Performance and Agreement Between WGS Variant Calling Pipelines Used for Bovine Tuberculosis Control: Toward International Standardization

Whole genome sequencing (WGS) and allied variant calling pipelines are a valuable tool for the control and eradication of infectious diseases, since they allow the assessment of the genetic relatedness of strains of animal pathogens. In the context of the control of tuberculosis (TB) in livestock, mainly caused by Mycobacterium bovis, these tools offer a high-resolution alternative to traditional molecular methods in the study of herd breakdown events. However, despite the increased use and efforts in the standardization of WGS methods in human tuberculosis around the world, the application of these WGS-enabled approaches to control TB in livestock is still in early development. Our study pursued an initial evaluation of the performance and agreement of four publicly available pipelines for the analysis of M. bovis WGS data (vSNP, SNiPgenie, BovTB, and MTBseq) on a set of simulated Illumina reads generated from a real-world setting with high TB prevalence in cattle and wildlife in the Republic of Ireland. The overall performance of the evaluated pipelines was high, with recall and precision rates above 99% once repeat-rich and problematic regions were removed from the analyses. In addition, when the same filters were applied, distances between inferred phylogenetic trees were similar and pairwise comparison revealed that most of the differences were due to the positioning of polytomies. Hence, under the studied conditions, all pipelines offer similar performance for variant calling to underpin real-world studies of M. bovis transmission dynamics.

COVID-19 and chronic diabetes: the perfect storm for reactivation tuberculosis?: a case series

Background The coronavirus disease 2019 pandemic is predicted to have a net negative effect on tuberculosis control, with an estimated excess of 6.3 million tuberculosis cases and 1.4 million deaths by 2025. Programmatic issues such as the lockdown of tuberculosis services affect all patients, while biosocial factors have a differential impact on an individual’s risk for tuberculosis or adverse tuberculosis outcomes. Case presentation We report three Hispanic cases of incident tuberculosis (two males, 43 and 44 years old; one female, 49 years old) after resolution of coronavirus disease episodes. Coincidentally, all cases shared a common risk factor: a chronic history poorly controlled diabetes. Conclusions Our findings alert to the threat posed by the synergy between coronavirus disease and diabetes, on tuberculosis reactivation. In medium- to high-risk settings for tuberculosis, we recommend implementation of routine screening for latent tuberculosis infection in these cases, and preventive tuberculosis treatment in those who are positive.

Health System Productivity In Sub-Saharan Africa: Tuberculosis Control In High Burden Countries

Background: 21 of the 30 countries with a high tuberculosis (TB) burden are in Sub-Saharan Africa (SSA). SSA is also home to 74% of all HIV-positive TB patients reported worldwide in 2014. This paper analyses the productivity changes of TB programs and decompose this productivity down into technological change and technical efficiency. Method: this study was carried out in 16 SSA countries where TB is highly endemic and covers the period 2009-2016. The data is taken from the annual reports of global TB Program. We used the Hicks-Moorsteen index to compute and decompose total factor productivity (TFP), and the β-convergence and σ-convergence tests to check for convergence patterns among SSA countries. Results: The largest increase in the TFP (35.7%) in 2016 with respect to the base year corresponds to the cutbacks in inputs (9.1%) and a positive change in outputs (0.9%). We found that technological change has been the main driver of the TFP growth, and that increasing technical efficiency may be the first objective in efforts to improve the TFP of TB programs. Our findings support the hypothesis of convergence among SSA countries in the fight against TB. Moreover, corruption was considered as one of the most important determinants of tuberculosis control in SSA countries.Conclusion: the findings suggest that improving the technical efficiency of TB programs mainly calls for better resource allocation, capacity building in governance and management of programs, improved training of the health providers and stronger prevention policies. An efficient use of funds will arguably reduce the number of tuberculosis cases and TB burden. The Global Fund must closely monitor all the grants in its portfolio and respond decisively and urgently to any instances of corruption.

