Production and Evaluation of Antibodies and Phage Display-Derived Peptide Ligands for Immunomagnetic Separation of Mycobacterium bovis

This study describes the development and optimization of an immunomagnetic separation (IMS) method to isolate Mycobacterium bovis cells from lymph node tissues. Gamma-irradiated whole M. bovis AF2122/97 cells and ethanol-extracted surface antigens of such cells were used to produce M. bovis-speci?c polyclonal and monoclonal antibodies in rabbits and mice. They were also used to generate M. bovis-speci?c peptide ligands by phage display biopanning. The various antibodies and peptide ligands obtained were used to coat MyOne tosyl-activated Dynabeads (Life Technologies), singly or in combination, and evaluated for IMS. Initially, M. bovis capture from Middlebrook 7H9 broth suspensions (concentration range, 10 to 10⁵ CFU/ml) was evaluated by IMS combined with an M. bovis-speci?c touchdown PCR. IMS-PCR results and, subsequently, IMS-culture results indicated that the beads with greatest immunocapture capability for M. bovis in broth were those coated simultaneously with a monoclonal antibody and a biotinylated 12-mer peptide. These dually coated beads exhibited minimal capture (mean of 0.36% recovery) of 12 other Mycobacterium spp. occasionally encountered in veterinary tuberculosis (TB) diagnostic laboratories. When the optimized IMS method was applied to various M. bovis-spiked lymph node matrices, it demonstrated excellent detection sensitivities (50% limits of detection of 3.16 and 57.7 CFU/ml of lymph node tissue homogenate for IMS-PCR and IMS-culture, respectively). The optimized IMS method therefore has the potential to improve isolation of M. bovis from lymph nodes and hence the diagnosis of bovine tuberculosis.

Improved Detection of Mycobacterium bovis Infection in Bovine Lymph Node Tissue Using Immunomagnetic Separation (IMS)-Based Methods

Immunomagnetic separation (IMS) can selectively isolate and concentrate Mycobacterium bovis cells from lymph node tissue to facilitate subsequent detection by PCR (IMS-PCR) or culture (IMS-MGIT). This study describes application of these novel IMS-based methods to test for M. bovis in a survey of 280 bovine lymph nodes (206 visibly lesioned (VL), 74 non-visibly lesioned (NVL)) collected at slaughter as part of the Northern Ireland bovine TB eradication programme. Their performance was evaluated relative to culture. Overall, 174 (62.1%) lymph node samples tested positive by culture, 162 (57.8%) by IMS-PCR (targeting IS6110), and 196 (70.0%) by IMS-MGIT culture. Twelve (6.9%) of the 174 culture positive lymph node samples were not detected by either of the IMS-based methods. However, an additional 78 M. bovis positive lymph node samples (26 (12.6%) VL and 54 (73.0%) NVL) were detected by the IMS-based methods and not by culture. When low numbers of viable M. bovis are present in lymph nodes (e.g. in NVLs of skin test reactor cattle) decontamination prior to culture may adversely affect viability, leading to false negative culture results. In contrast, IMS specifically captures whole M. bovis cells (live, dead or potentially dormant) which are not subject to any deleterious treatment before detection by PCR or MGIT culture. During this study only 2.7% of NVL lymph nodes tested culture positive, whereas 73% of the same samples tested M. bovis positive by the IMS-based tests. Results clearly demonstrate that not only are the IMS-based methods more rapid but they have greater detection sensitivity than the culture approach currently used for the detection of M. bovis infection in cattle.. Adoption of the IMS-based methods for lymph node testing would have the potential to improve M. bovis detection in clinical samples.

Field-Isolated Genotypes of Mycobacterium bovis Vary in Virulence and Influence Case Pathology but Do Not Affect Outbreak Size

Strains of many infectious agents differ in fundamental epidemiological parameters including transmissibility, virulence and pathology. We investigated whether genotypes of Mycobacterium bovis (the causative agent of bovine tuberculosis, bTB) differ significantly in transmissibility and virulence, combining data from a nine-year survey of the genetic structure of the M. bovis population in Northern Ireland with detailed records of the cattle population during the same period. We used the size of herd breakdowns as a proxy measure of transmissibility and the proportion of skin test positive animals (reactors) that were visibly lesioned as a measure of virulence. Average breakdown size increased with herd size and varied depending on the manner of detection (routine herd testing or tracing of infectious contacts) but we found no significant variation among M. bovis genotypes in breakdown size once these factors had been accounted for. However breakdowns due to some genotypes had a greater proportion of lesioned reactors than others, indicating that there may be variation in virulence among genotypes. These findings indicate that the current bTB control programme may be detecting infected herds sufficiently quickly so that differences in virulence are not manifested in terms of outbreak sizes. We also investigated whether pathology of infected cattle varied according to M. bovis genotype, analysing the distribution of lesions recorded at post mortem inspection. We concentrated on the proportion of cases lesioned in the lower respiratory tract, which can indicate the relative importance of the respiratory and alimentary routes of infection. The distribution of lesions varied among genotypes and with cattle age and there were also subtle differences among breeds. Age and breed differences may be related to differences in susceptibility and husbandry, but reasons for variation in lesion distribution among genotypes require further investigation. © 2013 Wright et al.

