Emergence of an Australian-like pstS-null vancomycin resistant Enterococcus faecium clone in Scotland

Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics

The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.

Genetic analysis of vancomycin-variable Enterococcus faecium clinical isolates in Italy

PURPOSE

To investigate the occurrence of vancomycin-variable enterococci (VVE) in a hospital in central Italy.

METHODS

vanA positive but vancomycin-susceptible Enterococcus faecium isolates (VVE-S) were characterized by antibiotic susceptibility tests, molecular typing (PFGE and MLST), and WGS approach. The reversion of VVE-S to a resistant phenotype was assessed by exposure to increasing vancomycin concentrations, and the revertant isolates were used in filter mating experiments. qPCR was used to analyze the plasmid copy number.

RESULTS

Eleven putative VVE-S were selected. WGS revealed two categories of vanA cluster plasmid located: the first type showed the lack of vanR, the deletion of vanS, and an intact vanH/vanA/vanX cluster; the second type was devoid of both vanR and vanS and showed a deletion of 544-bp at the 5'-end of the vanH. Strains (n = 7) carrying the first type of vanA cluster were considered VVE-S and were able to regain a resistance phenotype (VVE-R) in the presence of vancomycin, due to a 44-bp deletion in the promoter region of vanH/vanA/vanX, causing its constitutive expression. VVE-R strains were not able to transfer resistance by conjugation, and the resistance phenotype was unstable: after 11 days of growth without selective pressure, the revertants were still resistant but showed a lower vancomycin MIC. A higher plasmid copy number in the revertant strains was probably related to the resistance phenotype.

CONCLUSION

We highlight the importance of VVE transition to VRE under vancomycin therapy resulting in a potential failure treatment. We also report the first-time identification of VVE-S isolates pstS-null belonging to ST1478.

New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data

The MLST scheme currently used for Enterococcus faecium typing was designed in 2002 and is based on putative gene functions and Enterococcus faecalis gene sequences available at that time. As a result, the original MLST scheme does not correspond to the real genetic relatedness of E. faecium strains and often clusters genetically distant strains to the same sequence types (ST). Nevertheless, typing has a significant impact on the subsequent epidemiological conclusions and introduction of appropriate epidemiological measures, thus it is crucial to use a more accurate MLST scheme. Based on the genome analysis of 1,843 E. faecium isolates, a new scheme, consisting of 8 highly discriminative loci, was created in this study. These strains were divided into 421 STs using the new MLST scheme, as opposed to 223 STs assigned by the original MLST scheme. The proposed MLST has a discriminatory power of D = 0.983 (CI95% 0.981 to 0.984), compared to the original scheme's D = 0.919 (CI95% 0.911 to 0.927). Moreover, we identified new clonal complexes with our newly designed MLST scheme. The scheme proposed here is available within the PubMLST database. Although whole genome sequencing availability has increased rapidly, MLST remains an integral part of clinical epidemiology, mainly due to its high standardization and excellent robustness. In this study, we proposed and validated a new MLST scheme for E. faecium, which is based on genome-wide data and thus reflects the tested isolates' more accurate genetic similarity. IMPORTANCE Enterococcus faecium is one of the most important pathogens causing health care associated infections. One of the main reasons for its clinical importance is a rapidly spreading resistance to vancomycin and linezolid, which significantly complicates antibiotic treatment of infections caused by such resistant strains. Monitoring the spread and relationships between resistant strains causing severe conditions represents an important tool for implementing appropriate preventive measures. Therefore, there is an urgent need to establish a robust method enabling strain monitoring and comparison at the local, national, and global level. Unfortunately, the current, extensively used MLST scheme does not reflect the real genetic relatedness between individual strains and thus does not provide sufficient discriminatory power. This can lead directly to incorrect epidemiological measures due to insufficient accuracy and biased results.

