Extrapulmonary tuberculosis in Pakistan: Challenges in diagnosis and detection of drug resistance

Bakgrunn: Pakistan er blant de fem landene med høyest forekomst av tuberkulose (TB) og legemiddelresistent TB. Ekstrapulmonær TB (EPTB) utgjør 20% av alle registrerte TB-pasienter, men det er lite informasjon om sykdomsmanifestasjon, bakteriologiske diagnoser og forekomst av legemiddelresistens i EPTB. Mål: Det overordnede målet var å studere EPTB i Pakistan og evaluere nytten av konvensjonelle og nye diagnostiske verktøy for å diagnostisere og oppdage legemiddelresistens hos pasienter med EPTB. Hovedmålet med den første studien var å beskrive sykdomstegnene blant pasienter med EPTB. Målet med den andre studien var å vurdere den diagnostiske ytelsen av en rask molekylær analyse, Xpert MTB/RIF (Xpert), og histologisk undersøkelse for tuberkuløs lymfadenitt. Målet med den tredje studien var å studere forekomsten av rifampicin og annen legemiddelresistens mot TB hos nye pasienter med EPTB, og den fjerde studien hadde som mål å vurdere forekomsten og den genetiske profilen til isoniazidresistens samt tilhørende resistens mot fluorokinolon og pyrazinamid. Materiale og metoder: I studie 1 ble det utført deskriptiv analyse av en retrospektiv kohort av TB-pasienter registrert nasjonalt i 2016. Studie 2 og 3 ble utført på en prospektiv kohort av pasienter med antatt EPTB ved et tertiært sykehus. I studie 2 ble personer som ikke hadde fått TB-behandling og hadde forstørrede lymfeknuter inkludert, og vevsprøver fra eksisjonsbiopsier ble undersøkt med histologi, Xpert og dyrkning. I studie 3 ble pasienter med pleural effusjon i tillegg til personene i studie 2 med forstørrede lymfeknuter, inkludert. Pleuravæske ble undersøkt for syrefastestaver (AFB)-mikroskopi, Xpert MTB/RIF og dyrkning. Fenotypisk legemiddelsusceptibilitetstesting (DST) ble utført ved bruk av automatisert flytende DST (MGIT 960), og genotypisk DST ble utført ved hjelp av line-probe-undersøkelser (LPA). I studie 4 ble et fem års retrospektiv DST-datasett analysert for pasienter som ble testet ved det nasjonale TB-referanselaboratoriet ved hjelp av både fenotypiske og genotypiske DST-metoder. Resultater: I studie 1 ble individuelle pasientdata samlet inn fra 54 092 registrerte TB-tilfeller i 2016. Blant disse hadde 15 790 pasienter EPTB. De tre vanligste formene for EPTB var pleural (29,6 %), lymfatisk (22,7%) og abdominal TB (21,0%). Pleural TB var den vanligste blant voksne (34,2%), mens abdominal TB var mest utbredt blant barn (38,4%). Sannsynligheten for å ha EPTB var 1,1 ganger høyere for kvinner, 2,0 ganger høyere for barn og 3,3 ganger høyere for innbyggere i provinsene nordvest i landet. Behandlingssuksessraten for alle typer EPTB som var inkludert i studien, var høy, bortsett fra for TB-meningitt. I studie 2 ble ytelsen til diagnostiske verktøy analysert i en kohort på 390 pasienter med forstørrede lymfeknuter. Blant disse var 11 (2,8%) positive ved AFB-mikroskopi, 124 (31,8%) ved Xpert, 137 (35,1%) ved dyrkning, og histopatologi viste TB hos 208 (53,3%). Ved bruk av kombinerte resultater ble lymfeknutetuberkulose diagnostisert hos 228 pasienter, hvorav 78% ble bekreftet ved bakteriologiske tester. Sammenlignet med Xpert hadde histopatologi høyere sensitivitet (93% mot 62%), men lavere spesifisitet (68% mot 83%), og i undergruppeanalyser var sensitiviteten til Xpert høyere hos pasienter med kort klinisk historie. I studie 3 ble bakteriologisk diagnose og forekomst av legemiddelresistens analysert hos 671 studiepersoner. TB ble bekreftet bakteriologisk hos 255, og DST-resultater var tilgjengelige for 72,5% (n = 185) av pasientene med EPTB. Multidrug resistant -TB ble rapportert hos 2,2% (95% CI, 0,6–5,4), resistens mot rifampicin hos 2,7% (95% CI, 0,9–6,2), isoniazid hos 7,6% (95% CI, 4,1–12,4), ethambutol hos 1,1% (95% CI, 0,1–3,9), pyrazinamid hos 2,2% (95% CI, 0,9–5,5) og fluorokinoloner hos 6,0% (95% CI, 3,0–10,4). Sensitiviteten og spesifisiteten til LPA-DST var henholdsvis 100% og 98,8% for rifampicin, isoniazid og fluorokinolon. DST-resultater for rifampicin var tilgjengelige for 82 pasienter ved alle tre metoder og av disse ble fem rapportert som rifampicinresistente ved Xpert, men bare én ble bekreftet ved LPA, og ingen ble bekreftet ved fenotypisk DST. I studie 4 ble et retrospektivt DST-datasett med 11 045 TB-pasienter analysert. Både fenotypiske og genotypiske DST-resultater var tilgjengelige for 80 % av tilfellene. Det ble rapportert en betydelig forskjell mellom resistens som ble påvist ved fenotypisk og genotypisk DST-metoder, med en uoverensstemmelse på 16% for rifampicin og isoniazid. Blant nye EPTB-pasienter med rifampicinsensitivitet ble isoniazidresistens påvist hos 6,8%, sammenlignet med 9,8% hos pasienter med PTB. Den genetiske profilen for isoniazidresistens var lik for PTB og EPTB, men forskjellen var statistisk signifikant mellom rifampicinresistente og rifampicinsensitive populasjoner når det gjaldt påviste mutasjoner knyttet til isoniazidresistens, med 87% mot 71,6% og forekomsten av katG-mutasjoner på 76,1% mot 41,2% og inhA-mutasjoner på 7,6% mot 30,2%, henholdsvis. Det ble observert en signifikant høyere forekomst av levofloxacinresistens i forbindelse med isoniazidresistens. Konklusjoner: Pleural- og lymfatisk TB utgjorde til sammen 50% av alle registrerte tilfeller av EPTB. TB ble diagnostisert ved kun hjelp av Xpert i 54% av tilfellene, mens kombinasjonen av Xpert og histopatologi bekreftet diagnosen i over 95% av alle tilfeller med TB i lymfeknuter. Forekomsten av rifampicin- og