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Tick-borne pathogens (TBPs) constitute an emerging public health concern favoured by multidimensional global changes. Amongst these, increase and spread of wild boar (Sus scrofa) populations are of special concern since this species can act as a reservoir of zoonotic pathogens and promote tick abundance. Thus, we aimed to make a first assessment of the risk by TBPs resulting from wild boar and ticks in the vicinity of a highly populated area. Between 2014 and 2016, we collected spleen samples and 2256 ticks from 261 wild boars (out of 438 inspected) in the metropolitan area of Barcelona (MAB; northeast Spain). We morphologically identified four tick species: Hyalomma lusitanicum (infestation prevalence: 33.6%), Dermacentor marginatus (26.9%), Rhipicephalus sanguineus sensu lato (18.9%) and R. bursa (0.2%). Ticks were pooled according to species and individual host. A total of 180 tick pools and 167 spleen samples were screened by real-time PCR and/or reverse line blot hybridization assay for Ehrlichia sp., Anaplasma sp., Babesia sp., Rickettsia sp., Borrelia burgdorferi sensu lato and Coxiella burnetii. Seventy-two out of the 180 tick pools were positive to Rickettsia spp. (minimum prevalence of 8.7%), including Rickettsia massiliae, R. slovaca and R. raoultii. We did not detect Rickettsia spp. in wild boar spleens nor other TBPs in ticks or wild boars. Since the ticks identified can bite humans, and the recorded spotted fever group (SFG) rickettsiae are zoonotic pathogens, there is a risk of SFG rickettsiae transmission for MAB inhabitants. Our results suggest a broader distribution of H. lusitanicum, competent vector for the Crimean-Congo haemorrhagic fever virus than previously known. Wild boar is not a Rickettsia spp. reservoir according to the spleen negative results. However, its abundance could favour tick life cycle and abundance, and its proximity to humans could promote the infection risk by Rickettsia spp.

Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based improvement of antibiotic stewardship measures in the hospital. To address this, we combined existing antimicrobial susceptibility testing (AST) from FPRRH, with whole genome sequencing (WGS) of 41 Staphylococcus aureus isolates (2017–2019). AST revealed 73 % (30 of 41) of isolates were resistant to one or more antibiotics and 29 % (12 of 41) were multi-drug resistant (MDR). Resistance phenotypes were largely explained by the presence of antibiotic resistance genes in WGS data. Five isolates were methicillin-resistant S. aureus (MRSA) and MDR. Although all isolates were susceptible to clindamycin, a 24 % carriage of erm genes suggests potential for rapid development of resistance. We inferred a population structure for the S. aureus isolates by comparing their core genomes. Twenty isolates formed a tight cluster corresponding to multilocus sequence typing clonal complex (CC) 152, a CC found to be particularly prevalent in northern Africa. The frequency of genes associated with methicillin, chloramphenicol and ciprofloxacin resistance were significantly lower among CC152 strains than non-CC152 strains; thus, in keeping with previous work, we find that CC152 is almost exclusively methicillin-sensitive S. aureus (MSSA). Also, in agreement with other studies, we observed that the occurrence of Panton–Valentine leukocidin toxin-encoding genes was significantly higher among CC152 strains than non-CC152 strains. However, we also observed that the coagulase gene was over-represented in this CC, further defining the virulence strategy of this important pathogen. By generating detailed information about the epidemiology of circulating S. aureus and their antibiotic susceptibility, our study has provided, for the first time, data on which evidence-based infection and AMR interventions at FPRRH can be based.

Background Ticks and tick-borne pathogens (TBPs) represent a significant economic burden to cattle farming in sub-Saharan Africa including Nigeria. However, in the northern part of this country, where the largest livestock population reside, little is known about the contemporary diversity of ticks and TBPs. This area is particularly vulnerable to climate change, undergoing marked transformation of habitat and associated flora and fauna that is also likely to include ticks. This study aimed to document the occurrence of tick species and Apicomplexan TBPs in cattle from North-Western Nigeria. Methods In 2017, ticks were collected from cattle in Zamfara and Sokoto States and identified morphologically. Additionally, a subset of ticks were screened molecularly for the detection of Apicomplexan DNA. Results A total of 494 adult ticks were collected from 80 cattle in Zamfara and 65 cattle in Sokoto State. Nine tick species were encountered, including seven Hyalomma spp. (i.e. Hyalomma dromedarii, Hyalomma impeltatum, Hyalomma impressum, Hyalomma marginatum, Hyalomma rufipes, Hyalomma truncatum and Hyalomma turanicum), Amblyomma variegatum and Rhipicephalus (Boophilus) decoloratus. All species were present in Zamfara, whereas only five species were found in Sokoto. Hyalomma rufipes was the most prevalent tick infesting cattle in Zamfara State (76.2%), while H. dromedarii was the most prevalent in Sokoto State (43.7%), confirming the widespread transfer of this species from camels onto livestock and its adaptation to cattle in the region. Of 159 ticks screened, 2 out of 54 (3.7%) from Zamfara State and 29 out of 105 (27.6%) from Sokoto State harboured DNA of Theileria annulata, the agent of tropical theileriosis.Conclusions This study confirms the presence of a broad diversity of tick species in cattle from North-Western Nigeria, providing the first locality records for Zamfara State. The occurrence of H. turanicum, recorded for the first time in Nigeria, indicates a distribution of this tick beyond Northern Africa. This study provides the first report for T. annulata in Nigeria. Given its enormous burden on livestock farming in North Africa and across Asia, further investigations are needed to better understand its epidemiology, vector transmission and potential clinical significance in cattle from Northern Nigeria and neighbouring Sahelian countries.