An Economic Evaluation Estimating the Clinical and Economic Burden of Increased Vancomycin-Resistant Enterococcus faecium Infection Incidence in Japan

INTRODUCTION

While incidence rates of vancomycin-resistant Enterococcus faecium have remained comparatively low in Japan, there have been increasing reports of more vancomycin-resistant Enterococcus (VRE) outbreaks, requiring costly measures to contain. Increased incidence of VRE in Japan may lead to more frequent and harder to contain outbreaks with current control measures, causing a significant burden to the healthcare system in Japan. This study aimed to demonstrate the clinical and economic burden of vancomycin-resistant E. faecium infections to the Japanese healthcare system and the impact of increasing rates of vancomycin resistance.

METHODS

A de novo deterministic analytic model was developed to assess the health economic outcomes of treating hospital-acquired VRE infections; patients are treated according to a two-line treatment strategy, dependent on their resistance status. The model considers hospitalisation costs and the additional cost of infection control. Scenarios investigated the current burden of VRE infections and the additional burden of increased incidence of VRE. Outcomes were assessed over a 1-year and 10-year time horizon from a healthcare payer's perspective in a Japanese setting. Quality-adjusted life years (QALYs) were valued with a willingness-to-pay threshold of ¥5,000,000 ($38,023), and costs and benefits were discounted at a rate of 2%.

RESULTS

Current VRE incidence levels in enterococcal infections in Japan equates to ¥130,209,933,636 ($996,204,669) in associated costs and a loss of 185,361 life years (LYs) and 165,934 QALYs over 10 years. A three-fold increase (1.83%) is associated with an additional ¥4,745,059,504 ($36,084,651) in total costs on top of the current cost burden as well as an additional loss of 683 LYs over a lifetime, corresponding to 616 QALYs lost.

CONCLUSION

Despite low incidence rates, VRE infections already represent a substantial economic burden to the Japanese healthcare system. The substantial increase in costs associated with a higher incidence of VRE infections could result in a significant economic challenge for Japan.

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.

Vancomycin-resistant Enterococcus sequence type 1478 spread across hospitals participating in the Canadian Nosocomial Infection Surveillance Program from 2013 to 2018

OBJECTIVE

To analyze the spread of a novel sequence type (ST1478) of vancomycin-resistant Enterococcus faecium across Canadian hospitals.

DESIGN

Retrospective chart review of patients identified as having ST1478 VRE bloodstream infection.

SETTING

Canadian hospitals that participate in the Canadian Nosocomial Infection Surveillance Program (CNISP).

METHODS

From 2013 to 2018, VRE bloodstream isolates collected from participating CNISP hospitals were sent to the National Microbiology Laboratory (NML). ST1478 isolates were identified using multilocus sequence typing, and whole-genome sequencing was performed. Patient characteristics and location data were collected for patients with ST1478 bloodstream infection (BSI). The sequence and patient location information were used to generate clusters of infections and assess for intrahospital and interhospital spread.

RESULTS

ST1478 VRE BSI occurred predominantly in a small number of hospitals in central and western Canada. Within these hospitals, infections were clustered on certain wards, and isolates often had <20 single-nucleotide variants (SNV) differences from one another, suggesting a large component of intrahospital spread. Furthermore, some patients with bloodstream infections were identified as moving from one hospital to another, potentially having led to interhospital spread. Genomic analysis of all isolates revealed close relatedness between isolates at multiple different hospitals (<20 SNV) not predicted from our epidemiologic data.

CONCLUSIONS

Both intrahospital and regional interhospital spread have contributed to the emergence of VRE ST1478 infections across Canada. Whole-genome sequencing provides evidence of spread that might be missed with epidemiologic investigation alone.

Interhospital transmission of vancomycin-resistant Enterococcus faecium in Aomori, Japan

Background

Spread of vancomycin-resistant Enterococcus (VRE) is a global concern as a significant cause of healthcare-associated infections. A series of VRE faecium (VREf) outbreaks caused by clonal propagation due to interhospital transmission occurred in six general hospitals in Aomori prefecture, Japan.