Improved Detection of Mycobacterium bovis in Bovine Tissues Using Immunomagnetic Separation Approaches

Immunomagnetic separation (IMS) represents a simple but effective method of selectively capturing and concentrating Mycobacterium bovis, the causative agent of bovine tuberculosis (bTB), from tissue samples. It is a physical cell separation technique that does not impact cell viability, unlike traditional chemical decontamination prior to culture. IMS is performed with paramagnetic beads coated with M. bovis-specific antibody and peptide binders. Once captured by IMS, M. bovis cells can be detected by either PCR or cultural detection methods. Increased detection rates of M. bovis, particularly from non-visibly lesioned lymph node tissues from bTB reactor animals, have recently been reported when IMS-based methods were employed.

Evaluation of the diagnostic potential of a novel field immunomagnetic separation-immunochromatographic lateral flow assay to detect Mycobacterium bovis cells in European badger (Meles meles) faeces

The European badger (Meles meles) is a natural reservoir for Mycobacterium bovis, the causative agent of Bovine Tuberculosis, and has consequently been implicated in transmission of the disease to cattle. This study describes application of a novel M. bovis-specific immunochromatographic (lateral flow) assay in combination with immunomagnetic separation (IMS-LFD), to test badger faeces samples. In total, 441 faeces samples from badgers of unknown disease status collected from latrines at 110 badger setts throughout Northern Ireland (NI) and 100 faeces samples from badgers of known infection status from Great Britain (GB) were tested. Faeces (approx. 1g) was homogenised in 9 ml phosphate buffered saline, filtered (70 µm), and then 6-8 ml subjected to the IMS-LFD test. Residual clarified faecal homogenates were subjected to automated IMS followed by MGIT™ liquid culture (AIMS-MGIT™ culture) and qPCR (AIMS-qPCR). Evidence for the presence of M. bovis was obtained for 78 (18%), 61 (14%) and 140 (32%) of 441 NI badger faeces samples, and 10 (10%), 41 (41%) and 56 (56%) of 100 GB badger faeces samples, by IMS-LFD, AIMS-MGIT culture and AIMS-qPCR tests, respectively. The IMS-LFD test was less sensitive than AIMS-qPCR for detection of M. bovis and was, therefore, detecting badgers shedding high numbers of M. bovis in their faeces only. However, these ‘super shedders’ may be primarily responsible for the spread of Bovine Tuberculosis so are, therefore, an important target. This non-invasive test could form the basis of a field surveillance tool to indicate infected badger groups which are actively spreading M. bovis.

Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations

Whole genome sequencing (WGS) technology holds great promise as a tool for the forensic epidemiology of bacterial pathogens. It is likely to be particularly useful for studying the transmission dynamics of an observed epidemic involving a largely unsampled 'reservoir' host, as for bovine tuberculosis (bTB) in British and Irish cattle and badgers. BTB is caused by Mycobacterium bovis, a member of the M. tuberculosis complex that also includes the aetiological agent for human TB. In this study, we identified a spatio-temporally linked group of 26 cattle and 4 badgers infected with the same Variable Number Tandem Repeat (VNTR) type of M. bovis. Single-nucleotide polymorphisms (SNPs) between sequences identified differences that were consistent with bacterial lineages being persistent on or near farms for several years, despite multiple clear whole herd tests in the interim. Comparing WGS data to mathematical models showed good correlations between genetic divergence and spatial distance, but poor correspondence to the network of cattle movements or within-herd contacts. Badger isolates showed between zero and four SNP differences from the nearest cattle isolate, providing evidence for recent transmissions between the two hosts. This is the first direct genetic evidence of M. bovis persistence on farms over multiple outbreaks with a continued, ongoing interaction with local badgers. However, despite unprecedented resolution, directionality of transmission cannot be inferred at this stage. Despite the often notoriously long timescales between time of infection and time of sampling for TB, our results suggest that WGS data alone can provide insights into TB epidemiology even where detailed contact data are not available, and that more extensive sampling and analysis will allow for quantification of the extent and direction of transmission between cattle and badgers. © 2012 Biek et al.

