Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture.

BACKGROUND: Anaplasma phagocytophilum is a zoonotic and obligate intracellular bacterium transmitted by ticks. In domestic ruminants, it is the causative agent of tick-borne fever, which causes significant economic losses in Europe. As A. phagocytophilum is difficult to isolate and cultivate, only nine genome sequences have been published to date, none of which originate from a bovine strain.Our goals were to; 1/ develop a sequencing methodology which efficiently circumvents the difficulties associated with A. phagocytophilum isolation and culture; 2/ describe the first genome of a bovine strain; and 3/ compare it with available genomes, in order to both explore key genomic features at the species level, and to identify candidate genes that could be specific to bovine strains. RESULTS: DNA was extracted from a bovine blood sample infected by A. phagocytophilum. Following a whole genome capture approach, A. phagocytophilum DNA was enriched 197-fold in the sample and then sequenced using Illumina technology. In total, 58.9% of obtained reads corresponded to the A. phagocytophilum genome, covering 85.3% of the HZ genome. Then by performing comparisons with nine previously-sequenced A. phagocytophilum genomes, we determined the core genome of these ten strains. Following analysis, 1281 coding DNA sequences, including 1001 complete sequences, were detected in the A. phagocytophilum bovine genome, of which four appeared to be unique to the bovine isolate. These four coding DNA sequences coded for "hypothetical proteins of unknown function" and require further analysis. We also identified nine proteins common to both European domestic ruminants tested. CONCLUSION: Using a whole genome capture approach, we have sequenced the first A. phagocytophilum genome isolated from a cow. To the best of our knowledge, this is the first time that this method has been used to selectively enrich pathogenic bacterial DNA from samples also containing host DNA. The four proteins unique to the A. phagocytophilum bovine genome could be involved in host tropism, therefore their functions need to be explored.

Multilocus sequence analysis of Anaplasma phagocytophilum reveals three distinct lineages with different host ranges in clinically ill French cattle.

Molecular epidemiology represents a powerful approach to elucidate the complex epidemiological cycles of multi-host pathogens, such as Anaplasma phagocytophilum. A. phagocytophilum is a tick-borne bacterium that affects a wide range of wild and domesticated animals. Here, we characterized its genetic diversity in populations of French cattle; we then compared the observed genotypes with those found in horses, dogs, and roe deer to determine whether genotypes of A. phagocytophilum are shared among different hosts. We sampled 120 domesticated animals (104 cattle, 13 horses, and 3 dogs) and 40 wild animals (roe deer) and used multilocus sequence analysis on nine loci (ankA, msp4, groESL, typA, pled, gyrA, recG, polA, and an intergenic region) to characterize the genotypes of A. phagocytophilum present. Phylogenic analysis revealed three genetic clusters of bacterial variants in domesticated animals. The two principal clusters included 98% of the bacterial genotypes found in cattle, which were only distantly related to those in roe deer. One cluster comprised only cattle genotypes, while the second contained genotypes from cattle, horses, and dogs. The third contained all roe deer genotypes and three cattle genotypes. Geographical factors could not explain this clustering pattern. These results suggest that roe deer do not contribute to the spread of A. phagocytophilum in cattle in France. Further studies should explore if these different clusters are associated with differing disease severity in domesticated hosts. Additionally, it remains to be seen if the three clusters of A. phagocytophilum genotypes in cattle correspond to distinct epidemiological cycles, potentially involving different reservoir hosts.

Surgical Management of a Salter-Harris Type I Distal Physeal Fracture of the Tibia in a Calf: A Case Report.

Fractures are common conditions in cattle, including tibial fractures. Physeal tibial fractures are more specific and less frequently met in field conditions. A calf with a Salter-Harris type I distal physeal fracture of the tibia was referred to the National Veterinary School of Toulouse (ENVT), France. Although the use of external fixators in the treatment of tibial fractures is common, distal physeal tibial fractures require a different and specific technique involving them. They were first used as a lever arm to reduce the fracture due to the severe displacement. A hock joint bypass was then performed. Six weeks after treatment, the calf recovered successfully from the use of the affected limb without any adverse sequelae. The present case provides management of a distal tibial fracture using external fixators. This innovative and accessible surgical technique may be used by veterinary practitioners in future similar cases of distal tibial fractures when pins in the distal end cannot be inserted.

Thoracic Tumor Associated with a Unilateral Empyema in a Beef Cow: A Case Report.

