Abstract Rationale Nontuberculous mycobacteria (NTM) contribute to progressive pulmonary disease, therapeutic challenges, and unclear infection acquisition. The Healthcare-Associated Links in Transmission (pHALT) study aims to standardize genomic epidemiologic investigation of NTM isolates by profiling NTM prevalent among people with cystic fibrosis (pwCF) across six participating CF centers. Methods Serial respiratory and healthcare environmental (dust/water biofilm) NTM isolates were collected from six US CF Centers. Whole genome sequencing (WGS) was performed to identify NTM to the subspecies level and assess relatedness. Clustering was defined by organism-specific single nucleotide polymorphisms (SNPs). Epidemiological investigation and respiratory/environmental isolate comparison are ongoing. Results As of November 2025, a total of 580 NTM isolates, (523 respiratory, 57 environmental) have undergone WGS. A total of 232 unique pwCF had NTM isolates. Over half of the subjects had one isolate (124/232, 53.4%), some had 1 isolate (108/232, 46.6%), and a few had 1 NTM taxon (32/232, 13.7%). Nineteen NTM taxa were identified in addition to some respiratory isolates identified as “NTM/Unknown.” In terms of respiratory isolates, M. abscessus ssp. abscessus (MAB) was the most prevalent NTM, followed by M. avium (MAV) and M. intracellulare ssp. intracellulare (MINT) (Table 1). Environmental isolates were primarily MAV and M. intracellulare ssp. chimaera (MCHIM). Core genome analysis revealed a total of 24 within-site clusters: 5 MAV, 5 M. chelonae (MCHE), 4 MCHIM, 3 MAB, 3 M. fortuitum (MFORT), 2 M. abscessus ssp. massiliense (MMAS), 1 MINT, and 1 M. porcinum (MPORC). Several taxa (MAB, MMAS, MCHE and MCHIM) formed clusters that span between sites. Some taxa (MCHIM, MAV, MCHE) had clustering with respiratory and environmental isolates. High pangenome similarity (≤10 SNPs & ≥95% shared genome) between isolates was found at greater rates in certain clusters of MPORC, MFORT, MCHE and MAV. Conclusions The pHALT study highlights that even in the era of CF modulators, NTM infections remain a concern. We found genomic diversity of NTM across the sites, with some site-specific variability in NTM prevalence, nonetheless shared clusters between sites were observed suggesting potential common sources of acquisition. Limitations to the study include the small representation of environmental isolates sequenced to date and the overrepresentation of respiratory isolates from two sites. Future analysis includes cluster surveillance. These results emphasize the need for routine subspeciation of clinical NTM isolates for outbreak surveillance. Genetic profiling of clinical and environmental isolates will improve our understanding of NTM acquisition and may guide future infection prevention. This abstract is funded by: Cystic Fibrosis Foundation
Gross et al. (2026) studied this question.