Extended-spectrum β-lactamase genes traverse theEscherichia colipopulations of ICU patients, staff and environment

Abstract

Over a three-month period, we monitored the population of extended-spectrum beta-lactam-resistant Escherichia coli (ESBL-EC) associated with the patients, staff and environment of an intensive care unit (ICU) in Guangzhou, China. Thirty-four clinical isolates were obtained from the same hospital 12 months later. A total of 165 isolates were characterised and whole-genome sequenced, with 24 isolates subjected to long-read sequencing. The diverse population included representatives of 59 different sequence types (STs). ICU patient and environmental isolates were largely distinct from staff isolates and clinical isolates. We observed five instances of highly similar isolates (0-13 core-gene SNPs) being obtained from different patients or bed unit environments. ESBL resistance in this collection was largely conferred by blaCTX-M genes, which were found in 96.4% of all isolates. The contexts of blaCTX-M genes were diverse, situated in multiple chromosomal positions and in various plasmids. We identified blaCTX-M-bearing plasmid lineages that were present in multiple STs across the surveillance, staff and clinical collections. Closer examination of ISEcp1-blaCTX-M transposition units shed light on the dynamics of their transmission, with evidence for the acquisition of chromosomal copies of blaCTX-M genes from specific plasmid lineages, and for the movement of blaCTX-M-55 from a ST1193 chromosome to a small mobilisable plasmid. A carbapenem-resistant ST167 strain isolated from a patient that had been treated with meropenem and piperacillin-tazobactam contained seven copies of blaCMY-146, which appears to have been amplified by IS1. Our data revealed limited persistence and movement of ESBL-EC strains in the ICU environment, but we observed circulating plasmid lineages playing an essential and ongoing role in shaping the cephalosporin-resistance landscape in the population examined.

Longitudinal genomic surveillance of a UK intensive care unit shows a lack of patient colonisation by multi-drug resistant Gram-negative pathogens

“…We inves+gated the colonisa+on dynamics of these isolates, iden+fying 11 pa+ents that had been colonised by more than one E. coli ST during their ICU stay. There was less dynamic ac+vity of colonising strains in QEHB ICU than what has been observed previously in nosocomial transmission events (6,(38)(39)(40). There was also no iden+fiable pahern in the gain (Figures 4 and S9) or loss (Figure 5) of E. coli strains.…”

“…The prevalence of MDR in ICUs globally is increasingly concerning, with mul+ple ICU colonisa+on studies iden+fying high incidences of MDR (5)(6)(7)9). Here, we inves+gated whether the ICU at QEHB had the same burden of MDR as that observed elsewhere.…”

“…Whilst this represents reasonable diversity in a single ICU, it is considerably less diverse that what has been reported elsewhere. A study in Guangzhou, China iden+fied, for example, 59 different STs over a three-month period (6). At QEHB ICU the most abundant STs were the common commensals ST69 and ST58, which were both observed at much lower levels in the Guangzhou ICU.…”

“…We focussed on the common commensal Gram-nega+ve organisms E. coli and Klebsiella which can cause invasive disease (e.g. pneumonia, bloodstream infec+ons), transmit between pa+ents, and are known to circulate in the ICU environment (5,6,34). E. coli and Klebsiella have been reported to exhibit high levels of MDR, including carbapenem resistance, in other ICU environments.…”

“…Mul+drug resistant organisms (MDROs) frequently carry a variety of virulence factors which help them to easily colonise the gut (3,4) and with the poten+al to be a risk of infec+on in this vulnerable popula+on. Recent studies in South East Asia and China have highlighted significant transmission of MDROs (including carbapenem resistant Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii) at high levels in the ICU environment (5)(6)(7)(8)(9). In some cases this transmission has been ahributed to breaches of infec+on preven+on and control (IPC) measures.…”