Tumors in cows are not frequently reported in the literature. They often represent unusual findings in live animals and are incidental at slaughter with rare positive therapeutic outcomes for farmers. A 9-year-old beef cow was referred to the hospital of ruminants of the National Veterinary School of Toulouse, France. The cow started to become sick 10 days prior, and major symptoms were anorexia, arched back, tachycardia, and tachypnea associated with significantly attenuated cardiac and pulmonary sounds upon right-sided auscultation. After specific investigations, a thoracic sarcoma associated with unilateral empyema was diagnosed. The empyema was treated, and supportive treatment was only performed for the tumor. Although the sarcoma remained, clinical improvement was significant, and the cow went back to her farm of origin. After the end of the withdrawal period, the cow recovered clinically but was culled by the owners for economic reasons. The present case report offers a continuum from the initial clinical signs motivating specific investigations to interesting laboratory findings, which were confirmed post-mortem.

First detection of Mycoplasma wenyonii in France: Identification, evaluation of the clinical impact and development of a new specific detection assay.

Mycoplasma wenyonii, a hemoplasma infecting cattle, was never detected in France. In 2014, evocative inclusions were observed in erythrocytes from cattle presenting milk drops, anemia, and edema in Brittany (France). A survey was then initiated to investigate the epidemiological situation and correlate mycoplasma detection with clinical signs. For this purpose, a new PCR assay targeting polC gene was designed. Comparative results with published PCR assays place this new one as more specific, allowing a one-step diagnosis without further sequencing. A total of 181 cows were included in this study and 4.97% (n = 9) were positive, resulting in the first molecular identification of M. wenyonii in France. All positive animals presented anemia, edema and milk drop. When selecting animals presenting evocative clinical signs, the prevalence of M. wenyonii in Brittany was estimated to 25.6%. Further studies are needed to evaluate the importance of the infection, the implication of arthropods and the existence of asymptomatic carriers.

Extracellular DNA: A Nutritional Trigger of Mycoplasma bovis Cytotoxicity.

Microbial access to host nutrients is a key factor of the host-pathogen interplay. With their nearly minimal genome, wall-less bacteria of the class Mollicutes have limited metabolic capacities and largely depend on host nutrients for their survival. Despite these limitations, host-restricted mycoplasmas are widely distributed in nature and many species are pathogenic for humans and animals. Yet, only partial information is available regarding the mechanisms evolved by these minimal pathogens to meet their nutrients and the contribution of these mechanisms to virulence. By using the ruminant pathogen Mycoplasma bovis as a model system, extracellular DNA (eDNA) was identified as a limiting nutrient for mycoplasma proliferation under cell culture conditions. Remarkably, the growth-promoting effect induced by supplementation with eDNA was associated with important cytotoxicity for actively dividing host cells, but not confluent monolayers. To identify biological functions mediating M. bovis cytotoxicity, we produced a library of transposon knockout mutants and identified three critical genomic regions whose disruption was associated with a non-cytopathic phenotype. The coding sequences (CDS) disrupted in these regions pointed towards pyruvate metabolism as contributing to M. bovis cytotoxicity. Hydrogen peroxide was found responsible for eDNA-mediated M. bovis cytotoxicity, and non-cytopathic mutants were unable to produce this toxic metabolic compound. In our experimental conditions, no contact between M. bovis and host cells was required for cytotoxicity. Further analyses revealed important intra-species differences in eDNA-mediated cytotoxicity and H2O2 production, with some strains displaying a cytopathic phenotype despite no H2O2 production. Interestingly, the genome of strains PG45 and HB0801 were characterized by the occurrence of insertion sequences (IS) at close proximity to several CDSs found disrupted in non-cytopathic mutants. Since PG45 and HB0801 produced no or limited amount of H2O2, IS-elements might influence H2O2 production in M. bovis. These results confirm the multifaceted role of eDNA in microbial communities and further identify this ubiquitous material as a nutritional trigger of M. bovis cytotoxicity. M. bovis may thus take advantage of the multiple sources of eDNA in vivo to modulate its interaction with host cells, a way for this minimal pathogen to overcome its limited coding capacity.

[Persistent Bartonella infection: epidemiological and clinical implications]. / Epidémiologie des infections persistantes à Bartonella et conséquences cliniques.