Risk Factors of Pulmonary Tuberculosis and Countermeasures: A Literature Review

BACKGROUND: Tuberculosis is still the primary infectious disease in the world due to HIV/AIDS. In the 2015-2019 strategic plan of the Ministry of Health, infectious diseases are one of the main priorities that must create a Healthy Indonesia. The prevalence rate of pulmonary tuberculosis cases in Indonesia is 539,000 new cases each year, with the number of deaths around 101,000 per year. Acid Fast Bacilli (AFB) (+) incidence rate is around 110/ 100,000 population. AIM: This study aimed to identify the influencing factors and efforts to overcome pulmonary tuberculosis disease. MATERIALS AND METHODS: The research method was carried out by tracing the research reports/articles related to pulmonary tuberculosis incidence as many as 38 selected articles. RESULT: Factors that influence tuberculosis infection incidence include age, income level (socioeconomic), housing conditions, the behavior of opening windows every morning, smoking, and a history of contact with tuberculosis patients. There are various countermeasures undertaken to overcome pulmonary tuberculosis, one of which uses a tissue model. This model involves many stakeholders whose duty is to provide knowledge and record the number of sufferers. The stages of action to control tuberculosis include discovery, treatment, and surveillance. CONCLUSION: Facts in the field show that several factors can affect the success of implementing pulmonary tuberculosis control. Therefore, it is necessary to participate in all society components and involve other agencies beyond the health agency so the reduction in the incidence of pulmonary tuberculosis can be appropriately realized.

Addressing constraints to informal providers’ involvement in tuberculosis control: a qualitative study of patent medicine dealers and tuberculosis programme managers

Background A major constraint to tuberculosis control is low case finding with under-reporting to national authorities. Evidence shows that Patent Medicine Dealers are first port of call for most people with symptoms of tuberculosis, yet there is poor referral of such clients to tuberculosis treatment facilities for further evaluation. This study investigated constraints to involvement of Patent Medicine Dealers in tuberculosis control. Methods This was a cross-sectional qualitative study among Patent Medicine Dealers and Tuberculosis Control Programme Managers in Ebonyi State Nigeria. Sixty-four Patent Medicine Dealers and five Tuberculosis Control Programme Managers were interviewed using Focus Group Discussion and In-Depth Interview respectively. Data was collected with electronic audio-recording device and analyzed using thematic approach. Results There are some knowledge gaps about tuberculosis signs, symptoms, free-treatment policy and mode of operation of care service among Patent Medicine Dealers. Patent Medicine Dealers and Tuberculosis Control Programme Managers are willing to collaborate in tuberculosis control effort but constant demand for incentives by Patent Medicine Dealers and inability of National Tuberculosis Control Programme to keep up with such demands are obvious constraints. Conclusions Knowledge gaps in tuberculosis, its control, constant demand for incentives by Patent Medicine Dealers and inability of National Tuberculosis Control Programme to satisfy such demands are constraints to involvement of Patent Medicine Dealers in tuberculosis control. More robust engagement of Patent Medicine Dealers in tuberculosis control with clear job description through tuberculosis education and provision of incentives to support them are recommended policy approaches to improve linkage of clients to tuberculosis treatment facilities.

Pengendalian Tuberkulosis pada Masa Pandemi Covid-19 di Puskesmas Elopada Kabupaten Sumba Barat Daya Propinsi Nusa Tenggara Timur Tahun 2020

