The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for Dichelobacter nodosus

The prevalence, virulence, and serogroups of Dichelobacter nodosus and prevalence of Fusobacterium necrophorum in footrot lesions of sheep and cattle in Morocco

Background and Aim: Footrot is a contagious disease of ruminants leading to severe economic losses. This study aimed to estimate the prevalence, virulence, and serogroups of Dichelobacter nodosus and the prevalence of Fusobacterium necrophorum in footrot lesions of sheep and cattle. Materials and Methods: A total of 106 pathogenic lesion samples were taken from 74 sheep and 32 cattle exhibiting typical footrot lesions and were analyzed for the presence of D. nodosus and F. necrophorum by real-time polymerase chain reaction (PCR). Both virulence and serogroup were estimated for D. nodosus positive samples. Results: Among the 106 samples, 89 were positive by PCR for F. necrophorum, D. nodosus, or both. Dichelobacter nodosus was detected at a rate of 78.3% versus 28.3% for F. necrophorum. Virulent D. nodosus strains were detected in 67.5% of positive samples, with a higher rate in sheep (73.4%) than in cattle (47.4%). Benign D. nodosus strains were detected in 57.8% of samples, with a lower prevalence rate in sheep (50%) than in cattle (84.2%). The positive samples of D. nodosus revealed the presence of three dominant serogroups (D, H, I) and three minor serogroups (G, C, A) by serogroup-specific multiplex PCR. Conclusion: The findings provided information on the prevalence of D. nodosus and F. necrophorum strains in footrot lesions of sheep and cattle in some regions of Morocco, which will be useful for developing an effective autovaccine for the prevention of this disease in cattle and sheep in these regions. Keywords: cattle, Dichelobacter nodosus, footrot, Fusobacterium necrophorum, polymerase chain reaction, sheep.

Natural Mycoplasma Infection Reduces Expression of Pro-Inflammatory Cytokines in Response to Ovine Footrot Pathogens

Ovine footrot is a complex multifactorial infectious disease, causing lameness in sheep with major welfare and economic consequences. Dichelobacter nodosus is the main causative bacterium; however, footrot is a polymicrobial disease with Fusobacterium necrophorum, Mycoplasma fermentans and Porphyromonas asaccharolytica also associated. There is limited understanding of the host response involved. The proinflammatory mediators, interleukin (IL)-1β and C-X-C Motif Chemokine Ligand 8 (CXCL8), have been shown to play a role in the early response to D. nodosus in dermal fibroblasts and interdigital skin explant models. To further understand the response of ovine skin to bacterial stimulation, and to build an understanding of the role of the cytokines and chemokines identified, primary ovine interdigital fibroblasts and keratinocytes were isolated, cultured and stimulated. The expression of mRNA and protein release of CXCL8 and IL-1β were measured after stimulation with LPS, D. nodosus or F. necrophorum, which resulted in increased transcript levels of IL-1β and CXCL8 in the M. fermentans-free cells. However, only an increase in the CXCL8 protein release was observed. No IL-1β protein release was detected, despite increases in IL-1β mRNA, suggesting the signal for intracellular pre-IL-1β processing may be lacking when culturing primary cells in isolation. The keratinocytes and fibroblasts naturally infected with M. fermentans showed little response to the LPS, a range of D. nodosus preparations or heat-inactivated F. necrophorum. Primary single cell culture models complement ex vivo organ culture models to study different aspects of the host response to D. nodosus. The ovine keratinocytes and fibroblasts infected with M. fermentans had a reduced response to the experimental bacterial stimulation. However, in the case of footrot where Mycoplasma spp. are associated with diseased feet, this natural infection gives important insights into the impact of multiple pathogens on the host response.

Impact of Strain Variation of Dichelobacter nodosus on Disease Severity and Presence in Sheep Flocks in England

AprV2 and aprB2 are variants of the apr gene of Dichelobacter nodosus, the cause of footrot in sheep. They are putative markers for severe and mild disease expression. The aim of our study was to investigate the distribution of aprV2 and aprB2 in flocks with and without footrot. Our hypotheses were that both strains are present in endemically affected flocks, with aprB2 and aprV2 associated with mild and virulent phenotypes respectively but that D. nodosus is not present in flocks without footrot. Alternatively, aprB2 persists in flocks without footrot. Despite extensive searching over 3 years only three flocks of sheep without footrot were identified. D. nodosus was not detected in these three flocks. In one further flock, only mild interdigital dermatitis was observed, and only aprB2 was detected. Twenty-four flocks with endemic footrot of all severities were sampled on three occasions and all were positive for D. nodosus and the aprV2 variant; aprB2 was detected in only 11 of these flocks. AprB2 was detected as a co-infection with aprV2 in the 22% of samples positive for aprB2 and was more likely in mild footrot phenotypes than severe. Dichelobacter nodosus serogroups were not associated with footrot phenotype. We conclude that D. nodosus, even aprB2 strains, do not persist in flocks in the absence of footrot. Our results support the hypothesis that aprB2 is associated with mild footrot phenotypes. Finally, we conclude that given the small number of flocks without footrot that were identified, footrot is highly endemic in English sheep flocks.

