Genomic surveillance reveals clusters driving drug-resistant tuberculosis in Argentina

Tuberculosis that resists the main drugs used to treat it is a persistent public health threat. Between 2013–2022, researchers led by Noemí Yokobori and collaborators set out to map the genetic fingerprints of multidrug-resistant Mycobacterium tuberculosis circulating in Argentina. They analyzed 1,189 bacterial isolates collected over that decade to understand how resistance was spreading and which versions of the bacterium were most common. The team used a mixed laboratory strategy, combining PCR-based methods with whole-genome sequencing, and brought together epidemiological, geographic distribution and microbiological data to build a fuller picture. Their work sits at the start of a new genomic era for tuberculosis surveillance, where detailed genetic data can be used to spot transmission chains, detect imported strains and identify clusters of related cases. The study’s scope across years and regions allowed the team to see both long-term patterns and more recent events, including active local transmission and shifts in the importance of particular strain groups over time.

The study applied PCR-based methods together with whole-genome sequencing—building on next-generation sequencing technologies—to genotype each isolate and link genetic patterns to patient and location data. Of the 1,189 multidrug-resistant Mycobacterium tuberculosis isolates, 75.7% belonged to a cluster, showing that most cases were part of chains of related infections rather than isolated or unique events. The Euro-American lineage4 was virtually predominant across the samples. Four principal clusters, named M, Ra, Rb and Callao2 strains, together accounted for 45.9% of the newly diagnosed cases in the dataset, although their relative weight changed over the study period. The analysis found that the proportion of orphan (single, unclustered) and clustered cases varied across Argentina’s regions. A preliminary genomic analysis highlighted several local transmission chains of the Callao2 strain, which had been imported from Peru, and identified a superspreading event occurring circa 2020. The investigators note that a good performance of the current second-line regimes can be expected for most of the cases examined.

These findings show the practical value of combining PCR-based methods and whole-genome sequencing in routine surveillance: genetic data can reveal which strains are fueling outbreaks, where imported strains take hold, and where public health action should focus. The dominance of a few clusters—especially M, Ra, Rb and Callao2—means targeted investigations and contact tracing around those groupings could interrupt transmission chains. The discovery of active local transmission and a superspreading event around 2020 for the imported Callao2 strain highlights how quickly resistant strains can amplify if not detected. Because the study suggests most cases remain susceptible to existing second-line regimes, timely detection and treatment could prevent further resistance amplification. The authors recommend heightening suspicion of drug-resistance and enhancing timely and active surveillance in specific risk groups as concrete steps to manage tuberculosis in Argentina and reduce both spread and the evolution of more resistant forms.