Coccidiosis caused by Eimeria species is a well-recognized disease of livestock. Enteric Eimeria infections are common, but disease usually only manifests when infection intensity is abnormally high. Campylobacter species are important zoonotic enteric bacterial pathogens for which livestock are important reservoir hosts. The diversity and epidemiology of ovine Eimeria and Campylobacter infections on two farms in north-western England were explored through a 24-month survey of shedding in sheep feces. Most animals were infected with at least one of 10 different Eimeria species, among which E. bakuensis and E. ovinoidalis were most common. An animal's age and the season of sampling were associated with the probability and intensity of Eimeria infection. Season of sampling was also associated with the probability of Campylobacter infection. Interestingly, higher intensities of Eimeria infections were significantly more common in animals not co-infected with Campylobacter. We explored the determinants of E. bakuensis and E. ovinoidalis infections, observing that being infected with either significantly increased the likelihood of infection with the other. The prevalence of E. ovinoidalis infections was significantly lower in sheep infected with Campylobacter. Recognition that co-infectors shape the dynamics of parasite infection is relevant to the design of effective infection control programmes.

Coccidiosis caused by Eimeria species is a well-recognized disease of livestock. Enteric Eimeria infections are common, but disease usually only manifests when infection intensity is abnormally high. Campylobacter species are important zoonotic enteric bacterial pathogens for which livestock are important reservoir hosts. The diversity and epidemiology of ovine Eimeria and Campylobacter infections on two farms in north-western England were explored through a 24-month survey of shedding in sheep feces. Most animals were infected with at least one of 10 different Eimeria species, among which E. bakuensis and E. ovinoidalis were most common. An animal's age and the season of sampling were associated with the probability and intensity of Eimeria infection. Season of sampling was also associated with the probability of Campylobacter infection. Interestingly, higher intensities of Eimeria infections were significantly more common in animals not co-infected with Campylobacter. We explored the determinants of E. bakuensis and E. ovinoidalis infections, observing that being infected with either significantly increased the likelihood of infection with the other. The prevalence of E. ovinoidalis infections was significantly lower in sheep infected with Campylobacter. Recognition that co-infectors shape the dynamics of parasite infection is relevant to the design of effective infection control programmes.

Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based improvement of antibiotic stewardship measures in the hospital. To address this, we combined existing antimicrobial susceptibility testing (AST) from FPRRH, with whole genome sequencing (WGS) of 41 Staphylococcus aureus isolates (2017–2019). AST revealed 73 % (30 of 41) of isolates were resistant to one or more antibiotics and 29 % (12 of 41) were multi-drug resistant (MDR). Resistance phenotypes were largely explained by the presence of antibiotic resistance genes in WGS data. Five isolates were methicillin-resistant S. aureus (MRSA) and MDR. Although all isolates were susceptible to clindamycin, a 24 % carriage of erm genes suggests potential for rapid development of resistance. We inferred a population structure for the S. aureus isolates by comparing their core genomes. Twenty isolates formed a tight cluster corresponding to multilocus sequence typing clonal complex (CC) 152, a CC found to be particularly prevalent in northern Africa. The frequency of genes associated with methicillin, chloramphenicol and ciprofloxacin resistance were significantly lower among CC152 strains than non-CC152 strains; thus, in keeping with previous work, we find that CC152 is almost exclusively methicillin-sensitive S. aureus (MSSA). Also, in agreement with other studies, we observed that the occurrence of Panton–Valentine leukocidin toxin-encoding genes was significantly higher among CC152 strains than non-CC152 strains. However, we also observed that the coagulase gene was over-represented in this CC, further defining the virulence strategy of this important pathogen. By generating detailed information about the epidemiology of circulating S. aureus and their antibiotic susceptibility, our study has provided, for the first time, data on which evidence-based infection and AMR interventions at FPRRH can be based.

BackgroundTicks and tick-borne pathogens (TBPs) represent a significant economic burden to cattle farming in sub-Saharan Africa including Nigeria. However, in the northern part of this country, where the largest livestock population reside, little is known about the contemporary diversity of ticks and TBPs. This area is particularly vulnerable to climate change, undergoing marked transformation of habitat and associated flora and fauna that is also likely to include ticks. This study aimed to document the occurrence of tick species and Apicomplexan TBPs in cattle from North-Western Nigeria.MethodsIn 2017, ticks were collected from cattle in Zamfara and Sokoto States and identified morphologically. Additionally, a subset of ticks were screened molecularly for the detection of Apicomplexan DNA.ResultsA total of 494 adult ticks were collected from 80 cattle in Zamfara and 65 cattle in Sokoto State. Nine tick species were encountered, including sevenHyalommaspp. (i.e.Hyalomma dromedarii, Hyalomma impeltatum, Hyalomma impressum, Hyalomma marginatum, Hyalomma rufipes, Hyalomma truncatumandHyalomma turanicum),Amblyomma variegatumandRhipicephalus(Boophilus)decoloratus. All species were present in Zamfara, whereas only five species were found in Sokoto.Hyalomma rufipeswas the most prevalent tick infesting cattle in Zamfara State (76.2%), whileH. dromedariiwas the most prevalent in Sokoto State (43.7%), confirming the widespread transfer of this species from camels onto livestock and its adaptation to cattle in the region.Of 159 ticks screened, 2 out of 54 (3.7%) from Zamfara State and 29 out of 105 (27.6%) from Sokoto State harboured DNA ofTheileria annulata, the agent of tropical theileriosis.ConclusionsThis study confirms the presence of a broad diversity of tick species in cattle from North-Western Nigeria, providing the first locality records for Zamfara State. The occurrence ofH. turanicum, recorded for the first time in Nigeria, indicates a distribution of this tick beyond Northern Africa.This study provides the first report forT. annulatain Nigeria. Given its enormous burden on livestock farming in North Africa and across Asia, further investigations are needed to better understand its epidemiology, vector transmission and potential clinical significance in cattle from Northern Nigeria and neighbouring Sahelian countries.

Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate that fungi form critical components of putative microbial interaction networks, where the strength and frequency of interactions varies with host taxonomy. Host phylogeny drives differences in overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in mammals and for the bacterial microbiome. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.SIGNIFICANCE STATEMENTMicrobes perform vital metabolic functions that shape the physiology of their hosts. However, almost all research to date in wild animals has focused exclusively on the bacterial microbiota, to the exclusion of other microbial groups. Although likely to be critical components of the host microbiome, we have limited knowledge of the drivers of fungal composition across host species. Here we show that fungal community composition is determined by host species identity and phylogeny, and that fungi form extensive interaction networks with bacteria in the microbiome of a diverse range of animal species. This highlights the importance of microbial interactions as mediators of microbiome-health relationships in the wild.

A Gram-stain-negative, obligatory anaerobic spirochete, CHPAT, was isolated from the rectal tissue of a Holstein-Friesian cow. On the basis of 16S rRNA gene comparisons, CHPAT was most closely related to the human oral spirochete, Treponema parvum, with 88.8 sequence identity. Further characterisation on the basis of recA gene sequence analysis, cell morphology, pattern of growth and physiological profiling identified marked differences with respect to other recognised species of the genus Treponema. Microscopically, the helical cells measured approximately 1–5μm long and 0.15–0.25μm wide, with two to five irregular spirals. Transmission electron microscopy identified four periplasmic flagella in a 2 : 4 : 2 arrangement. CHPAT grew independently of serum, demonstrated no evidence of haemolytic activity and possessed an in vitro enzyme activity profile that is unique amongst validly named species of the genus Treponema, exhibiting C4 esterase, α-galactosidase and β-galactosidase activity. Taken together, these data indicate that CHPAT represents a novel species of the genus Treponema, for which the name Treponema rectale is proposed. The type strain of Treponema rectale is CHPAT (=DSM 103679T=NCTC 13848T). © 2017 IUMS.

Mapping the public health threat of tickborne pathogens requires quantification of not only the density of infected host-seeking ticks but also the rate of human exposure to these ticks. To efficiently sample a high number of persons in a short time, we used a mass-participation outdoor event. In June 2014, we sampled ≈500 persons competing in a 2-day mountain marathon run across predominantly tick-infested habitat in Scotland. From the number of tick bites recorded and prevalence of tick infection with Borrelia burgdoferi sensu lato and B. miyamotoi, we quantified the frequency of competitor exposure to the pathogens. Mass-participation outdoor events have the potential to serve as excellent windows for epidemiologic study of tickborne pathogens; their concerted use should improve spatial and temporal mapping of human exposure to infected ticks.

Introduction. Bartonella species are increasingly recognized as agents of culture-negative endocarditis. However, to date, almost all human cases have been associated with two members of the genus, Bartonella henselae and Bartonella quintana. B. henselae infections are zoonotic, with domestic cats serving as reservoir hosts for the pathogen. Bartonella clarridgeiae also exploits cats as reservoir hosts, but its zoonotic potential is far less established.\ud \ud Case presentation. A 34-year-old male presented with palpitations after a history of aortic incompetence. During surgery for an aortic valve replacement, two vegetations were found on the aortic valve. PCR analysis of the vegetation demonstrated the presence of Bartonella species and so the patient was treated post-operatively with ceftriaxone and doxycycline, making a good recovery. Further PCR-based analysis of the patient’s aortic vegetation confirmed the presence of B. clarridgeiae .\ud \ud Conclusion. This report expands the number of Bartonella species associated with endocarditis and provides clear evidence that B. clarridgeiae should be considered a zoonotic pathogen.

The composition of the mammalian gut microbiota can be influenced by a multitude of environmental variables such as diet and infections. Studies investigating the effect of these variables on gut microbiota composition often sample across multiple separate populations and habitat types. In this study we explore how variation in the gut microbiota of the house mouse (Mus musculus domesticus) on the Isle of May, a small island off the east coast of Scotland, is associated with environmental and biological factors. Our study focuses on the effects of environmental variables, specifically trapping location and surrounding vegetation, as well as the host variables sex, age, body weight and endoparasite infection, on the gut microbiota composition across a fine spatial scale in a freely interbreeding population. We found that differences in gut microbiota composition were significantly associated with the trapping location of the host, even across this small spatial scale. Sex of the host showed a weak association with microbiota composition. Whilst sex and location could be identified as playing an important role in the compositional variation of the gut microbiota, 75% of the variation remains unexplained. Whereas other rodent studies have found associations between gut microbiota composition and age of the host or parasite infections, the present study could not clearly establish these associations. We conclude that fine spatial scales are important when considering gut microbiota composition and investigating differences among individuals. This work was supported by The Natural Environment Research Council (NERC) [grant number NE/L002604/1] as part of the Envision Doctoral Training Programme studentship (URL: https://nerc.ukri.org/) which was awarded to SG. This work was also supported by the Biotechnology and Biological Sciences Research Council [grant number BB/J014508/1], a Doctoral Training Programme studentship (URL: https://bbsrc.ukri.org/) awarded to SY and JF. The funders did not play any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. peer-reviewed

