The impact of changing the cut-off threshold of the interferon-gamma (IFN-γ) assay for diagnosing bovine tuberculosis in Ireland

In Ireland, the interferon-gamma (IFN-γ) assay is routinely used as an ancillary test interpreted in parallel with the single intradermal comparative tuberculin test (SICTT) to maximize the detection of bovine tuberculosis (bTB) infected animals. Up until 2018, a positive test result was recorded in the IFN-γ ELISA assay following whole blood stimulation with purified protein derivative (PPD)-bovine (B), PPD-avian (A) and nil sample (N), using the interpretation criteria, B-N > 50 optical density units (OD), B > 100 and B-A > 0. Following a review of available data, the threshold of the B-A component changed to B-A > 80. As predicting the impact of changing the cut-off thresholds for the IFN-γ test de novo is challenging, the aims of this study were to follow animals that initially tested negative using the new IFN-γ assay interpretation criteria and investigate their future risk of disclosure with bTB, with a focus on animals that otherwise would have been removed when using the older interpretation criteria (0 < B-A ≤ 80). Enrolled animals (n = 28,669 cattle from 527 herds) were followed up for two years (2019-2021), or to point of bTB detection or death. At the end of follow-up, 1151 (4.0%) of enrolled animals were bTB cases. The majority of these cases were diagnosed using SICTT (80.5%). The cumulative number of positive animals that would have been removed if the old cut-off (0 < B-A ≤ 80) was used amounted to 1680 cattle (5.9% of the enrolled cohort). Of these, 127 (7.5%) were diagnosed with bTB during follow-up. In contrast, 1024 of the 1151 cattle which subsequently tested positive during the study period following a negative IFN-γ test would not have been identified with the old or new IFN-γ cut-off criteria. Survival analysis showed that animals that would have been removed under the old interpretation criteria were at increased risk of a positive diagnosis with bTB during follow-up compared to other test negative animals. A newly developed risk prediction model (using a Cox proportional hazard model) showed that age, animal number of SICTT tests, number of inconclusive SICTT tests, B-A (IFN-γ assay), B-N (IFN-γ assay), animals from store herds and the percentage of the rest of the herd that were positive during the breakdown were statistically significantly associated with bTB detection. However, inclusion of the IFN-γ OD variables did not show added value in terms of prediction performance of the model.

Investigation of the association between the Enferplex bovine tuberculosis antibody test and the future risk of bovine tuberculosis in irish cattle in infected herds: a pilot field study

The Single Intradermal Comparative Tuberculin Test (SICTT) and the interferon-gamma (IFN-γ) assay are the approved diagnostic tests for bovine tuberculosis (bTB) in Ireland. The aim of this pilot study was to explore if there was any added diagnostic benefit from applying the Enferplex bTB test (an antibody test) in severe bTB herd breakdowns after the removal of cattle that had tested positive to the SICTT and the IFN-γ test. In addition to the normal bTB testing and management protocols, the animals in these herds that tested negative to SICTT and the IFN-γ test were followed forward for a period of two years. All animals were tested by Enferplex at enrolment. The time to subsequent bTB detection (diagnosed with SICTT/IFN-γ tests or detection of visible lesions at routine slaughter) for animals that tested positive or negative to the Enferplex bTB test at the start of the study was compared using Kaplan-Meier survival curves and Cox based survival models. Of the 484 enrolled animals (from 11 herds), 171 (35.3%) and 151 (31.1%) initially tested positive in the Enferplex assay under the high sensitivity and high specificity interpretation settings respectively. The results of the survival analysis showed that there was no difference in the survival time to a positive diagnosis with bTB during the follow-up period between animals initially classified as positive and negative by the Enferplex test. Further research is warranted to explore the potential benefit of using the Enferplex test in other scenarios.

Inferring bovine tuberculosis transmission between cattle and badgers via the environment and risk mapping

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is one of the most challenging and persistent health issues in many countries worldwide. In several countries, bTB control is complicated due to the presence of wildlife reservoirs of infection, i.e. European badger (Meles meles) in Ireland and the UK, which can transmit infection to cattle. However, a quantitative understanding of the role of cattle and badgers in bTB transmission is elusive, especially where there is spatial variation in relative density between badgers and cattle. Moreover, as these two species have infrequent direct contact, environmental transmission is likely to play a role, but the quantitative importance of the environment has not been assessed. Therefore, the objective of this study is to better understand bTB transmission between cattle and badgers via the environment in a spatially explicit context and to identify high-risk areas. We developed an environmental transmission model that incorporates both within-herd/territory transmission and between-species transmission, with the latter facilitated by badger territories overlapping with herd areas. Model parameters such as transmission rate parameters and the decay rate parameter of M. bovis were estimated by maximum likelihood estimation using infection data from badgers and cattle collected during a 4-year badger vaccination trial. Our estimation showed that the environment can play an important role in the transmission of bTB, with a half-life of M. bovis in the environment of around 177 days. Based on the estimated transmission rate parameters, we calculate the basic reproduction ratio (R) within a herd, which reveals how relative badger density dictates transmission. In addition, we simulated transmission in each small local area to generate a first between-herd R map that identifies high-risk areas.

Bovine tuberculosis in youngstock cattle: A narrative review

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, remains a high-priority global pathogen of concern. The role of youngstock animals in the epidemiology of bTB has not been a focus of contemporary research. Here we have aimed to collate and summarize what is known about the susceptibility, diagnosis, transmission (infectiousness), and epidemiology to M. bovis in youngstock (up to 1-year of age). Youngstock are susceptible to M. bovis infection when exposed, with the capacity to develop typical bTB lesions. Calves can be exposed through similar routes as adults, via residual infection, contiguous neighborhood spread, wildlife spillback infection, and the buying-in of infected but undetected cattle. Dairy systems may lead to greater exposure risk to calves relative to other production systems, for example, via pooled milk. Given their young age, calves tend to have shorter bTB at-risk exposure periods than older cohorts. The detection of bTB varies with age when using a wide range of ante-mortem diagnostics, also with post-mortem examination and confirmation (histological and bacteriological) of infection. When recorded as positive by ante-mortem test, youngstock appear to have the highest probabilities of any age cohort for confirmation of infection post-mortem. They also appear to have the lowest false negative bTB detection risk. In some countries, many calves are moved to other herds for rearing, potentially increasing inter-herd transmission risk. Mathematical models suggest that calves may also experience lower force of infection (the rate that susceptible animals become infected). There are few modeling studies investigating the role of calves in the spread and maintenance of infection across herd networks. One study found that calves, without operating testing and control measures, can help to maintain infection and lengthen the time to outbreak eradication. Policies to reduce testing for youngstock could lead to infected calves remaining undetected and increasing onwards transmission. Further studies are required to assess the risk associated with changes to testing policy for youngstock in terms of the impact for within-herd disease control, and how this may affect the transmission and persistence of infection across a network of linked herds.

