Whole-genome sequencing of carbapenem-resistant gram-negative bacteria in patients with cirrhosis

Objectives In patients with liver cirrhosis, colonization and infection with carbapenem-resistant gram-negative bacteria (CRGN) are associated with high mortality prior and after liver transplantation. Since the epidemiological context of newly occurring carbapenem resistance (CR) often remains unclear, approaches to identify transmission routes are urgently needed to avoid the spread of CRGN.

Methods Among 351 patients evaluated for liver transplantation and screened for CRGN between 2009 and 2018, 18 CRGN were isolated from 17 patients. In these strains, whole-genome sequencing was performed to assess the genotype and phenotype of CR as well as phylogenetic relationship. Clinical records in patients with closely related strains were dissected to identify potential routes of transmission.

Results Carbapenem-resistant Klebsiella pneumoniae (n = 8) and Pseudomonas aeruginosa (n = 7) were the predominating pathogens. In silico detection of antimicrobial resistance genes for all bacterial strains revealed a diverse spectrum of carbapenemases (VIM-1, VIM-2, OXA-48-like, OXA-24-like and OXA-51-like), each of which was unique to exclusively one of these strains. Core genome phylogenetic analysis for strains of each bacterial species suggested a potential relationship of three K. pneumoniae isolates. However, the subsequent in-detail genomic analysis of these strains unveiled differences in several chromosomal loci including a locus involved in colistin resistance. No evidence of plasmid hospitalism conveying CR was detected. From first clinical de novo CRGN detection onwards, patients with closely related strains had never simultaneously been admitted to a particular ward, nor had they crossed paths within in-house facilities on the same day.

Conclusion Our data suggest that the phenotypically identified “carbapenem resistance” in our cohort of liver cirrhosis patients was a result of several different underlying genetic mechanisms. In regard to the apparently close relation of three particular isolates, there was no molecular or clinical evidence of in-hospital transmission of CR genes. Since CRGN transmission may occur in very few cases despite strict in-house hygiene measures, comprehensive hygiene concepts including healthcare and nursing providers are warranted.

Publication History

Article published online:
04 January 2021