Recombination within and between species of the alpha proteobacterium Bartonella infecting rodents.
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ABSTRACT:
SUBMITTER: Paziewska A
PROVIDER: S-EPMC3011088 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The alpha-Proteobacterium Bartonella is a common parasite of voles and mice, giving rise to short-lived (4 weeks to 2 months) infections. Here, we report high sequence diversity in genes of the VirB/VirD type IV secretion system (T4SS), amongst Bartonella from natural rodent populations in NE Poland. The VirB5 protein is predicted to consist of three conserved alpha helices separated by loops of variable length which include numerous indels. The C-terminal domain includes repeat stretches of KEK residues, reflecting underlying homopolymeric stretches of adenine residues. A total of 16 variants of VirB5, associated with host identity, but not bacterial taxon, were identified from 22 Bartonella isolates. One was clearly a recombinant from two others, another included an insertion of two KEK repeats. The virB5 gene appears to evolve via both mutation and recombination, as well as slippage mediated insertion/deletion events. The recombinational units are thought to be relatively short, as there was no evidence of linkage disequilibrium between virB5 and the bepA locus only 5.5 kb distant. The diversity of virB5 is assumed to be related to immunological role of this protein in Bartonella infections; diversity of virB5 may assist persistence of Bartonella in the rodent population, despite the relatively short (3-4 weeks) duration of individual infections. It is clear from the distribution of virB5 and bepA alleles that recombination within and between clades is widespread, and frequently crosses the boundaries of conventionally recognised Bartonella species.
| S-EPMC3391547 | biostudies-literature
Project description:Bartonella species are hemotropic, facultative intracellular bacteria, some of which cause zoonoses, that are widely disseminated among many mammals, including humans. During infection in humans, vascular endothelial cells play a crucial role as a replicative niche for Bartonella, and some are capable of promoting vascular proliferation. Along with well-studied pathogenic factors such as a trimeric autotransporter adhesin BadA or VirB/D4 type IV secretion system, bacteria-secreted protein BafA is also involved in Bartonella-induced vasoproliferation. Genes encoding BafA orthologs have been found in the genomes of most Bartonella species, but their functionality remains unclear. In this study, we focused on three cat-derived zoonotic species (B. henselae, B. koehlerae, and B. clarridgeiae) and two rodent-derived species (B. grahamii and B. doshiae) and compared the activity of BafA derived from each species. Recombinant BafA proteins of B. henselae, B. koehlerae, B. clarridgeiae, and B. grahamii, species that also cause human disease, induced cell proliferation and tube formation in cultured endothelial cells, while BafA derived from B. doshiae, a species that is rarely found in humans, showed neither activity. Additionally, treatment of cells with these BafA proteins increased phosphorylation of both vascular endothelial growth factor receptor 2 and extracellular signal-regulated kinase 1/2, with the exception of B. doshiae BafA. Differential bafA mRNA expression and BafA secretion among the species likely contributed to the differences in the cell proliferation phenotype of the bacteria-infected cells. These findings suggest that the biological activity of BafA may be involved in the infectivity or pathogenicity of Bartonella species in humans.
| S-EPMC10016083 | biostudies-literature
Project description: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.