Rapid-bTB: a novel lateral flow test able to differentiate Mycobacterium bovis from Mycobacterium tuberculosis in sputum

Background: A novel lateral flow, immunochromatographic assay (LFD) specific for Mycobacterium bovis, the cause of bovine tuberculosis and zoonotic TB, was recently developed at Queen’s University Belfast. The LFD detects whole M. bovis cells, in contrast to other commercially available LFD tests (BD MGITTM TBc ID, SD Bioline TB Ag MPT 64, Capilia TB-Neo kit) which detect MPT64 antigen secreted during growth. The new LFD test has been evaluated in the veterinary context, and its specificity for M. bovis in the broadest sense (i.e. subsp. bovis, subsp. caprae and BCG) and sensitivity to detect M. bovis in positive MGIT™ liquid cultures was demonstrated comprehensively.
Methods: Preliminary work was carried out by researchers at Queen’s University Belfast to optimise sputum sample preparation, estimate the limit of detection (LOD) of the LFD with M. bovis-spiked sputum samples, and check LFD specificity by testing a broad range of non-tuberculous Mycobacterium spp. (NTM) and other bacterial genera commonly encountered in sputum samples (Haemophilus, Klebsiella, Pseudomonas, Staphylococcus). In the Cameroon laboratory direct detection of M. bovis in human sputa was attempted, and 50 positive sputum MGIT™ cultures and 33 cultures of various Mycobacterium spp. originally isolated from human sputa were tested.
Results: Sputum sample preparation consisted of digestion with 1% NALC for 30 min, centrifugation at 3000g for 20 min, PBS wash, centrifugation again, and pellet resuspended in KPL blocking buffer before 100 µl was applied to the LFD. The LOD of the LFD applied to M. bovis-spiked sputum was estimated to be 104 CFU/ml. A small number of confirmed Ziehl-Neelsen ‘3+’ M. bovis positive sputum samples were tested directly but no positive LFD results were obtained. All of the sputum MGIT™ cultures and mycobacterial cultures (including M. tuberculosis, M. africanum, M. bovis, M. intracellulare, M. scrofulaceum, M. fortuitum, M. peregrinum, M. interjectum) tested LFD negative when read after 15 min except for the M. bovis cultures, thereby confirming specificity of LFD for M. bovis in the clinical microbiology context.
Conclusions: Results indicate that the ‘Rapid-bTB’ LFD is a very specific test, able to differentiate M. bovis from M. tuberculosis, M. africanum, and a range of NTM isolated from human sputa in MGITTM liquid cultures. However, the LFD lacks sufficient sensitivity to be applied earlier in the diagnostic process to directly test human sputa.

Tuberculosis among Iron Age individuals from Tyva, South Siberia: palaeopathological and biomolecular findings

The study focuses on the evidence for tuberculosis apparent in an Iron Age population recovered from the cemetery of Aymyrlyg, Tyva (Tuva), South Siberia. A recent wholly molecular study of five of the cases confirmed the presence of Mycobacterium tuberculosis (MTB) complex DNA in four of the individuals. In all cases the disease was caused by strains of Mycobacterium bovis rather than Mycobacterium tuberculosis and represents the first positive identification of the bovine form of the disease in archaeological human remains. Details of the palaeopathological characteristics of the cases are provided in the current paper, while the molecular observations are extended to include a quantitative evaluation of the surviving mycobacterial DNA using real-time PCR. The observation that bovine tuberculosis was the pathogen responsible is discussed in terms of current understanding of the evolution of the MTB complex as well as the implications for future ancient DNA studies in this area.

Detectability of bovine TB using the tuberculin skin test does not vary significantly according to pathogen genotype within Northern Ireland

Strains of many infectious diseases differ in parameters that influence epidemic spread, for example virulence, transmissibility, detectability and host specificity. Knowledge of inter-strain variation can be exploited to improve management and decrease disease incidence. Bovine tuberculosis (bTB) is increasingly prevalent among farmed cattle in the UK, exerting a heavy economic burden on the farming industry and government. We aimed to determine whether strains of Mycobacterium bovis (the causative agent of bTB) identified and classified using genetic markers (spoligotyping and multi-locus VNTR analysis) varied in response to the tuberculin skin test; this being the primary method of bTB detection used in the UK. Inter-strain variation in detectability of M. bovis could have important implications for disease control. The skin test is based on a differential delayed type hypersensitivity (DTH) response to intradermal injections of purified protein derivative (PPD) from M. bovis (PPD-B) and Mycobacterium avium (PPD-A). We searched for an association between skin test response (PPD-B skin rise minus PPD-A skin rise) and M. bovis genotype at the disclosing test in culture-confirmed cases using a field dataset consisting of 21,000 isolates belonging to 63 genotypes of M. bovis from cattle in Northern Ireland. We found no substantial variation among genotypes (estimated responses clustered tightly around the mean) controlling for animal sex, breed and test effects. We also estimated the ratio of skin test detected to undetected cases (i.e. cases only detected at abattoir). The skin test detection ratio varied among abattoirs with some detecting a greater proportion of cases than others but this variation was unrelated to the community composition of genotypes within each abattoir catchment. These two lines of evidence indicate that M. bovis genotypes in Northern Ireland have similar detectability using the skin test.

