Population genetics, taxonomy, phylogeny and evolution of Borrelia burgdorferi sensu lato

Nested coevolutionary networks shape the ecological relationships of ticks, hosts, and the Lyme disease bacteria of the Borrelia burgdorferi (s.l.) complex

Background

The bacteria of the Borrelia burgdorferi (s.l.) (BBG) complex constitute a group of tick-transmitted pathogens that are linked to many vertebrate and tick species. The ecological relationships between the pathogens, the ticks and the vertebrate carriers have not been analysed. The aim of this study was to quantitatively analyse these interactions by creating a network based on a large dataset of associations. Specifically, we examined the relative positions of partners in the network, the phylogenetic diversity of the tick’s hosts and its impact on BBG circulation. The secondary aim was to evaluate the segregation of BBG strains in different vectors and reservoirs.

Results

BBG circulates through a nested recursive network of ticks and vertebrates that delineate closed clusters. Each cluster contains generalist ticks with high values of centrality as well as specialist ticks that originate nested sub-networks and that link secondary vertebrates to the cluster. These results highlighted the importance of host phylogenetic diversity for ticks in the circulation of BBG, as this diversity was correlated with high centrality values for the ticks. The ticks and BBG species in each cluster were not significantly associated with specific branches of the phylogeny of host genera (R² = 0.156, P = 0.784 for BBG; R² = 0.299, P = 0.699 for ticks). A few host genera had higher centrality values and thus higher importance for BBG circulation. However, the combined contribution of hosts with low centrality values could maintain active BBG foci. The results suggested that ticks do not share strains of BBG, which were highly segregated among sympatric species of ticks.

Conclusions

We conclude that BBG circulation is supported by a highly redundant network. This network includes ticks with high centrality values and high host phylogenetic diversity as well as ticks with low centrality values. This promotes ecological sub-networks and reflects the high resilience of BBG circulation. The functional redundancy in BBG circulation reduces disturbances due to the removal of vertebrates as it allows ticks to fill other biotic niches.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1803-z) contains supplementary material, which is available to authorized users.

Parallelisms and Contrasts in the Diverse Ecologies of the Anaplasma phagocytophilum and Borrelia burgdorferi Complexes of Bacteria in the Far Western United States

Anaplasma phagocytophilum and Borrelia burgdorferi are two tick-borne bacteria that cause disease in people and animals. For each of these bacteria, there is a complex of closely related genospecies and/or strains that are genetically distinct and have been shown through both observational and experimental studies to have different host tropisms. In this review we compare the known ecologies of these two bacterial complexes in the far western USA and find remarkable similarities, which will help us understand evolutionary histories and coadaptation among vertebrate host, tick vector, and bacteria. For both complexes, sensu stricto genospecies (those that infect humans) share a similar geographic range, are vectored mainly by ticks in the Ixodes ricinus-complex, utilize mainly white-footed mice (Peromyscus leucopus) as a reservoir in the eastern USA and tree squirrels in the far west, and tend to be generalists, infecting a wider variety of vertebrate host species. Other sensu lato genospecies within each complex are generally more specialized, occurring often in local enzootic cycles within a narrow range of vertebrate hosts and specialized vector species. We suggest that these similar ecologies may have arisen through utilization of a generalist tick species as a vector, resulting in a potentially more virulent generalist pathogen that spills over into humans, vs. utilization of a specialized tick vector on a particular vertebrate host species, promoting microbe specialization. Such tight host-vector-pathogen coupling could also facilitate high enzootic prevalence and the evolution of host immune-tolerance and bacterial avirulence.

Recurrent evolution of host and vector association in bacteria of the Borrelia burgdorferi sensu lato species complex

Background

The Borrelia burgdorferi sensu lato (s.l.) species complex consists of tick-transmitted bacteria and currently comprises approximately 20 named and proposed genospecies some of which are known to cause Lyme Borreliosis. Species have been defined via genetic distances and ecological niches they occupy. Understanding the evolutionary relationship of species of the complex is fundamental to explaining patterns of speciation. This in turn forms a crucial basis to frame testable hypotheses concerning the underlying processes including host and vector adaptations.

Results

Illumina Technology was used to obtain genome-wide sequence data for 93 strains of 14 named genospecies of the B. burgdorferi species complex and genomic data already published for 18 additional strain (including one new species) was added. Phylogenetic reconstruction based on 114 orthologous single copy genes shows that the genospecies represent clearly distinguishable taxa with recent and still ongoing speciation events apparent in Europe and Asia. The position of Borrelia species in the phylogeny is consistent with host associations constituting a major driver for speciation. Interestingly, the data also demonstrate that vector associations are an additional driver for diversification in this tick-borne species complex. This is particularly obvious in B. bavariensis, a rodent adapted species that has diverged from the bird-associated B. garinii most likely in Asia. It now consists of two populations one of which most probably invaded Europe following adaptation to a new vector (Ixodes ricinus) and currently expands its distribution range.

Conclusions

The results imply that genotypes/species with novel properties regarding host or vector associations have evolved recurrently during the history of the species complex and may emerge at any time. We suggest that the finding of vector associations as a driver for diversification may be a general pattern for tick-borne pathogens. The core genome analysis presented here provides an important source for investigations of the underlying mechanisms of speciation in tick-borne pathogens.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3016-4) contains supplementary material, which is available to authorized users.

Multiple independent transmission cycles of a tick-borne pathogen within a local host community

Many pathogens are maintained by multiple host species and involve multiple strains with potentially different phenotypic characteristics. Disentangling transmission patterns in such systems is often challenging, yet investigating how different host species contribute to transmission is crucial to properly assess and manage disease risk. We aim to reveal transmission cycles of bacteria within the Borrelia burgdorferi species complex, which include Lyme disease agents. We characterized Borrelia genotypes found in 488 infected Ixodes ricinus nymphs collected in the Sénart Forest located near Paris (France). These genotypes were compared to those observed in three sympatric species of small mammals and network analyses reveal four independent transmission cycles. Statistical modelling shows that two cycles involving chipmunks, an introduced species, and non-sampled host species such as birds, are responsible for the majority of tick infections. In contrast, the cycle involving native bank voles only accounts for a small proportion of infected ticks. Genotypes associated with the two primary transmission cycles were isolated from Lyme disease patients, confirming the epidemiological threat posed by these strains. Our work demonstrates that combining high-throughput sequence typing with networks tools and statistical modeling is a promising approach for characterizing transmission cycles of multi-host pathogens in complex ecological settings.

Vectors as Epidemiological Sentinels: Patterns of Within-Tick Borrelia burgdorferi Diversity

Hosts including humans, other vertebrates, and arthropods, are frequently infected with heterogeneous populations of pathogens. Within-host pathogen diversity has major implications for human health, epidemiology, and pathogen evolution. However, pathogen diversity within-hosts is difficult to characterize and little is known about the levels and sources of within-host diversity maintained in natural populations of disease vectors. Here, we examine genomic variation of the Lyme disease bacteria, Borrelia burgdorferi (Bb), in 98 individual field-collected tick vectors as a model for study of within-host processes. Deep population sequencing reveals extensive and previously undocumented levels of Bb variation: the majority (~70%) of ticks harbor mixed strain infections, which we define as levels Bb diversity pre-existing in a diverse inoculum. Within-tick diversity is thus a sample of the variation present within vertebrate hosts. Within individual ticks, we detect signatures of positive selection. Genes most commonly under positive selection across ticks include those involved in dissemination in vertebrate hosts and evasion of the vertebrate immune complement. By focusing on tick-borne Bb, we show that vectors can serve as epidemiological and evolutionary sentinels: within-vector pathogen diversity can be a useful and unbiased way to survey circulating pathogen diversity and identify evolutionary processes occurring in natural transmission cycles.