| S-EPMC4973202 | biostudies-literature
Project description:BackgroundCaviomorph rodents, some of the oldest Leishmania spp. hosts, are widely dispersed in Brazil. Despite both experimental and field studies having suggested that these rodents are potential reservoirs of Leishmania parasites, not more than 88 specimens were analyzed in the few studies of natural infection. Our hypothesis was that caviomorph rodents are inserted in the transmission cycles of Leishmania in different regions, more so than is currently recognized.MethodologyWe investigated the Leishmania infection in spleen fragments of 373 caviomorph rodents from 20 different species collected in five Brazilian biomes in a period of 13 years. PCR reactions targeting kDNA of Leishmania sp. were used to diagnose infection, while Leishmania species identification was performed by DNA sequencing of the amplified products obtained in the HSP70 (234) targeting. Serology by IFAT was performed on the available serum of these rodents.Principal findingsIn 13 caviomorph rodents, DNA sequencing analyses allowed the identification of 4 species of the subgenus L. (Viannia): L. shawi, L. guyanensis, L. naiffi, and L. braziliensis; and 1 species of the subgenus L. (Leishmania): L. infantum. These include the description of parasite species in areas not previously included in their known distribution: L. shawi in Thrichomys inermis from Northeastern Brazil and L. naiffi in T. fosteri from Western Brazil. From the four other positive rodents, two were positive for HSP70 (234) targeting but did not generate sequences that enabled the species identification, and another two were positive only in kDNA targeting.Conclusions/significanceThe infection rate demonstrated by the serology (51.3%) points out that the natural Leishmania infection in caviomorph rodents is much higher than that observed in the molecular diagnosis (4.6%), highlighting that, in terms of the host species responsible for maintaining Leishmania species in the wild, our current knowledge represents only the "tip of the iceberg."
| S-EPMC4263410 | biostudies-literature
Project description:Chromosomal inversions disrupt recombination in heterozygotes by both reducing crossing-over within inverted regions and increasing it elsewhere in the genome. The reduction of recombination in inverted regions facilitates the maintenance of hybridizing species, as outlined by various models of chromosomal speciation. We present a comprehensive comparison of the effects of inversions on recombination rates and on nucleotide divergence. Within an inversion differentiating Drosophila pseudoobscura and Drosophila persimilis, we detected one double recombinant among 9,739 progeny from F(1) hybrids screened, consistent with published double-crossover frequencies observed within species. Despite similar rates of exchange within and between species, we found no sequence-based evidence of ongoing gene exchange between species within this inversion, but significant exchange was inferred within species. We also observed greater differentiation at regions near inversion breakpoints between species versus within species. Moreover, we observed strong "interchromosomal effect" (higher recombination in inversion heterozygotes between species) with up to 9-fold higher recombination rates along collinear segments of chromosome two in hybrids. Further, we observed that regions most susceptible to changes in recombination rates corresponded to regions with lower recombination rates in homokaryotypes. Finally, we showed that interspecies nucleotide divergence is lower in regions with greater increases in recombination rate, potentially resulting from greater interspecies exchange. Overall, we have identified several similarities and differences between inversions segregating within versus between species in their effects on recombination and divergence. We conclude that these differences are most likely due to lower frequency of heterokaryotypes and to fitness consequences from the accumulation of various incompatibilities between species. Additionally, we have identified possible effects of inversions on interspecies gene exchange that had not been considered previously.
| S-EPMC3171675 | biostudies-literature
Project description:Bartonella spp. comprise an ecologically successful group of microorganisms that infect erythrocytes and have adapted to different hosts, which include a wide range of mammals, besides humans. Rodents are reservoirs of about two-thirds of Bartonella spp. described to date; and some of them have been implicated as causative agents of human diseases. In our study, we performed molecular and phylogenetic analyses of Bartonella spp. infecting wild rodents from five different Brazilian biomes. In order to characterize the genetic diversity of Bartonella spp., we performed a robust analysis based on three target genes, followed by sequencing, Bayesian inference, and maximum likelihood analysis. Bartonella spp. were detected in 25.6% (117/457) of rodent spleen samples analyzed, and this occurrence varied among different biomes. The diversity analysis of gltA sequences showed the presence of 15 different haplotypes. Analysis of the phylogenetic relationship of gltA sequences performed by Bayesian inference and maximum likelihood showed that the Bartonella species detected in rodents from Brazil was closely related to the phylogenetic group A detected in other cricetid rodents from North America, probably constituting only one species. Last, the Bartonella species genogroup identified in the present study formed a monophyletic group that included Bartonella samples from seven different rodent species distributed in three distinct biomes. In conclusion, our study showed that the occurrence of Bartonella bacteria in rodents is much more frequent and widespread than previously recognized.ImportanceIn the present study, we reported the occurrence of Bartonella spp. in some sites in Brazil. The identification and understanding of the distribution of this important group of bacteria may allow the Brazilian authorities to recognize potential regions with the risk of transmission of these pathogens among wild and domestic animals and humans. In addition, our study accessed important gaps in the biology of this group of bacteria in Brazil, such as its low host specificity, high genetic diversity, and relationship with other Bartonella spp. detected in rodents trapped in America. Considering the diversity of newly discovered Bartonella species and the great ecological plasticity of these bacteria, new studies with the aim of revealing the biological aspects unknown until now are needed and must be performed around the world. In this context, the impact of Bartonella spp. associated with rodents in human health should be assessed in future studies.
