Extensive acquisition of carbapenem-resistant Acinetobacter baumannii in Intensive Care Unit patients is driven by widespread environmental contamination

Abstract

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major public health concern globally. Often studied in the context of hospital outbreaks, little is known about the persistence and evolutionary dynamics of endemic CRAB populations. A three-month prospective observational study was conducted in a 28-bed intensive care unit (ICU) in Hangzhou, China. A total of 3985, 964 and 119 samples were collected from the hospital environment, patients and staff, respectively. CRAB were isolated from 10.75% of collected samples (n = 551) and whole-genome sequenced. The ICU CRAB population was dominated by OXA-23-producing global clone 2 isolates (99.27 % of all isolates) that could be divided into 20 distinct clusters. CRAB was persistently present in the ICU, driven by regular introductions of distinct clusters. The hospital environment was heavily contaminated, with CRAB isolated from bed units on 183/335 (54.63 %) sampling occasions but from patients on only 72/299 (24.08 %) occasions. CRAB was spread to adjacent bed units and rooms and following re-location of patients within the ICU. We also observed that, over the course of this study, three different plasmids had transferred between CRAB strains in the ICU. The epidemiology of CRAB in this setting contrasted with previously described clonal outbreaks in high-income countries, highlighting the importance of environmental CRAB reservoirs in ICU epidemiology. There is an urgent need for targeted infection prevention and control interventions in endemic settings that can address the global threat posed by this against this multidrug-resistant opportunistic pathogen.

Changes to an intensive care unitAcinetobacter baumanniipopulation following COVID-19 disruptions and targeted infection prevention interventions

“…To determine the genomic contexts of these bla OXA-23 genes, we examined 19 hybrid-assembled complete GC2 genomes, and screened the collection of 213 GC2 draft genomes with signature sequences indicative of the Tn2006 or Tn2009 insertions identified in our first study. 10 This revealed that the chromosomal positions encountered in the first study accounted for bla OXA-23 carriage in all GC2 isolates collected here (Figure 2A; Table S3). Additionally, one hybrid-assembled genome (DETAB-E2110) contained two copies of Tn2006, with the second copy found in the 13,545 bp plasmid pDETAB10::Tn2006 (Figure S4).…”

“…In August-October 2019, we conducted a 13-week genomic surveillance study of CRAB in a 28-bed intensive care unit (ICU) located in Hangzhou, China. 10 We found that the ICU . CRAB population was dominated by representatives of global clone 2 (GC2), which is one of two clones that account for the majority of CRAB globally.…”

“…In August-October 2019, we conducted a 13-week genomic surveillance study of CRAB in a 28-bed intensive care unit (ICU) located in Hangzhou, China. 10 We found that the ICU CRAB population was dominated by representatives of global clone 2 (GC2), which is one of two clones that account for the majority of CRAB globally. 3 Consistent with global reports, carbapenem resistance in this GC2 population was conferred by the bla OXA-23 carbapenemase gene, which was present in composite transposons Tn2006 or Tn2009 inserted at several different chromosomal sites.…”

“…3 Consistent with global reports, carbapenem resistance in this GC2 population was conferred by the bla OXA-23 carbapenemase gene, which was present in composite transposons Tn2006 or Tn2009 inserted at several different chromosomal sites. 10 Comparative analyses revealed that the GC2 population in this ICU was phylogenetically diverse, and the diversity appeared to have been shaped by independent introductions of multiple distinct GC2 clusters to the ICU. We detected putative CRAB transmission events between bed units and rooms within the ICU, and the spatiotemporal co-location of diverse CRAB clusters facilitated three horizontal gene transfer events over the course of the study.…”

“…We detected putative CRAB transmission events between bed units and rooms within the ICU, and the spatiotemporal co-location of diverse CRAB clusters facilitated three horizontal gene transfer events over the course of the study. 10 Informed by that first study, we planned to implement a set of IPC interventions, then perform a follow-up study to evaluate their effectiveness in reducing the prevalence of CRAB in the ICU. However, ICU operations were interrupted by the outbreak of COVID-19 in early 2020, and access to the ICU was restricted.…”