Globally, tuberculosis is still a major health problems including in Indonesia.The program has been implemented however,the tuberculosis cases are still high considering the condition during the COVID-19 pandemic. The purpose of this article is to provide an overview of tuberculosis during the COVID-19 pandemic at the Elopada Health Center through qualitative inquiry by interviewing with one person and three head of the health center in the tuberculosis service department and two village heads. Meanwhile, the triangulation informants consisted of tuberculosis manager in Southwest Sumba Regency and the head of the Controlling Division of infectious diseases. The results showed that the number of tuberculosis cases at the health center had an increase in cases with BTA+. Control measures providing tuberculosis services included active and passive case findings, diagnosis and treatment which were done manually and digitally,based on microscopic laboratory examinations and molecular rapid tests. Treatment and recording and reporting are done manually or digitally. During the pandemic, tuberculosis services were carried out separately from other patient services. The conclusion is that tuberculosis control at the Elopada Community Health Center is still being carried out during the pandemic by paying attention to health protocols and utilizing technology (social media). Key words: control, tuberkulosis, pandemic Covid-19, Elopada health center Abstrak Tuberkulosis masih menjadi perhatian sebagai salah satu masalah kesehatan utama di Indonesia maupun Global. Program sudah dijalankan namun sampai saat ini kasus tuberkulosis masih tinggi. Disamping itu kondisi saat ini menghadapi pandemi covid-19. Puskesmas menjadi ujung tombak dalam memberikan pelayanan kesehatan di masyarakat. Tujuan artikel ini adalah memberikan gambaran pengendalian tuberkulosis pada masa pandemi di Puskesmas Elopada. Jenis penelitian adalah kualitatif observatif yang melakukan wawancara dengan kepala puskesmas dan petugas bagian pelayanan tuberkulosis dan kepala desa. Sedangkan informan triangulasi terdiri dari pengelola tuberkulosis Kabupaten Sumba Barat Daya dan Kepala Bidang Pengendalian Penyakit Menular. Hasil penelitian menunjukkan bahwa jumlah kasus tuberkulosis di puskesmas Elopada terjadi peningkatan pada kasus dengan BTA+. Upaya pengendalian yang dilakukan memberikan pelayanan tuberkulosis meliputi penemuan kasus secara aktif dan pasif yang dilakukan secara manual dan berbasis internet, diagnosis penderita berdasarkan hasil pemeriksaan labotarorium secara mikroskopis dan menggunakan tes cepat molekuler. Pengobatan, pencatatan dan pelaporan dilakukan secara manual maupun digital. Selama masa pandemi pelayanan tuberkulosis dilakukan terpisah dengan pelayanan pasien lainnya. Kesimpulan pengendalian tuberkulosis di Puskesmas Elopada tetap dijalankan di masa pandemi dengan memperhatikan protokol kesehatan dan memanfaatkan teknologi (media sosial). Kata kunci: Pengendalian, tuberkulosis, Pandemi Covid-19, Puskesmas Elopada

Drug resistance in tuberculosis- resurvey in Wardha district, India after implementation of revised national TB control program

Level of drug resistance among new TB patients indicates the efficacy of any control programme. A drug resistance survey, as a part of global study in new pulmonary tuberculosis (NPTB) patients, was conducted in Wardha district, India under WHO /IUTLD in 2001, before the implementation of the Revised National Tuberculosis Control Programme (RNTCP) which was implemented in the district in 2002. The present study was conducted in Wardha district in 2014-2015, thirteen years after the implementation of RNTCP, and the drug resistance in isolates from NPTB patients was compared to the results of 2001 survey. The methodology used was same in both the surveys. : In addition to 132 isolates from Wardha, the study also included 112 isolates from adjoining city, Nagpur and total of 244 sputum isolates were subjected to drug sensitivity by standard 1% proportion method on Lowenstein Jensen’s medium. In addition molecular typing of resistant strains was done.: In Wardha, compared to 2001 survey, overall susceptibility to first line drugs washigher (94.7% vs 80.2%); and resistance to streptomycin (3% vs 7.6%) and isoniazid (2.2% vs 15.2%) were significantly lower (p≤ 0.05). MDR was 0.75% against 0.50% in the earlier study but the difference was statistically not significant. Only two MDR isolate were recovered, of which only one was from Wardha.After the implementation of RNTCP in Wardha District, drug resistancein new PTB patients has shown a decline and MDR continues to be low reflecting upon the efficiency of the program.