Early OXA-48-Producing Enterobacterales Isolates Recovered in a Spanish Hospital Reveal a Complex Introduction Dominated by Sequence Type 11 (ST11) and ST405 Klebsiella pneumoniae Clones

Abstract

Carbapenemase-producing Enterobacterales (CPE) have become an important public health concern. In our hospital, VIM enzymes were first detected in 2005, Klebsiella pneumoniae carbapenemase (KPC) enzymes in 2009, and OXA-48 enzymes in 2012. We assess the population biology of the first OXA-48-producing Enterobacterales isolates recovered in our hospital (2012 to 2013) where infections by other carbapenemases had been endemic for several years. Over a 21-month period, 71 isolates (61 Klebsiella pneumoniae, 5 Escherichia coli, 2 Klebsiella aerogenes, and 1 each of Enterobacter cloacae, Klebsiella oxytoca, and Citrobacter amalonaticus) recovered from clinical and surveillance specimens from 57 patients (22.8% nonhospitalized) were investigated for OXA-48-like-producing enzymes. Analyses for characterization and determination of the location of the blaOXA-48 gene, plasmid transferability, sequence, and clonal relatedness were performed. Most of the isolates also coproduced CTX-M-15 (57/71, 80.3%) and/or VIM-1 (7/71, 9.8%). K. pneumoniae was predominantly identified as sequence type 11 (ST11) (63.4%) and ST405 (9.8%) and E. coli as ST540, ST1406, ST3163, and ST4301. The blaOXA-48 gene was part of Tn1999.2 located at the tir gene of plasmids (ca. ≥50 kb) of the IncL/M group, also carrying blaVIM-1 and blaCTX-M-15 genes. We selected one ST11 K. pneumoniae isolate for whole-genome sequencing in which we studied the plasmid containing the blaOXA-48 gene. This plasmid was compared with indexed plasmids existing in NCBI database by the use of BRIG and MAUVE. Our data suggest a rapid spread of blaOXA-48 genes between commonly isolated high-risk clones of Enterobacterales species, frequently associated with antibiotic resistance. Moreover, the emergence of the multiresistant ST11 K. pneumoniae clone among nonhospitalized patients emphasizes the difficulty of preventing its dissemination into the community. IMPORTANCE We present results of microbiological analysis of the first Enterobacterales isolates that were isolated in 2012 in our institution expressing OXA-48 carbapenemase. This enzyme confers resistance to carbapenems, an important group of antibiotics widely used in the hospitals. OXA-48 carbapenemase is currently present in many parts of the world, but it is found particularly frequently in the Mediterranean area. It was disseminated at the Ramón y Cajal Hospital and found to be associated with a particular Klebsiella pneumoniae strain, so-called high-risk clone ST11, which was previously found in our institution in association with other enzymes such as CTX-M-15, VIM-1, and KPC-3. This clone might have acquired a plasmid harboring the blaOXA-48 gene. Our results point out the importance of local epidemiology in the dissemination and maintenance of multidrug-resistant bacteria.

Genomic analysis of the initial dissemination of carbapenem-resistant Klebsiella pneumoniae clones in a tertiary hospital

“…Nevertheless, little is known at the genomic level about the initial colonization and subsequent dispersion of these isolates in hospitals. Most studies have analysed the specific bacterial clone and plasmid(s) responsible for the first cases detected [38]. Extending these analyses beyond the initial period and complete genome analysis of the corresponding isolates allows a better characterization of the colonizing strains and genes, revealing the relationships among isolates.…”

Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients

“…These plasmids share a highly conserved backbone and differ mainly by the presence/absence of various insertions; for simplicity, they are all referred to as pOXA-48 throughout the text. This plasmid type is frequently associated with K. pneumoniae high-risk clones 16 , such as the sequence types 11 (ST11), ST15, ST101, and ST405 6 , 15 , 17 , 18 , which are able to readily spread between hospitalized patients producing outbreaks of infections 19 , 20 . Previous epidemiological studies strongly suggested the possibility of within-patient pOXA-48 transfer 20 – 25 , indicating that pOXA-48 would be an ideal study system to investigate the nosocomial dissemination of carbapenem resistance.…”

Dissemination routes of the carbapenem resistance plasmid pOXA-48 in a hospital setting

“…The bla oχA-48 gene is usually encoded in an IncL, broad-host-range conjugative plasmid called pOXA-48 8 (Figure S1). This plasmid is frequently associated with K. pneumoniae high-risk clones 12 , such as the sequence types 11 (ST11), ST15, ST101, and ST405 6,13–15 , which are able to readily spread between hospitalized patients producing outbreaks of infections 16,17 . Previous epidemiological studies strongly suggested the possibility of within-patient pOXA-48 transfer 17–21 , indicating that pOXA-48 would be an ideal study system to investigate the nosocomial dissemination of carbapenem resistance.…”