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

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.

Bacteraemia due to Microbacterium paraoxydans in a patient with chronic kidney disease, refractory hypertension and sarcoidosis.

INTRODUCTION: Microbacterium spp. are yellow-pigmented Gram-positive coryneform rods found in various environmental sources, such as soil and water samples. They rarely cause human infection, mostly infecting immunocompromised patients and catheter insertion sites, making them challenging to identify in clinical settings. CASE PRESENTATION: We report a case of a 61-year-old female on long-term prednisone therapy for sarcoidosis with minimal exposure to environmental sources, who presented with an overtly infected Hickman catheter site and presyncope. The patient had a central venous catheter (CVC) that had been in place for the previous 6 years for treatment of refractory hypertension and congestive heart failure. Blood cultures obtained from the CVC on initial presentation were positive for a mixed infection, which was subcultured and grew Staphylococcus aureus, Staphylococcus epidermidis, Acinetobacter radioresistens and Leifsonia aquatica based on the Becton Dickinson Phoenix Automated Microbiology System. The L. aquatica, designated as isolate 4120, was further analysed, since infections associated with this organism are uncommon, and it was the only organism to grow from the patient's catheter tip. Matrix-assisted laser desorption ionization-time of flight MS identified isolate 4120 as Microbacterium paraoxydans. To resolve the conflicting results, additional analyses of isolate 4120 were carried out and compared to several reference strains. Isolate 4120 was found to have intermediate susceptibility to ciprofloxacin and non-susceptibility to vancomycin. Morphology, susceptibility, biochemical characteristics and whole-genome sequencing confirmed the clinical isolate as Microbacterium paraoxydans. CONCLUSION: In this case, we identified an organism that is rarely seen in clinical settings and characterized it with a comprehensive laboratory analysis. The patient in our case responded to replacement of the CVC, and treatment with levofloxacin by mouth and intravenous vancomycin.