Summary
Background
Multidrug-resistant tuberculosis (MDR-TB) is a significant threat to
tuberculosis elimination worldwide. Understanding the transmission pattern
is crucial for its control. We used a genomic epidemiological approach to
assess the recent transmission of MDR-TB and potential risk factors for
transmission.
Methods
In a population-based retrospective study, we performed
variable-number-of-tandem-repeat (VNTR) genotyping, followed by whole-genome
sequencing (WGS) of isolates from all MDR-TB patients in Shanghai, China,
2009-2012. We measured strain diversity within and between genomically
clustered patients. Genomic and epidemiologic data were combined to
construct transmission networks.
Findings
367 (5%) of 7982 patients with tuberculosis had MDR tuberculosis and
324 (88%) of these had isolates available for genomic analysis. 103 (32%) of
the 324 MDR strains were in 38 genomic clusters that differed by 12 or fewer
single nucleotide polymorphisms (SNPs), indicating recent transmission of
MDR strains. Patients who had delayed diagnosis or were older than 45 years
had high risk of recent transmission. 235 (73%) patients with MDR
tuberculosis probably had transmission of MDR strains. Transmission network
analysis showed that 33 (87%) of the 38 clusters accumulated additional
drug-resistance mutations through emergence or fixation of mutations during
transmission. 68 (66%) of 103 clustered MDR strains had compensatory
mutations of rifampicin resistance.
Interpretation
Recent transmission of MDR strains, with increasing drug-resistance,
helps drive the MDR-TB epidemic in Shanghai, China. WGS provides a measure
of the heterogeneity of drug-resistant mutations within and between hosts
and enhances our ability to determine the transmission patterns of
MDR-TB.
Funding
National Science and Technology Major Project, National Natural
Science Foundation of China, and US National Insitutes of Health.