Background\ud Landscape structure can affect pathogen prevalence and persistence with consequences for human and animal health. Few studies have examined how reservoir host species traits may interact with landscape structure to alter pathogen communities and dynamics. Using a landscape of islands and mainland sites we investigated how natural landscape fragmentation affects the prevalence and persistence of the zoonotic tick-borne pathogen complex Borrelia burgdorferi(sensu lato), which causes Lyme borreliosis. We hypothesized that the prevalence of B. burgdorferi (s.l.) would be lower on islands compared to the mainland and B. afzelii, a small mammal specialist genospecies, would be more affected by isolation than bird-associated B. garinii and B. valaisiana and the generalist B. burgdorferi (sensu stricto).\ud Methods\ud Questing (host-seeking) nymphal I. Ricinus ticks (n = 6567) were collected from 12 island and 6 mainland sites in 2011, 2013 and 2015 and tested for B. burgdorferi(s.l.). Deer abundance was estimated using dung transects.\ud Results\ud The prevalence of B. burgdorferi (s.l.) was significantly higher on the mainland (2.5%, 47/1891) compared to island sites (0.9%, 44/4673) (P < 0.01). While all four genospecies of B. burgdorferi (s.l.) were detected on the mainland, bird-associated species B. garinii and B. valaisiana and the generalist genospecies B. burgdorferi(s.s.) predominated on islands.\ud Conclusion\ud We found that landscape structure influenced the prevalence of a zoonotic pathogen, with a lower prevalence detected among island sites compared to the mainland. This was mainly due to the significantly lower prevalence of small mammal-associated B. afzelii. Deer abundance was not related to pathogen prevalence, suggesting that the structure and dynamics of the reservoir host community underpins the observed prevalence patterns, with the higher mobility of bird hosts compared to small mammal hosts leading to a relative predominance of the bird-associated genospecies B. garinii and generalist genospecies B. burgdorferi (s.s.) on islands. In contrast, the lower prevalence of B. afzelii on islands may be due to small mammal populations there exhibiting lower densities, less immigration and stronger population fluctuations. This study suggests that landscape fragmentation can influence the prevalence of a zoonotic pathogen, dependent on the biology of the reservoir host.

In contrast to the conditions in most laboratory studies, wild animals are routinely challenged by multiple infections at once, and these infections can interact in complex ways. This means that the impact of a parasite on its host’s physiology and fitness cannot be fully assessed in isolation, and requires consideration of the interactions with other co-infections. Here we examine the impact of two common blood parasites in the field vole (Microtus agrestis): Babesia microti and Bartonella spp., both of which have zoonotic potential. We collected longitudinal and cross-sectional data from four populations of individually-tagged wild field voles. This included data on biometrics, life history, ectoparasite counts, presence/absence of microparasites, immune markers and, for a subset of voles, more detailed physiological and immunological measurements. This allowed us to monitor infections over time and to estimate components of survival and fecundity. We confirm, as reported previously, that B. microti has a preventative effect on infection by Bartonella spp., but that the reverse is not true. We observe gross splenomegaly following B. microti infection, and an increase in IL-10 production along with some weight loss following Bartonella spp. infection. However, these animals appeared otherwise healthy and we detect no impact of infection on survival or fecundity due to the two haemoparasite taxa. This is particularly remarkable in the case of B. microti which induces apparently drastic long-term changes to spleen sizes, but without major adverse effects. Our work sheds light on the ecologies of these important zoonotic agents, and more generally on the influence that interactions among multiple parasites have on their hosts in the wild.

The Toll-like receptor (TLR) genes are a conserved family of genes central to the innate immune response to pathogen infection. They encode receptor proteins, recognise pathogen associated molecular patterns (PAMPs) and trigger initial immune responses. In some host-pathogen systems, it is reported that genetic differences, such as single nucleotide polymorphisms (SNPs), associate with disease resistance or susceptibility. Little is known about TLR gene diversity in the European badger (Meles meles). We collected DNA from UK badgers, carried out PCR amplification of the badger TLR2 gene and exon 3 of TLR4 and determined DNA sequences for individual badgers for TLR2 (n=61) and TLR4 exon 3 (n=59). No polymorphism was observed in TLR4. Three TLR2 amino acid haplotype variants were found. Ninety five percent of badgers were homozygous for one common haplotype (H1), the remaining three badgers had genotypes H1/H3, H1/H2 and H2/H2. By broad comparison with other species, diversity in TLR genes in badgers seems low. This could be due to a relatively localised sampling or inherent low genetic diversity. Further studies are required to assess the generality of the low observed diversity and the relevance to the immunological status of badgers.

The animal immune response has hitherto been viewed primarily in the context of resistance only. However, individuals, can also employ a tolerance strategy to maintain good health in the face of on-going infection. To shed light on the genetic and physiological basis of tolerance, we use a natural population of field voles, Microtus agrestis, to search for an association between the expression of the transcription factor Gata3, previously identified as a marker of tolerance in this system, and polymorphism in 84 immune and non-immune genes. Our results show clear evidence for an association between Gata3 expression and polymorphism in the Fcer1a gene, with the explanatory power of this polymorphism being comparable to that of other non-genetic variables previously identified as important predictors of Gata3 expression. We also uncover the possible mechanism behind this association using an existing protein-protein interaction network for the mouse model rodent, Mus musculus, which we validate using our own expression network for M. agrestis. Our results suggest that the polymorphism in question may be working at the transcriptional level, leading to changes in the expression of the Th2-related genes, Tyrosine-protein kinase BTK and Tyrosine-protein kinase TXK, and hence potentially altering the strength of the Th2 response, of which Gata3 is a mediator. We believe our work has implications for both treatment and control of infectious disease.