Seroconversion against antigen MPB83 in badgers (Meles meles) vaccinated with multiple doses of BCG strain Sofia

Serological diagnosis of Mycobacterium bovis infection in badgers (Meles meles) has relied primarily on antibody recognition of MPB83, a sero-dominant antigen of M. bovis. Most vaccine studies in badgers to date have used the Bacille Calmette-Guerin (BCG) Danish strain, a low producer of MPB83. Due to a supply shortage of the BCG Danish strain, the BCG Sofia SL222 strain has been considered as an alternative vaccine. This strain is a high producer of MPB83 raising the possibility that vaccinated animals will test sero-positive in diagnostic assays that use this antigen. In this study we vaccinated a group of eleven badgers with BCG Sofia SL222 by injection via the intramuscular route and a booster vaccine dose was similarly delivered at 12 weeks and 64 weeks. Primary vaccination did not result in measured detection of antibodies against MPB83 in any badger during the first twelve weeks using serum or whole blood tested by the Dual Path Platform (DPP) VetTB, however, MPB83 antibodies were detected in a semi-quantitative ELISA assay. Following delivery of booster BCG at 12 weeks and 64 weeks, antibody responses against MPB83 were recorded in badgers using whole blood and serum on DPP VetTB and by ELISA. At all time points, vaccination was also associated with the in vitro production of gamma interferon (IFN-γ) following stimulation of lymphocytes with bovine and avian tuberculin (PPD) but not with MPB83 or M. bovis specific antigen CFP-10. The results indicate that serological diagnosis of tuberculosis using tests that target MPB83 may be compromised if badgers are repeatedly vaccinated with BCG Sofia.

Numbers of close contacts of individuals infected with SARS-CoV-2 and their association with government intervention strategies

Background

Contact tracing is conducted with the primary purpose of interrupting transmission from individuals who are likely to be infectious to others. Secondary analyses of data on the numbers of close contacts of confirmed cases could also: provide an early signal of increases in contact patterns that might precede larger than expected case numbers; evaluate the impact of government interventions on the number of contacts of confirmed cases; or provide data information on contact rates between age cohorts for the purpose of epidemiological modelling. We analysed data from 140,204 close contacts of 39,861 cases in Ireland from 1st May to 1st December 2020.

Results

Negative binomial regression models highlighted greater numbers of contacts within specific population demographics, after correcting for temporal associations. Separate segmented regression models of the number of cases over time and the average number of contacts per case indicated that a breakpoint indicating a rapid decrease in the number of contacts per case in October 2020 preceded a breakpoint indicating a reduction in the number of cases by 11 days.

Conclusions

We found that the number of contacts per infected case was overdispersed, the mean varied considerable over time and was temporally associated with government interventions. Analysis of the reported number of contacts per individual in contact tracing data may be a useful early indicator of changes in behaviour in response to, or indeed despite, government restrictions. This study provides useful information for triangulating assumptions regarding the contact mixing rates between different age cohorts for epidemiological modelling.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12889-021-12318-y.

Protective immunity against tuberculosis in a free-living badger population vaccinated orally with Mycobacterium bovis Bacille Calmette-Guérin

Vaccination of badgers with Mycobacterium bovis Bacille Calmette-Guérin (BCG) has been shown to protect badgers against tuberculosis in experimental trials. During the 3-year County Kilkenny BCG vaccine field study, badgers were treated orally with placebo (100% in Zone A), BCG (100% in Zone C) or randomly assigned 50%: 50% treatment with BCG or placebo (Zone B). At the end of the study, 275 badgers were removed from the trial area and subjected to detailed post-mortem examination followed by histology and culture for M. bovis. Among these badgers, 83 (30.2%) were captured for the first time across the three zones, representing a non-treated proportion of the population. Analysis of the data based on the infection status of treated animals showed a prevalence of 52% (95% CI: 40%-63%) infection in Zone A (placebo), 39% (95% CI: 17%-64%) in Zone B (placebo) and 44% (95% CI: 20%-70%) in Zone B (BCG vaccinated) and 24% (95% CI: 14%-36%) in Zone C (BCG vaccinated). There were no statistically significant differences in the proportion of animals with infection involving the lung and thoracic lymph nodes, extra-thoracic infection or in the distribution and severity scores of histological lesions. Among the 83 non-treated badgers removed at the end of the study, the infection prevalence of animals in Zone A (prevalence = 46%, 95% CI: 32%-61%) and Zone B (prevalence = 44%, 95% CI: 23%-67%) was similar to the treated animals in these zones. However, in Zone C, no evidence of infection was found in any of the untreated badgers (prevalence = 0%, 95% CI: 0%-14%). This is consistent with an indirect protective effect in the non-vaccinated badgers leading to a high level of population immunity. The results suggest that BCG vaccination of badgers could be a highly effective means of reducing the incidence of tuberculosis in badger populations.

RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course

Bovine tuberculosis, caused by infection with members of the Mycobacterium tuberculosis complex, particularly Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including RNA sequencing, has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analysed the transcriptome of bovine whole peripheral blood samples collected at −1 week pre-infection and +1, +2, +6, +10, and +12 weeks post-infection time points. Differentially expressed genes were catalogued and evaluated at each post-infection time point relative to the −1 week pre-infection time point and used for the identification of putative candidate host transcriptional biomarkers for M. bovis infection. Differentially expressed gene sets were also used for examination of cellular pathways associated with the host response to M. bovis infection, construction of de novo gene interaction networks enriched for host differentially expressed genes, and time-series analyses to identify functionally important groups of genes displaying similar patterns of expression across the infection time course. A notable outcome of these analyses was identification of a 19-gene transcriptional biosignature of infection consisting of genes increased in expression across the time course from +1 week to +12 weeks post-infection.

Estimation of the serial interval and proportion of pre-symptomatic transmission events of COVID- 19 in Ireland using contact tracing data

BACKGROUND

The serial interval is the period of time between the onset of symptoms in an infector and an infectee and is an important parameter which can impact on the estimation of the reproduction number. Whilst several parameters influencing infection transmission are expected to be consistent across populations, the serial interval can vary across and within populations over time. Therefore, local estimates are preferable for use in epidemiological models developed at a regional level. We used data collected as part of the national contact tracing process in Ireland to estimate the serial interval of SARS-CoV-2 infection in the Irish population, and to estimate the proportion of transmission events that occurred prior to the onset of symptoms.

RESULTS

After data cleaning, the final dataset consisted of 471 infected close contacts from 471 primary cases. The median serial interval was 4 days, mean serial interval was 4.0 (95% confidence intervals 3.7, 4.3) days, whilst the 25th and 75th percentiles were 2 and 6 days respectively. We found that intervals were lower when the primary or secondary case were in the older age cohort (greater than 64 years). Simulating from an incubation period distribution from international literature, we estimated that 67% of transmission events had greater than 50% probability of occurring prior to the onset of symptoms in the infector.

CONCLUSIONS

Whilst our analysis was based on a large sample size, data were collected for the primary purpose of interrupting transmission chains. Similar to other studies estimating the serial interval, our analysis is restricted to transmission pairs where the infector is known with some degree of certainty. Such pairs may represent more intense contacts with infected individuals than might occur in the overall population. It is therefore possible that our analysis is biased towards shorter serial intervals than the overall population.

A molecularly defined skin test reagent for the diagnosis of bovine tuberculosis compatible with vaccination against Johne's Disease

Tuberculin Purified Protein Derivatives (PPDs) exhibit multiple limitations: they are crude extracts from mycobacterial cultures with largely unknown active components; their production depends on culture of mycobacteria requiring expensive BCL3 production facilities; and their potency depends on the technically demanding guinea pig assay. To overcome these limitations, we developed a molecularly defined tuberculin (MDT) by adding further antigens to our prototype reagent composed of ESAT-6, CFP-10 and Rv3615c (DIVA skin test, DST). In vitro screening using PBMC from infected and uninfected cattle shortlisted four antigens from a literature-based list of 18 to formulate the MDT. These four antigens plus the previously identified Rv3020c protein, produced as recombinant proteins or overlapping synthetic peptides, were formulated together with the three DST antigens into the MDT to test cattle experimentally and naturally infected with M. bovis, uninfected cattle and MAP vaccinated calves. We demonstrated significant increases in MDT-induced skin responses compared to DST in infected animals, whilst maintaining high specificity in unvaccinated or MAP vaccinated calves. Further, MDT can also be applied in in vitro blood-based interferon-gamma release assays. Thus, MDT promises to be a robust diagnostic skin and blood test reagent overcoming some of the limitations of PPDs and warrants full validation.

