Rapid Acquisition and Transmission of Drug Resistance Amongst Beijing Lineage Mycobacterium tuberculosis in Vietnam

Whole genome sequencing (WGS) and phenotypic drug susceptibility testing was performed on a collection of 2,542 Mycobacterium tuberculosis (Mtb) isolates from tuberculosis (TB) patients recruited in Ho Chi Minh City (HCMC), Vietnam, to investigate Mtb diversity, the prevalence and phylodynamics of drug resistance, and in silico resistance prediction with sequencing data. Amongst isolates tested phenotypically against first-line drugs, we observed high rates of streptomycin [STR, 37.7% (N=573/1,520)] and isoniazid resistance [INH, 25.7% (N=459/1,786)], and lower rates of resistance to rifampicin [RIF, 4.9% (N=87/1,786)] and ethambutol [EMB, 4.2% (N=75/1,785)]. Resistance to STR and INH was predicted moderately well when applying the TB-Profiler algorithm to WGS data (sensitivities of 0.81 and 0.87 respectively), while resistance to RIF and EMB was predicted relatively poorly (sensitivities of 0.70 and 0.44 respectively). Rates of multidrug-resistance [(MDR, 3.9% (N=69/1,786)], and resistance to a number of second-line drugs [Para-aminosalicylic acid (29.6% N=79/267), Amikacin (15.4% N=41/267) and Moxifloxacin (21.3%), N=57/267], were found to be high within a global context. Comparing rates of drug resistance among lineages, and exploring the dynamics of resistance acquisition through time, suggest the Beijing lineage (lineage 2.2) acquires de novo resistance mutations at higher rates and suffers no apparent fitness cost acting to impede the transmission of resistance. We infer resistance to INH and STR to have arisen earlier, on average, than resistance to RIF, and to be more widespread across the phylogeny. The high prevalence of ‘background’ INH resistance, combined with high rates of RIF mono-resistance (20.7%, N=18/87) suggests that rapid assays for INH resistance will be valuable in this setting. These tests will allow the detection of INH mono-resistance, and will allow MDR isolates to be distinguished from isolates with RIF mono-resistance. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work, or researchers involved in this work, received funding from the National Health and Medical Research Council Australia, the Wellcome Trust UK, The Agency for Science, Technology and Research Singapore, The National University of Singapore, the Munz Chair of Cardiovascular Prediction and Prevention at the Baker Heart and Diabetes Institute Australia, and the NIHR Cambridge Biomedical Research Centre UK. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All study protocols for PTB and TBM studies were approved by the Institutional Research Board of Pham Ngoc Thach Hospital for TB and Lung Disease, HCMC Health Services and the Oxford Tropical Research Ethics Committee, UK. Approval for the genomics study was granted from the Health Sciences Human Ethics Sub-Committee at the University of Melbourne, Australia (ID:1340458). Written informed consent was obtained from all patients. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Mtb genome data from a subset of PTB patients have been previously described. These genomes are available at the European Nucleotide Archive (accession ID PRJNA355614; ). The remaining Mtb genome data will be available via the NCBI database upon publication of this manuscript.