Emergence of carbapenem-resistant clonal complex 2 in multiple hospitals in São Paulo state, Brazil.

Carbapenem-resistant (CRAB) is a common pathogen prevalent in Brazilian hospitals. Worldwide, dissemination of CRAB is associated with the Clonal Complex 2 (CC2); in South America, however, CC1, 15, 25, and 79 are the most prevalent clones. In July 2020, our reference laboratory received the first CC2 isolates from a COVID-19 hospital, and, in the following months, this clone was detected in 15 other Brazilian institutions. To understand the clonal structure of this emerging pathogen, we characterize 89 isolates by whole-genome sequencing and antimicrobial susceptibility testing. Disk diffusion revealed resistance to all beta-lactams, aminoglycosides, fluoroquinolones, folate pathway antagonists, and tetracyclines, but susceptibility to polymyxin B. Resistome analysis identified diverse antimicrobial resistance genes, including the associated with Tn, and in AbGRI3, conferring resistance to beta-lactams and aminoglycosides, respectively. Fine-scale phylogeny based on single nucleotide polymorphisms (SNPs) revealed that Brazilian CRAB CC2 isolates were closely related, presenting up to 755 SNPs in pairwise comparison. We did not observe hospital-specific subclones, indicating multiple introductions and/or inter-hospital dissemination. This study reports the rapid arrival and spread of CRAB CC2 isolates in multiple hospitals, likely driven by infection control deficiencies experienced during the COVID-19 pandemic.