Aspiration is associated with nontuberculous mycobacterial (NTM) pulmonary disease and airway dysbiosis is associated with increased inflammation. We examined whether NTM disease was associated with a distinct airway microbiota and immune profile.297 oral wash and induced sputum samples were collected from 106 participants with respiratory symptoms and imaging abnormalities compatible with NTM. Lower airway samples were obtained in 20 participants undergoing bronchoscopy. 16S rRNA gene and nested mycobacteriome sequencing approaches characterised microbiota composition. In addition, inflammatory profiles of lower airway samples were examined.The prevalence of NTM⁺cultures was 58%. Few changes were noted in microbiota characteristics or composition in oral wash and sputum samples among groups. Among NTM⁺samples, 27% of the lower airway samples were enriched withMycobacterium. A mycobacteriome approach identifiedMycobacteriumin a greater percentage of samples, including some nonpathogenic strains. In NTM⁺lower airway samples, taxa identified as oral commensals were associated with increased inflammatory biomarkers.The 16S rRNA gene sequencing approach is not sensitive in identifying NTM among airway samples that are culture-positive. However, associations between lower airway inflammation and microbiota signatures suggest a potential role for these microbes in the inflammatory process in NTM disease.

The role of fitness in transmission of drug-resistant strains has been explored in previous studies; but has not been established for F15/LAM4/KZN strains, which were responsible for the extensively drug-resistant tuberculosis (XDR-TB) outbreak in Tugela Ferry, South Africa. The biological fitness of 15 clinical strains representing the F15/LAM4/KZN, Beijing, F11 and F28 families was determined by growth, viability and competition assays and correlated with DNA sequencing of eight genes associated with drug resistance and putative compensatory mechanisms. Similar growth rates were observed among susceptible, multidrug-resistant (MDR) and XDR strains of the KZN and F28 genotypes. In contrast, Beijing and F11 MDR strains demonstrated significantly reduced fitness. Resistant strains exhibited heterogeneous fitness profiles in competition with different susceptible strains, suggesting strain dependence. In addition, co-culture growth rates were consistently higher than independent growth rates in 13/14 competition pairs. All 14 drug-resistant strains retained viability, at a low CFU/mL, when paired with susceptible strains. The persistence of such resistant strains could consequently support the acquisition of additional drug-resistance-conferring mutations and/or the evolution of compensatory mechanisms. Frequently occurring mutations were detected in KZN and F28 resistant strains whereas, the Beijing MDR strain harboured a less common katG mutation and the F11 MDR strain had no katG mutation. Contrary to drug-resistant Beijing and F11 strains, the successful transmission of KZN strains, particularly during the outbreak, may be attributed to the presence of drug-resistance-conferring mutations associated with little or no associated fitness costs. Amplified growth in co-culture may be suggestive of in vivo trans-complementation.

Background: Oral samples show promise for tuberculosis (TB) diagnosis, but data from different sample types and sputum-scarce individuals remain limited. Methods: We evaluated Xpert MTB/RIF Ultra (Ultra) in symptomatic clinic attendees (cohort A, n = 891) and people initiating antiretroviral therapy without symptom screening (cohort B, n = 258). In cohort A, we collected oral washes (OWs) and, separately, tongue swabs (flocked or foam with heat). In cohort B, we collected OWs, 3 flocked tongue swabs (1 heated, 2 pooled), and, separately, buccal swabs and periodontal brushes. Sputum induction was offered, and different culture methods were applied to a subset of cohort B tongue swabs. Results: In cohort A, Ultra sensitivity was 80% (95% confidence interval [CI], 56%–94%) for OWs, 59% (95% CI, 53%–65%) for flocked swabs, and 65% (95% CI, 58%–72%) for foam swabs, with high specificity. Foam swabs detected more people with Ultra sputum semi-quantitation categories of low or less than flocked swabs (53% [95% CI, 41%–64%] vs 37% [95% CI, 29%–46%]). In cohort B, OWs and single heated swabs had sensitivities of 71% (95% CI, 42%–92%) and 64% (95% CI, 35%–87%), respectively. Pooled tongue swabs, buccal swabs, and brushes had lower sensitivity. MGIT960 showed the highest sensitivity (64% [95% CI, 35%–87%]) among culture methods. Oral sampling identified TB in sputum-scarce people: 25% (7/28) positive by flocked or foam swabs (cohort A); 18% (10/56) were OW and 23% (13/56) single swab positive (cohort B). In cohort B, this could double Ultra positivity if induction were unavailable. Conclusions: Ultra on OWs or foam swabs offers higher sensitivity than other oral methods and effectively detects TB in sputum-scarce individuals.