most virulent but harbors one of the most reduced genomes. Carrión’s disease, the infection caused by B. bacilliformis, has been afflicting poor rural populations for centuries in the high-altitude valleys of the South American Andes, where the pathogen’s distribution is probably restricted by its sand fly vector’s range. Importantly, Carrión’s disease satisfies the criteria set by the World Health Organization for a disease amenable to elimination. However, to date, there are no genome-level studies to identify potential footprints of B. bacilliformis (patho)adaptation. Our comparative genomic approach demonstrates that the evolution of this intracellular pathogen is shaped predominantly via mutation. Analysis of strains having publicly-available genomes shows high mutational divergence of core genes leading to multiple sub-species. We infer that the sub-speciation event might have happened recently where a possible adaptive divergence was accelerated by intermediate emergence of a mutator phenotype. Also, within a sub-species the pathogen shows inter-clonal adaptive evolution evidenced by non-neutral accumulation of convergent amino acid mutations. A total of 67 non-recombinant core genes (over-representing functional categories like DNA repair, glucose metabolic process, ATP-binding and ligase) were identified as candidates evolving via adaptive mutational convergence. Such convergence, both at the level of genes and their encoded functions, indicates evolution of B. bacilliformis clones along common adaptive routes, while there was little diversity within a single clone.

How host-restriction, intracellularity and genome reduction interplay to exert or maintain virulence is poorly characterized. The fact that B. bacilliformis is the most pathogenic Bartonella and has a highly reduced genome makes it an attractive model to gain insights into (patho)adaptive evolution of intracellular pathogens. Also, B. bacilliformis is known to lack many virulence genes present in other Bartonella, indicating unique strategies of (patho)adaptation. Our study reveals a prevalent nature of mutational force in B. bacilliformis evolution with two distinct outcomes: (a) mutational divergence leading to sub-speciation, possibly recently, via accelerated accumulation and fixation of favorable mutations mediated by a mutator phenotype; and (b) mutational convergence between clones of a sub-species exhibiting shared functional trajectories of adaptive evolution. Our findings highlight positions accumulating adaptive mutations in candidate genes, offering future functional studies to elucidate B. bacilliformis virulence evolution, and of broad application to intracellular pathogens with a reduced gene repertoire.

Prevalence and Diversity of Bartonella Species in Rodents from Georgia (Caucasus)

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 commonly 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.

Multi-Locus Sequence Typing of Bartonella bacilliformis DNA Performed Directly from Blood of Patients with Oroya's Fever During a Peruvian Outbreak

Background

Bartonella bacilliformis is the etiological agent of Carrion’s disease, a neglected tropical poverty-linked illness. This infection is endemic of Andean regions and it is estimated that approximately 1.7 million of South Americans are at risk. This bacterium is a fastidious slow growing microorganism, which is difficult and cumbersome to isolate from clinical sources, thereby hindering the availability of phylogenetic relationship of clinical samples. The aim of this study was to perform Multi Locus Sequence Typing of B. bacilliformis directly in blood from patients diagnosed with Oroya fever during an outbreak in Northern Peru.

Methodology/Principal Findings

DNA extracted among blood samples from patients diagnosed with Oroya’s fever were analyzed with MLST, with the amplification of 7 genetic loci (ftsZ, flaA, ribC, rnpB, rpoB, bvrR and groEL) and a phylogenetic analysis of the different Sequence Types (ST) was performed. A total of 4 different ST were identified. The most frequently found was ST1 present in 66% of samples. Additionally, two samples presented a new allelic profile, belonging to new STs (ST 9 and ST 10), which were closely related to ST1.

Conclusions/Significance

The present data demonstrate that B. bacilliformis MLST studies may be possible directly from blood samples, being a promising approach for epidemiological studies. During the outbreak the STs of B. bacilliformis were found to be heterogeneous, albeit closely related, probably reflecting the evolution from a common ancestor colonizing the area. Additional studies including new samples and areas are needed, in order to obtain better knowledge of phylogenetic scenario B. bacilliformis.

The bacteria Bartonella bacilliformis is the etiological agent of Carrion’s disease, which is a neglected poverty-related disease, related to Mountain Andean valleys of Peru, Colombia and Ecuador. This disease, in absence of treatment presents a high mortality during the acute phase, called Oroya’s Fever. The second phase is characterized by the development of dermal eruptions, known as “Verruga peruana” (Peruvian wart). This bacterium is a fastidious slow growing microorganism, being difficult and cumbersome to isolate from clinical sources. Then, the available data about phylogenetic relationship in clinical samples are really scarce, but suggesting high variability. The aim of the study was to perform direct blood analysis of B. bacilliformis Multi Locus Sequence Typing (MLST), a genotyping tool, in patients with Oroya fever during an outbreak. The present study demonstrates that the direct blood PCR, followed by nucleotide sequencing and MLST is a technique useful in the phylogenic characterization of this fastidious microorganism endemic from Andean regions. In this study, we demonstrate that the outbreak of Oroya’s fever was caused by closely related Sequence Typing (ST) microorganisms and, additionally, new STs have been described.

