Mycobacterium bovis in California dairies: a case series of 2002-2013 outbreaks

Selective sweep sites and SNP dense regions differentiate Mycobacterium bovis isolates across scales

Mycobacterium bovis, a bacterial zoonotic pathogen responsible for the economically and agriculturally important livestock disease bovine tuberculosis (bTB), infects a broad mammalian host range worldwide. This characteristic has led to bidirectional transmission events between livestock and wildlife species as well as the formation of wildlife reservoirs, impacting the success of bTB control measures. Next Generation Sequencing (NGS) has transformed our ability to understand disease transmission events by tracking variant sites, however the genomic signatures related to host adaptation following spillover, alongside the role of other genomic factors in the M. bovis transmission process are understudied problems. We analyzed publicly available M. bovis datasets collected from 700 hosts across three countries with bTB endemic regions (United Kingdom, United States, and New Zealand) to investigate if genomic regions with high SNP density and/or selective sweep sites play a role in Mycobacterium bovis adaptation to new environments (e.g., at the host-species, geographical, and/or sub-population levels). A simulated M. bovis alignment was created to generate null distributions for defining genomic regions with high SNP counts and regions with selective sweeps evidence. Random Forest (RF) models were used to investigate evolutionary metrics within the genomic regions of interest to determine which genomic processes were the best for classifying M. bovis across ecological scales. We identified in the M. bovis genomes 14 and 132 high SNP density and selective sweep regions, respectively. Selective sweep regions were ranked as the most important in classifying M. bovis across the different scales in all RF models. SNP dense regions were found to have high importance in the badger and cattle specific RF models in classifying badger derived isolates from livestock derived ones. Additionally, the genes detected within these genomic regions harbor various pathogenic functions such as virulence and immunogenicity, membrane structure, host survival, and mycobactin production. The results of this study demonstrate how comparative genomics alongside machine learning approaches are useful to investigate further the nature of M. bovis host-pathogen interactions.

Association of Exposure to Cattle with Self-Reported History of TB Among Dairy Workers

BACKGROUND

Mycobacterium bovis (bTB) is a potential health hazard to dairy workers. This study uses the One Health wholistic framework for examining bovine tuberculosis (TB) and its relationship to human health. This approach can help bridge surveillance data gaps and contribute to disease control and prevention programs for dairy farm workers, cattle, and the environment. The primary objective of this study was to compare the self-reported history of TB among dairy workers in Bailey County, Texas, with occupational categories of risk and exposure to TB.

METHODS

A cross-sectional study was conducted among dairy workers. Job positions were used as a proxy for exposure to cattle-high and medium/low. We employed bivariate analyses to examine differences between groups using both the chi-square test and the nonparametric Kruskal-Wallis test.

RESULTS

Of the 293 dairy workers invited, 77.0% (n = 225) participated. No statistically significant associations were found between job categories and reported history of TB exposure. Workers in the high group were younger, Guatemalan males with lower levels of formal education, more likely to be single with no children, and cohabitating with coworkers compared with the medium/low group.

CONCLUSION/APPLICATION TO PRACTICE

Self-reported TB history among dairy workers is an imprecise measure of being previously diagnosed with TB. Dairy workers at risk for occupationally acquired TB could be tested for TB before employment and tested periodically thereafter, and more expeditiously treated if a positive test is obtained. Future studies should focus on the feasibility of offering on-farm health services, such as TB screening.

Zoonotic Tuberculosis in Humans: Control, Surveillance, and the One Health Approach

Zoonotic tuberculosis is a reemerging infectious disease in high-income countries and a neglected one in low- and middle-income countries. Despite major advances in its control as a result of milk pasteurization, its global burden is unknown, especially due the lack of surveillance data. Additionally, very little is known about control strategies. The purpose of this review was to contextualize the current knowledge about the epidemiology of zoonotic tuberculosis and to describe the available evidence regarding surveillance and control strategies in high-, middle-, and low-income countries. We conducted this review enriched by a One Health perspective, encompassing its inherent multifaceted characteristics. We found that the burden of zoonotic tuberculosis is likely to be underreported worldwide, with higher incidence in low-income countries, where the surveillance systems are even more fragile. Together with the lack of specific political commitment, surveillance data is affected by lack of a case definition and limitations of diagnostic methods. Control measures were dependent on risk factors and varied greatly between countries. This review supports the claim that a One Health approach is the most valuable concept to build capable surveillance systems, resulting in effective control measures. The disease characteristics and suggestions to implement surveillance and control programs are discussed.