Inbred mouse strains, living in simple laboratory environments far removed from nature, have been shown to vary consistently in their immune response. However, wildlife populations are typically outbreeding and face a multiplicity of challenges, parasitological and otherwise. In this study we seek evidence of consistent difference in immunological profile amongst individuals in the wild. We apply a novel method in this context, using longitudinal (repeated capture) data from natural populations of field voles, Microtus agrestis, on a range of life history and infection metrics, and on gene expression levels. We focus on three immune genes, IFN-γ, Gata3, and IL-10, representing respectively the Th1, Th2 and regulatory elements of the immune response. Our results show that there was clear evidence of consistent differences between individuals in their typical level of expression of at least one immune gene, and at most all three immune genes, after other measured sources of variation had been taken into account. Furthermore, individuals that responded to changing circumstances by increasing expression levels of Gata3 had a correlated increase in expression levels of IFN-γ. Our work stresses the importance of acknowledging immunological variation amongst individuals in studies of parasitological and infectious disease risk in wildlife populations.

A novel bacterium, strain Ru1T, was encountered during a survey of spirochaetes living in the gastrointestinal tract of ruminants. Comparative analysis of 16S rRNA gene sequence data indicated that strain Ru1T clustered within the genus Treponema but shared at most 86.1 sequence similarity with other recognised species of the genus Treponema. Further phylogenetic analysis based on partial recombinase A (recA) gene sequence comparisons, together with phenotypic characterization, also demonstrated the divergence of strain Ru1T from other recognised species of the genus Treponema. Microscopically, strain Ru1T appeared as a very small, highly motile, helical spirochaete with eight periplasmic flagella in a 4: 8: 4 arrangement. It exhibited C8 esterase lipase, leucine arylamidase, I²-galactosidase and I²-glucosidase activity. A distinctive, serum-independent growth pattern was also observed, characterized by colonies with an absence of the local haemolysis that is typical of many pathogenic treponemes. On the basis of these data, strain Ru1T is considered to represent a novel species of the genus Treponema, for which the name Treponema ruminis sp. nov. is proposed. The type strain is Ru1T (=DSM 103462T=NCTC 13847T). © 2017 IUMS.

Bovine digital dermatitis (BDD) is a serious infectious inflammatory lameness causing pain and suffering to many cattle worldwide and which has severe economic implications. This study set out to investigate relationships between the treponemes considered causal of BDD and the local inflammatory response of the bovine host. Here we describe, for the first time, the isolation of bovine foot skin keratinocytes and fibroblasts as separate cell lineages. These cell lines were then exposed to treponeme whole-cell sonicates, and the gene expression of selected host inflammatory mediators investigated using quantitative reverse transcriptase PCR. Several genes, including those encoding RANTES/CCL5, MMP12, TNFα, TGFβ and TIMP3 were significantly upregulated in fibroblasts exposed to whole-cell sonicates derived from BDD treponeme phylotypes. For each of the above genes there were similar fibroblast expression increases for all three BDD treponeme phylotypes tested, suggesting common virulence mechanisms. With bovine foot skin keratinocytes, we were unable to detect expression of RANTES/CCL5 and after incubation with BDD treponeme constituents we were unable to observe any significant changes in expression of inflammatory mediators tested. These contrasting results suggest fibroblasts rather than keratinocytes may be an important shared target of pathogenesis for BDD treponemes.

The field vole ( Microtus agrestis) is a known maintenance host of Mycobacterium microti. Previous studies have shown that infected animals develop tuberculosis. However, the disease is also known in cats and is sporadically reported from humans and other mammalian species. We examined trapped field voles from an endemic area, using a range of diagnostic approaches. These confirmed that a combination of gross and histological examination with culture is most appropriate to identify the true prevalence of the disease, which was shown to be more than 13% at times when older animals that have previously been shown to be more likely to develop the disease dominate the population. The thorough pathological examination of diseased animals showed that voles generally develop systemic disease with most frequent involvement of spleen and liver, followed by skin, lymph nodes, and lungs. The morphology of the lesions was consistent with active disease, and their distribution suggested skin wounds or oral and/or aerogenic infection as the main portal of entry. The demonstration of mycobacteria in open skin lesions, airways, and salivary glands indicated bacterial shedding from the skin and with sputum and saliva. This suggests not only the environment but also direct contact and devouring as likely sources of infection.

Sheep infected with Anaplasma phagocytophilum, the causative agent of tick-borne fever (TBF), develop humoral immune responses 7–14 days after infection. Those individuals that survive acute TBF develop persistent infection, which may last for several months or even for life. The persistence of infection and recurrent bacteraemia is thought to be due to p44-mediated antigenic variation. The present study mapped linear B-cell epitopes within the hypervariable region (HVR) of the surface membrane protein P44 and investigated whether the development of antibodies against B cell epitopes within the HVR was preceded by the expression of p44 variants. Serum samples obtained from five sheep infected with the Old Sourhope strain of A. phagocytophilum (AP-OS) were used to detect antibody reactivity against 20-mer overlapping synthetic peptides spanning the HVR of two p44 variants which were expressed during primary bacteraemia and 3 variants expressed during secondary bacteraemia. The results showed that all five p44 variants of AP-OS have dominant B-cell epitopes residing mainly in the 3rd and 7th of the 10–11 peptides mapping each HVR. Antibody reactivity against peptides of the HVR of all the variants was characterised by a gradual rise, reaching peak levels in samples obtained 24 days post-inoculation (dpi) followed by a gradual decline. Anamnestic responses to whole cell antigens and to some of the dominant antigenic epitopes were detected in some of the animals, which were monitored for 52 weeks.