Proteins of Bartonella bacilliformis: Candidates for Vaccine Development

Bartonella bacilliformis is the etiologic agent of Carrión's disease or Oroya fever. B. bacilliformis infection represents an interesting model of human host specificity. The notable differences in clinical presentations of Carrión's disease suggest complex adaptations by the bacterium to the human host, with the overall objectives of persistence, maintenance of a reservoir state for vectorial transmission, and immune evasion. These events include a multitude of biochemical and genetic mechanisms involving both bacterial and host proteins. This review focuses on proteins involved in interactions between B. bacilliformis and the human host. Some of them (e.g., flagellin, Brps, IalB, FtsZ, Hbp/Pap31, and other outer membrane proteins) are potential protein antigen candidates for a synthetic vaccine.

Classification of Bartonella strains associated with straw-colored fruit bats (Eidolon helvum) across Africa using a multi-locus sequence typing platform

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.

Bats, with over 1000 recognized species, represent about 20% of all classified mammalian species worldwide. These mammals have a wide range of ecologies and life-history traits, and are now widely recognized as important reservoirs of many pathogens. Bartonella species have been found distributed in a wide range of mammalian species, including bats. About half of recognized Bartonella species, including one bat-associated species, have been associated with human illness. Previous studies have shown that Bartonella species are extremely diverse, with or without evident specificity to their mammalian hosts. Possessing many unique aspects, bartonellae can serve as a useful biological marker to study how microorganisms have evolved and diversified along with their animal hosts in evolutionary history. In this study, we applied multi-locus sequence typing, or MLST, to study the genetic differences of straw-colored fruit bat (Eidolon helvum)-associated Bartonella species. Our studies suggest Bartonella species have both exchanged genetic materials among species through recombination events and lost genes that are perhaps superfluous to their life cycles, which includes an intracellular stage in mammals.

Oroya fever and verruga peruana: bartonelloses unique to South America

Bartonella bacilliformis is the bacterial agent of Carrión's disease and is presumed to be transmitted between humans by phlebotomine sand flies. Carrión's disease is endemic to high-altitude valleys of the South American Andes, and the first reported outbreak (1871) resulted in over 4,000 casualties. Since then, numerous outbreaks have been documented in endemic regions, and over the last two decades, outbreaks have occurred at atypical elevations, strongly suggesting that the area of endemicity is expanding. Approximately 1.7 million South Americans are estimated to be at risk in an area covering roughly 145,000 km2 of Ecuador, Colombia, and Peru. Although disease manifestations vary, two disparate syndromes can occur independently or sequentially. The first, Oroya fever, occurs approximately 60 days following the bite of an infected sand fly, in which infection of nearly all erythrocytes results in an acute hemolytic anemia with attendant symptoms of fever, jaundice, and myalgia. This phase of Carrión's disease often includes secondary infections and is fatal in up to 88% of patients without antimicrobial intervention. The second syndrome, referred to as verruga peruana, describes the endothelial cell-derived, blood-filled tumors that develop on the surface of the skin. Verrugae are rarely fatal, but can bleed and scar the patient. Moreover, these persistently infected humans provide a reservoir for infecting sand flies and thus maintaining B. bacilliformis in nature. Here, we discuss the current state of knowledge regarding this life-threatening, neglected bacterial pathogen and review its host-cell parasitism, molecular pathogenesis, phylogeny, sand fly vectors, diagnostics, and prospects for control.

Global distribution of Bartonella infections in domestic bovine and characterization of Bartonella bovis strains using multi-locus sequence typing

Bartonella bovis is commonly detected in cattle. One B. bovis strain was recently isolated from a cow with endocarditis in the USA, suggesting its role as an animal pathogen. In the present study, we investigated bartonella infections in 893 cattle from five countries (Kenya, Thailand, Japan, Georgia, and Guatemala) and 103 water buffaloes from Thailand to compare the prevalence of the infection among different regions and different bovid hosts. We developed a multi-locus sequence typing (MLST) scheme based on nine loci (16S rRNA, gltA, ftsZ, groEL, nuoG, ribC, rpoB, ssrA, and ITS) to compare genetic divergence of B. bovis strains, including 26 representatives from the present study and two previously described reference strains (one from French cows and another from a cow with endocarditis in the USA). Bartonella bacteria were cultured in 6.8% (7/103) of water buffaloes from Thailand; all were B. bovis. The prevalence of bartonella infections in cattle varied tremendously across the investigated regions. In Japan, Kenya, and the Mestia district of Georgia, cattle were free from the infection; in Thailand, Guatemala, and the Dusheti and Marneuli districts of Georgia, cattle were infected with prevalences of 10-90%. The Bartonella isolates from cattle belonged to three species: B. bovis (n=165), B. chomelii (n=9), and B. schoenbuchensis (n=1), with the latter two species found in Georgia only. MLST analysis suggested genetic variations among the 28 analyzed B. bovis strains, which fall into 3 lineages (I, II, and III). Lineages I and II were found in cattle while lineage III was restricted to water buffaloes. The majority of strains (17/28), together with the strain causing endocarditis in a cow in the USA, belonged to lineage I. Further investigations are needed to determine whether B. bovis causes disease in bovids.

