Sheridan, E. A. | Search bioRxiv

bioRxiv2024

The presence of an ESBL-encoding plasmid reported during a Klebsiella pneumoniae nosocomial outbreak in the United Kingdom

The presence of extended-spectrum {beta}-lactamase (ESBL) encoding plasmids in bacteria contributes towards rising resistance rates, mortality and healthcare costs in clinical settings. An EBSL-encoding plasmid, pESBL-PH was identified during a nosocomial outbreak of Klebsiella pneumoniae ST628 at a United Kingdom general district hospital in 2018. A plasmid from the earliest 2018 K. pneumoniae strain discovered during the outbreak was assembled using both Oxford nanopore long reads and illumina short reads, yielding a fully closed plasmid, pESBL-PH-2018. pESBL-PH-2018 was queried against the complete NCBI RefSeq Plasmid Database, comprising 93,823 plasmids, downloaded on July 16, 2024. To identify structurally similar plasmids, strict thresholds were applied: both a shared hash ratio > 0.9 and a mash similarity [≥] 0.98. This returned 61 plasmids belonging to 13 unique sequence types (STs) hosts. The plasmids were detected in 13 unique countries, dating from 2012-2023, associated with a range of infections including bacteremia. Low numbers of single nucleotide polymorphisms (SNPs) were identified between pESBL-PH-2018 and query plasmids, further confirming their relatedness. The AMR region of the plasmids varied; interestingly IS26 mediated-tandem amplification of resistance genes, including the ESBL blaCTX-M-15 was identified in two independent strains raising their copy number to three. Furthermore, the genomic background of strains carrying a pESBL-PH-2018-like plasmid were analyzed, revealing truncation of the chromosomal ompK36 porin gene and carbapenemase resistance gene carriage on accessory plasmids in 17.85% and 26.78% of strains with a complete chromosome available. This analysis reveals the widespread dissemination of an ESBL-encoding plasmid in a background of resistance-encoding strains, requiring active surveillance.

microbiology↗

bioRxiv2021

Plasmids as donors of Insertion Sequence elements mediating colistin resistance in Klebsiella pneumoniae

Colistin is a last resort antibiotic for the treatment of carbapenemase producing Klebsiella pneumoniae (CRKP). In line with rising colistin use worldwide, colistin resistant Klebsiella pneumoniae (K. pneumoniae) isolates have emerged. The disruption of mgrB by insertion sequences (ISs) has been widely reported worldwide representing a mechanism mediating colistin resistance. Evidence suggests plasmids encode mobilizable IS elements which preferentially integrate into the mgrB gene in K. pneumoniae causing gene inactivation and colistin resistance. Recognised IS elements targeting mgrB include ISL3 (ISKpn25), IS5 (ISKpn26), ISKpn14 and IS903B-like elements. K. pneumoniae represents the single largest species carrying plasmids encoding these IS elements. For IS presence among species, 1000 BLASTn hits were downloaded and filtered for plasmids. Additionally, the top 120 BLASTn non-duplicate circularised plasmid contig hits for each IS element were typed for incompatibility (Inc) group and carbapenemase gene presence. IS903B was found in 28 unique Inc groups, while ISKpn25 was largely carried by IncFIB(pQil) plasmids. ISKpn26 and ISKpn14 were most often found associated with IncFII(pHN7A8) plasmids. Of the 34 unique countries which contained any of the IS elements, ISKpn25 was identified from 26. ISKpn26, ISKpn14, and IS903B insertion sequences were identified from 89.3%, 44.9% and 23.9% plasmid samples from China. Plasmids carrying ISKpn25, ISKpn14, and ISKpn26 IS elements are 12.18, 27.0, and 44.43 times more likely to carry carbapenemase genes relative to plasmids carrying the IS element IS903B. Moreover, plasmids carrying ISKpn26, ISKpn25, and ISKpn14 were 6.10, 28.82, and 31.47 times more likely to be sourced from a clinical environmental setting than the environment relative to IS903B IS harboring plasmid. ISKpn25 present on IncFIB(pQil) sourced from clinical settings is established across multiple countries, while ISKpn26, ISKpn14, and IS903B appear most often in China. High carbapenemase presence in tandem with IS elements may help promote an extensively drug resistant profile in K. pneumoniae limiting already narrow therapeutic treatment options.

microbiology↗