The Herd-Level Sensitivity of Abattoir Surveillance for Bovine Tuberculosis: Simulating the Effects of Current and Potentially Modified Meat Inspection Procedures in Irish Cattle

Estimated Prevalence of Tuberculosis in Ruminants from Slaughterhouses in Constantine Province (Northeastern Algeria): A 10-Year Retrospective Survey (2011–2020)

Tuberculosis (TB) is considered one of the most widespread and devastating zoonotic diseases in low-income countries, with a cosmopolitan distribution. The aim of this 10-year retrospective survey (from 2011 to 2020) was to determine the frequency of bovine, ovine, and goat tuberculosis in different local slaughterhouses across Constantine Province, Algeria. The control of livestock carcasses was systematically performed by veterinarian inspectors, after each stage of the slaughter process. The routine abattoir inspection included the detection of visible abnormalities on different organs and lymph nodes. The overall prevalence of tuberculosis recorded in slaughtered animals was 0.83%, with the following distribution among species: 2.73% in cattle, 0.001% in sheep, and 0.0% in goats. During the study period, there was a strong correlation (R = 0.82) (p < 0.01) between tuberculosis occurrence and the number of slaughtered cattle. Fluctuations in monthly TB prevalence ranged from 2% to 24.8% between 2018 and 2020, although there were no statistically significant correlations between infection and the age or gender of the animals, except for the year 2020 when a significantly higher (p = 0.017) percentage of TB cases were recorded in female cattle compared to male cattle. The average monthly weight of the confiscated livers and lungs ranged significantly (p ≤ 0.05) from 150 kg to 350 kg. The study results provide baseline data regarding livestock tuberculosis monitoring in the area of Constantine, Algeria, indicating that the disease incidence is not highly alarming, yet remains a serious public and animal health issue in the screened region.

Accuracy of Tests for Diagnosis of Animal Tuberculosis: Moving Away from the Golden Calf (and towards Bayesian Models)

The last decades have seen major efforts to develop new and improved tools to maximize our ability to detect tuberculosis-infected animals and advance towards the objective of disease control and ultimately eradication. Nevertheless, there is still uncertainty regarding test performance due to the wide range of specificity and especially sensitivity estimates published in the scientific literature. Here, we performed a systematic review of the literature on studies that evaluated the performance of tuberculosis diagnostic tests used in animals through Bayesian Latent Class Models (BLCMs), which do not require the application of a (fallible) reference procedure to classify animals as infected with tuberculosis or not. BLCM-based sensitivity and specificity estimates deviated from those obtained using a reference procedure for certain antemortem tests: an overall lower sensitivity of skin tests and serology and a higher sensitivity of interferon-gamma (IFN-γ) assays was reported. In the case of postmortem diagnostic tests, sensitivity estimates from BLCMs were similar to estimates from studies based on other methodologies. For specificity, the range of BLCM-based estimates was narrower than those based on a reference test, reaching values close to 100% (but lower in the case of IFN-γ assays). In conclusion, Bayesian methods have been increasingly applied for the evaluation of tuberculosis diagnostic tests in animals, yielding results that differ (sometimes substantially) from previously reported test performance in the literature, particularly for in vivo tests and sensitivity estimates. Newly developed models that allow adjustment for relevant factors (e.g., age, breed, region, and herd size) can contribute to the generation of more unbiased estimates of test performance. Nevertheless, although BLCMs for tuberculosis do not require the use of an imperfect reference procedure and are therefore not influenced by its limited performance, they require careful implementation, and transparent systematic reporting should be the norm.

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.

Use of Slaughterhouses as Sentinel Points for Genomic Surveillance of Foot-and-Mouth Disease Virus in Southern Vietnam

The genetic diversity of foot-and-mouth disease virus (FMDV) poses a challenge to the successful control of the disease, and it is important to identify the emergence of different strains in endemic settings. The objective of this study was to evaluate the sampling of clinically healthy livestock at slaughterhouses as a strategy for genomic FMDV surveillance. Serum samples (n = 11,875) and oropharyngeal fluid (OPF) samples (n = 5045) were collected from clinically healthy cattle and buffalo on farms in eight provinces in southern and northern Vietnam (2015-2019) to characterize viral diversity. Outbreak sequences were collected between 2009 and 2019. In two slaughterhouses in southern Vietnam, 1200 serum and OPF samples were collected from clinically healthy cattle and buffalo (2017 to 2019) as a pilot study on the use of slaughterhouses as sentinel points in surveillance. FMDV VP1 sequences were analyzed using discriminant principal component analysis and time-scaled phylodynamic trees. Six of seven serotype-O and -A clusters circulating in southern Vietnam between 2017-2019 were detected at least once in slaughterhouses, sometimes pre-dating outbreak sequences associated with the same cluster by 4-6 months. Routine sampling at slaughterhouses may provide a timely and efficient strategy for genomic surveillance to identify circulating and emerging FMDV strains.