Bartonella are Gram-negative hemotropic bacteria that infect a wide range of mammals. At least 14 Bartonella species or subspecies have been reported to be pathogenic for humans and animals. Wild and domestic animals represent a large reservoir. Reservoir species usually display chronic bacteremia. This explains some aspects of the epidemiology of these infections, and especially vector-borne transmission. The molecular mechanisms of persistent infection have clinical consequences both for occasional hosts and for human and animal reservoirs. An increasing number of clinical cases are being described in reservoir species that were previously considered to remain asymptomatic.

"Candidatus anaplasma camelii" in one-humped camels (Camelus dromedarius) in Morocco: a novel and emerging anaplasma species?

BACKGROUND: There has been a growing interest in camel anaplasmosis due to its recent emergence in this reservoir species and concerns for its zoonotic potential. The epidemiology of anaplasmosis in camels therefore remains poorly understood mostly because camels belong to marginalised poor and often transhumant populations whose interests are largely neglected. Most studies of anaplasmosis in camels have relied on microscopy and serology for diagnosis and only three studies, undertaken in Tunisia, Saudia Arabia and China, have used molecular diagnostics. The present work characterises Anaplasmataceae strains circulating in the Camelus dromedarius reservoir in Morocco using PCR. METHODS: Camels (n = 106) were randomly sampled from 6 regions representing different agro-ecological areas in southern Morocco. Whole blood was collected and screened using PCR methods targeting the gene groEL. Anaplasmataceae strains were characterised by sequence analysis of the gene groEL. RESULTS: A total of 39.62% (42/106) camels screened were positive for Anaplasmataceae spp. GenBank BLAST analysis of five positive sequenced samples revealed that all strains were 100% identical to "Candidatus Anaplasma camelii". Phylogenetic investigation and genetic characterisation of the aligned segment (650 bp) of the gene groEL confirmed high similarity with A. platys. CONCLUSION: This study demonstrates the circulation of a previously unidentified species of the genus Anaplasma in Morocco which is genetically close to the agent causing canine anaplasmosis but whose main reservoir is thought to be Camelus dromedarius. TRIAL REGISTRATION NUMBER: This study is not a clinical trial and therefore a trial registration number does not apply.

Immune response of mature cows subjected to annual booster vaccination against neonatal calf diarrhoea with two different commercial vaccines: A non-inferiority study.

Neonatal calf diarrhoea can have important economic consequences. Scour vaccines are available against some of the most frequent pathogens responsible for this disease: Bovine Rotavirus (BoRV), Bovine Coronavirus (BoCV) and E. coli K99. In this multi-centre, randomised, blinded study, adult cows vaccinated with a trivalent vaccine marketed for years (Rotavec™ Corona, MSD Animal Health - RC) prior to last parturition were revaccinated 12-15 months later, prior to the upcoming parturition, with either a single injection of a recently marketed vaccine (Bovigen™ Scour, Virbac - BS), or RC. The aim of this trial was to verify whether BS is not inferior to RC for the stimulation of the immune response and the passive transfer to calves in these conditions. A total of 136 multiparous dairy cows, from 5 different herds and located in 3 countries (France, UK and Germany) were enrolled in the study. Sixty-five cows were vaccinated with BS and 71 with RC. Antibody levels, measured by competitive ELISA and represented as percentage of inhibition (PI), were assessed in the cow's serum (on the day of vaccination: D0 and on days 21, 42 and at calving), in the colostrum and in the serum of calves in the first week of life. Differences in means of PI between groups and the 95% confidence interval (CI) were calculated. The non-inferiority threshold was set at -10%. The relationships between antibody levels in the colostrum and the vaccination-calving interval (VCI) or the inter-booster vaccination interval (IBVI) were also analysed. All the lower margins of the 95% CI of the difference in means of PI, in all samples and for the 3 pathogens assessed, were above -10%. This result shows that BS is not inferior to RC for the stimulation of the immune response against BoRV, BoCV and E. coli K99 and the passive transfer of immunity to calves when this vaccine is administered to their dams previously vaccinated with RC. Furthermore, no correlation was found between PI values in the colostrum and the VCI or IBVI. The ratio of animals with a PI ≥ 95% in the colostrum, among cows with similar intervals, was not significantly different between groups, for all antigens tested. Therefore, this study shows that a single injection of the heterologous vaccine BS can be used as a booster in cattle previously vaccinated with RC.

Opening the black box of Anaplasma phagocytophilum diversity: current situation and future perspectives.