isoniazidresistens var lavere blant nye EPTB-pasienter sammenlignet med PTB, men forskjellen var ikke statistisk signifikant. Den genetiske profilen for isoniazidresistens og tilhørende resistens mot fluorokinolon og pyrazinamid var sammenlignbar mellom EPTB og PTB.Background: Pakistan is among the top five high-burden countries for tuberculosis (TB) and drug-resistant TB. Extrapulmonary TB (EPTB) accounts for 20% of all notified TB patients but there is little information on disease manifestations, bacteriological diagnoses, and prevalence of anti-TB drug resistance in EPTB. Objective: The overall objective was to study EPTB in Pakistan, and evaluate the usefulness of conventional and new diagnostic tools in diagnosing and detecting drug resistance in EPTB patients. The first study primarily aimed to describe the disease manifestations among EPTB patients notified in Pakistan. The second study aimed to assess the performance of a rapid molecular assay, Xpert MTB/RIF (Xpert), and histological examination in the diagnoses of tuberculous lymphadenitis. The third study aimed to determine the prevalence of rifampicin and other anti-TB drug resistance in new EPTB patients and the fourth study aimed to assess the prevalence and genetic profile of isoniazid resistance and associated resistance to fluoroquinolone and pyrazinamide. Material and Methods: In study-1, descriptive analysis was performed on a retrospective cohort of TB patients notified nationwide in 2016. Studies 2 and 3 were performed on a prospective cohort of patients presumed to have EPTB in a tertiary care hospital. In study-2, TB treatment naïve people with enlarged lymph nodes were included and excision biopsy specimens were tested by histology, Xpert, and culture. In study-3, patients with pleural effusion in addition to people in study-2 with enlarged lymph nodes were included. Pleural fluid sediments were tested for smear, Xpert MTB/RIF, and culture. Phenotypic drug susceptibility testing (DST) was performed using automated liquid DST (MGIT 960) and genotypic DST by line-probe assays (LPA). For study-4, a five-year retrospective DST data set was analyzed of TB patients tested in the National TB reference laboratory by phenotypic and/or genotypic DST methods. Results: In study-1, individual patient data was collected of 54092 TB cases notified in 2016. Among 15790 EPTB patients included, the three most common forms of EPTB were pleural (29.6%), lymphatic (22.7%), and abdominal TB (21.0%). Pleural TB was the most common among adults (34.2%) and abdominal TB in children (38.4%). The likelihood of having EPTB, was 1.1 times high for females, 2.0 times for children, and 3.3 times for residents of provinces in the Northwest. The treatment success rate for all types of EPTB included in the study was high except for TB meningitis. In study-2, the performance of diagnostic tools in a cohort of 390 patients with enlarged lymph nodes was analyzed and among these 11 (2.8%) were positive by AFB microscopy, 124 (31.8%) by Xpert, 137 (35.1%) by culture, and histopathology was consistent with TB in 208 (53.3%). Using composite results, lymph node TB was diagnosed in 228 of which 78% were bacteriologically confirmed. Histopathology compared to Xpert had higher sensitivity (93 vs. 62%) but lower specificity (68 vs.83%) and in sub-group analysis, the sensitivity of Xpert was higher in patients with short clinical history. In study-3, bacteriological diagnosis and prevalence of drug resistance was analyzed in 671 study participants. Bacteriologically confirmed TB was diagnosed in 255 and DST results were available for 72.5% (n=185) of EPTB patients. MDR-TB was reported in 2.2% (95% CI, 0.6–5.4)., resistance to rifampicin in 2.7% (95% CI, 0.9–6.2), isoniazid in 7.6% (95% CI, 4.1–12.4), ethambutol in 1.1% (95% CI, 0.1–3.9), pyrazinamide in 2.2% (95%CI, 0.9–5.5) and fluoroquinolones in 6.0% (95% CI, 3.0–10.4). The sensitivity and specificity of LPA-DST was 100% and 98.8% respectively for rifampicin, isoniazid, and fluoroquinolone. Rifampicin results were available by all three methods for 82 patients and of these five were reported rifampicin resistant by Xpert and only one was confirmed by LPA and none by phenotypic DST. In study-4, a retrospective DST data set of 11045 TB patients was analyzed. Both phenotypic and genotypic DST results were available for 80% of cases. A significant difference was reported between resistance detected by phenotypic and genotypic DST methods with 16% discordance in rifampicin and isoniazid. Among rifampicin-sensitive new EPTB, isoniazid resistance was 6.8% compared to 9.8% in PTB. The genetic profile of isoniazid resistance was similar in PTB and EPTB but the difference was statistically significant between rifampicin-resistant and sensitive populations for isoniazid-resistant conferring mutations detected in 87% vs 71.6%, the prevalence of katG mutations in 76.1% vs 41.2% and inhA in 7.6% vs 30.2% respectively. A significantly higher levofloxacin resistance was seen associated with isoniazid resistance. Conclusions: Pleural and lymphatic TB collectively comprised 50% of all notified EPTB cases. TB was diagnosed by Xpert alone in 54%, while in combination with histopathology in more than 95% of all TB lymph node cases. Rifampicin and isoniazid resistance was lower in the new EPTB compared to PTB; the difference was not statistically significant. The genetic profile of isoniazid resistance and associated fluoroquinolone and pyrazinamide resistance in EPTB was comparable with PTB.Doktorgradsavhandlin