Evaluation of the Dual Path Platform (DPP) VetTB assay for the detection of Mycobacterium bovis infection in badgers

Bovine tuberculosis (bTB), caused by Mycobacterium bovis, represents a major animal health issue. In the United Kingdom and the Republic of Ireland, European badgers (Meles meles) have been shown to act as a reservoir of M. bovis infection, hindering the eradication of bTB in livestock. The availability of suitable diagnostic assays, particularly those that may be applied in a "trap-side" setting, would facilitate the implementation of a wider range of disease control strategies. Here we evaluate the Dual Path Platform (DPP) VetTB assay, a lateral-flow type test for detecting antibodies to M. bovis antigens (MPB83 and ESAT-6/CFP-10). Both serum and whole blood were evaluated as diagnostic samples. Additionally, two methods were evaluated for interpretation of test results (qualitative interpretation by eye and quantitative measurement using an optical reader). The antibody response to MPB83 detected by the DPP VetTB assay increased significantly following experimental M. bovis infection of badgers, whilst the response to ESAT-6/CFP-10 showed no significant change. In sera from TB-free captive and naturally M. bovis infected wild badgers the MPB83 response exhibited a sensitivity of 55 % by eye and quantitative reader (95 % CI: 40-71 and 38-71, respectively), with slightly lower specificity when read by eye (93 % compared to 98 %; 95 % CI: 85-100 and 90-100, respectively). In whole blood, the DPP VetTB assay MPB83 response exhibited a sensitivity of 65 % (95 % CI: 50-80) when interpreted by eye and 53 % (95 % CI: 36-69) using quantitative values, whilst the specificity was 94 % and 98 % respectively (95 % CI: 88-100 and 90-100). Comparison with contemporaneous diagnostic test results from putatively naturally infected and TB-free badgers demonstrated varying levels of agreement. Using sera from naturally M. bovis infected and TB-free badgers, with post mortem confirmation of disease status, the DPP VetTB assay exhibited a sensitivity of 60 % (95 % CI: 41-77) when interpreted using quantitative values (specificity 95 %; 95 % CI: 76-100), and 67 % (95 % CI: 50-84) when read by eye (specificity 95 %; 95 % CI: 86-100). Further work is required to robustly characterize the DPP VetTB assay's performance in a wider selection of samples, and in the practical and epidemiological contexts in which it may be applied.

Characteristics of Mycobacterium bovis infected herds tested with the interferon-gamma assay

The IFN-γ (interferon gamma) assay is used in Ireland as an ancillary diagnostic test to the single intradermal comparative tuberculin test (SICTT) to maximise the detection of Mycobacterium bovis infected animals (bTB) in cattle herds. Understanding the relationships between herd and animal risk factors and IFN-γ test results is critical to enable the development and evaluation of policy measures on how best to use the test. In this study, we set out to characterise Irish herds with IFN-γ test positive animals in terms of herd size, number of SICTT reactors and number of IFN-γ positive tests, and to evaluate the IFN-γ test in terms of the test cut-off values. The results showed that larger herds with more SICTT reactors were likely to have more IFN-γ positives in the herd, and herds with an IFN-γ test positive animal that was also positive for bTB lesions at post-mortem had higher numbers of IFN-γ positive animals in the herd. Raising the cut-off values for the IFN-γ test only marginally decreased the combined sensitivity of the IFN-γ and the SICTT for diagnosis of bTB lesioned animals. The analysis has provided valuable information on the performance of the IFN-γ test as it is used under current bTB infection levels in Ireland.

New serological platform for detecting antibodies against Mycobacterium tuberculosis complex in European badgers

European badgers (Meles meles) have been identified as wildlife reservoirs for Mycobacterium bovis in the UK and Ireland, and may also have a role in the epidemiology of animal tuberculosis in other European regions. Thus, detection of M. bovis‐infected badgers may be required for the purposes of surveillance and monitoring of disease levels in infected populations. Current serological assays to detect M. bovis infection in live badgers, while rapid and inexpensive, show limited diagnostic sensitivity. Here we describe and evaluate new ELISA platforms for the recognition of the P22 multiprotein complex derived from the purified protein derivative (PPD) of M. bovis. The recognition of IgG against P22 multiprotein complex derived from PPD‐B was tested by ELISA in the serum of badgers from the UK, Ireland and Spain. TB infection in the badgers was indicated by the presence of M. bovis in tissues by culture and histology at post‐mortem examination and TB‐free status was established by repeated negativity in the interferon γ release assay (IGRA). In experimentally infected badgers, humoral antibody responses against P22 developed within 45 days post‐infection. The ELISA tests showed estimated sensitivity levels of 74–82% in experimentally and naturally infected badgers with specificities ranging from 75% to 100% depending on the badger population tested. The P22 multi‐antigen based ELISAs provide a sensitive and specific test platform for improved tuberculosis surveillance in badgers.

Simultaneous measurement of antigen-induced CXCL10 and IFN-γ enhances test sensitivity for bovine TB detection in cattle

Bovine tuberculosis (BTB) is a disease of economic and zoonotic importance caused mainly by Mycobacterium bovis. In addition to the tuberculin skin test, an interferon-gamma (IFN-γ) release assay (IGRA) blood test has been incorporated in the BTB control programs of numerous countries as an ancillary test to the skin test. A potential disadvantage of the IGRA assay is that it relies solely on the measurement of a single readout (i.e. IFN-γ) for the detection of BTB. In this study we have assessed the practical use of CXCL10 as an additional biomarker for the diagnosis of BTB in the setting of the current testing approach alongside IGRA. To do so, we have assessed both IFN-γ and CXCL10 readouts in blood cultures from a variety of different BTB cattle groups stimulated with standard tuberculin reagents and also with more specific defined antigens (ESAT-6, CFP-10 and Rv3615c). When using a tuberculin based whole blood assay, CXCL10 alone could not substitute for IFN-γ as the analyte measured in the test without reducing the sensitivity of detecting BTB animals. However, when used as an additional test readout, CXCL10 identified BTB animals that failed to induce IFN-γ responses. When tested in non-infected animals, the use of the dual biomarker system had the potential to lower overall test specificity, however this could be overcome by raising the cut-off values for CXCL10 test positivity. Taken together, the results demonstrate that in particular settings, measurement of CXCL10 has the potential to complement the current use of IFN-γ in blood assays to maximise the detection of BTB.