Lyme disease, caused by a bacteria carried by deer ticks, is the most common vector-borne disease in North America and over 30,000 cases are reported each year in the United States. Ticks may be infected with multiple strains of the Lyme disease bacteria, which differ in transmissibility and the harm they pose to humans. In this study, we collected 98 infected deer ticks from across the United States and southern Canada. We used genetic techniques to investigate the diversity of the Lyme disease bacteria infecting each individual tick. We find that 70% of ticks are infected with multiple strains of the Lyme disease bacteria, indicating that humans may be exposed to and infected with multiple bacterial strains from a single tick bite. We also find evidence that the Lyme disease bacteria is evolving in response to the immune defenses of its natural hosts (including rodents and birds). Our study shows that individual ticks and other disease vectors can be studied as epidemiological sentinels, which reveal the extensive diversity of pathogens circulating in natural disease cycles and how they are evolving.

Diversifying forest communities may change Lyme disease risk: extra dimension to the dilution effect in Europe

Lyme disease is caused by bacteria of theBorrelia burgdorferigenospecies complex and transmitted by Ixodid ticks. In North America only one pathogenic genospecies occurs, in Europe there are several. According to the dilution effect hypothesis (DEH), formulated in North America, nymphal infection prevalence (NIP) decreases with increasing host diversity since host species differ in transmission potential. We analysedBorreliainfection in nymphs from 94 forest stands in Belgium, which are part of a diversification gradient with a supposedly related increasing host diversity: from pine stands without to oak stands with a shrub layer. We expected changing tree species and forest structure to increase host diversity and decrease NIP. In contrast with the DEH, NIP did not differ between different forest types. Genospecies diversity however, and presumably also host diversity, was higher in oak than in pine stands. Infected nymphs tended to harbourBorrelia afzeliiinfection more often in pine stands whileBorrelia gariniiandBorrelia burgdorferiss. infection appeared to be more prevalent in oak stands. This has important health consequences, since the latter two cause more severe disease manifestations. We show that the DEH must be nuanced for Europe and should consider the response of multiple pathogenic genospecies.

TRANSLATING ECOLOGY, PHYSIOLOGY, BIOCHEMISTRY, AND POPULATION GENETICS RESEARCH TO MEET THE CHALLENGE OF TICK AND TICK-BORNE DISEASES IN NORTH AMERICA

Emerging and re-emerging tick-borne diseases threaten public health and the wellbeing of domestic animals and wildlife globally. The adoption of an evolutionary ecology framework aimed to diminish the impact of tick-borne diseases needs to be part of strategies to protect human and animal populations. We present a review of current knowledge on the adaptation of ticks to their environment, and the impact that global change could have on their geographic distribution in North America. Environmental pressures will affect tick population genetics by selecting genotypes able to withstand new and changing environments and by altering the connectivity and isolation of several tick populations. Research in these areas is particularly lacking in the southern United States and most of Mexico with knowledge gaps on the ecology of these diseases, including a void in the identity of reservoir hosts for several tick-borne pathogens. Additionally, the way in which anthropogenic changes to landscapes may influence tick-borne disease ecology remains to be fully understood. Enhanced knowledge in these areas is needed in order to implement effective and sustainable integrated tick management strategies. We propose to refocus ecology studies with emphasis on metacommunity-based approaches to enable a holistic perspective addressing whole pathogen and host assemblages. Network analyses could be used to develop mechanistic models involving multihost-pathogen communities. An increase in our understanding of the ecology of tick-borne diseases across their geographic distribution will aid in the design of effective area-wide tick control strategies aimed to diminish the burden of pathogens transmitted by ticks.

Borrelia Genotyping in Lyme Disease

Borrelia burgdorferisensu lato is the causative agent of Lyme borreliosis, multisystem disorder characterized by a wide spectrum of clinical manifestations. Different borrelia species can lead to distinct clinical presentations, but some species were associated with defined clinical manifestation likeBorrelia afzeliiwith skin manifestations,Borrelia gariniiwith central nervous system disorders andBorrelia burgdorferisensu stricto with Lyme arthritis.Ixodesticks represent the main vectors ofB. burgdorferisensu lato; wild animals, lizards and birds are the natural reservoir of borrelia. Genotyping of borrelia strains is of great importance for epidemiological, clinical, and evolutionary studies. Numerous methods are available for the genotyping ofB. burgdorferisensu lato based either on whole genome or PCR based typing. Typing methods differ in their approach and target, many of them were implemented more or less successfully for diagnostic purposes.

Molecular identification of Borrelia genus in questing hard ticks from Portugal: Phylogenetic characterization of two novel Relapsing Fever-like Borrelia sp

In the last decades, several studies have reported pathogenic species of Borrelia related to those that cause Tick-borne Relapsing Fever (RF), but unexpectedly suggesting their transmission by hard ticks, known vectors of Borrelia burgdorferi sensu lato (B. burgdorferi s.l.) species, rather than by soft ticks. This study was designed to update the presence of B. burgdorferi s.l. species in ticks from several districts of mainland Portugal, where Ixodes ricinus had been previously described. Ticks (a total of 2915 specimens) were collected in seven districts throughout the country, and analyzed using molecular methods. Three nested-PCR protocols, targeting the flagellin gene (flaB), the intergenic spacer region (IGS) located between 5S and 23S rRNA, and the glpQ gene, and a conventional PCR targeting the 16S rRNA, were used for Borrelia DNA detection. Borrelia DNA was detected in 3% of the ticks from Braga, Vila Real, Lisboa, Setúbal, Évora and Faro districts. The obtained amplicons were sequenced and analyzed by BLASTn, and 15/63 (24%) matched with homologous sequences from Borrelia lusitaniae and 15/63 (24%) with B. garinii, being these the most prevalent species. DNA from B. burgdorferi sensu stricto (s.s.), B. valaisiana and B. afzelii were detected in 7/63 (11%), 6/63 (10%), and 2/63 (3%) of the specimens, respectively. Unexpectedly, DNA sequence (flaB) analysis from eight (13%) samples, two from Rhipicephalus sanguineus and six from Haemaphysalis punctata tick species, revealed high homology with RF-like Borrelia. Phylogenetic analyses obtained from three genetic markers (16S rRNA, flaB, and glpQ) confirmed their congruent inclusion in a strongly supported RF cluster, where they segregated in two subgroups which differ from the other Relapsing Fever species. Therefore, the results confirm the circulation of multiple species of B. burgdorferi s.l. over a wide geographic range, covering most of the Portuguese mainland territory. Surprisingly, the obtained data also revealed two putative Relapsing Fever-like Borrelia species in different species of hard ticks, possibly disclosing the circulation of novel RF-like Borrelia species with different associated tick vectors.

Trans-Atlantic exchanges have shaped the population structure of the Lyme disease agent Borrelia burgdorferi sensu stricto

The origin and population structure of Borrelia burgdorferi sensu stricto (s.s.), the agent of Lyme disease, remain obscure. This tick-transmitted bacterial species occurs in both North America and Europe. We sequenced 17 European isolates (representing the most frequently found sequence types in Europe) and compared these with 17 North American strains. We show that trans-Atlantic exchanges have occurred in the evolutionary history of this species and that a European origin of B. burgdorferi s.s. is marginally more likely than a USA origin. The data further suggest that some European human patients may have acquired their infection in North America. We found three distinct genetically differentiated groups: i) the outgroup species Borrelia bissettii, ii) two divergent strains from Europe, and iii) a group composed of strains from both the USA and Europe. Phylogenetic analysis indicated that different genotypes were likely to have been introduced several times into the same area. Our results demonstrate that irrespective of whether B. burgdorferi s.s. originated in Europe or the USA, later trans-Atlantic exchange(s) have occurred and have shaped the population structure of this genospecies. This study clearly shows the utility of next generation sequencing to obtain a better understanding of the phylogeography of this bacterial species.

