Unveiling the genome of a high-risk pandrug-resistant Klebsiella pneumoniae emerging in the Brazilian Amazon region, 2022

Abstract

BACKGROUND: Pandrug-resistant (PDR) K. pneumoniae has been reported sporadically in many countries and remains rare in Brazil. OBJECTIVES: This study unraveled the genetic determinants involved with the PDR background of a clinical ST11 K. pneumoniae recovered in the Brazilian Amazon region, where K. pneumoniae genomic and epidemiological information is scarce. METHODS: Kp196 was submitted to the antimicrobial susceptibility test by the Disk-Diffusion method and MIC determination. The whole genome sequencing was obtained and the sequence type was determined by cgMLST. Its intrinsic and acquired resistome was assessed by CARD and comparison with wild-type genes. FINDINGS: The analyses revealed that Kp196 belonged to the pandemic ST11 and presented the PDR phenotype. Its acquired resistome was composed of a huge set of clinically relevant resistance determinants, including blaCTX-M-15 and blaNDM-1, all found in the vicinity of mobile platforms. Considering its intrinsic resistome, the multidrug resistance, especially to colistin, tigecycline and fluoroquinolones, was multifactorial and attributed to modifications (indels, missense mutations, and gene disruption) in several housekeeping genes (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35-36-37). The Kp196 intrinsic resistome was also observed in a ST11 environmental strain, although harbouring distinct acquired resistomes. CONCLUSIONS: An accumulation of different resistance mechanisms regarding the intrinsic resistome accounts for a more stable resistome, strongly contributing to the Kp196 PDR phenotype.