Nosocomial infections caused by vancomycin-resistant Enterococcus in a Japanese general hospital and molecular genetic analysis

Detection of glycopeptide resistance and virulence genes in enterococci isolated from cheese and investigation of the clonal relationship of E. faecium species with rectal surveillance isolates

OBJECTIVE

This study aimed to investigate the presence of glycopeptide resistance and virulence genes in Enterococcus spp. isolated from cheese and the clonal relationship of E. faecium species with rectal surveillance isolates.

MATERIALS AND METHOD

The study included 50 E. faecium species identified by the BD Phoenix 100 automatic identification system from surveillance cultures sent to the Kahramanmaraş Sütçü İmam University's microbiology laboratory and Enterococcus species from various packaged and unpackaged cheese samples. Multiplex polymerase chain reaction was used to investigate the presence of glycopeptide resistance and virulence genes in enterococci isolates. The clonal relationship between E. faecium isolates was evaluated using the Enterobacterial Repetitive Intergenic Consensus polymerase chain reaction method.

RESULTS

Bacterial growth was detected in 33 of the cheese samples. The study included E. faecium and E. faecalis species. Glycopeptide resistance genes were detected in 11 E. faecalis isolates, including vanD (61.1 %) and vanB (44.4 %). None of the glycopeptide resistance genes were detected in E. faecium isolates. Additionally, virulence genes were detected in 5 (31.25 %) E. faecium and 12 (66.6 %) E. faecalis isolates. Glycopeptide resistance genes were more common in isolates from packaged cheeses (p = 0.045).

CONCLUSION

Four E. faecium strains isolated from cheeses were closely related to the rectal surveillance isolates. This suggests that the health risks associated with enterococci in cheese must be carefully analyzed.

Analysis of a persistent outbreak with vancomycin-resistant Enterococcus faecium revealed the need for an adapted diagnostic algorithm

OBJECTIVES

The study institute was challenged with an outbreak of different vancomycin-resistant Enterococcus faecium (VREfm), including vanA- and/or vanB-containing isolates. Remarkably, screening overnight enriched specimens using a vanA and vanB real-time polymerase chain reaction (PCR) gave positive results for vanB with very low cycle threshold values, whereas VREfm-specific enrichment cultures remained negative. This paper describes the analysis of the diagnostic results leading to adaptation of the diagnostic algorithm.

METHODS

The results of vanA and vanB screening PCR and VREfm-specific culture (Brilliance VRE) were collected and combined with genotyping data of the identified VREfm isolates. During the outbreak, a second VREfm-specific culture medium (CHROMagar VRE) was introduced, and the results were compared with the results obtained with Brilliance VRE agar.

RESULTS

Thirty-five patients were identified as VREfm carriers, in which four different strains were identified: vanA (STnew-CT7088) and/or vanB (ST80-CT1065, ST117-CT7117 and ST117-CT7118). Complementing the PCR results, culture and genotyping revealed that culture with Brilliance VRE agar was inadequate for detection of the vanB ST117 isolates identified, irrespective of the minimum inhibitory concentration of vancomycin. In contrast, CHROMagar VRE was able to detect the vanB ST117 isolates and other tested isolates correctly.

CONCLUSIONS

The vanB ST117 isolates were detected inadequately by the VREfm-specific culture media, possibly contributing to unnoticed spread of VREfm. For this reason, CHROMagar VRE was evaluated during the outbreak and subsequently implemented in routine diagnostics, replacing Brilliance VRE agar.

Enhanced automated detection of outbreaks of a rare antimicrobial-resistant bacterial species

Surveillance of antimicrobial resistance (AMR) is a crucial strategy to combat AMR. Using routine surveillance data, we could detect and control hospital outbreaks of AMR bacteria as early as possible. Previously, we developed a framework for automatic detection of clusters of AMR bacteria using SaTScan, a free cluster detection tool integrated into WHONET. WHONET is a free software used globally for microbiological surveillance data management. We applied this framework to data from the Japan Nosocomial Infections Surveillance (JANIS), one of the world's most comprehensive and largest national AMR surveillance systems. Although WHONET-SaTScan has several cluster detection algorithms, no published studies have compared how different algorithms can produce varying results in cluster detection. Here, we conducted a comparison to detect clusters of vancomycin-resistant enterococci (VRE), which has been rare in Japan, by analyzing combinations of resistance to several key antimicrobials ("resistance profiles") using the comprehensive national routine AMR surveillance data of JANIS and validated the detection capabilities of each algorithm using publicly available reports of VRE clusters. All publicly reported VRE hospital outbreaks were detected as statistical clusters using the space-time uniform algorithm implemented in WHONET-SaTScan. In contrast, only 18.8% of the publicly reported outbreaks were detected using another algorithm (space-time permutation). The space-time uniform algorithm was also effective in identifying hospital wards affected by outbreaks attributed to specific resistance profiles. Although half of the publicly reported outbreaks were attributed to VRE resistant to five particular antimicrobials, four other resistance profiles also contributed to the outbreaks, highlighting the diversity of AMR bacteria within these occurrences. Our comparison revealed a clear advantage in using an algorithm (space-time uniform) for detecting VRE clusters in WHONET-SaTScan based on national surveillance data and further demonstrated the capability to distinguish detected clusters based on resistance profiles.

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.

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.

Human Adult Microbiota in a Static Colon Model: AhR Transcriptional Activity at the Crossroads of Host–Microbe Interaction

Functional symbiotic intestinal microbiota regulates immune defense and the metabolic processing of xenobiotics in the host. The aryl hydrocarbon receptor (AhR) is one of the transcription factors mediating host–microbe interaction. An in vitro static simulation of the human colon was used in this work to analyze the evolution of bacterial populations, the microbial metabolic output, and the potential induction of AhR transcriptional activity in healthy gut ecosystems. Fifteen target taxa were explored by qPCR, and the metabolic content was chromatographically profiled using SPME-GC-MS and UPLC-FLD to quantify short-chain fatty acids (SCFA) and biogenic amines, respectively. Over 72 h of fermentation, the microbiota and most produced metabolites remained stable. Fermentation supernatant induced AhR transcription in two of the three reporter gene cell lines (T47D, HepG2, HT29) evaluated. Mammary and intestinal cells were more sensitive to microbiota metabolic production, which showed greater AhR agonism than the 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) used as a positive control. Some of the SCFA and biogenic amines identified could crucially contribute to the potent AhR induction of the fermentation products. As a fundamental pathway mediating human intestinal homeostasis and as a sensor for several microbial metabolites, AhR activation might be a useful endpoint to include in studies of the gut microbiota.