Abattoir survey of bovine tuberculosis in tanta, centre of the Nile delta, with in silico analysis of gene mutations and protein-protein interactions of the involved mycobacteria

Bovine tuberculosis is a transboundary disease of high economic and public health burden worldwide. In this study, post-mortem examination of 750 cattle and buffalo in Tanta abattoir, Centre of the Nile Delta, revealed visible TB in 4% of animals and a true prevalence of 6.85% (95% CI: 5.3%-8.9%). Mycobacterial culture, histopathology and RT-PCR targeting all members of M. tuberculosis complex were performed, upon which 85%, 80% and 100% of each tested lesions were confirmed as TB, respectively. Mpb70-targeting PCR was conducted on ten RT-PCR positive samples for sequencing and identified nine Mycobacterium (M.) bovis strains and, interestingly, one M. tuberculosis (Mtb) strain from a buffalo. Bioinformatics tools were used for prediction of mutations, nucleotide polymorphisms, lineages, drug resistance and protein-protein interactions (PPI) of the sequenced strains. The Mtb strain was resistant to rifampicin, isoniazid and streptomycin, and to the best of our knowledge, this is the first report of multidrug resistant (MDR)-Mtb originating from buffaloes. Seven M. bovis strains were resistant to ethambutol and ethionamide. Such resistances were associated with KatG, rpoB, rpsL, embB and ethA genes mutations. Other mutations and nucleotide polymorphisms were also predicted, some are reported for the first time and require experimental work for validation. PPI revealed more interactions than what would be expected for a random set of proteins of similar size and had dense interactions between nodes that are biologically connected, as a group. Two M. bovis strains belonged to BOV AFRI lineage (Spoligotypes BOV 1; BOV 2) and eight strains belonged to East-Asian (Beijing) lineage. In conclusion, visible TB was prevalent in the study area, RT-PCR is the best to confirm the disease, MDR-Mtb is associated with buffalo TB, and mycobacteria of different lineages carry many resistance genes to chemotherapeutic agents used in treatment of human TB constituting a major public health risk.

Use of Network Analysis and Spread Models to Target Control Actions for Bovine Tuberculosis in a State from Brazil

Livestock movements create complex dynamic interactions among premises that can be represented, interpreted, and used for epidemiological purposes. These movements are a very important part of the production chain but may also contribute to the spread of infectious diseases through the transfer of infected animals over large distances. Social network analysis (SNA) can be used to characterize cattle trade patterns and to identify highly connected premises that may act as hubs in the movement network, which could be subjected to targeted control measures in order to reduce the transmission of communicable diseases such as bovine tuberculosis (TB). Here, we analyzed data on cattle movement and slaughterhouse surveillance for detection of TB-like lesions (TLL) over the 2016-2018 period in the state of Rio Grande do Sul (RS) in Brazil with the following aims: (i) to characterize cattle trade describing the static full, yearly, and monthly snapshots of the network contact trade, (ii) to identify clusters in the space and contact networks of premises from which animals with TLL originated, and (iii) to evaluate the potential of targeted control actions to decrease TB spread in the cattle population of RS using a stochastic metapopulation disease transmission model that simulated within-farm and between-farm disease spread. We found heterogeneous densities of premises and animals in the study area. The analysis of the contact network revealed a highly connected (~94%) trade network, with strong temporal trends, especially for May and November. The TLL cases were significantly clustered in space and in the contact network, suggesting the potential for both local (e.g., fence-to-fence) and movement-mediated TB transmission. According to the disease spread model, removing the top 7% connected farms based on degree and betweenness could reduce the total number of infected farms over three years by >50%. In conclusion, the characterization of the cattle network suggests that highly connected farms may play a role in TB dissemination, although being close to infected farms was also identified as a risk factor for having animals with TLL. Surveillance and control actions based on degree and betweenness could be useful to break the transmission cycle between premises in RS.

Development and Application of a Prioritization Tool for Animal Health Surveillance Activities in Ireland

Decisions around animal health management by stakeholders are often subject to resource limitation, therefore prioritization processes are required to evaluate whether effort is attributed appropriately. The objectives of this study were to develop and apply a surveillance prioritization process for animal health surveillance activities in Ireland. An exploratory sequential mixed research methods design was utilized. A prioritization tool was developed for surveillance activities and implemented over two phases. During the first phase, a survey was conducted which asked stakeholders to prioritize diseases/conditions by importance for Irish agriculture. In the second phase, experts identified the most important surveillance objectives, and allocated resources to the activities that they considered would best meet the surveillance objectives, for each disease/condition. This study developed a process and an accompanying user-friendly practical tool for animal disease surveillance prioritization which could be utilized by other competent authorities/governments. Antimicrobial resistance and bovine tuberculosis were ranked top of the endemic diseases/conditions in the Irish context, while African swine fever and foot and mouth disease were ranked top of the exotic diseases/conditions by the stakeholders. The study showed that for most of the diseases/conditions examined in the prioritization exercise, the respondents indicated a preference for a combination of active and passive surveillance activities. Future extensions of the tool could include prioritization on a per species basis.