Methods

The number of patients with VREf was obtained from thirty seven hospitals participating in the local network of Aomori prefecture. Thirteen hospitals performed active screening tests for VRE. Whole genome sequencing analysis was performed.

Results

The total number of cases with VREf amounted to 500 in fourteen hospitals in Aomori from Jan 2018 to April 2021. It took more than three years for the frequency of detection of VRE to return to pre-outbreak levels. The duration and size of outbreaks differed between hospitals according to the countermeasures available at each hospital. Whole genome sequencing analysis indicated vanA-type VREf ST1421 for most samples from six hospitals.

Conclusions

This was the first multi-jurisdictional outbreak of VREf sequence type 1421 in Japan. In addition to strict infection control measures, continuous monitoring of VRE detection in local medical regions and smooth and immediate communication among hospitals are required to prevent VREf outbreaks.

Centre-specific bacterial pathogen typing affects infection-control decision making

Whole-genome sequencing is becoming the de facto standard for bacterial outbreak surveillance and infection prevention. This is accompanied by a variety of bioinformatic tools and needs bioinformatics expertise for implementation. However, little is known about the concordance of reported outbreaks when using different bioinformatic workflows. In this multi-centre proficiency testing among 13 major Dutch healthcare-affiliated centres, bacterial whole-genome outbreak analysis was assessed. Centres who participated obtained two randomized bacterial datasets of Illumina sequences, a Klebsiella pneumoniae and a Vancomycin-resistant Enterococcus faecium, and were asked to apply their bioinformatic workflows. Centres reported back on antimicrobial resistance, multi-locus sequence typing (MLST), and outbreak clusters. The reported clusters were analysed using a method to compare landscapes of phylogenetic trees and calculating Kendall–Colijn distances. Furthermore, fasta files were analysed by state-of-the-art single nucleotide polymorphism (SNP) analysis to mitigate the differences introduced by each centre and determine standardized SNP cut-offs. Thirteen centres participated in this study. The reported outbreak clusters revealed discrepancies between centres, even when almost identical bioinformatic workflows were used. Due to stringent filtering, some centres failed to detect extended-spectrum beta-lactamase genes and MLST loci. Applying a standardized method to determine outbreak clusters on the reported de novo assemblies, did not result in uniformity of outbreak-cluster composition among centres.

The Role of Whole Genome Sequencing in the Surveillance of Antimicrobial Resistant Enterococcus spp.: A Scoping Review

Enterococcus spp. have arisen as important nosocomial pathogens and are ubiquitous in the gastrointestinal tracts of animals and the environment. They carry many intrinsic and acquired antimicrobial resistance genes. Because of this, surveillance of Enterococcus spp. has become important with whole genome sequencing emerging as the preferred method for the characterization of enterococci. A scoping review was designed to determine how the use of whole genome sequencing in the surveillance of Enterococcus spp. adds to our knowledge of antimicrobial resistance in Enterococcus spp. Scoping review design was guided by the PRISMA extension and checklist and JBI Reviewer's Guide for scoping reviews. A total of 72 articles were included in the review. Of the 72 articles included, 48.6% did not state an association with a surveillance program and 87.5% of articles identified Enterococcus faecium. The majority of articles included isolates from human clinical or screening samples. Significant findings from the articles included novel sequence types, the increasing prevalence of vancomycin-resistant enterococci in hospitals, and the importance of surveillance or screening for enterococci. The ability of enterococci to adapt and persist within a wide range of environments was also a key finding. These studies emphasize the importance of ongoing surveillance of enterococci from a One Health perspective. More studies are needed to compare the whole genome sequences of human enterococcal isolates to those from food animals, food products, the environment, and companion animals.

