Unmasking the Hidden Burden: What "Culture-Negative" Really Means for TB
- Ray Sullivan
- Jun 21
- 3 min read
Tuberculosis (TB) remains a major global health challenge, and accurate diagnosis is crucial for effective treatment and preventing spread. While highly sensitive molecular tests like Cepheid’s GeneXpert MTB/RIF Ultra (Ultra) have revolutionized TB detection, especially for patients with low bacterial levels (paucibacillary TB), they've also introduced a puzzling phenomenon: detecting Mycobacterium tuberculosis (Mtb) DNA in sputum even when traditional cultures come back negative.
These "discordant" results (Ultra-positive, culture-negative) have long been a mystery. Do they indicate false positives, or a true, but hard-to-detect, TB infection? Yingda Xie, at the Rutgers New Jersey Medical School, Public Health Research Institute, led an international research team to shed light on this crucial question.
The researchers conducted a detailed sub-study in three high-burden TB settings in Africa (Uganda, Kenya, and South Africa). They identified 66 symptomatic adults with these "discordant" results. To understand their significance, these individuals were compared to two control groups:
• Sputum-negative controls: Individuals who were negative on all TB tests, including Ultra and cultures.
• Sputum-positive controls: Individuals who tested positive on Ultra and had Mtb growth in cultures.
Over 12 months, participants were assessed for various TB biomarkers, including:
• Mtb bacterial biomarkers: Mtb growth in augmented or follow-up sputum cultures, and Mtb mRNA in baseline sputum.
• TB-associated host transcriptional signatures: Gene expression patterns in the host's blood that indicate TB infection.
The study yielded several key and unexpected findings:
• High Prevalence of Biomarkers in Discordants: At baseline, 51.5% of discordant participants had at least one TB-associated biomarker, with 16.7% showing Mtb bacterial biomarkers. Over the 12-month follow-up, 26.5% of untreated discordant participants continued to show Mtb biomarkers.
• No Significant Difference from "Sputum-Negative" Controls: Perhaps the most striking discovery was that symptomatic "sputum-negative" individuals had similar, unexpectedly high rates of TB biomarkers and microbiologic progression compared to the discordant group. For instance, 26.9% of sputum-negatives had Mtb biomarkers at baseline, and 42.3% had a positive host-response signatures, which was not statistically different from the discordant group.
• Sputum-Negatives Becoming Ultra-Positive: An astounding 30% of untreated sputum-negative participants converted to Ultra-positive at their month 2 follow-up visit. This suggests a fluid line between these groups, often separated only by the variability in detecting low bacterial burdens.
• Limited Progression to Culture-Confirmed TB: Despite the high biomarker prevalence, only one untreated discordant and one untreated sputum-negative participant (about 3% and 2% respectively) developed culture-confirmed TB over 12 months. This aligns with historical estimates of untreated TB progression rates.
These findings challenge the initial hypothesis that Ultra-positive, culture-negative results specifically indicate active or incipient TB. Instead, the study suggests that a substantial proportion of all symptomatic, culture-negative individuals may have undiagnosed TB, regardless of their initial Ultra status.
This hidden population could have significant implications:
• Potential for Transmission: Recent evidence shows that Mtb can be aerosolized even from sputum-negative individuals. If many culture-negative individuals are indeed infected, they could contribute to ongoing TB transmission, potentially leading to millions of missed cases annually.
• Need for More Comprehensive Diagnostics: The study highlights a critical need for more comprehensive diagnostic approaches that can reliably detect sputum culture-negative TB, considering its infectiousness, pathology, and risk of progression. This goes beyond simply identifying Mtb DNA and calls for a deeper understanding of the disease's trajectory in these patients.
• Low CD4 Counts Associated with Biomarkers: A post-hoc analysis revealed that culture-negative individuals with positive TB biomarkers had significantly lower median CD4 counts, regardless of their Ultra status, suggesting a link to immune status.
In conclusion, this research broadens our understanding of TB, suggesting that many symptomatic individuals deemed "culture-negative" may indeed harbor undetected Mycobacterium tuberculosis. This points to a considerable, undiagnosed population requiring further investigation to guide future diagnostic strategies and public health interventions.
Xie YL, Modi N, Lopez K, Reiss R, Robledo J, Eichberg C, Hapeela N, Nakabugo E, Anyango I, Arora K, Odero R, Van Heerden J, Zemanay W, Kaipilyawar VS, Kennedy S, Banada P, Nakiyingi L, Joloba ML, Centner C, McCarthy K, Ellner J, Salgame P, Alland D, Dorman SE. Prominence of Mycobacterium tuberculosis biomarkers among sputum culture-negative clinic attendees, independent of Ultra status. J Infect Public Health. 2025 Jul;18(7):102791. doi: 10.1016/j.jiph.2025.102791. Epub 2025 Apr 24. PMID: 40315556.
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