Evidence for Host-Genotype Associations of Borrelia burgdorferi Sensu Stricto

Different genotypes of the agent of Lyme disease in North America, Borrelia burgdorferi sensu stricto, show varying degrees of pathogenicity in humans. This variation in pathogenicity correlates with phylogeny and we have hypothesized that the different phylogenetic lineages in North America reflect adaptation to different host species. In this study, evidence for host species associations of B. burgdorferi genotypes was investigated using 41 B. burgdorferi-positive samples from five mammal species and 50 samples from host-seeking ticks collected during the course of field studies in four regions of Canada: Manitoba, northwestern Ontario, Quebec, and the Maritimes. The B. burgdorferi genotypes in the samples were characterized using three established molecular markers (multi-locus sequence typing [MLST], 16S-23S rrs-rrlA intergenic spacer, and outer surface protein C sequence [ospC] major groups). Correspondence analysis and generalized linear mixed effect models revealed significant associations between B. burgdorferi genotypes and host species (in particular chipmunks, and white-footed mice and deer mice), supporting the hypotheses that host adaptation contributes to the phylogenetic structure and possibly the observed variation in pathogenicity in humans.

Complex population structure of Borrelia burgdorferi in southeastern and south central Canada as revealed by phylogeographic analysis

Lyme disease, caused by the bacterium Borrelia burgdorferi sensu stricto, is an emerging zoonotic disease in Canada and is vectored by the blacklegged tick, Ixodes scapularis. Here we used Bayesian analyses of sequence types (STs), determined by multilocus sequence typing (MLST), to investigate the phylogeography of B. burgdorferi populations in southern Canada and the United States by analyzing MLST data from 564 B. burgdorferi-positive samples collected during surveillance. A total of 107 Canadian samples from field sites were characterized as part of this study, and these data were combined with existing MLST data for samples from the United States and Canada. Only 17% of STs were common between both countries, while 49% occurred only in the United States, and 34% occurred only in Canada. However, STs in southeastern Ontario and southwestern Quebec were typically identical to those in the northeastern United States, suggesting a recent introduction into this region from the United States. In contrast, STs in other locations in Canada (the Maritimes; Long Point, Ontario; and southeastern Manitoba) were frequently unique to those locations but were putative descendants of STs previously found in the United States. The picture in Canada is consistent with relatively recent introductions from multiple refugial populations in the United States. These data thus point to a geographic pattern of populations of B. burgdorferi in North America that may be more complex than simply comprising northeastern, midwestern, and Californian groups. We speculate that this reflects the complex ecology and spatial distribution of key reservoir hosts.

Flying ticks: anciently evolved associations that constitute a risk of infectious disease spread

Ticks are important vectors of emerging zoonotic diseases affecting human and animal health worldwide. Ticks are often found on wild birds, which have been long recognized as a potential risk factor for dissemination of ticks and tick-borne pathogens (TBP), thus raising societal concerns and prompting research into their biology and ecology. To fully understand the role of birds in disseminating some ticks species and TBP, it is important to consider the evolutionary relationships between birds, ticks and transmitted pathogens. In this paper we reviewed the possible role of birds in the dissemination of TBP as a result of the evolution of host-tick-pathogen associations. Birds are central elements in the ecological networks of ticks, hosts and TBP. The study of host-tick-pathogen associations reveals a prominent role for birds in the dissemination of Borrelia spp. and Anaplasma phagocytophilum, with little contribution to the possible dissemination of other TBP. Birds have played a major role during tick evolution, which explains why they are by far the most important hosts supporting the ecological networks of ticks and several TBP. The immune response of birds to ticks and TBP has been largely overlooked. To implement effective measures for the control of tick-borne diseases, it is necessary to study bird-tick and bird-pathogen molecular interactions including the immune response of birds to tick infestation and pathogen infection.

Similarities in murine infection and immune response to Borrelia bissettii and Borrelia burgdorferi sensu stricto

In 1982, Borrelia burgdorferi sensu stricto (ss) was identified as the aetiological agent of Lyme disease. Since then an increasing number of Borrelia burgdorferi sensu lato (sl) species have been isolated in the United States. To date, many of these species remain understudied despite mounting evidence associating them with human illness. Borrelia bissettii is a spirochaete closely related to B. burgdorferi that has been loosely associated with human illness. Using an experimental murine infection model, we compared the infectivity and humoral immune response with a North American isolate of B. bissettii and B. burgdorferi using culture, molecular and serological methods. The original B. bissettii cultures were unable to infect immunocompetent mice, but were confirmed to be infectious after adaptation in immunodeficient animals. B. bissettii infection resulted in spirochaete burdens similar to B. burgdorferi in skin, heart and bladder whereas significantly lower burdens were observed in the joint tissues. B. bissettii induced an antibody response similar to B. burgdorferi as measured by both immunoblotting and the C6 ELISA. Additionally, this isolate of B. bissettii was sequenced on the Ion Torrent PGM, which successfully identified many genes orthologous to mammalian virulence factors described in B. burgdorferi. Similarities seen between both infections in this well-characterized murine model contribute to our understanding of the potential pathogenic nature of B. bissettii. Infection dynamics of B. bissettii, and especially the induced humoral response, are similar to B. burgdorferi, suggesting this species may contribute to the epidemiology of human borreliosis.

Evolutionary aspects of emerging Lyme disease in Canada

In North America, Lyme disease (LD) is a tick-borne zoonosis caused by the spirochete bacterium Borrelia burgdorferi sensu stricto, which is maintained by wildlife. Tick vectors and bacteria are currently spreading into Canada and causing increasing numbers of cases of LD in humans and raising a pressing need for public health responses. There is no vaccine, and LD prevention depends on knowing who is at risk and informing them how to protect themselves from infection. Recently, it was found in the United States that some strains of B. burgdorferi sensu stricto cause severe disease, whereas others cause mild, self-limiting disease. While many strains occurring in the United States also occur in Canada, strains in some parts of Canada are different from those in the United States. We therefore recognize a need to identify which strains specific to Canada can cause severe disease and to characterize their geographic distribution to determine which Canadians are particularly at risk. In this review, we summarize the history of emergence of LD in North America, our current knowledge of B. burgdorferi sensu stricto diversity, its intriguing origins in the ecology and evolution of the bacterium, and its importance for the epidemiology and clinical and laboratory diagnosis of LD. We propose methods for investigating associations between B. burgdorferi sensu stricto diversity, ecology, and pathogenicity and for developing predictive tools to guide public health interventions. We also highlight the emergence of B. burgdorferi sensu stricto in Canada as a unique opportunity for exploring the evolutionary aspects of tick-borne pathogen emergence.

Molecular identification and bioinformatics analysis of a potential anti-vector vaccine candidate, 15-kDa salivary gland protein (Salp15), from Ixodes affinis ticks

Salp15, a 15-kDa salivary gland protein plays an important role in tick blood-feeding and transmission of Borrelia burgdorferi, the causative agent of Lyme borreliosis. The comparative studies reveal that Salp15 is a genetically conserved protein across various Ixodes species. In this study, we have identified a Salp15 homolog, designated as Iaff15, from Ixodes affinis ticks that are the principal enzootic vectors of B. burgdorferi sensu stricto in the southeastern part of the United States. Comparison of the annotated amino acid sequences showed that Iaff15 share 81% homology with I. sinensis Salp15 homolog and 64% homology with I. scapularis Salp15. Phylogenetic analysis revealed that Iaff15 come within the same clade with I. sinensis, I. scapularis, and I. pacificus Salp15 homologs. The bioinformatics analysis of the posttranslational modifications prediction revealed that all the Salp15 family members contain glycosylation sites. In addition, Iaff15 carried a higher number of Casein Kinase II phosphorylation sites in comparison to the other Salp15 family members. Collectively, high sequence conservation distributed over the entire amino acids sequence not only suggests an important role for Iaff15 in I. affinis blood feeding and vector-pathogen interactions but may also lead to the development of an anti-vector vaccine against this group of ticks.