Anaplasma phagocytophilum is a zoonotic obligate intracellular bacterium known to be transmitted by ticks belonging to the Ixodes persulcatus complex. This bacterium can infect several mammalian species, and is known to cause diseases with variable symptoms in many domestic animals. Specifically, it is the causative agent of tick-borne fever (TBF), a disease of important economic impact in European domestic ruminants, and human granulocytic anaplasmosis (HGA), an emerging zoonotic disease in Asia, USA and Europe. A. phagocytophilum epidemiological cycles are complex and involve different ecotypes, vectors, and mammalian host species. Moreover, the epidemiology of A. phagocytophilum infection differs greatly between Europe and the USA. These different epidemiological contexts are associated with considerable variations in bacterial strains. Until recently, few A. phagocytophilum molecular typing tools were available, generating difficulties in completely elucidating the epidemiological cycles of this bacterium. Over the last few years, many A. phagocytophilum typing techniques have been developed, permitting in-depth epidemiological exploration. Here, we review the current knowledge and future perspectives regarding A. phagocytophilum epidemiology and phylogeny, and then focus on the molecular typing tools available for studying A. phagocytophilum genetic diversity.

A new multiple-locus variable-number tandem repeat analysis reveals different clusters for Anaplasma phagocytophilum circulating in domestic and wild ruminants.

BACKGROUND: Anaplasma phagocytophilum is a tick-borne intragranulocytic alpha-proteobacterium. It is the causative agent of tick-borne fever in ruminants, and of human granulocytic anaplasmosis in humans, two diseases which are becoming increasingly recognized in Europe and the USA. However, while several molecular typing tools have been developed over the last years, few of them are appropriate for in-depth exploration of the epidemiological cycle of this bacterium. Therefore we have developed a Multiple-Locus Variable number tandem repeat (VNTR) Analysis typing technique for A. phagocytophilum. METHODS: Five VNTRs were selected based on the HZ human-derived strain genome, and were tested on the Webster human-derived strain and on 123 DNA samples: 67 from cattle, 7 from sheep, 15 from roe deer, 4 from red deer, 1 from a reindeer, 2 from horses, 1 from a dog, and 26 from ticks. RESULTS: From these samples, we obtained 84 different profiles, with a diversity index of 0.96 (0.99 for vertebrate samples, i.e. without tick samples). Our technique confirmed that A. phagocytophilum from roe deer or domestic ruminants belong to two different clusters, while A. phagocytophilum from red deer and domestic ruminants locate within the same cluster, questioning the respective roles of roe vs red deer as reservoir hosts for domestic ruminant strains in Europe. As expected, greater diversity was obtained between rather than within cattle herds. CONCLUSIONS: Our technique has great potential to provide detailed information on A. phagocytophilum isolates, improving both epidemiological and phylogenic investigations, thereby helping in the development of relevant prevention and control measures.

Endocarditis in cattle caused by Bartonella bovis.

This study aimed to determine the role of Bartonella as an endocarditis agent in cattle. Bartonella bovis was identified by PCR, gene sequences analysis, and specific internal transcribed spacer amplicon product size in 2 bovine endocarditis cases with high antibody titers, which demonstrates that B. bovis is a pathogen for cattle.

Broad-range PCR-TTGE for the first-line detection of bacterial pathogen DNA in ticks.

Ticks are known or suspected vectors for a wide range of bacterial pathogens. One of the first steps for tick-borne risk assessment is the detection of these pathogens in their vectors. In the present study, a broad-range PCR amplification of the eubacterial gene encoding the 16S rRNA gene combined with Temporal Temperature Gradient gel Electrophoresis (TTGE) was evaluated as a method allowing the one-step detection of bacterial pathogen DNA in ticks. Firstly, DNA extracts from bacteria known to be tick-borne pathogens, i.e., Borrelia burgdorferi lato sensu, Anaplasma phagocytophilum, Spotted Fever Group (SFG) Rickettsia spp., were used to establish a TTGE pathogen DNA reference marker. Secondly, we used broad-range PCR-TTGE to detect the presence of DNA from these three pathogens in 55 DNA extracts from pools of 10 nymphal Ixodes ricinus ticks, which have been previously shown to carry DNA from at least one of those bacteria by specific PCR. Among the 20 B. burgdorferi specific-PCR samples, 15 (75%) were also found to be positive using PCR-TTGE. Sixteen of the seventeen (94%) Rickettsia spp. PCR-specific samples were positive using PCR-TTGE detection and all PCR-specific positive extracts (11/11, 100%) for A. phagocytophilum were also positive using PCR-TTGE. Moreover, we identified unexpected bacterial sequences that were not related to any of the three pathogens such as a sequence related to Spiroplasma sp. Thus, broad-range PCR-TTGE allowed the single step detection of DNA from up to 3 pathogens in the same co-infected samples as well as detection of DNA from unexpected bacteria.

