Snapshot of Defense Systems in Multidrug Resistant Klebsiella pneumoniae

Abstract

ObjectivesThe defense mechanisms in bacterial pathogens protect them from host immune systems, bacteriophage infections and stringent environmental conditions. This study explores the defense-systems in multidrug resistant Klebsiella pneumoniae isolated from Ghanaian hospital ICUs focusing on CRISPR-cas, restriction-modification and toxin-antitoxin systems (TAs). MethodGenomic DNA of K. pneumoniae environmental (NS2) and clinical (PS4) strains were subjected to whole genome sequencing using Illumina and assembled with SPAdes (v3.13.1). CRISPR-cas, restriction-modification and TAs were identified using PADLOC, defense finder and TADB3.0 respectively. ResultsThe strains harbor diverse defense systems. Relative to reference K. pneumoniae with 10 defense systems, NS2 has twelve and PS4, five. CRISPR-Cas systems were found only in NS2, while both strains have type I, II and IV restriction and modification systems. The strains have > 30 characterized and novel TAs (type I, II, IV, VIII) similar to reference K. pneumoniae. NS2 harbors more TAs than PS4 both on chromosomes and plasmids. The strains have comparable resistance determinants to more than six classes of antibiotics. ConclusionThe genome of strains encodes similar clinically relevant defense-systems indicating possibility of microbial exchange from fomites and humans. They could leverage the defense-systems to propagate resistance in high-risk environments such as the hospital. Fomite-resident strain with high levels of resistance could increase infection risk in the ICU; hence, should also be prioritized.