Epidemiological, phylogenetic, and resistance heterogeneity amongAcinetobacter baumanniiin a major US Deep South healthcare center

Abstract

Acinetobacter baumannii(Ab) disease in the U.S. is commonly attributed to outbreaks of one or two monophyletic carbapenem resistance (CR)Ablineages that vary by region. However, there is limited knowledge regardingAbepidemiology and population structure in the U.S. Deep South, and few studies compare contemporary CR and carbapenem-susceptible (Cs)Ab, despite prevalence of the latter. We performed a 12-year time series analysis of Ab cases in a large hospital in Birmingham, AL, and 89 isolates from an ongoing surveillance project started in November 2021 were analyzed by whole genome sequencing and antibiotic susceptibility testing (AST). Cumulative CR rate among 2462 cases since 2011 was 19.4%, with increased rates during winter months resulting from seasonal changes in CsAbincidence. Sequenced CRAbbelonged to clonal complex (CC) 1, CC108, CC250, CC2, and CC499. Most CRAbCCs were comprised of isolates that clustered apart from U.S. counterparts in phylogenetic analysis, despite being identified in unrelated cases occurring ≥3 months apart. In contrast, 38/47 (81%) CsAbisolates each belonged to a distinct CC. CRAbisolates displayed lineage-distinct AST features, including unique carbapenem resistance genetic determinants and presumptive heteroresistance behaviors unique to CC108 and CC499 isolates. This first comprehensive analysis ofAbcases in the U.S. Deep South revealed epidemiological trends consistent with those in other regions and an unusually high degree of phylogenetic diversity among regional CRAbisolates. We also describe emergent U.S. CRAblineages whose unconventional antimicrobial resistance features must be integrated into ongoing diagnostic, treatment, and surveillance efforts.