Ovine footrot: A review of current knowledge

Footrot is a contagious foot disease mainly affecting sheep. It is caused by the Gram-negative anaerobic bacterium Dichelobacter nodosus. Warm, wet environmental conditions favour development of footrot, and under perfect conditions, it takes just 2-3 weeks from infection to manifestation of clinical signs. Affected sheep show lameness of various degrees and often graze while resting on their carpi. Local clinical signs vary in severity and extent from interdigital inflammation (benign footrot) to underrunning of the complete horn shoe in advanced stages of virulent footrot. Laboratory diagnosis ideally involves collection of four-foot interdigital swab samples followed by competitive real time PCR, allowing for detection of the presence of D. nodosus and differentiation between benign and virulent strains. Laboratory-based diagnostics at the flock level based on risk-based sampling and pooling of interdigital swab samples are recommended. The list of treatment options of individual sheep includes careful removal of the loose undermined horn, local or systemic administration of antimicrobials, systemic administration of non-steroidal anti-inflammatories (NSAIDs) and disinfectant footbathing. Strategies for control at the flock level are manifold and depend on the environmental conditions and the procedures traditionally implemented by the respective country. Generally, measures consist of treatment/culling of infected sheep, vaccination and prevention of reinfection of disease-free flocks. Gaining deeper insight into the beneficial effects of NSAIDs, screening for eco-friendly footbath solutions, developing better vaccines, including the development of a robust, reproducible infection model and elucidation of protective immune responses, as well as the elaboration of effective awareness training programs for sheep farmers, are relevant research gaps.

Genomic heterogeneity of Dichelobacter nodosus within and between UK sheep flocks and between age groups within a flock

Background

Footrot and interdigital dermatitis are endemic infectious diseases in all sheep farming regions, impairing welfare and production. The development of efficacious vaccines against the primary causative pathogen has been hampered by the extensive antigenic diversity of Dichelobacter nodosus. Understanding the heterogeneity of the pathogen within and between flocks is essential if the feasibility of bespoke vaccine production is to be assessed for use in the U.K.

Results

In this study 56 ewe and lamb isolates from 9 flocks were compared by D. nodosus serogroup and Multi Locus Sequence Type which provides significantly enhanced discriminatory power for molecular epidemiology. Serogroup heterogeneity between flocks ranged from two to five unique serogroups per flock. Three flocks contained isolates of two serogroups, two flocks contained isolates of three serogroups and one flock included isolates of five serogroups. Analysis of 25 isolates from one flock with high prevalence of lameness, identified that serogroup and sequence type was significantly correlated with age. Significantly higher proportion of lambs were infected with serogroup B (principally ST85) as opposed to serogroup H (principally ST86), which predominated amongst adult sheep.

Conclusions

Genomic heterogeneity of the pathogen was significantly lower within flock compared to heterogenicity observed between flocks. Furthermore, this study indicates that within a flock, the host-pathogen dynamics and susceptibility to particular D. nodosus strains may be age dependent.

Characterization of two putative Dichelobacter nodosus footrot vaccine antigens identifies the first lysozyme inhibitor in the genus

The Gram-negative anaerobic bacterium Dichelobacter nodosus (Dn) causes footrot in ruminants, a debilitating and highly contagious disease that results in necrotic hooves and significant economic losses in agriculture. Vaccination with crude whole-cell vaccine mixed with multiple recombinant fimbrial proteins can provide protection during species-specific outbreaks, but subunit vaccines containing broadly cross-protective antigens are desirable. We have investigated two D. nodosus candidate vaccine antigens. Macrophage Infectivity Potentiator Dn-MIP (DNO_0012, DNO_RS00050) and Adhesin Complex Protein Dn-ACP (DNO_0725, DNO_RS06795) are highly conserved amongst ~170 D. nodosus isolates in the https://pubmlst.org/dnodosus/ database. We describe the presence of two homologous ACP domains in Dn-ACP with potent C-type lysozyme inhibitor function, and homology of Dn-MIP to other putative cell-surface and membrane-anchored MIP virulence factors. Immunization of mice with recombinant proteins with a variety of adjuvants induced antibodies that recognised both proteins in D. nodosus. Notably, immunization with fimbrial-whole-cell Footvax vaccine induced anti-Dn-ACP and anti-Dn-MIP antibodies. Although all adjuvants induced high titre antibody responses, only antisera to rDn-ACP-QuilA and rDn-ACP-Al(OH)₃ significantly prevented rDn-ACP protein from inhibiting lysozyme activity in vitro. Therefore, a vaccine incorporating rDn-ACP in particular could contribute to protection by enabling normal innate immune lysozyme function to aid bacterial clearance.

