Colistin is a last resort antibiotic for the treatment of carbapenemase producing Klebsiella pneumoniae (CRKP) and other extensively drug resistant (XDR) gram-negative bacterial isolates. In line with rising colistin use worldwide, colistin resistant Klebsiella pneumoniae (K. pneumoniae) isolates have emerged. Insertion sequences (IS) integrating into the mgrB gene represents a significant mechanism mediating the emergence of colistin resistance in clinical settings. The disruption of mgrB by ISs has been widely reported worldwide. 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 each IS element. The nucleotide reference sequence for ISKpn25, ISKpn26, ISKpn14 and IS903B were downloaded from IS finder. The BLATSn tool from NCBI was used to retrieve sequences producing significant alignment. 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. Metadata pertaining to each sample was retrieved, including isolate source information to aid the understanding of the clinical threat posed by IS elements. 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. India, USA, and Italy were the isolation origin country for 16.6%, 13.3%, and 9.2%, respectively of the ISKpn25 insertions identified in plasmids. In contrast, ISKpn26, ISKpn14, and IS903B insertion sequences were identified from 89.3%, 44.9% and 23.9% plasmid samples from China. The stratification of carbapenemase genes presence and isolation source between ISKpn25, ISKpn26, ISKpn14 and IS903B bearing plasmids was markedly different. A significant difference between IS elements and the distribution of carbapenemase genes (χ2(3, N = 480) = 155.12, p = <.001) was detected. In addition, a significant difference between IS elements and source isolation distribution (χ2(3, N = 382) = 46.97, p = <.001) was also observed. Post hoc analysis revealed IS903B has a significantly different (p = <.001) carbapenemase and source isolation distribution relative to ISKpn26, ISKpn14 or ISKpn25. The odds ratio revealed 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, the odds ratio reveled 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 plasmids. 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. IS element mobilisation into the mgrB gene has been linked to colistin treatment therapy, while carbapenemase gene presence has been associated with the epidemic success of K. pneumoniae in clinical settings. Plasmids which harbour both carbapenemases and IS elements may engender an extensively drug resistant phenotype during colistin therapy in hospitals.
Colistin resistance beyond carbapenems: molecular epidemiology of multi-drug resistant Klebsiella pneumoniae from an Italian hospital