| S-EPMC5118926 | biostudies-literature
Project description:Here, we describe for the first time the prevalence and genetic properties of Bartonella organisms in wild rodents in Japan. We captured 685 wild rodents throughout Japan (in 12 prefectures) and successfully isolated Bartonella organisms from 176 of the 685 rodents (isolation rate, 25.7%). Those Bartonella isolates were all obtained from the rodents captured in suburban areas (rate, 51.8%), but no organism was isolated from the animals captured in city areas. Sequence analysis of rpoB and gltA revealed that the Bartonella isolates obtained were classified into eight genetic groups, comprising isolates closely related to B. grahamii (A-I group), B. tribocorum and B. elizabethae (B-J group), B. tribocorum and B. rattimassiliensis (C-K group), B. rattimassiliensis (D-L group), B. phoceensis (F-N group), B. taylorii (G-O group), and probably two additional novel Bartonella species groups (E-M and H-P). B. grahamii, which is one of the potential causative agents of human neuroretinitis, was found to be predominant in Japanese rodents. In terms of the relationships between these Bartonella genetic groups and their rodent species, (i) the A-I, E-M, and H-P groups appear to be associated with Apodemus speciosus and Apodemus argenteus; (ii) the C-K, D-L, and F-N groups are likely implicated in Rattus rattus; (iii) the B-J group seems to be involved in Apodemus mice and R. rattus; and (iv) the G-O group is probably associated with A. speciosus and Clethrionomys voles. Furthermore, dual infections with two different genetic groups of bartonellae were found in A. speciosus and R. rattus. These findings suggest that the rodent in Japan might serve as a reservoir of zoonotic Bartonella infection.
| S-EPMC2519277 | biostudies-literature
Project description:Worldwide, Bartonella infections are known to inflict a wide range of mammals and, within rodents alone, more than 20 Bartonella species have been detected. There is, however, a lack of studies on the presence of Bartonella spp. in rodents in the Baltic region. We analysed 580 individuals belonging to eight small rodent species trapped in coastal and continental areas of Lithuania during 2015-2016. The presence of Bartonella DNA was examined by real-time PCR targeting the ssrA gene. The molecular characterization of the bacteria strains was based on sequence analysis of two housekeeping genes (rpoB, groEL) and the intergenic spacer region (ITS). For the rodents overall, the prevalence of Bartonella spp. was 54.8%, while the prevalence figures for each of the individual species were 8.3% in M. musculus, 15.8% in A. agrarius, 33.3% in M. arvalis, 42.4% in M. glareolus, 53.4% in M. oeconomus, 57.5% in M. minutus, 79.6% in A. flavicollis to 80% in M. agrestis. Sequence analysis revealed that the Bartonella strains belonged to the B. grahamii, B. taylorii, B. rochalimae, B. tribocorum, B. coopersplainsensis and B. doshiae genogroups. The highest Bartonella infection rates and the highest species diversity were both detected in rodents captured in the coastal area. To our knowledge, these are the first reports of the presence of B. coopersplainsensis, B. doshiae and B. tribocorum in Lithuania.
