Sputum isolates of Mycobacterium abscessus may not reflect a patient’s full bacterial diversity because subclones with differing antimicrobial resistance profiles may also be be present, according to study data published in Clinical Infectious Diseases.

Children with cystic fibrosis (CF) are at a particularly high risk for life-threatening M abscessus infections and recent data from adults concerning inpatient subclones suggests within-patient diversity may also be a relevant concern in pediatric patients with CF. To investigate this concept, whole genome sequencing of 32 isolates of M abscessus from multiple body sites of 2 patients with CF who received a lung transplantation and subsequent management in the United Kingdom in 2015 was performed.

Clustering analysis of single nucleotide variants showed multiple subpopulations in each patient, which were differentially abundant between sputum, lung samples, chest wounds, and pleural fluid. Further, sputum isolates did not represent overall within-patient diversity nor did they allow for detection of mutations previously associated with macrolide resistance (rrl 2058/2059).  The frequency of variants present changed, with some being present at intermediate frequencies before lung transplants. The time of transplant coincided with extensive variation, suggesting that this was disruptive for the microbial community. Transplantation did not clear the infections and both patients died as a result of M abscessus infection.

The investigators stated that, “based on this data, we would question how useful the phenotypic testing of isolates recovered from a limited number of sputum samples is for guiding antimicrobial therapy, as this strategy is unlikely to capture the diversity present in the full sample.” The results suggested that a wider diversity is present in patients with chronic M abscessus infections, although this diversity is not well sampled with sputum and body site influences the subpopulation structure. Therefore, widespread sampling of multiple sites is recommended, as this would provide more accuracy in building antimicrobial resistance profiles and may be necessary for guiding treatment prior to transplant.

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The feasibility of obtaining biopsies, which carries a clinical risk in patients awaiting transplantation, was acknowledged by the investigators. Alternatively, they suggested that deep sequencing of sputum isolates may be a solution, potentially capturing a sufficient fraction of the total within patient diversity, especially with regard to minor variants conferring resistance.

Reference

Shaw LP, Doyle RM, Kavaliunaite E, et al. Children with cystic fibrosis are infected with multiple subpopulations of Mycobacterium abscessus with different antimicrobial resistance profiles. Clin Infect Dis. 2019;69:1678-1686.