A vanA vancomycin-resistant Enterococcus faecium ST80 outbreak resulting from a single importation event

Emergence and ongoing outbreak of ST80 vancomycin-resistant Enterococcus faecium in Guangdong province, China from 2021 to 2023: a multicenter, time-series and genomic epidemiological study

BACKGROUND

Surveillance systems revealed that the prevalence of vancomycin-resistant Enterococcus faecium (VREfm) has increased. We aim to investigate the epidemiological and genomic characteristics of VREfm in China.

METHODS

We collected 20,747 non-redundant E. faecium isolates from inpatients across 19 hospitals in six provinces between January 2018 and June 2023. VREfm was confirmed by antimicrobial susceptibility testing. The prevalence was analyzed using changepoint package in R. Genomic characteristics were explored by whole-genome sequencing.

RESULTS

5.59% (1159/20,747) of E. faecium isolates were resistant to vancomycin. The prevalence of VREfm increased in Guangdong province from 5% before 2021 to 20-50% in 2023 (p < 0.0001), but not in the other five provinces. Two predominant clones before 2021, ST17 and ST78, were substituted by an emerging clone, ST80, from 2021 to 2023 (88.63%, 195/220). All ST80 VREfm from Guangdong formed a single lineage (SC11) and were genetically distant from the ST80 VREfm from other countries, suggesting a regional outbreak. All ST80 VREfm in SC11 carried a new type of plasmid harbouring a vanA cassette, which was embedded in a Tn1546-like structure flanked by IS1678 and ISL3. However, no conjugation-related gene was detected and no transconjugant was obtained in conjugation experiment, indicating that the outbreak of ST80 VREfm could be attributed to clonal transmission.

CONCLUSIONS

We revealed an ongoing outbreak of ST80 VREfm with a new vanA-harbouring plasmid in Guangdong, China. This clone has also been identified in other provinces and countries, foreboding a risk of wider spreading shortly. Continuous surveillance is needed to inform public health interventions.

A novel molecular assay conducted on the BD Max system to facilitate reflex testing for vanA and vanB in clinical isolates of enterococci

Infections caused by vancomycin-resistant enterococci (VRE) are common. Real-time PCR assays targeting vanA and vanB facilitate screening of patients in healthcare settings to limit the risk of dissemination, especially amongst those at high-risk of infection or with limited treatment options. Such assays are commonly performed as reflex testing procedures where they augment phenotypic techniques and shorten turnaround time to benefit timely clinical management. 'Random access' and 'sample-to-result' real-time PCR platforms are suited for this application as they are of low complexity and less technically demanding. Modelled on these attributes, we configured a real-time PCR assay (VRE BD) for detection of vanA/B in clinical isolates of enterococci, adapted for the BD Max System (Becton Dickinson). We applied an unconventional approach by testing suspensions of microorganisms in water to circumvent the traditional pre-analytical genomic extraction process. Our objective of this study was to assess the performance of this assay for detection of VRE in cultures by validating against a traditional real-time PCR assay based on the LightCycler 2.0 platform (Roche, VRE RO). A high level of analytical sensitivity and specificity (≥99.0%) for both genes was obtained when testing suspensions derived from blood agar. Results for suspensions obtained from chromID VRE (Edwards Group) showed a similar level of performance for vanA detection (100%), but not for the vanB target (≥90.9%) where a lesser number of isolates were available for testing. However, our results for VRE detection in isolates from these media were repeatable and reproducible, and equated to positive and negative predictive values of ≥95.2% and ≥97.8%, respectively. Furthermore, the VRE BD assay was also able to accurately detect VRE in clinical and spiked BacT/ALERT (bioMérieux) blood cultures. Thus, the technical simplicity, short turnaround time and robustness of this high performing assay for VRE is suitable for reflex testing. In addition, the format developed for the BD Max platform has potential application for reflex testing other molecular targets of clinical importance.

