Detecting, mapping, and suppressing the spread of a decade-longPseudomonas aeruginosanosocomial outbreak with genomics

Abstract

ABSTRACTWhole-genome sequencing is revolutionizing bacterial outbreak investigation but its application to the clinic remains limited. In 2020, prospective and retrospective surveillance detected aPseudomonas aeruginosaoutbreak with 254 isolates collected from 82 patients in 27 wards of a hospital. Its origin was dated to the late 90s, just after the facility opened, and patient-to-patient and environment-to-patient cases of transmission were inferred. Over time, two epidemic subclones evolved in separate hosts and hospital areas, including newly opened wards, and hospital-wide sampling confirmed reservoirs persisted in the plumbing. Pathoadaptive mutations in genes associated with virulence, cell wall biogenesis, and antibiotic resistance were identified. While the latter correlated with the acquisition of phenotypic resistances to 1st (cephalosporin), 2nd (carbapenems) and 3rd (colistin) lines of treatment, maximum parsimony suggested that a truncation in a lipopolysaccharide component coincided with the emergence of a subclone prevalent in chronic infections. Since initial identification, extensive infection control efforts guided by routine, near real-time surveillance have proved successful at slowing transmission.SIGNIFICANCE STATEMENTEvery year, millions of hospital-associated infections are threatening patient lives. This, in a world in which rates of resistances to existing antibiotics are increasing. And this, at a time dubbed the post-antibiotic era when new drugs are scarce. But now is also the golden age of genomics. Here, applying this transformative technology to the clinic revealed an outbreak ofPseudomonas aeruginosa, resistant to last line antibiotics, that had escaped detection for decades. The mapping of transmission chains, through hospital floors, pointed to environmental reservoirs in intensive care units but also provided critical insights into the evolution and adaptation of this pathogen. Genomic data, shared in near real-time with the hospital, resulted in targeted interventions and the prevention of new cases.