Identification of the minimal cytolytic unit for streptolysin S and an expansion of the toxin family

BACKGROUND

Streptolysin S (SLS) is a cytolytic virulence factor produced by the human pathogen Streptococcus pyogenes and other Streptococcus species. Related "SLS-like" toxins have been characterized in select strains of Clostridium and Listeria, with homologous clusters bioinformatically identified in a variety of other species. SLS is a member of the thiazole/oxazole-modified microcin (TOMM) family of natural products. The structure of SLS has yet to be deciphered and many questions remain regarding its structure-activity relationships.

RESULTS

In this work, we assessed the hemolytic activity of a series of C-terminally truncated SLS peptides expressed in SLS-deficient S. pyogenes. Our data indicate that while the N-terminal poly-heterocyclizable (NPH) region of SLS substantially contributes to its bioactivity, the variable C-terminal region of the toxin is largely dispensable. Through genome mining we identified additional SLS-like clusters in diverse Firmicutes, Spirochaetes and Actinobacteria. Among the Spirochaete clusters, naturally truncated SLS-like precursors were found in the genomes of three Lyme disease-causing Borrelia burgdorferi sensu lato (Bbsl) strains. Although unable to restore hemolysis in SLS-deficient S. pyogenes, a Bbsl SLS-like precursor peptide was converted to a cytolysin using purified SLS biosynthetic enzymes. A PCR-based screen demonstrated that SLS-like clusters are substantially more prevalent in Bbsl than inferred from publicly available genome sequences.

CONCLUSIONS

The mutagenesis data described herein indicate that the minimal cytolytic unit of SLS encompasses the NPH region of the core peptide. Interestingly, this region is found in all characterized TOMM cytolysins, as well as the novel putative TOMM cytolysins we discovered. We propose that this conserved region represents the defining feature of the SLS-like TOMM family. We demonstrate the cytolytic potential of a Bbsl SLS-like precursor peptide, which has a core region of similar length to the SLS minimal cytolytic unit, when modified with purified SLS biosynthetic enzymes. As such, we speculate that some Borrelia have the potential to produce a TOMM cytolysin, although the biological significance of this finding remains to be determined. In addition to providing new insight into the structure-activity relationships of SLS, this study greatly expands the cytolysin group of TOMMs.

The Borrelia afzelii outer membrane protein BAPKO_0422 binds human factor-H and is predicted to form a membrane-spanning β-barrel

The deep evolutionary history of the Spirochetes places their branch point early in the evolution of the diderms, before the divergence of the present day Proteobacteria. As a spirochete, the morphology of the Borrelia cell envelope shares characteristics of both Gram-positive and Gram-negative bacteria. A thin layer of peptidoglycan, tightly associated with the cytoplasmic membrane, is surrounded by a more labile outer membrane (OM). This OM is rich in lipoproteins but with few known integral membrane proteins. The outer membrane protein A (OmpA) domain is an eight-stranded membrane-spanning β-barrel, highly conserved among the Proteobacteria but so far unknown in the Spirochetes. In the present work, we describe the identification of four novel OmpA-like β-barrels from Borrelia afzelii, the most common cause of erythema migrans (EM) rash in Europe. Structural characterization of one these proteins (BAPKO_0422) by SAXS and CD indicate a compact globular structure rich in β-strand consistent with a monomeric β-barrel. Ab initio molecular envelopes calculated from the scattering profile are consistent with homology models and demonstrate that BAPKO_0422 adopts a peanut shape with dimensions 25×45 Å (1 Å=0.1 nm). Deviations from the standard C-terminal signature sequence are apparent; in particular the C-terminal phenylalanine residue commonly found in Proteobacterial OM proteins is replaced by isoleucine/leucine or asparagine. BAPKO_0422 is demonstrated to bind human factor H (fH) and therefore may contribute to immune evasion by inhibition of the complement response. Encoded by chromosomal genes, these proteins are highly conserved between Borrelia subspecies and may be of diagnostic or therapeutic value.

Borrelia persica: In vitro cultivation and characterization via conventional PCR and multilocus sequence analysis of two strains isolated from a cat and ticks from Israel

Borrelia persica, one of the pathogenic agents of tick-borne relapsing fever, is transmitted by the soft tick Ornithodoros tholozani. It causes infections in humans as well as in animals. In this study, we developed a medium, termed Pettenkofer/LMU Bp, for reliable in vitro cultivation. Cell densities up to 5.2×10(7) viable cells/ml were achieved over at least 40 passages. The cultivable B. persica strain isolated from a cat was further analyzed by amplification of the flaB gene using conventional PCR. In addition, seven housekeeping genes (clpA, clpX, pepX, pyrG, recG, rplB and uvrA) of this B. persica strain and a second strain isolated out of pooled ticks from Israel were amplified and the phylogenetic relationships among Borrelia species were analyzed. The results of the conventional PCR and the multilocus sequence analysis confirmed our isolates as B. persica.

Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi

BACKGROUND

Rapid and accurate retrieval of whole genome sequences of human pathogens from disease vectors or animal reservoirs will enable fine-resolution studies of pathogen epidemiological and evolutionary dynamics. However, next generation sequencing technologies have not yet been fully harnessed for the study of vector-borne and zoonotic pathogens, due to the difficulty of obtaining high-quality pathogen sequence data directly from field specimens with a high ratio of host to pathogen DNA.

RESULTS

We addressed this challenge by using custom probes for multiplexed hybrid capture to enrich for and sequence 30 Borrelia burgdorferi genomes from field samples of its arthropod vector. Hybrid capture enabled sequencing of nearly the complete genome (~99.5 %) of the Borrelia burgdorferi pathogen with 132-fold coverage, and identification of up to 12,291 single nucleotide polymorphisms per genome.

CONCLUSIONS

The proprosed culture-independent method enables efficient whole genome capture and sequencing of pathogens directly from arthropod vectors, thus making population genomic study of vector-borne and zoonotic infectious diseases economically feasible and scalable. Furthermore, given the similarities of invertebrate field specimens to other mixed DNA templates characterized by a high ratio of host to pathogen DNA, we discuss the potential applicabilty of hybrid capture for genomic study across diverse study systems.

Interactions between tick and transmitted pathogens evolved to minimise competition through nested and coherent networks

Natural foci of ticks, pathogens, and vertebrate reservoirs display complex relationships that are key to the circulation of pathogens and infection dynamics through the landscape. However, knowledge of the interaction networks involved in transmission of tick-borne pathogens are limited because empirical studies are commonly incomplete or performed at small spatial scales. Here, we applied the methodology of ecological networks to quantify >14,000 interactions among ticks, vertebrates, and pathogens in the western Palearctic. These natural networks are highly structured, modular, coherent, and nested to some degree. We found that the large number of vertebrates in the network contributes to its robustness and persistence. Its structure reduces interspecific competition and allows ample but modular circulation of transmitted pathogens among vertebrates. Accounting for domesticated hosts collapses the network’s modular structure, linking groups of hosts that were previously unconnected and increasing the circulation of pathogens. This framework indicates that ticks and vertebrates interact along the shared environmental gradient, while pathogens are linked to groups of phylogenetically close reservoirs.