Tuberculosis Prevalence Among US Crop-Workers, 2000 to 2012: Trends and Contributing Factors

OBJECTIVE

We intend to study tuberculosis (TB) in one of the poorest communities in the US, hired agriculture workers, for most recent years (2000 to 2012) including the last recession period.

METHODS

Time-chart, simple mean differences, and logistic regressions were used to describe TB-prevalence and risk factors among US crop-workers. Data were drawn from the National Agricultural Workers Survey (NAWS).

RESULTS

A high TB-prevalence was found among crop-workers with a dramatically increasing trend in recent years. Hispanic ethnicity, having farmworker family members, the presence of health insurance, and good spoken English were associated with an increased TB-prevalence.

CONCLUSION

We found risk factors related to ethnicity and poor access to health care, a strong association between agriculture activity and TB, and an increase of TB-cases due to the 2008 downturn in this underserved population. We urge the health authorities to control this epidemic.

Whole Genome Sequencing of Mycobacterium bovis Isolated From Livestock in the United States, 1989-2018

The United States official bovine tuberculosis (bTB) eradication program has utilized genotyping for Mycobacterium bovis isolates since 2000 and whole genome sequencing was implemented in 2013. The program has been highly successful, yet as bTB prevalence has reached historic lows, a small number of new bTB-affected cattle herds occur annually. Therefore, understanding the epidemiology of bTB transmission is critically important, in order to target limited resources for surveillance and achieve eradication. This evaluation described the diversity and epidemiology of M. bovis isolates identified in the USA livestock. Isolates from animals within the bTB endemic area of Michigan were excluded. Broad diversity was found among 1,248 isolates, collected from affected cattle and farmed cervids herds and fed cattle during 1989–2018. Nearly 70% of isolates from 109 herds/cases during 1999–2018 were European clonal complex 1 and 30% were European clonal complex 2. The sources of infection based on the herd investigation were known for 41% of herds/cases and 59% were not epidemiologically linked to another USA origin herd. Whole genome sequencing results were consistent with the investigation findings and previously unrecognized links between herds and cases were disclosed. For herds/cases with an unknown source of infection, WGS results suggested several possible sources, including undocumented cattle movement, imported cattle and humans. The use of WGS in new cases has reduced the time and costs associated with epidemiological investigations. Within herd SNP diversity was evaluated by examining 18 herds with 10 or more isolates sequenced. Forty percent of isolates had not diverged or accumulated any SNPs, and 86% of the isolates had accumulated 3 or fewer SNPs. The results of WGS does not support a bTB reservoir in USA cattle. The bTB eradication program appears to be highly effective as the majority of herds/cases in the USA are unique strains with limited herd to herd transmission.

Factors Affecting Herd Status for Bovine Tuberculosis in Dairy Cattle in Northern Thailand

The objective of this case-control study was to identify farm-level risk factors associated with bovine tuberculosis (bTB) in dairy cows in northern Thailand. Spatial analysis was performed to identify geographical clustering of case-farms located in Chiang Mai and Chiang Rai provinces in northern Thailand. To identify management factors affecting bTB status, a matched case-control study was conducted with 20 case-farms and 38 control-farms. Case-farms were dairy farms with at least single intradermal tuberculin test- (SIT-) reactor(s) in the farms during 2011 to 2015. Control-farms were dairy farms with no SIT-reactors in the same period and located within 5 km from case-farms. Questionnaires were administered for data collection with questions based on epidemiological plausibility and characteristics of the local livestock industry. Data were analyzed using multiple logistic regressions. A significant geographic cluster was identified only in Chiang Mai province (p < 0.05). The risk factor associated with presence of SIT-reactors in dairy herds located in this region was purchasing dairy cows from dealers (OR = 5.85, 95% CI = 1.66-20.58, and p = 0.006). From this study, it was concluded that geographic clustering was identified for dairy farms with SIT-reactors in these provinces, and the cattle movements through cattle dealers increased the risks for SIT-reactor farm status.

