Systematic Comparison of Epidemic and Non-Epidemic Carbapenem Resistant Klebsiella pneumoniae Strains

Abstract

Over the past few decades, extensively drug resistant (XDR) resistant Klebsiella pneumoniae has become a notable burden to healthcare all over the world. Especially carbapenemase-producing strains are problematic due to their capability to withstand even last resort antibiotics. Some sequence types (STs) of K. pneumoniae are significantly more prevalent in hospital settings in comparison to other equally resistant strains. This provokes the question whether or not there are phenotypic characteristics that may render certain K. pneumoniae more suitable for epidemic dispersal between patients, hospitals, and different environments. In this study, we selected seven epidemic and non-epidemic carbapenem resistant K. pneumoniae isolates for extensive systematic characterization for phenotypic and genotypic qualities in order to identify potential factors that precede or emerge from epidemic successfulness. Studied characteristics include growth rates and densities in different conditions (media, temperature, pH, resource levels), tolerance to alcohol and drought, inhibition between strains, ability to compensate pH, as well as various genomic features. Overall, there are clear differences between isolates, yet, only drought tolerance was found to notably associate with non-epidemic K. pneumoniae strains. We further report a preliminary study on the potential to control K. pneumoniae ST11 with an antimicrobial component produced by a non-epidemic K. pneumoniae. This component initially restricts bacterial growth, but stable resistance develops rapidly in vitro.

High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study

“…KL51 (n = 111/307, 36.1%) and KL64 (n = 104/307, 33.8%) were dominant K-loci types in this study, whereas KL1, KL2, KL5, KL20, KL17, KL51, KL54, KL57 and KL64 are the reported K-loci types from other Indian studies [ 31 ]. KL51 is reported from isolates from the United States, Sweden, United Kingdom [ 34 ], Thailand [ 35 ], and Lebanon [ 36 ]. The phylogenetic tree of the 307 isolates shows the correlation between capsular locus type and sequence type, for example of KL51 with ST231, and of KL64 with ST147 and ST395 ( Supplementary Figure 1 ).…”

Strain-level bacterial typing directly from patient samples using optical DNA mapping

“…Whole-genome sequences of the samples were used to assign each sample to its correct SG for each of the tested SG resolutions to confirm the ODM data. The E. coli samples EC3-4, EC7-11, and EC18 had been previously sequenced by Fröding et al 34 (assembly accession numbers GCA_013171465.1, GCA_013172225.1, GCA_01317276 5.1, GCA_013174205.1, GCA_013176495.1, GCA_013176595.1, GCA_013176845.1, and GCA_013176885.1) and the K. pneumoniae samples KP2-3, KP7, and KP9 by Koskinen et al 35 (GCA_016056235.1, GCA_015831445.1, GCA_016056215.1, and GCA_015831545.1). These assemblies were all downloaded from GenBank.…”

“…These assemblies were all downloaded from GenBank. The samples KP1, KP4-6, and KP8 were sequenced and assembled using the same method as the other K. pneumoniae samples 35 . The remaining samples were sequenced for this study in the following way.…”

A Nationwide Genomic Study of Clinical Klebsiella pneumoniae Carrying bla OXA-232 and rmtF in China

“…In addition, the novel ST (ST-V, gapA1-infB1-mdh-1-pgi8-phoE1-rpoB1-tonB447) was a single-locus variant of ST15 with variation at the tonB gene. KL51 was reported from the United States, Sweden, the United Kingdom ( 33 ), Thailand ( 34 ), and Lebanon ( 35 ). KL112 has been reported from Russia ( 36 ).…”