An Invasive Mammal (the Gray Squirrel, Sciurus carolinensis) Commonly Hosts Diverse and Atypical Genotypes of the Zoonotic Pathogen Borrelia burgdorferi Sensu Lato

Invasive vertebrate species can act as hosts for endemic pathogens and may alter pathogen community composition and dynamics. For the zoonotic pathogen Borrelia burgdorferisensu lato, the agent of Lyme borreliosis, recent work shows invasive rodent species can be of high epidemiological importance and may support host-specific strains. This study examined the role of gray squirrels (Sciurus carolinensis) (n = 679), an invasive species in the United Kingdom, as B. burgdorferi sensu lato hosts. We found that gray squirrels were frequently infested with Ixodes ricinus, the main vector of B. burgdorferi sensu lato in the United Kingdom, and 11.9% were infected with B. burgdorferi sensu lato. All four genospecies that occur in the United Kingdom were detected in gray squirrels, and unexpectedly, the bird-associated genospecies Borrelia garinii was most common. The second most frequent infection was with Borrelia afzelii. Genotyping of B. garinii and B. afzelii produced no evidence for strains associated with gray squirrels. Generalized linear mixed models (GLMM) identified tick infestation and date of capture as significant factors associated with B. burgdorferi sensu lato infection in gray squirrels, with infection elevated in early summer in squirrels infested with ticks. Invasive gray squirrels appear to become infected with locally circulating strains of B. burgdorferi sensu lato, and further studies are required to determine their role in community disease dynamics. Our findings highlight the fact that the role of introduced host species in B. burgdorferi sensu lato epidemiology can be highly variable and thus difficult to predict.

Vector potential and population dynamics for Amblyomma inornatum

We studied the natural life cycle of Amblyomma inornatum and its vector potential in South Texas. This tick is distributed throughout South Texas and most of Central America. A. inornatum represented 1.91% of the ticks collected by carbon dioxide traps during a study of free-living ticks in the Tamaulipan Biotic Province in South Texas. The life cycle of A. inornatum in South Texas showed a clear seasonal pattern consistent with one generation per year. Nymphs emerged in the spring with a peak in February through May. Adults emerged in the summer with a peak in July through September. Detection of A. inornatum larvae was negatively correlated with saturation deficit and positively correlated with rain in the previous few months. Adult activity was positively correlated with temperature and rain in the previous five weeks. Using PCR we detected the presence of species related to Candidatus Borrelia lonestari, Borrelia burgdorferi, Rickettsia species (Candidatus Rickettsia amblyommii), Ehrlichia chaffeensis, and another Ehrlichia related to Ehrlichia ewingii. Finally we sequenced the mitochondrial 16S rRNA genes and found that A. inornatum is most closely related to Amblyomma parvum. This is the first report of the life cycle, vector potential and phylogeny of A. inornatum.

Phylogenomic identification of regulatory sequences in bacteria: an analysis of statistical power and an application to Borrelia burgdorferi sensu lato

Phylogenomic footprinting is an approach for ab initio identification of genome-wide regulatory elements in bacterial species based on sequence conservation. The statistical power of the phylogenomic approach depends on the degree of sequence conservation, the length of regulatory elements, and the level of phylogenetic divergence among genomes. Building on an earlier model, we propose a binomial model that uses synonymous tree lengths as neutral expectations for determining the statistical significance of conserved intergenic spacer (IGS) sequences. Simulations show that the binomial model is robust to variations in the value of evolutionary parameters, including base frequencies and the transition-to-transversion ratio. We used the model to search for regulatory sequences in the Lyme disease species group (Borrelia burgdorferi sensu lato) using 23 genomes. The model indicates that the currently available set of Borrelia genomes would not yield regulatory sequences shorter than five bases, suggesting that genome sequences of additional B. burgdorferi sensu lato species are needed. Nevertheless, we show that previously known regulatory elements are indeed strongly conserved in sequence or structure across these Borrelia species. Further, we predict with sufficient confidence two new RpoS binding sites, 39 promoters, 19 transcription terminators, 28 noncoding RNAs, and four sets of coregulated genes. These putative cis- and trans-regulatory elements suggest novel, Borrelia-specific mechanisms regulating the transition between the tick and host environments, a key adaptation and virulence mechanism of B. burgdorferi. Alignments of IGS sequences are available on BorreliaBase.org, an online database of orthologous open reading frame (ORF) and IGS sequences in Borrelia.

IMPORTANCE

While bacterial genomes contain mostly protein-coding genes, they also house DNA sequences regulating the expression of these genes. Gene regulatory sequences tend to be conserved during evolution. By sequencing and comparing related genomes, one can therefore identify regulatory sequences in bacteria based on sequence conservation. Here, we describe a statistical framework by which one may determine how many genomes need to be sequenced and at what level of evolutionary relatedness in order to achieve a high level of statistical significance. We applied the framework to Borrelia burgdorferi, the Lyme disease agent, and identified a large number of candidate regulatory sequences, many of which are known to be involved in regulating the phase transition between the tick vector and mammalian hosts.

Evolution and population genomics of the Lyme borreliosis pathogen, Borrelia burgdorferi

Population genomic studies have the potential to address many unresolved questions about microbial pathogens by facilitating the identification of genes underlying ecologically important traits, such as novel virulence factors and adaptations to humans or other host species. Additionally, this framework improves estimations of population demography and evolutionary history to accurately reconstruct recent epidemics and identify the molecular and environmental factors that resulted in the outbreak. The Lyme disease bacterium, Borrelia burgdorferi, exemplifies the power and promise of the application of population genomics to microbial pathogens. We discuss here the future of evolutionary studies in B. burgdorferi, focusing on the primary evolutionary forces of horizontal gene transfer, natural selection, and migration, as investigations transition from analyses of single genes to genomes.

Borrelia burgdorferi sensu lato spirochetes in wild birds in northwestern California: associations with ecological factors, bird behavior and tick infestation

Although Borrelia burgdorferi sensu lato (s.l.) are found in a great diversity of vertebrates, most studies in North America have focused on the role of mammals as spirochete reservoir hosts. We investigated the roles of birds as hosts for subadult Ixodes pacificus ticks and potential reservoirs of the Lyme disease spirochete B. burgdorferi sensu stricto (s.s.) in northwestern California. Overall, 623 birds representing 53 species yielded 284 I. pacificus larvae and nymphs. We used generalized linear models and zero-inflated negative binomial models to determine associations of bird behaviors, taxonomic relationships and infestation by I. pacificus with borrelial infection in the birds. Infection status in birds was best explained by taxonomic order, number of infesting nymphs, sampling year, and log-transformed average body weight. Presence and counts of larvae and nymphs could be predicted by ground- or bark-foraging behavior and contact with dense oak woodland. Molecular analysis yielded the first reported detection of Borrelia bissettii in birds. Moreover, our data suggest that the Golden-crowned Sparrow (Zonotrichia atricapilla), a non-resident species, could be an important reservoir for B. burgdorferi s.s. Of 12 individual birds (9 species) that carried B. burgdorferi s.l.-infected larvae, no birds carried the same genospecies of B. burgdorferi s.l. in their blood as were present in the infected larvae removed from them. Possible reasons for this discrepancy are discussed. Our study is the first to explicitly incorporate both taxonomic relationships and behaviors as predictor variables to identify putative avian reservoirs of B. burgdorferi s.l. Our findings underscore the importance of bird behavior to explain local tick infestation and Borrelia infection in these animals, and suggest the potential for bird-mediated geographic spread of vector ticks and spirochetes in the far-western United States.