Epidemiological investigation of bovine tuberculosis outbreaks in Uruguay (2011-2013)

Bovine tuberculosis (bTB) is a chronic disease of cattle caused by infection with the Mycobacterium bovis. While bTB prevalence in Uruguay has been low (<11 outbreaks/year) for the past 50 years as a consequence of a national control program, annual incidence increased in 2011 through 2013-15, 26 and 16 infected herds each year, raising concerns from livestock stakeholders and the government. The goal of this study was to assess the spatial dynamics of bTB in Uruguay from 2011 to 2013 and the association between bTB and potential demographic and movement risk factors at the herd level using data provided by the Uruguayan Ministry of Livestock, Agriculture, and Fisheries. Clustering of incident outbreaks was assessed using the Cuzick-Edwards' test and the Bernoulli model of the spatial scan statistic, and a conditional multivariable logistic regression model was used to assess risk factors associated with bTB in a subset of Uruguayan dairy farms. Significant (P<0.05) global clustering was detected in 2012, while high-risk local clusters were detected in southwestern (2011, 2012, 2013), northwestern (2012), and southeastern (2012) Uruguay. Increased risk of bTB in different regions of Uruguay suggests a potential role of animal movements in disease dissemination. Larger herds, higher numbers of animals purchased, and incoming steers to the farm were associated with increased odds of breaking with bTB, in agreement with previous studies but also suggesting other additional sources of risk. These results will contribute to enhanced effectiveness of bTB control programs in Uruguay with the ultimate objective of preventing or mitigating the impact of the disease in the human and animal populations of the country.

Multiple sampling and discriminatory fingerprinting reveals clonally complex and compartmentalized infections by M. bovis in cattle

The combination of new genotyping tools and a more exhaustive sampling policy in the analysis of infection by Mycobacterium tuberculosis has shown that infection by this pathogen is more complex than initially expected. Mixed infections, coexistence of clonal variants from a parental strain, and compartmentalized infections are all different modalities of this clonal complexity. Until recently, genotyping of Mycobacterium bovis in animal populations was based on spoligotyping and analysis of a single isolate per infection; therefore, clonal complexity is probably underdetected. We used multiple sampling combined with highly discriminatory MIRU-VNTR to study compartmentalized infections by M. bovis in a low-tuberculosis prevalence setting. We spoligotyped the M. bovis isolates from two or more anatomic locations sampled from 55 animals on 39 independent farms. Compartmentalized infections, with two different strains infecting independent lymph nodes in the same animal, were found in six cases (10.9%). MIRU-VNTR analysis confirmed that the compartmentalization was strict and that only one strain was present in each infected node. MIRU-VNTR analysis of additional infected animals on one of the farms confirmed that the compartmentalized infection was a consequence of superinfection, since the two strains were independently infecting other animals. This same analysis revealed the emergence of a microevolved clonal variant in one of the lymph nodes of the compartmentalized animal. Clonal complexity must also be taken into consideration in M. bovis infection, even in low-prevalence settings, and analyses must be adapted to detect it and increase the accuracy of molecular epidemiology studies.

Virulence of two strains of mycobacterium bovis in cattle following aerosol infection

Over the past two decades, highly virulent strains of Mycobacterium tuberculosis have emerged and spread rapidly in man, suggesting a selective advantage based on virulence. A similar scenario has not been described for Mycobacterium bovis infection in cattle (i.e. bovine tuberculosis). An epidemiological investigation of a recent outbreak of bovine tuberculosis in a USA dairy indicated that the causative strain of M. bovis (strain 10-7428) was particularly virulent, with rapid spread within the herd. In the present study, the virulence of this strain (10-7428) was directly compared in the target host with a well-characterized strain (95-1315) of relevance to the USA bovine tuberculosis eradication programme. Aerosol inoculation of 10(4) colony forming units of M. bovis 95-1315 (n = 8) or 10-7428 (n = 8) resulted in a similar distribution and severity of gross and microscopical lesions of tuberculosis as well as mycobacterial colonization, primarily affecting the lungs and lung-associated lymph nodes. Specific cell-mediated and antibody responses, including kinetics of the response, as well as antigen recognition profiles, were also comparable between the two treatment groups. Present findings demonstrate that M. bovis strains 95-1315 and 10-7428 have similar virulence when administered to cattle via aerosol inoculation. Other factors such as livestock management practices likely affected the severity of the outbreak in the dairy.