Wild Animal Tuberculosis: Stakeholder Value Systems and Management of Disease

When human health is put at risk from the transmission of animal diseases, the options for intervention often require input from stakeholders whose differing values systems contribute to decisions on disease management. Animal tuberculosis (TB), caused principally by Mycobacterium bovis is an archetypical zoonotic pathogen in that it can be transmitted from animals to humans and vice versa. Although elimination of zoonotic transmission of TB to humans is frequently promoted as the raison d'être for TB management in livestock, in many countries the control strategies are more likely based on minimizing the impact of sustained infection on the agricultural industry. Where wild animals are implicated in the epidemiology of the disease, the options for control and eradication can require involvement of additional stakeholder groups. Conflict can arise when different monetary and/or societal values are assigned to the affected animals. This may impose practical and ethical dilemmas for decision makers where one or more species of wild animal is seen by some stakeholders to have a greater value than the affected livestock. Here we assess the role of stakeholder values in influencing TB eradication strategies in a number of countries including Ireland, the UK, the USA, Spain, France, Australia, New Zealand and South Africa. What it reveals is that the level of stakeholder involvement increases with the complexity of the epidemiology, and that similar groups of stakeholders may agree to a set of control and eradication measures in one region only to disagree with applying the same measures in another. The level of consensus depends on the considerations of the reservoir status of the infected host, the societal values assigned to each species, the type of interventions proposed, ethical issues raised by culling of sentient wild animals, and the economic cost benefit effectiveness of dealing with the problem in one or more species over a long time frame. While there is a societal benefit from controlling TB, the means to achieve this requires identification and long-term engagement with all key stakeholders in order to reach agreement on ethical frameworks that prioritize and justify control options, particularly where culling of wild animals is concerned.

Investigation into the genetic diversity in toll-like receptors 2 and 4 in the European badger Meles meles

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.

Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

Members of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity yet distinct host tropism. Notably, while Mycobacterium bovis is highly virulent and pathogenic for cattle, the human pathogen M. tuberculosis is attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strains M. bovis AF2122/97 and M. tuberculosis H37Rv at both the global transcriptional and the translational level via RNA-sequencing and SWATH MS. Furthermore, a bovine alveolar macrophage infection time course model was used to investigate the shared and divergent host transcriptomic response to infection with M. tuberculosis H37Rv or M. bovis AF2122/97. Significant differential expression of virulence-associated pathways between the two bacilli was revealed, including the ESX-1 secretion system. A divergent transcriptional response was observed between M. tuberculosis H37Rv and M. bovis AF2122/97 infection of bovine alveolar macrophages, in particular cytosolic DNA-sensing pathways at 48 h post-infection, and highlights a distinct engagement of M. bovis with the bovine innate immune system. The work presented here therefore provides a basis for the identification of host innate immune mechanisms subverted by virulent host-adapted mycobacteria to promote their survival during the early stages of infection.

Cross reactive immune responses in cattle arising from exposure to Mycobacterium bovis and non-tuberculous mycobacteria

Accurate diagnosis of tuberculosis in cattle may be compromised in areas where there are high rates of exposure to environmental/non-tuberculous mycobacteria (NTM). This cross reaction of immune responses to Mycobacterium bovis antigens shared with NTMs can result in reduced specificity of commonly used diagnostic tests including tuberculin skin tests and the interferon gamma assay (IFN-ɣ). In this study we assessed the cross-reactive immune responses of M. bovis (infected) and NTM exposed animals to M. bovis and M. avium tuberculin, the ESAT6/CFP10 cocktail antigen, tuberculin derived from cultures of selected NTMs, and a panel of recombinant mycobacterium tuberculosis complex (MTBC) antigens sharing homology with orthologues in NTM. Gamma interferon (IFN-ɣ) responses were measured in whole blood cultures using the IFN-ɣ assay and the IFN-ɣ elispot assay on purified peripheral blood mononuclear cells (PBMC). We observed the expected strong IFN-ɣ response to PPD-B in the M. bovis infected animals that distinguished this group from non-infected NTM exposed cattle. The IFN-ɣ responses to PPD-N (M. nonchromogenicum), were relatively high in both infected and non-infected NTM exposed cattle, but were not significantly different to classify the true infection status of each group. The results indicated that the cross-reactive responses to PPD-B and/or PPD-A with PPD-N, likely arose from prior exposure to environmental non-tuberculous mycobacteria. The IFN-ɣ immune responses to the 10 R-Mag measured by the IFN-ɣ elispot assay revealed that three of the selected antigens, Rv3615 (ESpC), Rv0287 (esxG) and the ESAT6/CFP10, were immunogenic in the infected cattle, and distinguished the infected cattle from the non-infected NTM exposed animals. The combined data of PPDs and R-Mags derived from NTM mycobacteria may prove useful in future development of novel bTB diagnostic tests.

Pathogenesis of Mycobacterium bovis Infection: the Badger Model As a Paradigm for Understanding Tuberculosis in Animals

Tuberculosis in animals is caused principally by infection with Mycobacterium bovis and the potential for transmission of infection to humans is often the fundamental driver for surveillance of disease in livestock and wild animals. However, with such a vast array of species susceptible to infection, it is often extremely difficult to gain a detailed understanding of the pathogenesis of infection--a key component of the epidemiology in all affected species. This is important because the development of disease control strategies in animals is determined chiefly by an understanding of the epidemiology of the disease. The most revealing data from which to formulate theories on pathogenesis are that observed in susceptible hosts infected by natural transmission. These data are gathered from detailed studies of the distribution of gross and histological lesions, and the presence and distribution of infection as determined by highly sensitive bacteriology procedures. The information can also be used to establish the baseline for evaluating experimental model systems. The European badger (Meles meles) is one of a very small number of wild animal hosts where detailed knowledge of the pathogenesis of M. bovis infection has been generated from observations in natural-infected animals. By drawing parallels from other animal species, an experimental badger infection model has also been established where infection of the lower respiratory tract mimics infection and the disease observed in natural-infected badgers. This has facilitated the development of diagnostic tests and testing of vaccines that have the potential to control the disease in badgers. In this review, we highlight the fundamental principles of how detailed knowledge of pathogenesis can be used to evaluate specific intervention strategies, and how the badger model may be a paradigm for understanding pathogenesis of tuberculosis in any affected wild animal species.

IL-10 suppression of IFN-γ responses in tuberculin-stimulated whole blood from Mycobacterium bovis infected cattle

The measurement of bovine interferon-gamma (IFN-γ) forms the basis of a diagnostic test for bovine tuberculosis where Mycobacterium bovis sensitised effector T cells produce IFN-γ following in vitro stimulation with tuberculin antigens. In cattle infected with M. bovis it is also known that the anti-inflammatory IL-10 cytokine can inhibit in vitro production of IFN-γ leading to a reduced response in the IFN-γ diagnostic test. In order to investigate this in greater detail, whole blood samples from tuberculin skin test positive and negative cattle were stimulated with bovine and avian tuberculin antigens and in parallel with a neutralising anti-IL-10 monoclonal antibody. The results showed that IFN-γ protein levels increased when IL-10 activity was suppressed by Anti - IL-10. By using a standard diagnostic interpretation, the elevated levels of IFN-γ were shown to change the level of agreement between the performance of the single intradermal comparative tuberculin test (SICTT) and IFN-γ assay, depending on the tuberculin treatment. A transcriptomic analysis using RT-qPCR investigated the influence of IL-10 activity on expression of a suite of cytokine genes (IFNG, IL12B, IL10 and CXCL10) associated with antigen-stimulated production of IFN-γ. The IFNG and IL12B genes both experienced significant increases in expression in the presence of Anti-IL-10, while the expression of IL10 and CXCL10 remained unaffected.