Multilocus spacer analysis revealed highly homogeneous genetic background of Asian type of Borrelia miyamotoi

Borrelia miyamotoi, a member of the relapsing fever group borreliae, was first isolated in Japan and subsequently found in Ixodes ticks in North America, Europe and Russia. Currently, there are three types of B. miyamotoi: Asian or Siberian (transmitted mainly by Ixodes persulcatus), European (Ixodesricinus) and American (Ixodesscapularis and Ixodespacificus). Despite the great genetic distances between B. miyamotoi types, isolates within a type are characterised by an extremely low genetic variability. In particular, strains of B. miyamotoi of Asian type, isolated in Russia from the Baltic sea to the Far East, have been shown to be identical based on the analysis of several conventional genetic markers, such as 16S rRNA, flagellin, outer membrane protein p66 and glpQ genes. Thus, protein or rRNA - coding genes were shown not to be informative enough in studying genetic diversity of B. miyamotoi within a type. In the present paper, we have attempted to design a new multilocus technique based on eight non-coding intergenic spacers (3686bp in total) and have applied it to the analysis of intra-type genetic variability of В. miyamotoi detected in different regions of Russia and from two tick species, I. persulcatus and Ixodespavlovskyi. However, even though potentially the most variable loci were selected, no genetic variability between studied DNA samples was found, except for one nucleotide substitution in two of them. The sequences obtained were identical to those of the reference strain FR64b. Analysis of the data obtained with the GenBank sequences indicates a highly homogeneous genetic background of B. miyamotoi from the Baltic Sea to the Japanese Islands. In this paper, a hypothesis of clonal expansion of B. miyamotoi is discussed, as well as possible mechanisms for the rapid dissemination of one B. miyamotoi clone over large distances.

Genome Sequence of Borrelia chilensis VA1, a South American Member of the Lyme Borreliosis Group

Borrelia chilensis strain VA1 is a recently described South American member of the Borrelia burgdorferisensu lato complex from Chile. Whole-genome sequencing analysis determined its linear chromosome and plasmids lp54 and cp26, confirmed its membership in the Lyme borreliosis group, and will open new research avenues regarding its pathogenic potential.

Whole-Genome Sequence of Borrelia garinii Strain 935T Isolated from Ixodes persulcatus in South Korea

We report here the genome sequence of Borrelia garinii strain 935T isolated from Ixodes persulcatus in South Korea. The 1,176,739 bp (G+C content, 27.73%) genome consists of 1,194 coding regions, 4 rRNA genes, and 33 aminoacyl-tRNA synthetase genes. This is the first whole-genome report of a Korean Borrelia species isolate.

Prevalence of Borrelia burgdorferi sensu lato in rodents from Jiangxi, southeastern China region

In order to investigate the prevalence of B.burgdorferi sensu lato in rodents from Jiangxi province of southeastern China. Isolation of B.burgdoferi strains and PCR-based studies were carried out in 204 mice collected from six counties of Jiangxi province in May of 2011 and 2012. The results showed the prevalence of Lyme spirochetal infection among seven species of wild and peridomestic rodents in Jiangxi. 3 strains isolated from 204 mice were all belonged to Borrelia yangze sp.nov. The study firstly showed the role of rodents in maintaining the pathogen of Lyme disease in the environment from Jiangxi province and there existed at least one genotype of Lyme spirochetes in Jiangxi.

Pathogenic Landscape of Transboundary Zoonotic Diseases in the Mexico-US Border Along the Rio Grande

Transboundary zoonotic diseases, several of which are vector borne, can maintain a dynamic focus and have pathogens circulating in geographic regions encircling multiple geopolitical boundaries. Global change is intensifying transboundary problems, including the spatial variation of the risk and incidence of zoonotic diseases. The complexity of these challenges can be greater in areas where rivers delineate international boundaries and encompass transitions between ecozones. The Rio Grande serves as a natural border between the US State of Texas and the Mexican States of Chihuahua, Coahuila, Nuevo León, and Tamaulipas. Not only do millions of people live in this transboundary region, but also a substantial amount of goods and people pass through it everyday. Moreover, it occurs over a region that functions as a corridor for animal migrations, and thus links the Neotropic and Nearctic biogeographic zones, with the latter being a known foci of zoonotic diseases. However, the pathogenic landscape of important zoonotic diseases in the south Texas-Mexico transboundary region remains to be fully understood. An international perspective on the interplay between disease systems, ecosystem processes, land use, and human behaviors is applied here to analyze landscape and spatial features of Venezuelan equine encephalitis, Hantavirus disease, Lyme Borreliosis, Leptospirosis, Bartonellosis, Chagas disease, human Babesiosis, and Leishmaniasis. Surveillance systems following the One Health approach with a regional perspective will help identifying opportunities to mitigate the health burden of those diseases on human and animal populations. It is proposed that the Mexico-US border along the Rio Grande region be viewed as a continuum landscape where zoonotic pathogens circulate regardless of national borders.

Borrelia infection in Ixodes pararicinus ticks (Acari: Ixodidae) from northwestern Argentina

The aim of this work was to describe for the first time the presence of Borrelia burgdorferi sensu lato infecting ticks in Argentina. Unfed specimens of Ixodes pararicinus collected from vegetation in Jujuy Province were tested for Borrelia infection by PCR targeting the gene flagellin (fla), the rrfA-rrlB intergenic spacer region (IGS) and the 16S rDNA (rrs) gene. One male and one female of I. pararicinus collected in Jujuy were found to be positive to Borrelia infection with the three molecular markers tested. Phylogenetically, the Borrelia found in I. pararicinus from Jujuy belongs to the B. burgdorferi s.l complex, and it was similar to one of the genospecies detected in I. aragaoi from Uruguay. Also, this genospecies is closely related to two genospecies known from USA, Borrelia americana and the Borrelia sp. genospecies 1. The epidemiological risk that implies the infection with Borrelia in I. paracinus ticks from Argentina appears to be low because the genospecies detected is not suspected of having clinical relevance and there are no records of Ixodes ticks biting humans in the southern cone of South America. Further studies are needed to assess accurately if there is risk of borreliosis transmitted by ticks in South America.

First detection and molecular identification of Borrelia garinii spirochete from Ixodes ovatus tick ectoparasitized on stray cat in Taiwan

Borrelia garinii spirochete was detected for the first time in Ixodes ovatus tick ectoparasitized on stray cat in Taiwan. The genetic identity of this detected spirochete was determined by analyzing the gene sequence amplified by genospecies-specific polymerase chain reaction assays based on the 5S-23S intergenic spacer amplicon (rrf-rrl) and outer surface protein A (ospA) genes of B. burgdorferi sensu lato. Phylogenetic relationships were analyzed by comparing the sequences of rrf-rrl and ospA genes obtained from 27 strains of Borrelia spirochetes representing six genospecies of Borrelia. Seven major clades can be easily distinguished by neighbour-joining analysis and were congruent by maximum-parsimony method. Phylogenetic analysis based on rrf-rrl gene revealed that this detected spirochete (strain IO-TP-TW) was genetically affiliated to the same clade with a high homogeneous sequences (96.7 to 98.1% similarity) within the genospecies of B. garinii and can be discriminated from other genospecies of Borrelia spirochetes. Interspecies analysis based on the genetic distance values indicates a lower level (<0.022) of genetic divergence (GD) within the genospecies of B. garinii, and strain IO-TP-TW was genetically more distant ( >0.113) to the strains identified in I. ovatus collected from Japan and China. Intraspecies analysis also reveals a higher homogeneity (GD<0.005) between tick (strain IO-TP-TW) and human (strain Bg-PP-TW1) isolates of B. garinii in Taiwan. This study provides the first evidence of B. garinii isolated and identified in an I. ovatus tick in Asia, and the higher homogeneity of B. garinii between tick and human strain may imply the risk of human infection by I. ovatus bite.

Exploring Diversity among Norwegian Borrelia Strains Originating from Ixodes ricinus Ticks

Characterisation of Borrelia strains from Ixodes ricinus ticks is important in the epidemiological surveillance of vector-borne pathogens. Multilocus sequences analysis (MLSA) is a molecular genotyping tool with high discriminatory power that has been applied in evolutionary studies and for the characterisation of Borrelia genospecies. MLSA was used to study genetic variations in Borrelia strains isolated from I. ricinus ticks collected from the woodlands in Skodje. The results demonstrate that the 50 Borrelia strains were separated into 36 sequence types (STs) that were not previously represented in the MLST database. A distance matrix neighbour-joining tree (bootstrapped 500 iterations) showed four deeply branched clusters, and each deeply branched cluster represented one Borrelia genospecies. The mean pairwise genetic differences confirm the genospecies clustering. The combination of alleles separates the Borrelia strains from northwest Norway from the strains in the MLST database, thus identifying new STs. Although a highly divergent B. afzelii population could be expected, the heterogeneity among the B. garinii strains is more unusual. The present study indicates that the circulation of strains between migrating birds and stationary birds in this coastal region may play a role in the evolution of B. garinii strains.

