Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital

Abstract

Background: Klebsiella pneumoniae is a leading cause of extended-spectrum β-lactamase (ESBL)-producing hospital-associated infections, for which elderly patients are at increased risk.

Methods: We conducted a 1-year prospective cohort study, in which a third of patients admitted to 2 geriatric wards in a specialized hospital were recruited and screened for carriage of K. pneumoniae by microbiological culture. Clinical isolates were monitored via the hospital laboratory. Colonizing and clinical isolates were subjected to whole-genome sequencing and antimicrobial susceptibility testing.

Results: K. pneumoniae throat carriage prevalence was 4.1%, rectal carriage 10.8%, and ESBL carriage 1.7%, and the incidence of K. pneumoniae infection was 1.2%. The isolates were diverse, and most patients were colonized or infected with a unique phylogenetic lineage, with no evidence of transmission in the wards. ESBL strains carried blaCTX-M-15 and belonged to clones associated with hospital-acquired ESBL infections in other countries (sequence type [ST] 29, ST323, and ST340). One also carried the carbapenemase blaIMP-26. Genomic and epidemiological data provided evidence that ESBL strains were acquired in the referring hospital. Nanopore sequencing also identified strain-to-strain transmission of a blaCTX-M-15 FIBK/FIIK plasmid in the referring hospital.

Conclusions: The data suggest the major source of K. pneumoniae was the patient's own gut microbiome, but ESBL strains were acquired in the referring hospital. This highlights the importance of the wider hospital network to understanding K. pneumoniae risk and infection prevention. Rectal screening for ESBL organisms on admission to geriatric wards could help inform patient management and infection control in such facilities.

Figure 1.

Core genome phylogeny for Klebsiella isolated from patients in the study wards, indicating multi-locus sequence typing (MLST) and capsule locus (KL) genotypes, and antimicrobial resistance (AMR) phenotypes. The tree is a maximum-likelihood phylogeny inferred from 489069 single-nucleotide variants in 3769 core genes; all branches defining species or lineages (ie, clades of isolates sharing sequence types from MLST) have >90% bootstrap support. Scale bar indicates nucleotide divergence. Clusters of genomes with patristic distance ≤0.1% nucleotide divergence are highlighted. Curved lines indicate isolates from the same patient (green, carriage isolates; purple, infection isolates; black, carriage and infection isolates). K loci were identified using Kaptive software. AMR phenotypes, determined using Vitek2 and interpreted according to Clinical and Laboratory Standards Institute guidelines, are indicated in the heat map and colored by drug class according to the inset legend; Asterisks denote multidrug resistance (resistant to ≥3 drug classes). Amc, amoxicillin–clavulanic acid; Ami, amikacin; Amp, ampicillin; Caz, ceftazidime; Cip, ciprofloxacin; Cro, ceftriaxone; Fep, cefepime; Fox, cefoxitin; Gen, gentamicin; Kz, cefazolin; Mer, meropenem; Nor, norfloxacin; Sxt, trimethoprim-sulfamethoxazole; Tim, ticarcillin–clavulanic acid; Tmp, trimethoprim; Tob, tobramycin; Tzp, tazobactam-piperacillin.

Figure 2.

Multidrug-resistant extended-spectrum β-lactamase producing lineages associated with multiple patients in the study wards. A, Timelines for Caulfield Hospital (CH) and Alfred Hospital (AH) stays for patients in the CH study wards who were infected with sequence type (ST) 29 or colonized with ST323 Klebsiella pneumoniae. Details of all admissions to CH (study site) or AH (referring hospital) during the 1-year study period (1 April 2013 to 31 March 2014) were extracted from the hospital records of these patients. (Note that CH0274 and CH0142 short-term stays are all AH, not intensive care unit [ICU] or CH.) ID, identifier. B, Midpoint-rooted core genome phylogenetic trees for all ST29 and ST323 K. pneumoniae isolated at CH or AH during the study period. Tips are colored by hospital of corresponding specimen collection, according to inset legend. Isolates from the CH study wards are highlighted in gray. Branches are labeled with the number of chromosomal single-nucleotide variants (SNVs) defining the branch (black numbers, above branch) and the number of SNVs in the corresponding FIB_K/FII_K plasmid sequence, relative to the major genotype (red numbers, below branch; see Supplementary Figure S2 for plasmid tree; ∆, plasmid lost; chr, plasmid integrated into chromosome). Dates of isolation are given in dd/mm/yyyy format. Antimicrobial resistance (AMR) phenotypes, determined using Vitek2 and interpreted according to Clinical and Laboratory Standards Institute guidelines, are indicated in the heat map and colored by drug class according to inset legend. Amc, amoxicillin–clavulanic acid; Ami, amikacin; Amp, ampicillin; Caz, ceftazidime; Cip, ciprofloxacin; Cro, ceftriaxone; Fep, cefepime; Fox, cefoxitin; Gen, gentamicin; Kz, cefazolin; Mer, meropenem; Nor, norfloxacin; Sxt, trimethoprim-sulfamethoxazole; Tim, ticarcillin–clavulanic acid; Tmp, trimethoprim; Tob, tobramycin; Tzp, tazobactam-piperacillin.

Figure 3.

Carbapenemase producing lineage sequence type (ST) 340. A, Core genome phylogenetic tree of all ST340 isolates identified at Caulfield Hospital (CH) or Alfred Hospital (AH) during the study period. Branches are labeled with number of chromosomal single-nucleotide variants (SNVs). CSF, cerebrospinal fluid. Dates of isolation are given in dd/mm/yyyy format. Antimicrobial resistance (AMR) phenotypes, determined using Vitek2 and interpreted according to Clinical and Laboratory Standards Institute guidelines, are indicated in the heat map and colored by drug class according to inset legend. Amc, amoxicillin–clavulanic acid; Ami, amikacin; Amp, Ampicillin; Caz, ceftazidime; Cip, ciprofloxacin; Cro, ceftriaxone; Fep, cefepime; Fox, cefoxitin; Gen, gentamicin; Kz, cefazolin; Mer, meropenem; Nor, norfloxacin; Sxt, trimethoprim-sulfamethoxazole; Tim, ticarcillin-clavulanic acid; Tmp, trimethoprim; Tob, tobramycin; Tzp, tazobactam-piperacillin; B, Timelines for hospital stays; all admissions to CH (where study wards were located) or AH (referring hospital) during the 1-year study period (1 April 2013 to 31 March 2014) were extracted from hospital records of these patients. ICU, intensive care unit. C, Comparison of AMR regions in the 2 forms of IncC plasmid identified in these isolates; AMR genes and mobile elements genes are labeled and colored according to the inset legend; white arrows indicate genes of other or unknown functions. CP, carbapenemase producing, defined by presence of blaIMP-4 gene and phenotypic meropenem resistance (Mer in A); ESBLs, extended-spectrum β-lactamases.