Background Cases of Lyme borreliosis, a vector-borne zoonosis caused by bacteria in the Borrelia burgdorferi (sensu lato) species group, have increased in recent years in Europe. Knowledge of environmental factors associated with abundance of the tick vector Ixodes ricinus and the pathogen B. burgdorferi (s.l.) is of interest to understand responses to environmental changes, predict variation in risk and to inform management interventions. Methods Nineteen woodland sites across Scotland were surveyed in 2012 for B. burgdorferi (s.l.) infection in questing I. ricinus nymphs (n = 200 per site), deer abundance and vegetation. Climatic factors were extracted for each site. Six additional sites were surveyed for questing nymphs in both 2012 and 2013 (n = 200 per site and year) to test for variation in B. burgdorferi (s.l.) prevalence between years. Results The mean prevalence of B. burgdorferi (s.l.) across 19 sites was 1.7% (95% CI: 1.4–2.2%; range 0–6%), all four genospecies known to be present in the UK were detected: B. garinii, B. afzelii, B. burgdorferi (sensu stricto) and B. valaisiana. A higher prevalence of B. burgdorferi (s.l.), higher densities of nymphs and higher densities of infected nymphs were found at sites with warmer climates, estimated with growing degree-days. No association between infection prevalence in nymphs and woodland type (semi-natural mixed vs coniferous) or deer density was found. At six sites sampled in 2012 and 2013, there was a significant increase in B. afzelli prevalence at two sites and a decrease in B. garinii prevalence at one site. Conclusions This study highlights challenges for the prediction of risk of Lyme borreliosis, reflecting the sensitivity of both pathogen and vector ecology to habitat, host and climatic factors. Significant changes in the prevalence of individual genospecies at sites monitored across time are likely to be due to variability in the host community composition between years. Our results indicate the importance of monitoring dynamic variables such as reservoir host populations as well as climate and habitat factors over multiple years, to identify environmental factors associated with Lyme borreliosis risk. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1875-9) contains supplementary material, which is available to authorized users.

We collected 69 ticks from nine, free-ranging Amur tigers ( Panthera tigris altaica) between 2002 and 2011 and investigated them for tick-borne pathogens. DNA was extracted using alkaline digestion and PCR was performed to detect apicomplexan organisms. Partial 18S rDNA amplification products were obtained from 14 ticks from four tigers, of which 13 yielded unambiguous nucleotide sequence data. Comparative sequence analysis revealed all 13 partial 18S rDNA sequences were most similar to those belonging to strains of Hepatozoon felis (>564/572 base-pair identity, >99% sequence similarity). Although this tick-borne protozoon pathogen has been detected in wild felids from many parts of the world, this is the first record from the Russian Far East.

Treponema species are implicated in many diseases of humans and animals. Digital dermatitis (DD) treponemes are reported to cause severe lesions in cattle, sheep, pigs, goats, and wild elk, causing substantial global animal welfare issues and economic losses. The fastidiousness of these spirochetes has previously precluded studies investigating within-phylogroup genetic diversity. An archive of treponemes that we isolated enabled multilocus sequence typing to quantify the diversity and population structure of DD treponemes. Isolates (n = 121) were obtained from different animal hosts in nine countries on three continents. The analyses herein of currently isolated DD treponemes at seven housekeeping gene loci confirm the classification of the three previously designated phylogroups: the Treponema medium, Treponema phagedenis, and Treponema pedis phylogroups. Sequence analysis of seven DD treponeme housekeeping genes revealed a generally low level of diversity among the strains within each phylogroup, removing the need for the previously used “-like” suffix. Surprisingly, all isolates within each phylogroup clustered together, regardless of host or geographic origin, suggesting that the same sequence types (STs) can infect different animals. Some STs were derived from multiple animals from the same farm, highlighting probable within-farm transmissions. Several STs infected multiple hosts from similar geographic regions, identifying probable frequent between-host transmissions. Interestingly, T. pedis appears to be evolving more quickly than the T. medium or T. phagedenis DD treponeme phylogroup, by forming two unique ST complexes. The lack of phylogenetic discrimination between treponemes isolated from different hosts or geographic regions substantially contrasts with the data for other clinically relevant spirochetes. IMPORTANCE The recent expansion of the host range of digital dermatitis (DD) treponemes from cattle to sheep, goats, pigs, and wild elk, coupled with the high level of 16S rRNA gene sequence similarity across hosts and with human treponemes, suggests that the same bacterial species can cause disease in multiple different hosts. This multilocus sequence typing (MLST) study further demonstrates that these bacteria isolated from different hosts are indeed very similar, raising the potential for cross-species transmission. The study also shows that infection spread occurs frequently, both locally and globally, suggesting transmission by routes other than animal-animal transmission alone. These results indicate that on-farm biosecurity is important for controlling disease spread in domesticated species. Continued surveillance and vigilance are important for ascertaining the evolution and tracking any further host range expansion of these important pathogens.

Summary Following experimental or natural infection with Anaplasma phagocytophilum , the causative agent of tick-borne fever (TBF), sheep may be infected persistently for several months or years. In the present study, quantitative real-time polymerase chain reaction was used to investigate the duration and magnitude of primary bacteraemia and to establish whether the organism is present continuously in the peripheral blood after the period of primary bacteraemia and the cessation of clinical signs. Persistent infection was characterized by a clearly defined period of primary bacteraemia followed by recurrent cycles of bacteraemia, usually lasting a few days and of lower magnitude, interspersed by negative periods of variable duration in which bacterial DNA could not be detected. During a 150-day period of consecutive sampling of four sheep, A. phagocytophilum was detected on 64.25 ± 4.9 occasions, which means that on average bacterial DNA was detected in 42.8 ± 3.3 percent of all samples, with the positive days falling into 15–20 distinct cycles. Primary bacteraemia lasted for 15.5 ± 2.33 days, but secondary and subsequent cycles of bacteraemia were short-lived, with 61% of the cycles lasting only 1–2 days and 39% lasting for 3 or more days. Secondary and subsequent cycles of bacteraemia were not accompanied by febrile responses or other clinical features of TBF. For three animals, bacterial DNA was detected at 311, 318 and 358 days post infection, indicating the long-term persistence of A. phagocytophilum within peripheral blood.