Implementation of Visual-Only Swine Inspection in the European Union: Challenges, Opportunities, and Lessons Learned

ABSTRACT

Consumption of contaminated meat and poultry products is a major source of foodborne illness in the United States and globally. Meat inspection procedures, established more than 100 years ago to detect prevailing food safety issues of the time and largely harmonized around the world, do not effectively detect modern hazards and may inadvertently increase food safety risks by spreading contamination across carcasses. Visual-only inspection (VOI) is a significantly different, modernized meat inspection system that is data driven and minimizes physical manipulation of the carcass during inspection. It was developed based on scientific evidence and risk assessment and aims to better control current food safety hazards. In 2014, the European Union (EU) became the first supranational government in the world to require VOI for all swine herds slaughtered in member states that met certain epidemiologic and animal rearing conditions. Here, we review the implementation of this new inspection system with the goal of informing similar modernization efforts in other countries and for other commodities beyond pork. This article reports the results of a literature review and interviews conducted with nine experts in 2018 on the implementation of the EU's 2014 VOI regulation. Challenges, opportunities, and lessons learned about the implementation of the regulation are described for audiences interested in adapting inspection procedures to prevent and detect modern food safety hazards. Overall, implementation of VOI varies within and across member states, and among slaughterhouses of different sizes. This variation is due to disease risk patterns, supply chain conditions, and trade barriers. Before transitioning to a similar risk-based meat inspection system, other countries should consider the following: science-based research agendas to identify what food chain information best predicts herd health and foodborne hazards, regulatory system design that accurately reflects local hazards, and development of targeted VOI educational materials.

HIGHLIGHTS

Post-mortem surveillance of bovine tuberculosis in Ireland: herd-level variation in the probability of herds disclosed with lesions at routine slaughter to have skin test reactors at follow-up test

Post-mortem surveillance in Ireland discloses skin-test negative cattle with presumptive evidence of infection of Mycobacterium bovis (lesions at routine slaughter (LRS)), the causative agent of bovine tuberculosis (bTB). Laboratory confirmation of lesions has impacts on trade restrictions for herds, therefore if laboratory capacity was diminished, how herds are treated would require an informed risk policy. Here we report the proportion of herds with subsequent evidence of within-herd transmission, based on skin-test results. We assess how herd-size, herd-type, and bTB-history affect the probability of additional reactors at follow-up test using univariable and multivariable random-effects models. The study represents a rapid response to developing an evidential base for policy demands during an extraordinary event, the COVID-19 epidemic in Ireland. A dataset from 2005 to 2019 of breakdowns were collated. Overall, 20,116 breakdowns were initiated by LRS cases. During the index tests of these breakdowns, 3931 revealed ≥1 skin-test reactor animals (19.54%; ≥1 standard reactors: 3827; 19.02%). Increasing herd-size was associated with reactor disclosure on follow-up. For small herds (<33 animals), 11.74% of follow-up tests disclosed ≥1 reactor; 24.63% of follow-up tests from very large herds (>137) disclosed ≥1 reactors. Beef (13.87%) and “other” (13%) herd production types had lower proportion of index tests with reactors in comparison with dairy (28.27%) or suckler (20.48%) herds. Historic breakdown size during the previous 3-years was associated reactor disclosure risk on follow-up. Our results are useful for rapid tailored policy development aimed at identifying higher risk herds.

Assessment of the sensitivity of the bovine tuberculosis eradication program in a high prevalence region of Spain using scenario tree modeling