The value of histological examination in the diagnosis of tuberculous lymphadenitis in the era of rapid molecular diagnosis

Extrapulmonary tuberculosis often poses a diagnostic challenge. This study aimed to assess the value of histological examination in diagnosing tuberculous lymphadenitis (LNTB) when performed simultaneously with rapid molecular assay (Xpert MTB/RIF) testing. People presumed to have LNTB were prospectively enrolled in a tertiary care hospital. Excision biopsy was performed and tested by histology, Xpert, and culture. Of 390 lymph nodes, 11 (2.8%) were positive by AFB microscopy, 124 (31.8%) by Xpert, 137 (35.1%) by culture, and histopathology was consistent with TB in 208 (53.3%). Altogether, LNTB was diagnosed in 228 and bacteriologically confirmed TB in 178 cases. Against culture, histopathology versus Xpert had higher sensitivity (93 vs. 62%) but lower specificity (68 vs. 83%). In patients with short clinical history, a significantly higher number of Xpert-positive specimens were culture-positive. Among patients with histology suggestive of TB, no difference was seen in response to treatment between bacteriology positive and negative, but a significant slow response was noted in bacteriology confirmed TB with nonspecific histology. In a country like Pakistan, with high TB and low HIV prevalence, diagnosis is possible for more than 95% of LNTB when Xpert and histopathology examination is used in combination, compared to less than 60% by Xpert alone.publishedVersio