The performance of the interferon gamma assay when used as a diagnostic or quality assurance test in Mycobacterium bovis infected herds

There are two different contexts in the Irish bTB eradication programme in which the interferon-gamma assay (IFN-γ) is applied. Firstly, the IFN-γ assay is applied routinely to high risk cohorts in herds with four or more reactors to the SICTT. The IFN-γ test is then carried out on blood samples submitted to the laboratory within 8h of collection (diagnostic testing). Secondly, the use of the IFN-γ assay has recently been extended to test SICTT reactors as part of a general quality assurance (QA) scheme to monitor the performance of the SICTT. Blood samples from reactors are tested one day after blood collection (QA testing). In this study, we analysed the relative performance of the SICTT and IFN-γ when used in parallel as an 8h diagnostic test and as a 24h QA test on SICTT reactors. A total of 17,725 IFN-γ tests were included in the analysis (11,658 diagnostic tests and 6067 QA tests). Of the samples submitted for diagnostic testing, the proportion positive to IFN-γ decreased with the severity of interpretation of the SICTT result. Of the standard reactors that were tested with IFN-γ in the QA programme, 92.2% were positive to the IFN-γ test. Among animals that were SICTT -ve/IFN-γ +ve, 18.9% were positive at post-mortem compared to 11.8% of those that were SICTT +ve (standard reactor)/IFN-γ -ve. These results highlight the risk associated with retaining SICTT -ve/IFN-γ +ve animals, and suggest that prompt removal of these animals is necessary to reduce the potential for future transmission.

Antigen-Specific IP-10 Release Is a Sensitive Biomarker of Mycobacterium bovis Infection in Cattle

The most widely used ante-mortem diagnostic tests for tuberculosis in cattle are the tuberculin skin test and the interferon-gamma (IFN-γ) release assay, both of which measure cell-mediated immune responses to Mycobacterium bovis infection. However, limitations in the performance of these tests results in a failure to identify all infected animals. In attempting to increase the range of diagnostic tests for tuberculosis, measurement of the cytokine IP-10 in antigen-stimulated blood has previously been shown to improve the detection of M. tuberculosis and M. bovis infection, in humans and African buffaloes (Syncerus caffer), respectively. In the present study, 60 cattle were identified by the single intradermal comparative tuberculin test as tuberculosis reactors (n = 24) or non-reactors (n = 36) and the release of IFN-γ and IP-10 in antigen-stimulated whole blood from these animals was measured using bovine specific ELISAs. There was a strong correlation between IP-10 and IFN-γ production in these samples. Moreover, measurement of the differential release of IP-10 in response to stimulation with M. bovis purified protein derivative (PPD) and M. avium PPD distinguished between reactor and non-reactor cattle with a sensitivity of 100% (95% CI, 86%–100%) and a specificity of 97% (95% CI, 85%–100%). These results suggest that IP-10 might prove valuable as a diagnostic biomarker of M. bovis infection in cattle.

RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli

Mycobacterium bovis, the agent of bovine tuberculosis, causes an estimated $3 billion annual losses to global agriculture due, in part, to the limitations of current diagnostics. Development of next-generation diagnostics requires a greater understanding of the interaction between the pathogen and the bovine host. Therefore, to explore the early response of the alveolar macrophage to infection, we report the first application of RNA-sequencing to define, in exquisite detail, the transcriptomes of M. bovis-infected and non-infected alveolar macrophages from ten calves at 2, 6, 24 and 48 hours post-infection. Differentially expressed sense genes were detected at these time points that revealed enrichment of innate immune signalling functions, and transcriptional suppression of host defence mechanisms (e.g., lysosome maturation). We also detected differentially expressed natural antisense transcripts, which may play a role in subverting innate immune mechanisms following infection. Furthermore, we report differential expression of novel bovine genes, some of which have immune-related functions based on orthology with human proteins. This is the first in-depth transcriptomics investigation of the alveolar macrophage response to the early stages of M. bovis infection and reveals complex patterns of gene expression and regulation that underlie the immunomodulatory mechanisms used by M. bovis to evade host defence mechanisms.

Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq

Johne's disease, caused by infection with Mycobacterium avium subsp. paratuberculosis, (MAP), is a chronic intestinal disease of ruminants with serious economic consequences for cattle production in the United States and elsewhere. During infection, MAP bacilli are phagocytosed and subvert host macrophage processes, resulting in subclinical infections that can lead to immunopathology and dissemination of disease. Analysis of the host macrophage transcriptome during infection can therefore shed light on the molecular mechanisms and host-pathogen interplay associated with Johne's disease. Here, we describe results of an in vitro study of the bovine monocyte-derived macrophage (MDM) transcriptome response during MAP infection using RNA-seq. MDM were obtained from seven age- and sex-matched Holstein-Friesian cattle and were infected with MAP across a 6-h infection time course with non-infected controls. We observed 245 and 574 differentially expressed (DE) genes in MAP-infected versus non-infected control samples (adjusted P value ≤0.05) at 2 and 6 h post-infection, respectively. Functional analyses of these DE genes, including biological pathway enrichment, highlighted potential functional roles for genes that have not been previously described in the host response to infection with MAP bacilli. In addition, differential expression of pro- and anti-inflammatory cytokine genes, such as those associated with the IL-10 signaling pathway, and other immune-related genes that encode proteins involved in the bovine macrophage response to MAP infection emphasize the balance between protective host immunity and bacilli survival and proliferation. Systematic comparisons of RNA-seq gene expression results with Affymetrix(®) microarray data generated from the same experimental samples also demonstrated that RNA-seq represents a superior technology for studying host transcriptional responses to intracellular infection.

Discovery of a polyomavirus in European badgers (Meles meles) and the evolution of host range in the family Polyomaviridae

Polyomaviruses infect a diverse range of mammalian and avian hosts, and are associated with a variety of symptoms. However, it is unknown whether the viruses are found in all mammalian families and the evolutionary history of the polyomaviruses is still unclear. Here, we report the discovery of a novel polyomavirus in the European badger (Meles meles), which to our knowledge represents the first polyomavirus to be characterized in the family Mustelidae, and within a European carnivoran. Although the virus was discovered serendipitously in the supernatant of a cell culture inoculated with badger material, we subsequently confirmed its presence in wild badgers. The European badger polyomavirus was tentatively named Meles meles polyomavirus 1 (MmelPyV1). The genome is 5187 bp long and encodes proteins typical of polyomaviruses. Phylogenetic analyses including all known polyomavirus genomes consistently group MmelPyV1 with California sea lion polyomavirus 1 across all regions of the genome. Further evolutionary analyses revealed phylogenetic discordance amongst polyomavirus genome regions, possibly arising from evolutionary rate heterogeneity, and a complex association between polyomavirus phylogeny and host taxonomic groups.

The role of badgers in the epidemiology of Mycobacterium bovis infection (tuberculosis) in cattle in the United Kingdom and the Republic of Ireland: current perspectives on control strategies

Bovine tuberculosis (TB), caused by infection with Mycobacterium bovis, is a persistent problem in cattle herds in Ireland and the United Kingdom, resulting in hardship for affected farmers and substantial ongoing national exchequer expenditure. There is irrefutable scientific evidence that badgers are a reservoir of M. bovis infection and are implicated in the transmission of infection to cattle. A range of options for the control of TB in badgers is currently available or under development including culling of badgers, vaccination of badgers and cattle, and improved biosecurity to limit contact between the two species. It is unlikely that the eradication of TB from cattle will be achieved without the reservoir of M. bovis infection in badgers being controlled. The chances of success will, however, improve with greater knowledge of the disease in both species and an understanding of the epidemiological drivers of the transmission of infection between badgers and cattle.

Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis

Mycobacterium bovis is an intracellular pathogen that causes tuberculosis in cattle. Following infection, the pathogen resides and persists inside host macrophages by subverting host immune responses via a diverse range of mechanisms. Here, a high-density bovine microarray platform was used to examine the bovine monocyte-derived macrophage transcriptome response to M. bovis infection relative to infection with the attenuated vaccine strain, M. bovis Bacille Calmette-Guérin. Differentially expressed genes were identified (adjusted P-value ≤0.01) and interaction networks generated across an infection time course of 2, 6, and 24 h. The largest number of biological interactions was observed in the 24-h network, which exhibited scale-free network properties. The 24-h network featured a small number of key hub and bottleneck gene nodes, including IKBKE, MYC, NFKB1, and EGR1 that differentiated the macrophage response to virulent and attenuated M. bovis strains, possibly via the modulation of host cell death mechanisms. These hub and bottleneck genes represent possible targets for immuno-modulation of host macrophages by virulent mycobacterial species that enable their survival within a hostile environment.

RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis

Bovine tuberculosis, caused by infection with Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including gene expression microarrays and RNA-sequencing (RNA-seq), has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix^® GeneChip^® Bovine Genome Array platform from the same PBL-extracted RNA. A total of 3,250 differentially expressed (DE) annotated genes were detected in the M. bovis-infected samples relative to the controls (adjusted P-value ≤0.05), with the number of genes displaying decreased relative expression (1,671) exceeding those with increased relative expression (1,579). Ingenuity^® Systems Pathway Analysis (IPA) of all DE genes revealed enrichment for genes with immune function. Notably, transcriptional suppression was observed among several of the top-ranking canonical pathways including Leukocyte Extravasation Signaling. Comparative platform analysis demonstrated that RNA-seq detected a larger number of annotated DE genes (3,250) relative to the microarray (1,398), of which 917 genes were common to both technologies and displayed the same direction of expression. Finally, we show that RNA-seq had an increased dynamic range compared to the microarray for estimating differential gene expression.

Control strategies for wildlife tuberculosis in Ireland

The principal domestic maintenance host for Mycobacterium bovis is infected cattle. In countries where comprehensive surveillance schemes have been applied, tuberculosis rarely affects an animal to the extent that it presents with clinical disease. In the latter stages of an eradication campaign, the aim is to maintain the disease-free status of clear herds and eliminate foci of infection in herds as well as restricting movement of infected animals from these herds, other than to slaughter. However, the eradication of tuberculosis from cattle herds may be compromised if infected wildlife species, such as Eurasian badgers (Meles meles), share the same environment and contribute to transmission of infection. The options for dealing with tuberculosis in the wildlife reservoir hosts are limited to segregation of domestic animals from the wildlife, culling of the wildlife host or vaccination. Options are further limited by conservation and social reasons, particularly where culling is concerned. In Ireland and the UK, vaccination of badgers against M. bovis, if successfully employed, could directly facilitate the completion of bovine tuberculosis eradication. Programmes of research into vaccination of badgers are being undertaken in both countries, and there is clear evidence that vaccination induces protection. Vaccine trials in captive badgers have established that the M. bovis bacille Calmette-Guérin (BCG) vaccine can induce a protective response that limits the distribution and severity of tuberculosis disease following experimental challenge. In Ireland, a large-scale field trial of oral BCG vaccination is being conducted to measure the protection generated in wild badgers subjected to natural transmission of infection and to estimate vaccine efficacy. The results will provide a framework for the development and implementation of a national strategy to address the disease in badger populations and if successful will remove this major impediment to tuberculosis eradication from cattle.

Optimising and evaluating the characteristics of a multiple antigen ELISA for detection of Mycobacterium bovis infection in a badger vaccine field trial

A long-term research programme has been underway in Ireland to evaluate the usefulness of badger vaccination as part of the national bTB (bovine tuberculosis) control strategy. This culminated in a field trial which commenced in county Kilkenny in 2009 to determine the effects of badger vaccination on Mycobacterium bovis transmission in badgers under field conditions. In the present study, we sought to optimise the characteristics of a multiplex chemiluminescent assay for detection of M. bovis infection in live badgers. Our goal was to maximise specificity, and therefore statistical power, during evaluation of the badger vaccine trial data. In addition, we also aimed to explore the effects of vaccination on test characteristics. For the test optimisation, we ran a stepwise logistic regression with analytical weights on the converted Relative Light Units (RLU) obtained from testing blood samples from 215 badgers captured as part of culling operations by the national Department of Agriculture, Food and the Marine (DAFM). The optimised test was applied to two other datasets obtained from two captive badger studies (Study 1 and Study 2), and the sensitivity and specificity of the test was attained separately for vaccinated and non-vaccinated badgers. During optimisation, test sensitivity was maximised (30.77%), while retaining specificity at 99.99%. When the optimised test was then applied to the captive badger studies data, we observed that test characteristics did not vary greatly between vaccinated and non-vaccinated badgers. However, a different time lag between infection and a positive test result was observed in vaccinated and non-vaccinated badgers. We propose that the optimized multiplex immunoassay be used to analyse the vaccine trial data. In relation to the difference in the time lag observed for vaccinated and non-vaccinated badgers, we also present a strategy to enable the test to be used during trial evaluation.

Oral vaccination of badgers (Meles meles) against tuberculosis: comparison of the protection generated by BCG vaccine strains Pasteur and Danish

Vaccination of badgers by the subcutaneous, mucosal and oral routes with the Pasteur strain of Mycobacterium bovis bacille Calmette-Guérin (BCG) has resulted in significant protection against experimental infection with virulent M. bovis. However, as the BCG Danish strain is the only commercially licensed BCG vaccine for use in humans in the European Union it is the vaccine of choice for delivery to badger populations. As all oral vaccination studies in badgers were previously conducted using the BCG Pasteur strain, this study compared protection in badgers following oral vaccination with the Pasteur and the Danish strains. Groups of badgers were vaccinated orally with 10(8) colony forming units (CFU) BCG Danish 1331 (n = 7 badgers) or 10(8) CFU BCG Pasteur 1173P2 (n = 6). Another group (n = 8) served as non-vaccinated controls. At 12 weeks post-vaccination, the animals were challenged by the endobronchial route with 6 × 10(3) CFU M. bovis, and at 15 weeks post-infection, all of the badgers were euthanased. Vaccination with either BCG strain provided protection against challenge compared with controls. The vaccinated badgers had significantly fewer sites with gross pathology and significantly lower gross pathological severity scores, fewer sites with histological lesions and fewer sites of infection, significantly lower bacterial counts in the thoracic lymph node, and lower bacterial counts in the lungs than the control group. No differences were observed between either of the vaccine groups by any of the pathology and bacteriology measures. The ELISPOT analysis, measuring production of badger interferon - gamma (IFN-γ), was also similar across the vaccinated groups.

Identification of risk factors associated with disclosure of false positive bovine tuberculosis reactors using the gamma-interferon (IFNγ) assay

The gamma-interferon assay (IFNγ) is often used as an ancillary diagnostic test alongside the tuberculin skin test in order to detect Mycobacterium bovis infected cattle. The performance of the IFNγ test has been evaluated in many countries worldwide and wider usage as a disease surveillance tool is constrained due to the relatively low and inconsistent specificity at a herd and area level. This results in disclosure of a higher proportion of false positive reactors when compared with the skin test. In this study, we used cohorts of animals from low prevalence tuberculosis herds (n = 136) to assess a range of risk factors that might influence the specificity of the test. Univariate and multivariate logistic generalised estimating-equation (GEE) models were used to evaluate potential risk factors associated with a false positive IFNγ test result. In these herds, the univariate model revealed that the region of herd origin, the time of year when the testing was carried out, and the age of the animal were all significant risk factors. In the final multivariate models only animal age and region of herd origin were found to be significant risk factors. A high proportion of herds with multiple IFNγ false positive animals were located in one county, with evidence of within-herd clustering, suggesting a localised source of non-specific sensitization. Knowledge of the underlying factors influencing the IFNγ test specificity could be used to optimize the test performance in different disease level scenarios in order to reduce the disclosure rate of false positive reactors.