Remarkable diversity of tick or mammalian-associated Borreliae in the metropolitan San Francisco Bay Area, California

The diversity of Lyme disease (LD) and relapsing fever (RF)-group spirochetes in the metropolitan San Francisco Bay area in northern California is poorly understood. We tested Ixodes pacificus, I. spinipalpis, and small mammals for presence of borreliae in Alameda County in the eastern portion of San Francisco Bay between 2009 and 2012. Analyses of 218 Borrelia burgdorferi sensu lato (Bb sl) culture or DNA isolates recovered from host-seeking I. pacificus ticks revealed that the human pathogen Bb sensu stricto (hereinafter, B. burgdorferi) had the broadest habitat distribution followed by B. bissettii. Three other North American Bb sl spirochetes, B. americana, B. californiensis and B. genomospecies 2, also were detected at lower prevalence. OspC genotyping of the resultant 167 B. burgdorferi isolates revealed six ospC alleles (A, D, E3, F, H and K) in I. pacificus. A novel spirochete belonging to the Eurasian Bb sl complex, designated CA690, was found in a questing I. spinipalpis nymph. Borrelia miyamotoi, a relapsing-fever (RF) group spirochete recently implicated as a human pathogen, was detected in 24 I. pacificus. Three rodent species were infected with Bb sl: the fox squirrel (Sciurus niger) with B. burgdorferi, and the dusky-footed wood rat (Neotoma fuscipes) and roof rat (Rattus rattus) with B. bissettii. Another spirochete that clustered phylogenetically with the Spanish R57 Borrelia sp. in a clade distinct from both the LD and RF groups infected some of the roof rats. Together, eight borrelial genospecies were detected in ticks or small mammals from a single Californian county, two of which were related phylogenetically to European spirochetes.

Molecular Typing of Borrelia burgdorferi

Borrelia burgdorferi sensu lato is a group of spirochetes belonging to the genus Borrelia in the family of Spirochaetaceae. The spirochete is transmitted between reservoirs and hosts by ticks of the family Ixodidae. Infection with B. burgdorferi in humans causes Lyme disease or Lyme borreliosis. Currently, 20 Lyme disease-associated Borrelia species and more than 20 relapsing fever-associated Borrelia species have been described. Identification and differentiation of different Borrelia species and strains is largely dependent on analyses of their genetic characteristics. A variety of molecular techniques have been described for Borrelia isolate speciation, molecular epidemiology, and pathogenicity studies. In this unit, we focus on three basic protocols, PCR-RFLP-based typing of the rrs-rrlA and rrfA-rrlB ribosomal spacer, ospC typing, and MLST. These protocols can be employed alone or in combination for characterization of B. burgdorferi isolates or directly on uncultivated organisms in ticks, mammalian host reservoirs, and human clinical specimens.

Phylogeny of Mycoplasma bovis isolates from Hungary based on multi locus sequence typing and multiple-locus variable-number tandem repeat analysis

BACKGROUND

Mycoplasma bovis is an important pathogen causing pneumonia, mastitis and arthritis in cattle worldwide. As this agent is primarily transmitted by direct contact and spread through animal movements, efficient genotyping systems are essential for the monitoring of the disease and for epidemiological investigations. The aim of this study was to compare and evaluate the multi locus sequence typing (MLST) and the multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) through the genetic characterization of M. bovis isolates from Hungary.

RESULTS

Thirty one Hungarian M. bovis isolates grouped into two clades by MLST. Two strains had the same sequence type (ST) as reference strain PG45, while the other twenty nine Hungarian isolates formed a novel clade comprising five subclades. Isolates originating from the same herds had the same STs except for one case. The same isolates formed two main clades and several subclades and branches by MLVA. One clade contained the reference strain PG45 and three isolates, while the other main clade comprised the rest of the strains. Within-herd strain divergence was also detected by MLVA. Little congruence was found between the results of the two typing systems.

CONCLUSIONS

MLST is generally considered an intermediate scale typing method and it was found to be discriminatory among the Hungarian M. bovis isolates. MLVA proved to be an appropriate fine scale typing tool for M. bovis as this method was able to distinguish closely related strains isolated from the same farm. We recommend the combined use of the two methods for the genotyping of M. bovis isolates. Strains have to be characterized first by MLST followed by the fine scale typing of identical STs with MLVA.

Comparison of tick-borne microorganism communities in Ixodes spp. of the Ixodes ricinus species complex at distinct geographical regions

Characterizing the tick-borne microorganism communities of Ixodes ricinus (sheep tick) and Ixodes persulcatus (taiga tick) from the I. ricinus species complex in distinct geographical regions of Eastern Europe and European Russia, we demonstrated differences between the two ticks. Taiga ticks were more frequently mono- and co-infected than sheep ticks: 24.4 % (45/184 tested ticks) versus 17.5 % (52/297) and 4.3 % (8/184) versus 3.4 % (10/297), respectively. Ginsberg co-infection index values were significant at the various sites. Diversity of the tick-borne microorganism communities was estimated by the Shannon index, reaching values of 1.71 ± 0.46 and 1.20 ± 0.15 at the sheep-tick and the taiga-tick harbored sites, respectively. Richness of the tick-borne microorganism community in the sheep tick collection sites was about twice the value of the taiga tick collection sites. Future investigations are warranted to further characterize the peculiarities of the tick-borne microorganism communities among the ticks of the Ixodes ricinus complex.

Implications of climate change on the distribution of the tick vector Ixodes scapularis and risk for Lyme disease in the Texas-Mexico transboundary region

BACKGROUND

Disease risk maps are important tools that help ascertain the likelihood of exposure to specific infectious agents. Understanding how climate change may affect the suitability of habitats for ticks will improve the accuracy of risk maps of tick-borne pathogen transmission in humans and domestic animal populations. Lyme disease (LD) is the most prevalent arthropod borne disease in the US and Europe. The bacterium Borrelia burgdorferi causes LD and it is transmitted to humans and other mammalian hosts through the bite of infected Ixodes ticks. LD risk maps in the transboundary region between the U.S. and Mexico are lacking. Moreover, none of the published studies that evaluated the effect of climate change in the spatial and temporal distribution of I. scapularis have focused on this region.

METHODS

The area of study included Texas and a portion of northeast Mexico. This area is referred herein as the Texas-Mexico transboundary region. Tick samples were obtained from various vertebrate hosts in the region under study. Ticks identified as I. scapularis were processed to obtain DNA and to determine if they were infected with B. burgdorferi using PCR. A maximum entropy approach (MAXENT) was used to forecast the present and future (2050) distribution of B. burgdorferi-infected I. scapularis in the Texas-Mexico transboundary region by correlating geographic data with climatic variables.

RESULTS

Of the 1235 tick samples collected, 109 were identified as I. scapularis. Infection with B. burgdorferi was detected in 45% of the I. scapularis ticks collected. The model presented here indicates a wide distribution for I. scapularis, with higher probability of occurrence along the Gulf of Mexico coast. Results of the modeling approach applied predict that habitat suitable for the distribution of I. scapularis in the Texas-Mexico transboundary region will remain relatively stable until 2050.

CONCLUSIONS

The Texas-Mexico transboundary region appears to be part of a continuum in the pathogenic landscape of LD. Forecasting based on climate trends provides a tool to adapt strategies in the near future to mitigate the impact of LD related to its distribution and risk for transmission to human populations in the Mexico-US transboundary region.