Predictors of slow clinical response and extended treatment in patients with extra-pulmonary tuberculosis in Pakistan, A hospital-based prospective study

The optimal duration of treatment in different forms of extrapulmonary tuberculosis (EPTB) is not clearly defined. This study aimed to identify predictors of slow clinical response and extended anti-TB treatment in EPTB patients. Socio-demographic, clinical, and microbiological characteristics of EPTB patients registered for anti-TB treatment at a tertiary care hospital, were analysed for identification of predictors of extended treatment. A total of 251 patients (137 lymphadenitis, and 114 pleuritis) were included in the analysis. Treatment was extended to more than 6 months in 58/251 (23%) patients. In the multivariate regression analysis, culture-positive EPTB (p = 0.007) [OR (95% CI) = 3.81 (1.43, 10.11)], history of diabetes (p = 0.014) [OR (95% CI) = 25.18 (1.94, 325.83)], smokeless tobacco use (p = 0.002) [OR (95% CI) = 17.69 (2.80, 111.72)], and slow regression of local signs and symptoms after 2 months of treatment (p < 0.001) [OR (95% CI) = 17.09 [(5.79, 50.39)] were seen to be significantly associated with treatment extension. Identification of predictors of extended treatment can help clinical decisions regarding optimal duration of treatment. Further studies are needed to identify subgroups of EPTB patients who can benefit from a shorter or longer treatment regimen.publishedVersio

Extrapulmonary tuberculosis in Pakistan- A nation-wide multicenter retrospective study

Background Pakistan is fifth among high burden countries for tuberculosis. A steady increase is seen in extrapulmonary tuberculosis (EPTB), which now accounts for 20% of all notified TB cases. There is very limited information on the epidemiology of EPTB. This study was performed with the aim to describe the demographic characteristics, clinical manifestations and treatment outcomes of EPTB patients in Pakistan. Method We performed descriptive analysis on routinely collected data for cohorts of TB patients registered nationwide in 2016 at health facilities selected using stratified convenient sampling. Findings Altogether 54092 TB including 15790 (29.2%) EPTB cases were registered in 2016 at 50 study sites. The median age was 24 years for EPTB and 30 years for PTB patients. The crude prevalence of EPTB in females was 30.5% (95%CI; 29.9–31.0) compared to 27.9% (95%CI; 27.3–28.4) in males. The likelihood of having EPTB (OR), was 1.1 times greater for females, 2.0 times for children, and 3.3 times for residents of provinces in the North-West. The most common forms of EPTB were pleural (29.6%), lymphatic (22.7%) and abdominal TB (21.0%). Pleural TB was the most common clinical manifestation in adults (34.2%) and abdominal TB in children (38.4%). An increase in the prevalence of pleural and osteoarticular and decline in lymphatic and abdominal TB was observed with advancing age. Diversity in demography and clinical manifestations were noted between provinces. The treatment success rate for all type EPTB was significantly high compared to bacteriology confirmed PTB with the exception of EPTB affecting CNS with a high mortality rate. Conclusions The study provides an insight into demography, clinical manifestations and treatment outcomes of EPTB. Further studies are needed to explain significant diversities observed between provinces, specific risk factors and challenges concerning EPTB management.publishedVersio

Prevalence and genetic profiles of isoniazid resistance in tuberculosis patients: A multicountry analysis of cross-sectional data.