In spite of the efforts invested to eradicate bovine tuberculosis (bTB) in cattle, the disease is still present in several developed countries, including Spain. Among the factors related with disease persistence in high prevalence areas, the lack of sensitivity of the screening test for detection of infected herds [single intradermal tuberculin (SIT) test] can play a major role. Here, a scenario tree model mimicking the diagnostic test scheme in place in the region of Castilla y Leon (Spain) was developed to estimate the probability of detecting bTB in an infected-non detected officially tuberculosis free (OTF) herd (herd sensitivity, HSe). In order to do so the probability of detecting at least one positive animal in the SIT test with/without post-mortem (detection of lesions and culture) confirmation in an infected herd was estimated using Monte Carlo simulation through @RISK (Palisade Co, NY, USA). Uncertainty on the accuracy of the diagnostic tests was introduced in the model using distributions based on the literature. The performance of the model was evaluated by comparing the predicted number of SIT/post-mortem positive animals in infected herds with those observed in newly detected bTB-infected herds in the region in 2011-2015. The estimated HSe of the SIT test was 76.2% (95% probability interval: 19.8-97.6). According to the model, bTB infection would be then confirmed through culture in 65.3% (95% PI: 50.0-82.3) of the herds detected through the SIT test, so that overall the proportion of infected-non detected OTF herds in which the infection could be confirmed after the initial SIT test was 49.6% (95% PI: 9.75-80.3). The predicted HSe of both SIT test and culture was directly correlated with herd size. Results from the model suggest a moderate but highly variable HSe of the current surveillance system in place for bTB detection in OTF herds located in high prevalence areas, that could be maximized by performing multiple tests within a year as indicated in the Spanish eradication program (with a median SIT HSe of 87% when two consecutive tests were considered). In addition, these results highlight the usefulness of performing subsequent SIT tests to rule out infection in SIT-positive herds even when the causative agent cannot be isolated.

Assessment of the bovine tuberculosis elimination protocol in the United States

In this study, we analyzed the performance of the USDA's bovine tuberculosis (bTB) elimination protocol in a 1,000-cow closed dairy herd using an agent-based simulation model under different levels of initial bTB infection. We followed the bTB test sensitivity and specificity values used by the USDA in its model assessment. We estimated the net present value over a 20-yr horizon for a bTB-free milking herd and for bTB-infected herds following the USDA protocol. We estimated the expected time to identify the infection in the herd once it is introduced, its elimination time, the reproductive number (R₀), and effective reproduction number (R_e) under the USDA protocol. The optimal number of consecutive negative whole-herd tests (WHT) needed to declare a herd bTB-free with a 95% confidence under different bTB prevalence levels was derived. Our results support the minimum number of consecutive negative WHT required by the USDA protocol to declare a herd bTB-free; however, the number of consecutive negative WHT needed to eliminate bTB in a herd depends on the sensitivity and specificity of the tests. The robustness of the protocol was analyzed under conservative bTB test parameters from the literature. The cost of implementing the USDA protocol when 1 infected heifer is introduced in a 1,000-cow dairy herd is about $1,523,161. The average time until detection and the time required to eliminate bTB-infected animals from the herd, after 1 occult animal is introduced in the herd, were 735 and 119 d, respectively.

Further description of bovine tuberculosis trends in the United Kingdom and the Republic of Ireland, 2003-2015

Extending on earlier work, trends in bovine tuberculosis (bTB) from 2003 to 2015 are described for the countries of the UK and the Republic of Ireland using standardised definitions and measures. Based on measures of animal and herd incidence, there remains a stable situation of extremely low prevalence in Scotland and the Low Risk Area of England, and a higher but ongoing reduction in prevalence in the Republic of Ireland. In Northern Ireland, there has been a rising bTB trend during 2010–2015, although not to levels experienced during 2002–2004. In the High Risk Area and Edge Area of England during 2010–2015, the rising bTB trends have continued but with some recent evidence of stabilisation. In Wales, prevalence has fallen subsequent to a peak in 2008. The paper considers country-level differences in the light of key policy changes, which are presented in detail. This work is unique, and will assist policymakers when critically evaluating policy options for effective control and eradication. Ongoing updates of this analysis would be useful, providing an evidence base for country-level comparison of bTB trends into the future. The use of multivariable analytical methods should be considered, but will rely on substantial sharing of raw data across the five countries.

Further improvement in the control of bovine tuberculosis recurrence in Ireland

Ongoing objective assessment of national bovine tuberculosis (bTB) policy in Ireland is important to monitor efforts towards improved bTB control. The study objective was to investigate temporal trends in the risk of herd recurrence. The study included all herds derestricted following a bTB episode ending in 1998, 2008 or 2012. The respective ‘study periods’ were up to the end of 2001 for 1998-derestricted herds, to the end of 2011 for 2008-derestricted herds, and to the end of 2015 for 2012-derestricted herds. A multivariable Cox proportional-hazard model was developed to examine time to next restriction. The results from the model showed a continuing significant decreasing trend in herd recurrence of bTB in Ireland from 1998 until 2015: herds derestricted in 2008 were 0.75 (95 per cent CI 0.68 to 0.82) times as likely to develop a further restriction compared with 1998 herds, and herds derestricted in 2012 were 0.85 (95per cent CI 0.76 to 0.95) times as likely as 2008 herds. However, despite significant improvements, recurrence of bTB remains a concern, with 30.2 per cent (95 per cent CI 28.0 to 32.4 per cent) of herds derestricted in 2012 being re-restricted over the subsequent three years. Further work is needed to address the two key drivers of herd recurrence, namely residual infection and local reinfection.