A phylogenomic and molecular marker based proposal for the division of the genus Borrelia into two genera: the emended genus Borrelia containing only the members of the relapsing fever Borrelia, and the genus Borreliella gen. nov. containing the members of the Lyme disease Borrelia (Borrelia burgdorferi sensu lato complex)

The genus Borrelia contains two groups of organisms: the causative agents of Lyme disease and their relatives and the causative agents of relapsing fever and their relatives. These two groups are morphologically indistinguishable and are difficult to distinguish biochemically. In this work, we have carried out detailed comparative genomic analyses on protein sequences from 38 Borrelia genomes to identify molecular markers in the forms of conserved signature inserts/deletions (CSIs) that are specifically found in the Borrelia homologues, and conserved signature proteins (CSPs) which are uniquely present in Borrelia species. Our analyses have identified 31 CSIs and 82 CSPs that are uniquely shared by all sequenced Borrelia species, providing molecular markers for this group of organisms. In addition, our work has identified 7 CSIs and 21 CSPs which are uniquely found in the Lyme disease Borrelia species and eight CSIs and four CSPs that are specific for members of the relapsing fever Borrelia group. Additionally, 38 other CSIs, in proteins which are uniquely found in Borrelia species, also distinguish these two groups of Borrelia. The identified CSIs and CSPs provide novel and highly specific molecular markers for identification and distinguishing between the Lyme disease Borrelia and the relapsing fever Borrelia species. We also report the results of average nucleotide identity (ANI) analysis on Borrelia genomes and phylogenetic analysis for these species based upon 16S rRNA sequences and concatenated sequences for 25 conserved proteins. These analyses also support the distinctness of the two Borrelia clades. On the basis of the identified molecular markers, the results from ANI and phylogenetic studies, and the distinct pathogenicity profiles and arthropod vectors used by different Borrelia spp. for their transmission, we are proposing a division of the genus Borrelia into two separate genera: an emended genus Borrelia, containing the causative agents of relapsing fever and a novel genus, Borreliella gen. nov., containing the causative agents of Lyme disease.

Comparative population genomics of the Borrelia burgdorferi species complex reveals high degree of genetic isolation among species and underscores benefits and constraints to studying intra-specific epidemiological processes

Lyme borreliosis, one of the most frequently contracted zoonotic diseases in the Northern Hemisphere, is caused by bacteria belonging to different genetic groups within the Borrelia burgdorferi species complex, which are transmitted by ticks among various wildlife reservoirs, such as small mammals and birds. These features make the Borrelia burgdorferi species complex an attractive biological model that can be used to study the diversification and the epidemiology of endemic bacterial pathogens. We investigated the potential of population genomic approaches to study these processes. Sixty-three strains belonging to three species within the Borrelia burgdorferi complex were isolated from questing ticks in Alsace (France), a region where Lyme disease is highly endemic. We first aimed to characterize the degree of genetic isolation among the species sampled. Phylogenetic and coalescent-based analyses revealed clear delineations: there was a ∼50 fold difference between intra-specific and inter-specific recombination rates. We then investigated whether the population genomic data contained information of epidemiological relevance. In phylogenies inferred using most of the genome, conspecific strains did not cluster in clades. These results raise questions about the relevance of different strategies when investigating pathogen epidemiology. For instance, here, both classical analytic approaches and phylodynamic simulations suggested that population sizes and migration rates were higher in B. garinii populations, which are normally associated with birds, than in B. burgdorferi s.s. populations. The phylogenetic analyses of the infection-related ospC gene and its flanking region provided additional support for this finding. Traces of recombination among the B. burgdorferi s.s. lineages and lineages associated with small mammals were found, suggesting that they shared the same hosts. Altogether, these results provide baseline evidence that can be used to formulate hypotheses regarding the host range of B. burgdorferi lineages based on population genomic data.

Evolutionary genomics of Borrelia burgdorferi sensu lato: findings, hypotheses, and the rise of hybrids

Borrelia burgdorferi sensu lato (B. burgdorferi s.l.), the group of bacterial species represented by Lyme disease pathogens, has one of the most complex and variable genomic architectures among prokaryotes. Showing frequent recombination within and limited gene flow among geographic populations, the B. burgdorferi s.l. genomes provide an excellent window into the processes of bacterial evolution at both within- and between-population levels. Comparative analyses of B. burgdorferi s.l. genomes revealed a highly dynamic plasmid composition but a conservative gene repertoire. Gene duplication and loss as well as sequence variations at loci encoding surface-localized lipoproteins (e.g., the PF54 genes) are strongly associated with adaptive differences between species. There are a great many conserved intergenic spacer sequences that are candidates for cis-regulatory elements and non-coding RNAs. Recombination among coexisting strains occurs at a rate approximately three times the mutation rate. The coexistence of a large number of genomic groups within local B. burgdorferi s.l. populations may be driven by immune-mediated diversifying selection targeting major antigen loci as well as by adaptation to multiple host species. Questions remain regarding the ecological causes (e.g., climate change, host movements, or new adaptations) of the ongoing range expansion of B. burgdorferi s.l. and on the genomic variations associated with its ecological and clinical variability. Anticipating an explosive growth of the number of B. burgdorferi s.l. genomes sampled from both within and among species, we propose genome-based methods to test adaptive mechanisms and to identify molecular bases of phenotypic variations. Genome sequencing is also necessary for monitoring a likely increase of genetic admixture of previously isolated species and populations in North America and elsewhere.

That's my story, and I'm sticking to it--an update on B. burgdorferi adhesins

Adhesion is the initial event in the establishment of any infection. Borrelia burgdorferi, the etiological agent of Lyme disease, possesses myriad proteins termed adhesins that facilitate contact with its vertebrate hosts. B. burgdorferi adheres to host tissues through interactions with host cells and extracellular matrix, as well as other molecules present in serum and extracellular fluids. These interactions, both general and specific, are critical in the establishment of infection. Modulation of borrelial adhesion to host tissues affects the microorganisms's ability to colonize, disseminate, and persist. In this review, we update the current knowledge on structure, function, and role in pathogenesis of these “sticky” B. burgdorferi infection-associated proteins.

Daam1 is a regulator of filopodia formation and phagocytic uptake of Borrelia burgdorferi by primary human macrophages

Borrelia burgdorferi is the causative agent of Lyme disease, an infectious disease that primarily affects the skin, nervous system, and joints. Uptake of borreliae by immune cells is decisive for the course of the infection, and remodelling of the host actin cytoskeleton is crucial in this process. In this study, we showed that the actin-regulatory formin Daam1 is important in Borrelia phagocytosis by primary human macrophages. Uptake of borreliae proceeds preferentially through capture by filopodia and formation of coiling pseudopods that enwrap the spirochetes. Using immunofluorescence, we localized endogenous and overexpressed Daam1 to filopodia and to F-actin-rich uptake structures. Live-cell imaging further showed that Daam1 is enriched at coiling pseudopods that arise from the macrophage surface. This filopodia-independent step was corroborated by control experiments of phagocytic cup formation with latex beads. Moreover, siRNA-mediated knockdown of Daam1 led to a 65% reduction of borreliae-induced filopodia, and, as shown by the outside-inside staining technique, to a 50% decrease in phagocytic uptake of borreliae, as well as a 37% reduction in coiling pseudopod formation. Collectively, we showed that Daam1 plays a dual role in the phagocytic uptake of borreliae: first, as a regulator of filopodia, which are used for capturing spirochetes, and second, in the formation of the coiling pseudopod that enwraps the bacterial cell. These data identify Daam1 as a novel regulator of B. burgdorferi phagocytosis. At the same time, this is the first demonstration of a role for Daam1 in phagocytic processes in general.-Hoffmann, A.-K., Naj, X., Linder, S. Daam1 is a regulator of filopodia formation and phagocytic uptake of Borrelia burgdorferi by primary human macrophages.