Genome-wide association study identifies novel loci associated with resistance to bovine tuberculosis

Tuberculosis (TB) caused by Mycobacterium bovis is a re-emerging disease of livestock that is of major economic importance worldwide, as well as being a zoonotic risk there is significant heritability for host resistance to bovine TB (bTB) in dairy cattle. To identify resistance loci for bTB, we undertook a genome-wide association study in female Holstein-Friesian cattle with 592 cases and 559 age-matched controls from case herds. Cases and controls were categorised into distinct phenotypes: skin test and lesion positive vs skin test negative on multiple occasions, respectively these animals were genotyped with the Illumina BovineHD 700K BeadChip. Genome-wide rapid association using linear and logistic mixed models and regression (GRAMMAR), regional heritability mapping (RHM) and haplotype-sharing analysis identified two novel resistance loci that attained chromosome-wise significance, protein tyrosine phosphatase receptor T (PTPRT; P=4.8 × 10 -7) and myosin IIIB (MYO3B; P=5.4 × 10 -6). We estimated that 21% of the phenotypic variance in TB resistance could be explained by all of the informative single-nucleotide polymorphisms, of which the region encompassing the PTPRT gene accounted for 6.2% of the variance and a further 3.6% was associated with a putative copy number variant in MYO3B the results from this study add to our understanding of variation in host control of infection and suggest that genetic marker-based selection for resistance to bTB has the potential to make a significant contribution to bTB control.

Physiological stress in the Eurasian badger (Meles meles): Effects of host, disease and environment

A method for monitoring hypothalamic–pituitary–adrenal (HPA) responses of the Eurasian badger (Meles meles) to stressors was validated by measuring cortisol excretion in serum and faeces. Serum and faecal samples were collected under anaesthesia from live-captured, wild badgers and fresh faeces was collected from latrines at 15 social groups in County Down, Northern Ireland. Variation in levels of cortisol in wild badgers was investigated relative to disease status, season, age, sex, body mass, body condition and reproductive status and environmental factors that might influence stress. Faecal cortisol levels were significantly higher in animals testing culture-positive for Mycobacterium bovis. Prolonged elevation of cortisol can suppress immune function, which may have implications for disease transmission. There was a strong seasonal pattern in both serum cortisol, peaking in spring and faecal cortisol, peaking in summer. Cortisol levels were also higher in adults with poor body condition and low body mass. Faecal samples collected from latrines in grassland groups had significantly higher cortisol than those collected from woodland groups, possibly as a result of greater exposure to sources of environmental stress. This study is the first to investigate factors influencing physiological stress in badgers and indicates that serological and faecal excretion are valid indices of the HPA response to a range of stressors.

Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis

Mycobacterium bovis is the causal agent of bovine tuberculosis, one of the most important diseases currently facing the UK cattle industry. Here, we use high-density whole genome sequencing (WGS) in a defined sub-population of M. bovis in 145 cattle across 66 herd breakdowns to gain insights into local spread and persistence. We show that despite low divergence among isolates, WGS can in principle expose contributions of under-sampled host populations to M. bovis transmission. However, we demonstrate that in our data such a signal is due to molecular type switching, which had been previously undocumented for M. bovis. Isolates from farms with a known history of direct cattle movement between them did not show a statistical signal of higher genetic similarity. Despite an overall signal of genetic isolation by distance, genetic distances also showed no apparent relationship with spatial distance among affected farms over distances <5 km. Using simulations, we find that even over the brief evolutionary timescale covered by our data, Bayesian phylogeographic approaches are feasible. Applying such approaches showed that M. bovis dispersal in this system is heterogeneous but slow overall, averaging 2 km/year. These results confirm that widespread application of WGS to M. bovis will bring novel and important insights into the dynamics of M. bovis spread and persistence, but that the current questions most pertinent to control will be best addressed using approaches that more directly integrate WGS with additional epidemiological data.