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Molecular epidemiology study of rifampicin-resistant TB in Vietnam shows high resistance to other drugsVietnam’s TB Crisis Hides a Dangerous Pattern

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Key Takeaway
Consider that RR-TB in Vietnam frequently carries resistance to other first- and second-line drugs, necessitating comprehensive resistance testing.

This molecular epidemiology study used whole genome sequencing (WGS) to characterize 252 rifampicin-resistant (RR) Mycobacterium tuberculosis isolates from 10 provinces in Vietnam, including samples from the VQUIN MDR trial. The primary aim was to assess the molecular epidemiology of RR-TB and the concordance between genotypic and phenotypic resistance predictions.

Key findings include high concordance between Xpert MTB/RIF and WGS for rifampicin resistance prediction (positive predictive value 96.8%). Among RR isolates, 96.3% (235/244) harbored mutations associated with resistance to at least one other first- or second-line antibiotic. Concordance between phenotypic drug susceptibility testing (DST) and genomic predictions was high for rifampicin (87.0%), isoniazid (98.7%), and levofloxacin (94.8%), and for linezolid (100%), pretomanid (100%), and bedaquiline (93.3%) in a subset of 77 isolates. Additionally, RR strains were more likely to belong to lineage 2.2.1 compared to rifampicin-susceptible strains.

Limitations include that phenotypic DST was performed on only a subset of isolates (77), and the study did not report p-values or confidence intervals for most comparisons. As an observational molecular epidemiology study, causal inferences cannot be drawn.

These findings reinforce the importance of prompt and broad detection of drug resistance to guide effective treatment regimens for RR-TB in Vietnam.

Nguyen, a 34-year-old motorcycle driver in Hanoi, spent months coughing, losing weight, and missing work. When he finally went to the clinic, tests showed he had tuberculosis. But not just any kind — one that didn’t respond to standard drugs. By the time doctors found the right treatment, his infection had spread.

He’s not alone. Vietnam ranks among the top 20 countries with the most cases of drug-resistant TB. Nearly 10,000 people there face this form of TB each year. Standard treatments often fail. Delays in diagnosis mean patients suffer longer and can spread the disease before getting help.

This doesn’t mean this treatment is available yet.

Most clinics test for resistance to just one or two drugs. The assumption has long been: if TB resists rifampicin, the cornerstone drug, doctors start a second-line regimen. But what if that’s not enough?

But here’s the twist: new research shows most rifampicin-resistant TB in Vietnam doesn’t stop there. It’s already resistant to other key antibiotics — even before treatment begins.

Think of TB bacteria like locks and keys. Antibiotics are keys that fit specific bacterial locks. When a mutation occurs, the lock changes shape. The key no longer works. Rifampicin is one key. But in Vietnam, many of these bacterial “locks” have changed in multiple places at once.

That means the bacteria are not just resistant to rifampicin — they’re often resistant to isoniazid, levofloxacin, and even newer drugs like linezolid and bedaquiline. It’s like a lock that no longer fits any of the keys in your ring.

Scientists studied 252 TB samples from patients across 10 provinces. These weren’t just from big cities — they included rural areas often left out of research. Each sample was tested using whole genome sequencing, a method that reads the bacteria’s DNA like a book.

What they found stunned experts. Of the 244 confirmed rifampicin-resistant cases, 96% were also resistant to at least one other major drug. Even more surprising: one strain, called lineage 2.2.1, dominated across regions. It’s spreading — and it’s tough to treat.

One strain to rule them all

This strain isn’t new, but its reach is. It’s especially common in Hanoi and Ho Chi Minh City, but now shows up in provinces far from urban centers. That suggests it’s not just local spread — people may be carrying it from city to countryside, or vice versa.

The good news? Modern tests like Xpert MTB/RIF caught rifampicin resistance accurately in 97% of cases. And when researchers checked resistance predictions from DNA against lab tests, the match was strong — over 90% for most drugs.

For newer drugs, the news was even better. Linezolid and pretomanid resistance predictions were 100% accurate in tested samples. Bedaquiline was close behind at 93%. That means genetic testing could safely guide treatment without waiting weeks for lab cultures.

But there's a catch.

While DNA testing is fast and accurate, it’s still not available in many clinics across Vietnam. Most patients still rely on older, slower methods. That delay can cost lives. And even when tests are done, access to second-line drugs isn’t guaranteed.

Experts say this data changes the game. If most resistant TB is multi-resistant from the start, doctors need broader testing upfront — not step-by-step guesses. Waiting to see what fails wastes precious time.

For patients, this means faster, smarter treatment could be possible — if the system adapts. It’s not about new drugs alone. It’s about using the right ones sooner.

Still, there are limits. This study looked at lab-cultured samples, which can be harder to get from very sick patients. And while genome sequencing is powerful, it’s not perfect. Rare mutations might still slip through.

The road ahead starts now. Vietnam’s health leaders are using this data to push for wider access to genetic testing. Clinical labs are being trained. The goal: make advanced testing routine, not rare.

New trials are already in motion to test whether starting broad treatment based on DNA results leads to better outcomes. If so, this approach could spread to other high-burden countries — from Indonesia to South Africa.

For millions at risk, the message is clear: knowing more, faster, could save lives. And in the fight against TB, time is everything.

Study Details

EvidenceLevel 5
PublishedApr 2026
View Original Abstract ↓
Background: Vietnam is a top 20 burden country for multi-drug resistant/rifampicin-resistant tuberculosis (MDR/RR-TB), with nearly 10,000 cases a year. With the emergence of new diagnostic assays for M. tuberculosis and resistance, along with new drugs for both treatment and prevention, we sought to better understand the molecular epidemiology of RR-TB in this high-burden setting, through the study of clinical trial isolates from the VQUIN MDR trial. Methods: We assembled a sample of cultured isolates, collected from patients with confirmed RR-M. tuberculosis within 10 provinces, enriching for isolates from outside of the 2 major cities, Hanoi and Ho Chi Minh City. We subjected these isolates whole genome sequencing (WGS) and bioinformatic analysis, with a subset subject to phenotypic drug susceptibility testing to evaluate phenotypic/genotypic concordance. New genome sequences were phylogenetically contextualised to publicly-available M. tuberculosis genome sequences sampled in Vietnam from National Center for Biotechnology Information (NCBI) Sequence Read Archives (SRA). Results: Isolates from 252 RR-TB cases passed quality controls and were available for analysis. Xpert MTB/RIF had a high concordance with WGS-based rifampicin-resistance prediction (PPV=96.8%). Of the 244 isolates confirmed to be rifampicin resistant, a high proportion (235/244 = 96.3%) had mutations associated with resistance to at least one other first- or second-line antibiotic. Phenotypic drug susceptibility testing (DST) for rifampicin, isoniazid, and levofloxacin was completed for 77 isolates with a high concordance demonstrated between DST and genomic-based resistance predictions (67/77, 87.0% RIF; 76/77, 98.7% INH; 73/77, 94.8%LFX). High concordance was also observed with new and repurposed antibiotics linezolid (100%, 60/60), pretomanid (100%, 60/60), and bedaquiline (56/60, 93.3%). Rifampicin-resistant strains were more likely to be lineage 2.2.1, compared to rifampicin-susceptible M. tuberculosis strains in Vietnam, particularly in the major cities. Conclusions: The high prevalence of secondary drug-resistance beyond RIF and INH, along with the dominance of one major lineage across geographic regions, provides insights on the spread of MDR/RR-TB in Vietnam and reinforces the importance of prompt and broad detection of drug-resistance to inform the timely initiation of effective drug regimens.
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