Ultrasensitive DNA assay finds potential hidden TB burden in US hospital patients

Detection of Mycobacterium tuberculosis DNA in more than one in ten respiratory samples has raised concern that tuberculosis disease remains substantially underdiagnosed in the USA

Researchers at Boston University, Massachusetts, USA, have reported an unexpectedly high prevalence of Mycobacterium tuberculosis DNA in hospitalised patients in Boston, a finding that has challenged assumptions about tuberculosis (TB) burden in low-incidence settings. The study has indicated that TB disease may be under-recognised in the USA and has prompted renewed scrutiny of current diagnostic paradigms.

The team employed an ultrasensitive molecular platform known as the ‘Totally Optimized Polymerase Chain Reaction TB assay’ which they have developed to improve detection of low-level bacterial DNA. Analysis revealed the presence of TB DNA in between 12 and 16 per cent of respiratory samples obtained from predominantly US-born patients treated at Boston Medical Center. This proportion stands in stark contrast to the low incidence rates typically reported for the region as lower than 0.003 per cent.

Particularly notable was the observation that all three patients diagnosed during the study period with acute chest syndrome, a severe complication associated with sickle cell disease, tested positive for TB DNA. This association has raised concern about a possible underappreciated infectious component in a condition that carries substantial morbidity and mortality risk.

“We began this research with the intent of sourcing respiratory samples to support the ongoing development of a novel molecular assay for TB,” said Dr Guillermo Madico, a scientist at Boston University’s National Emerging Infectious Diseases Laboratories and co-inventor of the assay.

“What we found was completely unexpected. Our ultrasensitive test is detecting Mycobacterium tuberculosis DNA in patients who are unlikely to receive a TB diagnosis using current methods. This opens the possibility that there could be thousands of Americans infected with forms of TB disease that remain hidden from our current diagnostic tools – putting them at risk of more serious complications or potential transmission to others,” he said.

TB remains the leading cause of death from an infectious disease worldwide. In the USA, the disease killed nearly 600 individuals and affected more than 9,600 people in 2023, while an estimated 13 million individuals carry a latent infection. Despite sustained public health efforts, progress towards elimination has stalled, with reported infections having increased between 2021 and 2024.

The investigation, led by Dr Madico and Dr Edward C. Jones-López, was comprised of three studies conducted over a six-year period. The researchers analysed 297 respiratory samples from patients treated at Boston Medical Center and St Elizabeth’s Medical Center, Brighton, Massachusetts, USA. The assay demonstrated markedly greater sensitivity than conventional mycobacterial culture and standard molecular diagnostics, with the ability to detect TB DNA in samples that had tested negative by established approaches.

Demographic analysis has shown that 75 per cent of patients with detectable TB DNA were aged 50 years or older. This finding aligns with established epidemiological patterns in the USA, where many active TB cases arise through reactivation of latent infection acquired earlier in life. However, the study also identified a discrepancy in diagnostic concordance, as most DNA-positive patients returned negative results in conventional TB infection tests such as the tuberculin skin test and interferon-gamma release assays. This discordance, which has been associated with advanced age and poorer clinical outcomes, remains incompletely understood.

“These findings suggest we may be missing a significant burden of TB disease, particularly in older Americans and in patients with certain underlying conditions,” said Dr Jones-López, who conducted the research while at Boston Medical Center and Boston University Chobanian and Avedisian School of Medicine. 

“Most concerning is the potential association with acute chest syndrome in sickle cell patients. If confirmed and expanded upon in larger studies, this finding could lead to better health outcomes for patients with this potentially life-threatening condition,” he added.

The authors have emphasised that the findings remain preliminary and require validation through larger, prospective, multicentre investigations incorporating detailed clinical, radiological, immunological and microbiological correlation. Nevertheless, they have argued that the potential implications for both clinical practice and public health justify prompt dissemination.

The assay targets a gene involved in the assembly of the M. tuberculosis cell wall and has already undergone validation in more than 400 patients with suspected TB across study sites in Uganda, Brazil, as well as the USA. Although it remains a research-use-only platform pending its regulatory approval, the technology exemplifies the increasing capability of molecular diagnostics to detect infections at levels beyond the reach of traditional culture-based methods.

The findings have also highlighted a potential limitation in current diagnostic strategies which rely heavily on mycobacterial culture that requires viable organisms capable of growth under laboratory conditions. By contrast, the molecular assay can detect extremely low levels of bacterial DNA which may indicate earlier stages of disease or atypical presentations that do not conform to established diagnostic criteria. This further raises fundamental questions about how TB is defined and diagnosed in both clinical and epidemiological contexts.

For further reading please visit: 10.1038/s41467-026-70890-6