Evidence of Bartonella sp. in questing adult and nymphal Ixodes ricinus ticks from France and co-infection with Borrelia burgdorferi sensu lato and Babesia sp.

Ticks are known vectors for a wide range of pathogenic microorganisms. Their role in the transmission of some others is so far only suspected. Ticks can transmit multiple pathogens, however, little is known about the co-existence of these pathogens within questing ticks. We looked for the presence of DNA from three micro-organisms, Bartonella sp., Borrelia burgdorferi sensu lato and Babesia sp. which are known or suspected tick-borne pathogens, using a cohort of 92 questing Ixodes ricinus ticks collected from pastures in northern France. DNA was extracted from each individual tick and the presence of the three pathogens was investigated using Polymerase Chain Reaction (PCR) amplification. Nine among 92 samples (9.8%) demonstrated PCR products using Bartonella specific primers, 3 among 92 (3.3%) using Borrelia burgdorferi sensu lato specific primers and 19 among 92 (20.6%) using Babesia specific primers. Seven among 92 samples (7.6%) were PCR positive for at least two of the pathogens and one sample was positive for all three. Adult ticks (12/18; 67%) showed significantly higher infection rates compared to nymphs (11/74; 15%) for all three pathogens (P < 0.001). This study is the demonstration of the simultaneous presence of Bartonella sp., Borrelia burgdorferi sensu lato and Babesia sp. in questing Ixodes ricinus ticks.

Role of Hippoboscidae flies as potential vectors of Bartonella spp. infecting wild and domestic ruminants.

The putative role of biting flies in Bartonella transmission among ruminants was investigated. Amplification of the Bartonella citrate synthase gene from 83 Hippoboscidae was detected in 94% of 48 adult Lipoptena cervi flies, 71% of 17 adult Hippobosca equina flies, 100% of 20 adult Melophagus ovinus flies, and 100% of 10 M. ovinus pupae. Our findings suggest that Hippoboscidae play a role in the transmission of Bartonella among ruminants. The vertical transmission of Bartonella in M. ovinus and the presence of Bartonella DNA in all samples suggest a symbiotic association between Bartonella and M. ovinus.

Determination of an efficient and reliable method for DNA extraction from ticks.

Molecular detection of pathogenic microorganisms in ticks is based on DNA amplification of the target pathogen; therefore, extraction of DNA from the tick is a major step. In this study, we compared three different tick DNA extraction protocols based on an enzymatic digestion by proteinase K followed by DNA extraction by a commercial kit (method 1), or on mortar crushing, proteinase K digestion and phenol/chloroform DNA extraction (method 2) and fine crushing with a beads beater, proteinase K digestion and DNA extraction using a commercial kit (method 3). The absence of PCR inhibitors and the DNA quality were evaluated by PCR amplification of the tick mitochondrial 16S rRNA gene using tick-specific primers. With method 1, 23/30 (77%) of the samples were extracted; with method 2, 30/31 (97%) of the samples were extracted and with method 3, 30/30 (100%) of the samples were extracted. DNA extraction efficiency using method 3 is significantly higher than DNA extraction efficiency using method 1 (100% versus 77%, P < 0.05). There was no significant difference between methods 2 and 3. Method 3 was however more adapted to cohort studies than method 2. This technique was validated for cohort tick DNA extraction and applicable to the treatment of small samples such as nymphs and soft ticks with 100% efficiency.

Bartonella chomelii sp. nov., isolated from French domestic cattle (Bos taurus).

Two strains of bacteria isolated from the blood of French domestic cows were found to be similar to Bartonella species on the basis of phenotypic characteristics. Genotypic analysis based on sequence comparison of the 16S rRNA and citrate synthase (gltA) genes and on DNA-DNA hybridization showed that the two isolates represent a distinct and new species of Bartonella. Moreover, the phylogenetic analysis inferred from comparison of 16S rRNA and gltA sequences demonstrated that the new Bartonella species is related to other ruminant-derived Bartonella species. The name Bartonella chomelii is proposed for the new species. The type strain of Bartonella chomelii sp. nov. is A828T (=CIP 107869T=CCUG47497T).