This chapter contains sections titled: Fusobacterium Necrophorum Infection, Helicobacter Infections, Bartonella Infections, Staphylococcus Infections, Streptococcus Infections, Rhodococcus Equi Infection, Corynebacterium Infections, Dermatophilus Infections, Brachyspira Infections in Birds, Actinomyces Infections, Arcanobacterium Infections, Erysipelothrix Infections, Actinobacillus Infections, Haemophilus Infections, Moraxella Infections, Lawsonia Intracellularis Infections, Aeromonas Species Infections, Bordetella Species Infections, Suttonella Ornithicola Sp. Nov. Infections of Species of TIT and Long - Tailed TITS and References.-- et al.

Bartonella are hemoparasites exploiting a range of mammals as reservoir hosts. Several species are zoonotic pathogens. Fleas, lice, and other arthropods, such as ticks, have been implicated as vectors. While the competence of ticks as vectors of Bartonella species has recently been demonstrated, the epidemiological significance of ticks as vectors of Bartonella species in wildlife populations remains unknown. We used the presence of deer at study sites to control the presence of Ixodes ricinus ticks, and used this system to determine whether I. ricinus contributes to the epidemiology of Bartonella species infections in small mammals. Ticks were present at all sites with deer, but were absent from all sites without deer; however, the abundance of ticks on small mammals did not affect the probability of wood mice being infected with Bartonella species. Data presented here indicate that I. ricinus is not involved in the transmission of Bartonella in woodland rodents.

The water vole (Arvicola amphibius) is Britain’s most endangered mammal, having gained protection under Schedule 5 of the Wildlife and Countryside Act in 2008. We present an overview of a range of naturally occurring pathogens and parasites in this rare species, which might negatively impact population persistence for small or declining populations. Wild water voles were live-captured in 2004 and 2006 from sites throughout the UK and were screened for a range of pathogens. These included: Puumala virus, Campylobacter spp., Escherichia coli, Salmonella enterica, Leptospira spp., Bartonella spp., Toxoplasma gondii, Giardia spp., Cryptosporidium spp., Babesia microti and Trypanosoma spp. E. coli was the most prevalent with 46/74 (62.2%; 95% CI, 51–73) individuals infected. One vole was co-infected with seven different pathogens whilst 20% of individuals were pathogen-free.

Although the importance of rodents as reservoirs for a number of tick-borne infections is well established,\ud comparatively little is known about the potential role of shrews, despite them occupying similar habitats. To\ud address this, blood and tick samples were collected from common shrews (Sorex araneus) and field voles\ud (Microtus agrestis), a known reservoir of various tick-borne infections, from sites located within a plantation\ud forest in northern England over a 2-year period. Of 647 blood samples collected from shrews, 121 (18.7%)\ud showed evidence of infection with Anaplasma phagocytophilum and 196 (30.3%) with Babesia microti. By comparison,\ud of 1505 blood samples from field voles, 96 (6.4%) were positive for A. phagocytophilum and 458 (30.4%)\ud for Ba. microti. Both species were infested with the ticks Ixodes ricinus and Ixodes trianguliceps, although they had\ud different burdens: on average, shrews carried almost six times as many I. trianguliceps larvae, more than twice as\ud many I. ricinus larvae, and over twice as many nymphs (both tick species combined). The finding that the\ud nymphs collected from shrews were almost exclusively I. trianguliceps highlights that this species is the key\ud vector of these infections in this small mammal community. These findings suggest that common shrews are a\ud reservoir of tick-borne infections and that the role of shrews in the ecology and epidemiology of tick-borne\ud infections elsewhere needs to be comprehensively investigated.

Bartonella henselae is one of the most common zoonotic agents acquired from companion animals (cats) in industrialized countries. Nonetheless, although the prevalence of infections in cats is high, the number of human cases reported is relatively low. One hypothesis for this discrepancy is that B. henselae strains vary in their zoonotic potential. To test this hypothesis, we employed structured sampling to explore the population structure of B. henselae in the United Kingdom and to determine the distribution of strains associated with zoonotic disease within this structure. A total of 118 B. henselae strains were delineated into 12 sequence types (STs) using multilocus sequence typing. We observed that most (85%) of the zoonosis-associated strains belonged to only three genotypes, i.e., ST2, ST5, and ST8. Conversely, most (74%) of the feline isolates belonged to ST4, ST6, and ST7. The difference in host association of ST2, ST5, and ST8 (zoonosis associated) and ST6 (feline) was statistically significant ( P < 0.05), indicating that a few, uncommon STs were responsible for the majority of symptomatic human infections.