Draft genome sequence of Dichelobacter nodosus JKS-07 serogroup E from India

OBJECTIVES

Dichelobacter nodosus is an anaerobic bacterium with fastidious growth requirements that is the principal cause of footrot associated with lameness in sheep and goats. In India, D. nodosus serogroups B and E have been recorded as major causes of footrot. Here we report the draft genome sequence of a D. nodosus serogroup E strain (JKS-07) from a case of virulent footrot in India.

METHODS

The whole genome of the D. nodosus JKS-07 serogroup E was sequenced using an Illumina HiSeq 2500 platform and was annotated according to functional gene categories. De novo genome assembly and annotation were performed using Perl scripts developed in-house using the Nr/Nt and UniProt databases.

RESULTS

The assembled genome is 1389350bp and contains 1301 genes. The genome has 45 tRNAs and 9 rRNAs. The draft genome sequence will provide insight into the various genes and regulators involved in D. nodosus growth and survival.

CONCLUSION

Information on the genome of the D. nodosus serogroup E strain is important bearing in mind the fact that both serogroups B and E are associated with virulent footrot, either alone or frequently together. In order to develop an efficacious vaccine against virulent footrot, it is essential to know the serological diversity as well as the virulence status of the D. nodosus strains. Serogroups B and E are potential vaccine candidates to mitigate ovine footrot in India.

Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications

The PubMLST.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species and genera.  Although the PubMLST website was conceived as part of the development of the first multi-locus sequence typing (MLST) scheme in 1998 the software it uses, the Bacterial Isolate Genome Sequence database (BIGSdb, published in 2010), enables PubMLST to include all levels of sequence data, from single gene sequences up to and including complete, finished genomes.  Here we describe developments in the BIGSdb software made from publication to June 2018 and show how the platform realises microbial population genomics for a wide range of applications.  The system is based on the gene-by-gene analysis of microbial genomes, with each deposited sequence annotated and curated to identify the genes present and systematically catalogue their variation.  Originally intended as a means of characterising isolates with typing schemes, the synthesis of sequences and records of genetic variation with provenance and phenotype data permits highly scalable (whole genome sequence data for tens of thousands of isolates) means of addressing a wide range of functional questions, including: the prediction of antimicrobial resistance; likely cross-reactivity with vaccine antigens; and the functional activities of different variants that lead to key phenotypes.  There are no limitations to the number of sequences, genetic loci, allelic variants or schemes (combinations of loci) that can be included, enabling each database to represent an expanding catalogue of the genetic variation of the population in question.  In addition to providing web-accessible analyses and links to third-party analysis and visualisation tools, the BIGSdb software includes a RESTful application programming interface (API) that enables access to all the underlying data for third-party applications and data analysis pipelines.

Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites

BACKGROUND

Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by targeting housekeeping genes that provide resolution down to the family, genera, and sometimes species level. Unfortunately, this level of resolution is not sufficient in many applications where strain-level identification of bacteria is required (biodefense, forensics, clinical diagnostics, and outbreak investigations). Adding more genomic targets will increase the resolution, but the challenge is identifying the appropriate targets. VaST was developed to address this challenge by finding the minimum number of targets that, in combination, achieve maximum strain-level resolution for any strain complex. The final combination of target regions identified by the algorithm produce a unique haplotype for each strain which can be used as a fingerprint for identifying unknown samples in a TAS assay. VaST ensures that the targets have conserved primer regions so that the targets can be amplified in all of the known strains and it also favors the inclusion of targets with basal variants which makes the set more robust when identifying previously unseen strains.

RESULTS

We analyzed VaST's performance using a number of different pathogenic species that are relevant to human disease outbreaks and biodefense. The number of targets required to achieve full resolution ranged from 20 to 88% fewer sites than what would be required in the worst case and most of the resolution is achieved within the first 20 targets. We computationally and experimentally validated one of the VaST panels and found that the targets led to accurate phylogenetic placement of strains, even when the strains were not a part of the original panel design.

CONCLUSIONS

VaST is an open source software that, when provided a set of variant sites, can find the minimum number of sites that will provide maximum resolution of a strain complex, and it has many different run-time options that can accommodate a wide range of applications. VaST can be an effective tool in the design of strain identification panels that, when combined with TAS technologies, offer an efficient and inexpensive strain typing protocol.