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

Background

Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). In addition, we compare gene expression profiles generated using RNA-seq with those previously generated by us using the high-density Affymetrix® GeneChip® Bovine Genome Array platform from the same MDM-extracted RNA.

Results

A mean of 7.2 million reads from each MDM sample mapped uniquely and unambiguously to single Bos taurus reference genome locations. Analysis of these mapped reads showed 2,584 genes (1,392 upregulated; 1,192 downregulated) and 757 putative natural antisense transcripts (558 upregulated; 119 downregulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). Of the differentially expressed genes, 694 were common to both the sense and antisense data sets, with the direction of expression (i.e. up- or downregulation) positively correlated for 693 genes and negatively correlated for the remaining gene. Gene ontology analysis of the differentially expressed genes revealed an enrichment of immune, apoptotic and cell signalling genes. Notably, the number of differentially expressed genes identified from RNA-seq sense strand analysis was greater than the number of differentially expressed genes detected from microarray analysis (2,584 genes versus 2,015 genes). Furthermore, our data reveal a greater dynamic range in the detection and quantification of gene transcripts for RNA-seq compared to microarray technology.

Conclusions

This study highlights the value of RNA-seq in identifying novel immunomodulatory mechanisms that underlie host-mycobacterial pathogen interactions during infection, including possible complex post-transcriptional regulation of host gene expression involving antisense RNA.

Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis

Mycobacterium avium subspecies paratuberculosis is the causative agent of Johne's disease, an intestinal disease of ruminants with major economic consequences. Infectious bacilli are phagocytosed by host macrophages upon exposure where they persist, resulting in lengthy subclinical phases of infection that can lead to immunopathology and disease dissemination. Consequently, analysis of the macrophage transcriptome in response to M. avium subsp. paratuberculosis infection can provide valuable insights into the molecular mechanisms that underlie Johne's disease. Here, we investigate pan-genomic gene expression in bovine monocyte-derived macrophages (MDM) purified from seven age-matched females, in response to in vitro infection with M. avium subsp. paratuberculosis (multiplicity of infection 2:1) at intervals of 2 hours, 6 hours and 24 hours post-infection (hpi). Differentially expressed genes were identified by comparing the transcriptomes of the infected MDM to the non-infected control MDM at each time point (adjusted P-value threshold ≤ 0.10). 1050 differentially expressed unique genes were identified 2 hpi, with 974 and 78 differentially expressed unique genes detected 6 and 24 hpi, respectively. Furthermore, in the infected MDM the number of upregulated genes exceeded the number of downregulated genes at each time point, with the fold-change in expression for the upregulated genes markedly higher than that for the downregulated genes. Inspection and systems biology analysis of the differentially expressed genes revealed an enrichment of genes involved in the inflammatory response, cell signalling pathways and apoptosis. The transcriptional changes associated with cellular signalling and the inflammatory response may reflect different immuno-modulatory mechanisms that underlie host-pathogen interactions during infection.

Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis

Background

Mycobacterium bovis, the causative agent of bovine tuberculosis, is a major cause of mortality in global cattle populations. Macrophages are among the first cell types to encounter M. bovis following exposure and the response elicited by these cells is pivotal in determining the outcome of infection. Here, a functional genomics approach was undertaken to investigate global gene expression profiles in bovine monocyte-derived macrophages (MDM) purified from seven age-matched non-related females, in response to in vitro challenge with M. bovis (multiplicity of infection 2∶1). Total cellular RNA was extracted from non-challenged control and M. bovis-challenged MDM for all animals at intervals of 2 hours, 6 hours and 24 hours post-challenge and prepared for global gene expression analysis using the Affymetrix® GeneChip® Bovine Genome Array.

Results

Comparison of M. bovis-challenged MDM gene expression profiles with those from the non-challenged MDM controls at each time point identified 3,064 differentially expressed genes 2 hours post-challenge, with 4,451 and 5,267 differentially expressed genes detected at the 6 hour and 24 hour time points, respectively (adjusted P-value threshold ≤0.05). Notably, the number of downregulated genes exceeded the number of upregulated genes in the M. bovis-challenged MDM across all time points; however, the fold-change in expression for the upregulated genes was markedly higher than that for the downregulated genes. Systems analysis revealed enrichment for genes involved in: (1) the inflammatory response; (2) cell signalling pathways, including Toll-like receptors and intracellular pathogen recognition receptors; and (3) apoptosis.

Conclusions

The increased number of downregulated genes is consistent with previous studies showing that M. bovis infection is associated with the repression of host gene expression. The results also support roles for MyD88-independent signalling and intracellular PRRs in mediating the host response to M. bovis.

Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes

BACKGROUND

Mycobacterium bovis is the causative agent of bovine tuberculosis (BTB), a pathological infection with significant economic impact. Recent studies have highlighted the role of functional genomics to better understand the molecular mechanisms governing the host immune response to M. bovis infection. Furthermore, these studies may enable the identification of novel transcriptional markers of BTB that can augment current diagnostic tests and surveillance programmes. In the present study, we have analysed the transcriptome of peripheral blood leukocytes (PBL) from eight M. bovis-infected and eight control non-infected age-matched and sex-matched Holstein-Friesian cattle using the Affymetrix® GeneChip® Bovine Genome Array with 24,072 gene probe sets representing more than 23,000 gene transcripts.

RESULTS

Control and infected animals had similar mean white blood cell counts. However, the mean number of lymphocytes was significantly increased in the infected group relative to the control group (P = 0.001), while the mean number of monocytes was significantly decreased in the BTB group (P = 0.002). Hierarchical clustering analysis using gene expression data from all 5,388 detectable mRNA transcripts unambiguously partitioned the animals according to their disease status. In total, 2,960 gene transcripts were differentially expressed (DE) between the infected and control animal groups (adjusted P-value threshold ≤ 0.05); with the number of gene transcripts showing decreased relative expression (1,563) exceeding those displaying increased relative expression (1,397). Systems analysis using the Ingenuity® Systems Pathway Analysis (IPA) Knowledge Base revealed an over-representation of DE genes involved in the immune response functional category. More specifically, 64.5% of genes in the affects immune response subcategory displayed decreased relative expression levels in the infected animals compared to the control group.

CONCLUSIONS

This study demonstrates that genome-wide transcriptional profiling of PBL can distinguish active M. bovis-infected animals from control non-infected animals. Furthermore, the results obtained support previous investigations demonstrating that mycobacterial infection is associated with host transcriptional suppression. These data support the use of transcriptomic technologies to enable the identification of robust, reliable transcriptional markers of active M. bovis infection.

Impact of delayed processing of bovine peripheral blood on differential gene expression

RT-qPCR can be used to accurately determine expression levels of genes following RNA extraction from tissue samples. If blood is the source of total RNA, it is often desirable to process the samples immediately following collection because delays in processing for RNA extraction may influence mRNA expression estimates obtained from RT-qPCR analyses. However, this may not be feasible if the site of blood collection is distant from the processing laboratory. In the present study, the effects of delays in the processing of blood samples on mRNA expression data was investigated using a panel of 23 functionally diverse genes from five different gene ontology (GO) categories in peripheral blood sampled from ten age-matched healthy cattle. Venous blood was collected in Tempus™ Blood RNA tubes, which contain reagents that lyse blood cells immediately and stabilise the RNA signature (T(0)). Blood was also collected in conventional lithium heparin collection tubes, and stored at ambient temperature for T(4), T(6) and T(8)h, prior to total RNA extraction. The mRNA expression profiles of these 23 genes were determined by RT-qPCR and compared across the time course. Thirteen genes showed significant up- or down-fold changes in mRNA expression over the 8h time course. Among the GO categories, genes in the Immune response category showed the most differential expression. These results also demonstrated that the changes in mRNA expression for the IFNG gene, which encodes the cytokine IFN-γ, did not correspond to IFN-γ protein levels estimated using ELISA.