Dried blood spots for qPCR diagnosis of acute Bartonella bacilliformis infection

Bartonella bacilliformis is the etiological agent of a life-threatening illness. Thin blood smear is the most common diagnostic method for acute infection in endemic areas of Peru but remains of limited value because of low sensitivity. The aim of this study was to adapt a B. bacilliformis-specific real-time polymerase chain reaction (PCR) assay for use with dried blood spots (DBS) as a sampling method and assess its performance and use for the diagnosis and surveillance of acute Bartonella infection. Only two of 65 children (3%) that participated in this study had positive blood smears for B. bacilliformis, whereas 16 (including these two) were positive by PCR performed on DBS samples (24.6%). The use of DBS in combination with B. bacilliformis-specific PCR could be a useful tool for public health in identifying and monitoring outbreaks of infection and designing control programs to reduce the burden of this life-threatening illness.

Molecular typing of "Candidatus Bartonella ancashi," a new human pathogen causing verruga peruana

A recently described clinical isolate, "Candidatus Bartonella ancashi," was obtained from a blood sample of a patient presenting with verruga peruana in the Ancash region of Peru. This sample and a second isolate obtained 60 days later from the same patient were molecularly typed using multilocus sequence typing (MLST) and multispacer sequence typing (MST). The isolates were 100% indistinguishable from each other but phylogenetically distant from Bartonella bacilliformis and considerably divergent from other known Bartonella species, confirming their novelty.

Distribution of Bartonella henselae variants in patients, reservoir hosts and vectors in Spain

We have studied the diversity of B. henselae circulating in patients, reservoir hosts and vectors in Spain. In total, we have fully characterized 53 clinical samples from 46 patients, as well as 78 B. henselae isolates obtained from 35 cats from La Rioja and Catalonia (northeastern Spain), four positive cat blood samples from which no isolates were obtained, and three positive fleas by Multiple Locus Sequence Typing and Multiple Locus Variable Number Tandem Repeats Analysis. This study represents the largest series of human cases characterized with these methods, with 10 different sequence types and 41 MLVA profiles. Two of the sequence types and 35 of the profiles were not described previously. Most of the B. henselae variants belonged to ST5. Also, we have identified a common profile (72) which is well distributed in Spain and was found to persist over time. Indeed, this profile seems to be the origin from which most of the variants identified in this study have been generated. In addition, ST5, ST6 and ST9 were found associated with felines, whereas ST1, ST5 and ST8 were the most frequent sequence types found infecting humans. Interestingly, some of the feline associated variants never found on patients were located in a separate clade, which could represent a group of strains less pathogenic for humans.

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

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

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

Pathogen typing in the genomics era: MLST and the future of molecular epidemiology

Multi-locus sequence typing (MLST) is a high-resolution genetic typing approach to identify species and strains of pathogens impacting human health, agriculture (animals and plants), and biosafety. In this review, we outline the general concepts behind MLST, molecular approaches for obtaining MLST data, analytical approaches for MLST data, and the contributions MLST studies have made in a wide variety of areas. We then look at the future of MLST and their relative strengths and weaknesses with respect to whole genome sequence typing approaches that are moving into the research arena at an ever-increasing pace. Throughout the paper, we provide exemplar references of these various aspects of MLST. The literature is simply too vast to make this review comprehensive, nevertheless, we have attempted to include enough references in a variety of key areas to introduce the reader to the broad applications and complications of MLST data.

Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa

We propose that clonal evolution in micropathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure, a definition already widely used for all kinds of pathogens, although not clearly formulated by many scientists and rejected by others. The two main manifestations of clonal evolution are strong linkage disequilibrium (LD) and widespread genetic clustering ("near-clading"). We hypothesize that this pattern is not mainly due to natural selection, but originates chiefly from in-built genetic properties of pathogens, which could be ancestral and could function as alternative allelic systems to recombination genes ("clonality/sexuality machinery") to escape recombinational load. The clonal framework of species of pathogens should be ascertained before any analysis of biomedical phenotypes (phylogenetic character mapping). In our opinion, this model provides a conceptual framework for the population genetics of any micropathogen.

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

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