Special Issue: FRONTIERS IN HOST-PARASITE ECOLOGY AND EVOLUTION Jackson, J. A., Begon, M., Birtles, R., Paterson, S., Friberg, I. M., Hall, A., Lowe, A., Ralli, C., Turner, A., Zawadzka, M., Bradley, J. E. (2011). The analysis of immunological profiles in wild animals: a case study on immunodynamics in the field vole, Microtus agrestis: IMMUNODYNAMICS IN MICROTUS AGRESTIS. Molecular Ecology, 20 (5), 893-909

The aim of this study was to develop quantitative real-time (q)PCR assays to detect all known haemoplasma species, and a human housekeeping gene in order to demonstrate both successful DNA extraction from clinical samples and to test for sample inhibition, and to apply these qPCRs to human blood samples and blood smears. Sensitive and specific generic haemoplasma qPCR assays were developed to amplify haemoplasma species, as well as human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as an internal amplification control. An optimized technique for extracting DNA from stained blood smears was also developed. These methods were applied to anonymized blood samples obtained from 100 human immunodeficiency virus (HIV)-infected South Africans and 920 UK patients undergoing haematological examination, and to 15 blood smears recruited from previous studies describing human haemoplasmosis. Human GAPDH levels were acceptable in all but three of the blood samples and all but two of the blood smears. The latter could have arisen due to DNA degradation due to the old age (over 35 years) of these smears. Haemoplasma infection was found in one HIV-infected South African, but the species could not be characterized due to the very low levels of DNA present. This report describes novel extraction and qPCR methodologies for haemoplasma screening. Previously reported human haemoplasmosis based on cytological diagnosis alone should be viewed with caution.

Bartonella are ubiquitous Gram-negative pathogens that cause chronic blood stream infections in mammals. Two species most often responsible for human infection, B. henselae and B. quintana, cause prolonged febrile illness in immunocompetent hosts, known as cat scratch disease and trench fever, respectively. Fascinatingly, in immunocompromised hosts, these organisms also induce new blood vessel formation leading to the formation of angioproliferative tumors, a disease process named bacillary angiomatosis. In addition, they cause an endothelial-lined cystic disease in the liver known as bacillary peliosis. Unfortunately, there are as yet no completely satisfying small animal models for exploring these unique human pathologies, as neither species appears able to sustain infection in small animal models. Therefore, we investigated the potential use of other Bartonella species for their ability to recapitulate human pathologies in an immunodeficient murine host. Here, we demonstrate the ability of Bartonella taylorii to cause chronic infection in SCID/BEIGE mice. In this model, Bartonella grows in extracellular aggregates, embedded within collagen matrix, similar to previous observations in cat scratch disease, bacillary peliosis, and bacillary angiomatosis. Interestingly, despite overwhelming infection later in disease, evidence for significant intracellular replication in endothelial or other cell types was not evident. We believe that this new model will provide an important new tool for investigation of Bartonella–host interaction.

Bartonella is a genus of vector-borne bacteria that infect the red blood cells of mammals, and includes several human-specific and zoonotic pathogens. Bartonella grahamii has a wide host range and is one of the most prevalent Bartonella species in wild rodents. We studied the population structure, genome content and genome plasticity of a collection of 26 B. grahamii isolates from 11 species of wild rodents in seven countries. We found strong geographic patterns, high recombination frequencies and large variations in genome size in B. grahamii compared with previously analysed cat- and human-associated Bartonella species. The extent of sequence divergence in B. grahamii populations was markedly lower in Europe and North America than in Asia, and several recombination events were predicted between the Asian strains. We discuss environmental and demographic factors that may underlie the observed differences.

Two canine haemoplasma species have been recognised to date; Mycoplasma haemocanis (Mhc), which has been associated with anaemia in splenectomised or immunocompromised dogs, and “Candidatus Mycoplasma haematoparvum” (CMhp), recently described in an anaemic splenectomised dog undergoing chemotherapy. The study aim was to develop quantitative real-time PCR assays (qPCRs) incorporating an endogenous internal control to detect Mhc and CMhp and to apply these assays to DNA samples extracted from canine blood collected in Northern Tanzania (n = 100) and from dogs presented to a Trinidadian veterinary hospital (n = 185). QPCRs specific for Mhc and CMhp were designed using 16S rRNA gene sequence data, and each was duplexed with an assay specific for canine glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The assays detected ≤10 copies of a sequence-specific haemoplasma plasmid per reaction and neither assay showed cross-reactivity with 106 copies of the sequence-specific plasmid from the non-target canine haemoplasma species. Nineteen of the 100 Tanzanian samples (19%) were positive for Mhc alone and one (1%) was dually infected. One Trinidadian sample was negative for canine GAPDH DNA and was excluded from the study. Of the 184 remaining Trinidadian samples, nine (4.9%) were positive for Mhc alone, five (2.7%) for CMhp alone, and two (1.1%) dually infected. This is the first report of canine haemoplasma qPCR assays that use an internal control to confirm the presence of amplifiable sample DNA, and their application to prevalence studies. Mhc was the most commonly detected canine haemoplasma species.

Genetically distinct subpopulations have adapted to different niches, The emerging tick-borne pathogen Anaplasma phagocytophilum is under increasing scrutiny for the existence of subpopulations that are adapted to different natural cycles. Here, we characterized the diversity of A. phagocytophilum genotypes circulating in a natural system that includes multiple hosts and at least 2 tick species, Ixodes ricinus and the small mammal specialist I. trianguliceps. We encountered numerous genotypes, but only 1 in rodents, with the remainder limited to deer and host-seeking I. ricinus ticks. The absence of the rodent-associated genotype from host-seeking I. ricinus ticks was notable because we demonstrated that rodents fed a large proportion of the I. ricinus larval population and that these larvae were abundant when infections caused by the rodent-associated genotype were prevalent. These observations are consistent with the conclusion that genotypically distinct subpopulations of A. phagocytophilum are restricted to coexisting but separate enzootic cycles and suggest that this restriction may result from specific vector compatibility.