| S-EPMC6710269 | biostudies-literature
Project description:Our study highlights the surveillance of Bartonella species among rodents and their associated ectoparasites (ticks, fleas, lice, and mites) in several regions across Thailand. A total of 619 rodents and 554 pooled ectoparasites (287 mite pools, 62 flea pools, 35 louse pools, and 170 tick pools) were collected from 8 provinces within 4 regions of Thailand. Bandicota indica (279), Rattus rattus (163), and R. exulans (96) were the most prevalent species of rats collected in this study. Real-time PCR assay targeting Bartonella-specific ssrA gene was used for screening and each positive sample was confirmed by PCR using nuoG gene. The prevalence of Bartonella DNA in rodent (around 17%) was recorded in all regions. The highest prevalence of Bartonella species was found in B. savilei and R. rattus with the rate of 35.7% (5/14) and 32.5% (53/163), respectively. High prevalence of Bartonella-positive rodent was also found in B. indica (15.1%, 42/279), and R. norvegicus (12.5%, 5/40). In contrast, the prevalence of Bartonella species in ectoparasites collected from the rats varied significantly according to types of ectoparasites. A high prevalence of Bartonella DNA was found in louse pools (Polyplax spp. and Hoplopleura spp., 57.1%) and flea pools (Xenopsylla cheopis, 25.8%), while a low prevalence was found in pools of mites (Leptotrombidium spp. and Ascoschoengastia spp., 1.7%) and ticks (Haemaphysalis spp., 3.5%). Prevalence of Bartonella DNA in ectoparasites collected from Bartonella-positive rodents (19.4%) was significantly higher comparing to ectoparasites from Bartonella-negative rodents (8.7%). The phylogenetic analysis of 41 gltA sequences of 16 Bartonella isolates from rodent blood and 25 Bartonella-positive ectoparasites revealed a wide range of diversity among Bartonella species with a majority of sequences (61.0%) belonging to Bartonella elizabethae complex (11 rodents, 1 mite pool, and 5 louse pools), while the remaining sequences were identical to B. phoceensis (17.1%, 1 mite pool, 5 louse pools, and 1 tick pool), B. coopersplainensis (19.5%, 5 rodents, 1 louse pool, and 2 tick pools), and one previously unidentified Bartonella species (2.4%, 1 louse pool).
| S-EPMC4617648 | biostudies-literature
Project description:BackgroundHuman papillomavirus (HPV) has a causal role in cervical cancer with almost half a million new cases occurring each year. Presence of the carcinogenic HPV is necessary for the development of the invasive carcinoma of the genital tract. Therefore, persistent infection with carcinogenic HPV causes virtually all cervical cancers. Some aspects of the molecular evolution of this virus, as the putative importance of recombination in its evolutionary history, are an opened current question. In addition, recombination could also be a significant issue nowadays since the frequency of co-infection with more than one HPV type is not a rare event and, thus, new recombinant types could be currently being generated.ResultsWe have used human alpha-PV sequences from the public database at Los Alamos National Laboratory to report evidence that recombination may exist in this virus. A model-based population genetic approach was used to infer the recombination signal from the HPV DNA sequences grouped attending to phylogenetic and epidemiological information, as well as to clinical manifestations. Our results agree with recently published ones that use a different methodology to detect recombination associated to the gene L2. In addition, we have detected significant recombination signal in the genes E6, E7, L2 and L1 at different groups, and importantly within the high-risk type HPV16. The method used has recently been shown to be one of the most powerful and reliable procedures to detect the recombination signal.ConclusionWe provide new support to the recent evidence of recombination in HPV. Additionally, we performed the recombination estimation assuming the best-fit model of nucleotide substitution and rate variation among sites, of the HPV DNA sequence sets. We found that the gene with recombination in most of the groups is L2 but the highest values were detected in L1 and E6. Gene E7 was recombinant only within the HPV16 type. The topic deserves further study because recombination is an important evolutionary mechanism that could have high impact both in pharmacogenomics (i.e. on the influence of genetic variation on the response to drugs) and for vaccine development.
| S-EPMC1847806 | biostudies-literature