BACKGROUND: The surveillance of drug resistance among tuberculosis (TB) patients is central to combatting the global TB epidemic and preventing the spread of antimicrobial resistance. Isoniazid and rifampicin are two of the most powerful first-line anti-TB medicines, and resistance to either of them increases the risk of treatment failure, relapse, or acquisition of resistance to other drugs. The global prevalence of rifampicin resistance is well documented, occurring in 3.4% (95% CI 2.5%-4.4%) of new TB patients and 18% (95% CI 7.6%-31%) of previously treated TB patients in 2018, whereas the prevalence of isoniazid resistance at global and regional levels is less understood. In 2018, the World Health Organization (WHO) recommended a modified 6-month treatment regimen for people with isoniazid-resistant, rifampicin-susceptible TB (Hr-TB), which includes rifampicin, pyrazinamide, ethambutol, and levofloxacin. We estimated the global prevalence of Hr-TB among TB patients and investigated associated phenotypic and genotypic drug resistance patterns. METHODS AND FINDINGS: Aggregated drug resistance data reported to WHO from either routine continuous surveillance or nationally representative periodic surveys of TB patients for the period 2003-2017 were reviewed. Isoniazid data were available from 156 countries or territories for 211,753 patients. Among these, the global prevalence of Hr-TB was 7.4% (95% CI 6.5%-8.4%) among new TB patients and 11.4% (95% CI 9.4%-13.4%) among previously treated TB patients. Additional data on pyrazinamide and levofloxacin resistance were available from 6 countries (Azerbaijan, Bangladesh, Belarus, Pakistan, the Philippines, and South Africa). There were no cases of resistance to both pyrazinamide and levofloxacin among Hr-TB patients, except for the Philippines (1.8%, 95% CI 0.2-6.4) and Belarus (5.3%, 95% CI 0.1-26.0). Sequencing data for all genomic regions involved in isoniazid resistance were available for 4,563 patients. Among the 1,174 isolates that were resistant by either phenotypic testing or sequencing, 78.6% (95% CI 76.1%-80.9%) had resistance-conferring mutations in the katG gene and 14.6% (95% CI 12.7%-16.8%) in both katG and the inhA promoter region. For 6.8% (95% CI 5.4%-8.4%) of patients, mutations occurred in the inhA promoter alone, for whom an increased dose of isoniazid may be considered. The main limitations of this study are that most analyses were performed at the national rather than individual patient level and that the quality of laboratory testing may vary between countries. CONCLUSIONS: In this study, the prevalence of Hr-TB among TB patients was higher than the prevalence of rifampicin resistance globally. Many patients with Hr-TB would be missed by current diagnostic algorithms driven by rifampicin testing, highlighting the need for new rapid molecular technologies to ensure access to appropriate treatment and care. The low prevalence of resistance to pyrazinamide and fluoroquinolones among patients with Hr-TB provides further justification for the recommended modified treatment regimen

Population structure, biogeography and transmissibility of mycobacterium tuberculosis

Mycobacterium tuberculosis is a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity and biogeography remains incomplete. Here we use a combination of phylogenetics and dimensionality reduction to reevaluate the population structure of M. tuberculosis, providing an in-depth analysis of the ancient Indo-Oceanic Lineage 1 and the modern Central Asian Lineage 3, and expanding our understanding of Lineages 2 and 4. We assess sub-lineages using genomic sequences from 4939 pan-susceptible strains, and find 30 new genetically distinct clades that we validate in a dataset of 4645 independent isolates. We find a consistent geographically restricted or unrestricted pattern for 20 groups, including three groups of Lineage 1. The distribution of terminal branch lengths across the M. tuberculosis phylogeny supports the hypothesis of a higher transmissibility of Lineages 2 and 4, in comparison with Lineages 3 and 1, on a global scale. We define an expanded barcode of 95 single nucleotide substitutions that allows rapid identification of 69 M. tuberculosis sub-lineages and 26 additional internal groups. Our results paint a higher resolution picture of the M. tuberculosis phylogeny and biogeography.http://www.nature.com/naturecommunicationsam2022Medical Microbiolog

Delay in diagnosis of tuberculosis in Rawalpindi, Pakistan

<p>Abstract</p> <p>Background</p> <p>Delay in diagnosis and treatment of tuberculosis (TB) may enhance the chances of morbidity and mortality and play a key role in continuous transmission of the bacilli. The objective of this study was to describe health care seeking behavior of suspected TB patients and initial diagnostic work up prior to consultation and diagnosis at National TB Center (NTC).</p> <p>Findings</p> <p>Interviews of 252 sputum smear positive patients were taken from NTC, Rawalpindi. The duration between on-set of symptoms and start of treatment was considered as the total delay and correlated with general characteristics of TB patients. The proportion of males and females were 49.6% and 50.4% with median age of 25 and 24 years respectively. A median delay of 56 days (8 weeks) was observed which was significantly associated with age, cough and fever. More than 50% of the current patients had a history of contact with previously diagnosed TB patients. The majority of patients (63%) visited health care providers within three weeks of appearance of symptoms but only thirty five percent were investigated for TB diagnosis.</p> <p>Conclusion</p> <p>Cough and fever are being ignored as likely symptoms of TB by patients as well as health care providers resulting in delay. Engaging private practitioners through public private mix (PPM) approach for expansion of TB diagnosis and increasing public awareness could be more beneficial to reduce delay.</p

Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study

BACKGROUND : In many countries, regular monitoring of the emergence of resistance to anti-tuberculosis drugs is hampered by the limitations of phenotypic testing for drug susceptibility. We therefore evaluated the use of genetic sequencing for surveillance of drug resistance in tuberculosis. METHODS : Population-level surveys were done in hospitals and clinics in seven countries (Azerbaijan, Bangladesh, Belarus, Pakistan, Philippines, South Africa, and Ukraine) to evaluate the use of genetic sequencing to estimate the resistance of Mycobacterium tuberculosis isolates to rifampicin, isoniazid, ofloxacin, moxifloxacin, pyrazinamide, kanamycin, amikacin, and capreomycin. For each drug, we assessed the accuracy of genetic sequencing by a comparison of the adjusted prevalence of resistance, measured by genetic sequencing, with the true prevalence of resistance, determined by phenotypic testing. FINDINGS : Isolates were taken from 7094 patients with tuberculosis who were enrolled in the study between November, 2009, and May, 2014. In all tuberculosis cases, the overall pooled sensitivity values for predicting resistance by genetic sequencing were 91% (95% CI 87–94) for rpoB (rifampicin resistance), 86% (74–93) for katG, inhA, and fabG promoter combined (isoniazid resistance), 54% (39–68) for pncA (pyrazinamide resistance), 85% (77–91) for gyrA and gyrB combined (ofloxacin resistance), and 88% (81–92) for gyrA and gyrB combined (moxifloxacin resistance). For nearly all drugs and in most settings, there was a large overlap in the estimated prevalence of drug resistance by genetic sequencing and the estimated prevalence by phenotypic testing. INTERPRETATION : Genetic sequencing can be a valuable tool for surveillance of drug resistance, providing new opportunities to monitor drug resistance in tuberculosis in resource-poor countries. Before its widespread adoption for surveillance purposes, there is a need to standardise DNA extraction methods, recording and reporting nomenclature, and data interpretation.The Bill & Melinda Gates Foundation, the United States Agency for International Development, and the TB Alliance.www.thelancet.com/infectionhttp://www.thelancet.com/infectionam2018Medical Microbiolog

Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment

11 páginas, 2 figuras, 1 tablaInappropriately high breakpoints have resulted in systematic false-susceptible AST results to anti-TB drugs. MIC, PK/PD and clinical outcome data should be combined when setting breakpoints to minimise the emergence and spread of antimicrobial resistance.I. Comas was supported by PID2019-104477RB-I00 from the Spanish Science Ministry and by ERC (CoG 101001038)Peer reviewe

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis.

Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: In this systematic analysis, we used a candidate gene approach to identify mutations associated with resistance or consistent with susceptibility for 13 WHO-endorsed antituberculosis drugs. We collected existing worldwide MTBC whole-genome sequencing data and phenotypic data from academic groups and consortia, reference laboratories, public health organisations, and published literature. We categorised phenotypes as follows: methods and critical concentrations currently endorsed by WHO (category 1); critical concentrations previously endorsed by WHO for those methods (category 2); methods or critical concentrations not currently endorsed by WHO (category 3). For each mutation, we used a contingency table of binary phenotypes and presence or absence of the mutation to compute positive predictive value, and we used Fisher's exact tests to generate odds ratios and Benjamini-Hochberg corrected p values. Mutations were graded as associated with resistance if present in at least five isolates, if the odds ratio was more than 1 with a statistically significant corrected p value, and if the lower bound of the 95% CI on the positive predictive value for phenotypic resistance was greater than 25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: We analysed 41 137 MTBC isolates with phenotypic and whole-genome sequencing data from 45 countries. 38 215 MTBC isolates passed quality control steps and were included in the final analysis. 15 667 associations were computed for 13 211 unique mutations linked to one or more drugs. 1149 (7·3%) of 15 667 mutations were classified as associated with phenotypic resistance and 107 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was more than 80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were identified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: We present the first WHO-endorsed catalogue of molecular targets for MTBC drug susceptibility testing, which is intended to provide a global standard for resistance interpretation. The existence of this catalogue should encourage the implementation of molecular diagnostics by national tuberculosis programmes. Funding: Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation