Rapid expansion and extinction of antibiotic resistance mutations during treatment of acute bacterial respiratory infections

Abstract

Acute bacterial infections are often treated empirically, with the choice of antibiotic therapy updated during treatment. The effects of such rapid antibiotic switching on the evolution of antibiotic resistance in individual patients are poorly understood. Here we find that low-frequency antibiotic resistance mutations emerge, contract, and even go to extinction within days of changes in therapy. We analyzed Pseudomonas aeruginosa populations in sputum samples collected serially from 7 mechanically ventilated patients at the onset of respiratory infection. Combining short- and long-read sequencing and resistance phenotyping of 420 isolates revealed that while new infections are near-clonal, reflecting a recent colonization bottleneck, resistance mutations could emerge at low frequencies within days of therapy. We then measured the in vivo frequencies of select resistance mutations in intact sputum samples with resistance-targeted deep amplicon sequencing (RETRA-Seq), which revealed that rare resistance mutations not detected by clinically used culture-based methods can increase by nearly 40-fold over 5–12 days in response to antibiotic changes. Conversely, mutations conferring resistance to antibiotics not administered diminish and even go to extinction. Our results underscore how therapy choice shapes the dynamics of low-frequency resistance mutations at short time scales, and the findings provide a possibility for driving resistance mutations to extinction during early stages of infection by designing patient-specific antibiotic cycling strategies informed by deep genomic surveillance.

WITHDRAWN: How antimicrobial heteroresistance promotes bacterial adaptation to antimicrobial therapy – or not

“…In our case, HR favored variants in oprD and the MexAB-OprM efflux pump system. Variants in these genes are commonly found in P. aeruginosa from acute infections treated with the β-lactam antimicrobials meropenem and ceftazidime 39, 40, 41 . Moreover, oprD variants were previously found to confer fitness advantages in vivo 42 , especially in P. aeruginosa from lung infections 41 .…”

Evolution of Habitat-Dependent Antibiotic Resistance in Pseudomonas aeruginosa

“…This bacterium is able to grow in several body locations, being one of the main causative agents of chronic infections in the lungs of cystic fibrosis (CF) or chronic obstructive pulmonary disease (COPD) patients ( 3 ) and also being a major cause of urinary tract infections (UTIs) ( 9 , 10 ). In addition to its metabolic versatility, P. aeruginosa presents a characteristic low susceptibility to a large variety of antibiotics ( 11 – 14 ), and it has a high capacity to acquire further resistance to antibiotics, something that frequently occurs by the acquisition of mutations in patients under treatment ( 15 – 17 ).…”

Recent advances in therapeutic targets identification and development of treatment strategies towards Pseudomonas aeruginosa infections

“…Additionally, frequency of resistance emergence in P. aeruginosa populations can shift within days based on the nature and duration of antibiotic therapy, since rare mutations not found using culture-based strategies can expand over 5–12 days in riposte to antibiotic changes, while mutations conferring resistance to antibiotics that were not administered decrease and undergo extinction [ 43 ]. Another study reported that the higher tolerance of P. aeruginosa biofilm cells towards multiple antibiotics, such as gentamicin and colistin, is due to the presence of strains with inactivated flgE gene that display cell aggregation, reduced ability to adhere to surfaces, and a faster biofilm growth [ 44 ].…”