Application of the Enfer chemiluminescent multiplex ELISA system for the detection of Mycobacterium bovis infection in goats

A study was conducted to optimise a multiplex serological immunoassay for use in identification of goats infected with Mycobacterium bovis. To assess assay specificity, 31 goats with a history of being free from M. bovis infection were used. To determine assay sensitivity, 180 Single Intradermal Comparative Tuberculin test (SICTT) positive goats were recruited. Additionally, 286 SICTT negative goats classed as potentially exposed animals present in the same positive herds were also included in the study. The results of the assay demonstrated a specificity of 100%. The multiplex assay detected 57/60 SICTT (95.0%) positive animals in one M. bovis infected herd and 120/120 (100%) in a second herd. In a separate experiment, 28 M. caprae culture confirmed infected goats from Spain were assayed, of which 24 (85.7%) were found positive in the test. The results show that inclusion of an antibody based assay can improve the ability to identify M. bovis and M. caprae infected goats. With further development and validation the multiplex assay may prove to be a useful tool for control of M. bovis and M. caprae infection in goats.

Tuberculosis in cattle herds are sentinels for Mycobacterium bovis infection in European badgers (Meles meles): the Irish Greenfield Study

In Ireland badgers are removed in response to tuberculosis (TB) breakdowns in cattle herds (focal culling). Prevalence studies, conducted using a detailed post mortem and bacteriological examination, showed that 36-50% of badgers were infected with Mycobacterium bovis. Focal culling forms part of the medium term national strategy for the control of bovine TB in cattle and is based on the premise that badgers in areas with herd breakdowns have a higher prevalence of infection than the badger population at large. However, the hypothesis that cattle can be used as sentinels for infection in the badger population has never been formally tested. In this study we tested the hypothesis by determining the infection prevalence in badgers in areas where there had been historically, a consistently low prevalence of infection in cattle. Low cattle TB prevalence areas were defined as those herds with ≤ 2 standard reactors in the annual round of skin testing over the preceding 5 years (Greenfield sites). Using GIS, and adjusting for variation in land use, previous culling and cattle density, 198 Greenfield sites were identified and surveyed, and 138 areas with badger setts or signs of badger activity were identified. A single badger was removed from 87 sites and all were examined using detailed post mortem and bacteriological procedures. A prevalence of M. bovis infection of 14.9% was found in the Greenfield site badgers. This prevalence was significantly lower (P<0.001) than in badgers removed during focal culling (36.6%). The results validate the use of cattle as sentinels for TB in badgers and support the medium term national strategy for the control of bovine TB. The geographic variation in M. bovis infection prevalence in the Irish badger populations will be used when devising strategies for the incorporation of badger vaccination into the long term bovine TB control programme.

Bovine tuberculosis in Europe from the perspective of an officially tuberculosis free country: trade, surveillance and diagnostics

Switzerland has been officially free of bovine tuberculosis (OTF) since 1960. Since 1980 the control of bovine tuberculosis (bTB) has been reduced to passive abattoir surveillance. Isolated cases of bTB, partly due to reactivation of human Mycobacterium bovis infections with subsequent transmission to cattle, have been noticed in the last years. In Europe, the overall prevalence of bTB is slightly increasing. Both OTF and non-OTF countries report increases in the proportion of bTB positive cattle herds. Current bTB eradication and control programs in Europe are facing a range of challenges. Whole herd depopulation is becoming a less attractive option for economic reasons and due to animal welfare concerns. Live animal trade is increasing both at national and international levels. Regarding these tendencies and taking into account the chronicity of bTB infection, pre-movement testing is becoming increasingly important as a central tool for eradication and for protection against re-introduction of bTB. Pre-movement testing, however specifically focuses on the infection status in individuals, requiring a high level of diagnostic accuracy to correctly diagnose infected animals. Current screening tests for bTB, however, have been designed to meet demands as herd tests. This illustrates that the modification of existing and/or the development of new diagnostics for bTB might be needed. The tuberculin skin test (TST), the primary screening test for bTB may in certain situations have low sensitivity. The interferon gamma (IFN-γ) assay is accepted to be more sensitive compared to TST. Reduced specificity, however, especially in areas of low bTB prevalence raises concerns. New antigen combinations including Rv3615c, OmpATb and others have been shown to complement ESAT-6 and CFP-10 in the whole blood IFN-γ assay and resulted in improved sensitivity (compared to ESAT-6 and CFP-10) and specificity (compared to tuberculins). Lesion detection after slaughter represents a cost-effective procedure for passive surveillance of bTB, especially in areas of low prevalence or in regions free of bTB; however, its sensitivity is very low. This illustrates that trade is linked with a certain risk to re-introduce bTB in OTF regions or countries and that there may be delays in detecting a re-introduction of bTB. In conclusion, regarding the fact that some parameters linked with bTB programs are changing, the development of improved diagnostic tests with a high reliability for use as individual animal tests will be important for future eradication of bTB, in line with international commitment to high standard animal health programs.

Mycobacterium bovis infection in the Eurasian badger (Meles meles): the disease, pathogenesis, epidemiology and control

Eurasian badgers (Meles meles) are an important wildlife reservoir of tuberculosis (Mycobacterium bovis) infection in Ireland and the United Kingdom. As part of national programmes to control tuberculosis in livestock, considerable effort has been devoted to studying the disease in badgers and this has lead to a rapid increase in our knowledge of tuberculosis in this host. Tuberculosis in badgers is a chronic infection and in a naturally-infected population the severity of disease can vary widely, from latent infection (infection without clinical signs and no visible lesions) to severe disease with generalized pathology. The high prevalence of pulmonary infection strongly supports the lungs as the principal site of primary infection and that inhalation of infectious aerosol particles is the principal mode of transmission. However, other routes, including transmission via infected bite wounds, are known to occur. The ante-mortem diagnosis of infection is difficult to achieve, as clinical examination and immunological and bacteriological examination of clinical samples are insensitive diagnostic procedures. Because infection in the majority of badgers is latent, the gross post-mortem diagnosis is also insensitive. A definitive diagnosis can only be made by the isolation of M. bovis. However, to gain a high level of sensitivity in the bacteriological examination, a large number of tissues from each badger must be cultured and sensitive culture methods employed. The transmission and maintenance of M. bovis in badger populations are complex processes where many factors influence within-population prevalence and rates of transmission. Badger social structures and the longevity of infected animals make them an ideal maintenance host for M. bovis infection. Badgers are directly implicated in the transmission of infection to cattle and the inability to eradicate the disease from cattle is, in part, a consequence of the interactions between the two species. A detailed understanding and knowledge of the epidemiology and pathogenesis of the disease are recognized as fundamental for devising new strategies to control infection with a view to limiting interspecies transmission. Vaccination, in spite of formidable challenges, is seen as the best long-term strategy option and studies with captive badgers have shown that vaccination with M. bovis bacillus Calmette-Guérin (BCG) induces protection when delivered by a variety of routes. Continued research is required to develop effective technologies to control the disease both in badgers and cattle. A combination of strategies, which employ the optimal use and targeting of resources, is likely to make a significant contribution towards eradication of the disease.