Genomic analysis of inter-hospital transmission of vancomycin-resistant Enterococcus faecium sequence type 80 isolated during an outbreak in Hiroshima, Japan

Outbreaks caused by vancomycin-resistant enterococci that transcend jurisdictional boundaries are occurring worldwide. This study focused on a vancomycin-resistant enterococcus outbreak that occurred between 2018 and 2021 across two cities in Hiroshima, Japan. The study involved genetic and phylogenetic analyses using whole-genome sequencing of 103 isolates of vancomycin-resistant enterococci to identify the source and transmission routes of the outbreak. Phylogenetic analysis was performed using core genome multilocus sequence typing and core single-nucleotide polymorphisms; infection routes between hospitals were inferred using BadTrIP. The outbreak was caused by Enterococcus faecium sequence type (ST) 80 carrying the vanA plasmid, which was derived from strain A10290 isolated in India. Of the 103 isolates, 93 were E. faecium ST80 transmitted across hospitals. The circular vanA plasmid of the Hiroshima isolates was similar to the vanA plasmid of strain A10290 and transferred from E. faecium ST80 to other STs of E. faecium and other Enterococcus species by conjugation. The inferred transmission routes across hospitals suggest the existence of a central hospital serving as a hub, propagating vancomycin-resistant enterococci to multiple hospitals. Our study highlights the importance of early intervention at the key central hospital to prevent the spread of the infection to small medical facilities, such as nursing homes, with limited medical resources and a high number of vulnerable individuals.

TEMPORARY REMOVAL: The first investigation of a nosocomial outbreak caused by ST80 vancomycin-resistant Enterococci faecium in China

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Vancomycin-Resistant Enterococcus faecium and the emergence of new Sequence Types associated with Hospital Infection

Enterococcus faecium is a major cause of vancomycin-resistant enterococcal (VRE) infection. New variants of the pathogen have emerged and become dominant in healthcare settings. Two such examples, vanB ST796 and vanA ST1421 sequence types, originally arose in Australia and proceeded to cause VRE outbreaks in other countries. Of concern is the detection of a vancomycin variable enterococcal (VVE) variant of ST1421 in Europe that exhibits a vancomycin-susceptible phenotype but which can revert to resistant in the presence of vancomycin. The recent application of genome sequencing for increasing our understanding of the evolution and spread of VRE is also explored here.

Fattening Pigs Are a Reservoir of Florfenicol-Resistant Enterococci Harboring Oxazolidinone Resistance Genes

ABSTRACT

The use of florfenicol in farm animals may select enterococci that carry resistance genes that confer resistance to linezolid, a critically important oxazolidinone antibiotic used in human medicine. This cross-sectional study aimed to assess the occurrence of oxazolidinone resistance genes in florfenicol-resistant enterococci from fattening pigs in Switzerland and to characterize a subset of the isolates using whole genome sequencing. A total of 31 florfenicol-resistant enterococcal isolates were obtained from 27 (5%) of 565 cecal samples of fattening pigs from seven (11%) of 62 farms. Screening by PCR revealed the presence of cfr-poxtA in 1 of 31, optrA in 15 of 31, and poxtA in 15 of 31 enterococcal isolates. One randomly selected isolate per PCR-positive Enterococcus species and positive farm was selected for further analysis (n = 10). In nine of the 10 isolates, the presence of oxazolidinone resistance genes did not result in phenotypic resistance. Whole genome sequencing analysis showed the presence of E. faecalis (n = 1), E. faecium (n = 1), and E. hirae (n = 1), harboring optrA18, optrA7, and a new optrA allele, respectively. E. durans (n = 1), E. faecium (n = 4), and E. hirae (n = 1) carried the wild-type poxtA, and E. faecalis (n = 1) coharbored cfr(D) and poxtA2. Except for optrA7, all oxazolidinone resistance genes were found on plasmids. Multilocus sequence typing analysis identified E. faecalis ST19 and ST376, E. faecium ST80 belonging to hospital-adapted clade A1, and E. faecium ST21, ST55, ST269, and ST416 belonging to clade A2, which represents human commensals and animal strains. The occurrence of cfr(D), optrA, and poxtA in various porcine Enterococcus spp. demonstrates the spread of oxazolidinone resistance genes among enterococci from fattening pigs in Switzerland. The presence in one sample of poxtA-carrying E. faecium ST80 emphasizes the potential risk to human health through dissemination of strains carrying oxazolidinone resistance genes into the food chain.

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