Emergence of pstS-Null Vancomycin-Resistant Enterococcus faecium Clone ST1478, Canada, 2013-2018

Rates of vancomycin-resistant enterococci bloodstream infections have remained relatively low in Canada. We recently observed an increase of 113% in these infections rates, which coincided with emergence of Enterococcus faecium pstS-null sequence type 1478. The proportion of this sequence type increased from 2.7% to 38.7% for all tested isolates from 2013-2018.

Emergence of vancomycin-resistant Enterococcus faecium ST1421 lacking the pstS gene in Korea

Although multilocus sequence typing (MLST) has been used to study molecular epidemiology and to explore the population structure of Enterococcus faecium, vancomycin-resistant E. faecium (VREF) strains lacking the pstS gene that were non-typable using conventional MLST methods were reported recently. We found nationwide emergence of VREF isolates lacking pstS in Korea and hereby report the molecular characteristics of these isolates. Forty-six VREF isolates lacking the pstS gene were identified among 300 VREF rectal isolates collected from hospitalized patients between 2014 and 2015. MLST was performed and clonal relatedness was determined by pulsed-field gel electrophoresis (PFGE). Four VREF ST1421 isolates were whole-genome sequenced. Among the VREF rectal isolates lacking pstS, 98% were classified as ST1421, which has identical allelic profiles to ST17 for all housekeeping genes except pstS. PFGE pattern analyses revealed 32 pulsotypes. All isolates harbored Tn1546 components with various transposase and insertion sequences. The whole-genome sequencing of four VREF ST1421 isolates showed that the pstS gene region was deleted at various locations with considerable inversion. The pstS gene was also depleted in 12.1% of 33 VREF clinical isolates in 2006-2007 and in 11.8% of 59 clinical isolates in 2012-2013. VREF ST1421 strains lacking the pstS gene have emerged in Korea. The emergence and spread of pstS-deleted VREF strains pose a serious challenge for epidemiological investigation. Alternative molecular typing methods to MLST will be increasingly necessary.

State-Wide Genomic and Epidemiological Analyses of Vancomycin-Resistant Enterococcus faecium in Tasmania's Public Hospitals

From 2015 onwards, the number of vancomycin-resistant Enterococcus faecium (VREfm) isolates increased in Tasmania. Previously, we examined the transmission of VREfm at the Royal Hobart Hospital (RHH). In this study, we performed a state-wide analysis of VREfm from Tasmania's four public acute hospitals. Whole-genome analysis was performed on 331 isolates collected from screening and clinical specimens of VREfm. In silico multi-locus sequence typing (MLST) was used to determine the relative abundance of broad sequence types (ST) across the state. Core genome MLST (cgMLST) was then applied to identify potential clades within the ST groupings followed by single-nucleotide polymorphic (SNP) analysis. This work revealed that differences in VREfm profiles are evident between the state's two largest hospitals with the dominant vanA types being ST80 at the RHH and ST1421 at Launceston General Hospital (LGH). A higher number of VREfm cases were recorded at LGH (n = 54 clinical, n = 122 colonization) compared to the RHH (n = 14 clinical, n = 67 colonization) during the same time period, 2014-2016. Eleven of the clinical isolates from LGH were vanA and belonged to ST1421 (n = 8), ST1489 (n = 1), ST233 (n = 1), and ST80 (n = 1) whereas none of the clinical isolates from the RHH were vanA. For the recently described ST1421, cgMLST established the presence of individual clusters within this sequence type that were common to more than one hospital and that included isolates with a low amount of SNP variance (≤16 SNPs). A spatio-temporal analysis revealed that VREfm vanA ST1421 was first detected at the RHH in 2014 and an isolate belonging to the same cgMLST cluster was later collected at LGH in 2016. Inclusion of isolates from two smaller hospitals, the North West Regional Hospital (NRH) and the Mersey Community Hospital (MCH) found that ST1421 was present in both of these institutions in 2017. These findings illustrate the spread of a recently described sequence type of VREfm, ST1421, to multiple hospitals in an Australian state within a relatively short time span.