High Prevalence of vanM in Vancomycin-Resistant Enterococcus faecium Isolates from Shanghai, China

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.

Deciphering the Resistome and Mobiolme of an Avian-Associated Enterococus faecalis ST249 Clone that Acquired Vancomycin Resistance Isolated from Neutropenic Patient in Tunisia

This study aimed to characterize the first vancomycin-resistant Enterococcus faecalis (VREfs) isolate from patient with neutropenic in Tunisia by whole-genome sequencing (WGS). This strain was detected from routine rectal swab from an 8-year-old child with bone marrow aplasia, residing in a rural area, on September 20, 2021. The strain was isolated after 12 days of hospitalization at the National Bone Marrow Transplant Center. Minimum Inhibitory Concentrations of vancomycin and teicoplanin were >256 and 16 mg/L, respectively. WGS revealed that the strain belonged to the ST249 clone, exclusively reported in avian (poultry and ducks) vancomycin-susceptible E. faecalis isolates in six studies from four countries, primarily Denmark. The vanA gene was carried by the Tn1546 transposon mobilized by a pTW9-like plasmid. The ardA gene, a CRISPR-Cas system neutralization factor, was detected in this strain. In summary, this is the first report of avian-associated E. faecalis ST249 in clinical samples. Initially vancomycin susceptible, the strain acquired a pTW9-like plasmid carrying the classical vanA-Tn1546 transposon. This acquisition was facilitated by the sex pheromone-response mechanisms and the ardA gene and CRISPR-Cas system neutralization.

Analysis of molecular epidemiological characteristics and antimicrobial susceptibility of vancomycin-resistant and linezolid-resistant Enterococcus in China

BACKGROUND

This study investigates the distribution and characteristics of linezolid and vancomycin susceptibilities among Enterococcus faecalis (E. faecalis) and Enterococcus faecium (E. faecium) and explores the underlying resistance mechanisms.

METHODS

A total of 2842 Enterococcus clinical isolates from patients were retrospectively collected, and their clinical data were further analyzed. The minimum inhibitory concentrations (MICs) of vancomycin and linezolid were validated by broth dilution method. The resistance genes optrA, cfr, vanA, vanB and vanM were investigated using polymerase chain reaction (PCR). Housekeeping genes and resistance genes were obtianed through whole-genome sequencing (WGS).

RESULTS

Of the 2842 Enterococcus isolates, 88.5% (2516) originated from urine, with E. faecium accounted for 60.1% of these. The vanA gene was identified in 27/28 vancomycin resistant Enterococcus (VRE) isolates, 4 of which carried both vanA and vanM genes. The remaining strain was vanM positive. The optrA gene was identified in all E. faecalis isolates among linezolid resistant Enterococcus (LRE). E. faecium showed a higher multiple antibiotic resistance index (MAR index) compared to E. faecalis. The multi-locus sequence typing (MLST) showed the sequence type of E. faecium mainly belongs to clonal complex (CC) 17, nearly E. faecalis isolates analyzed were differentiated into 7 characteristics of sequence types (STs), among which ST16 of CC16 were the major lineage.

CONCLUSION

Urine was the primary source of VRE and LRE isolates in this study. E. faecium showed higher levels of resistance compared to E. faecalis. OptrA gene was detected in 91.6% of LRE, which could explain linezolid resistance, and van genes were detected in all vancomycin resistant Enterococcus strains, while vanA was a key resistance mechanism in VRE identified in this study.

Development of an ultrafast PCR to detect clinically relevant acquired vancomycin-resistance genes from cultured enterococci

BACKGROUND

VRE are increasingly described worldwide. Screening of hospitalized patients at risk for VRE carriage is mandatory to control their dissemination. Here, we have developed the Bfast [VRE Panel] PCR kit, a rapid and reliable quantitative PCR assay for detection of vanA, vanB, vanD and vanM genes, from solid and liquid cultures adaptable to classical and ultrafast real-time PCR platforms.

METHODS

Validation was carried out on 133 well characterized bacterial strains, including 108 enterococci of which 64 were VRE. Analytical performances were determined on the CFX96 Touch (Bio-Rad) and Chronos Dx (BforCure), an ultrafast qPCR machine. Widely used culture plates and broths for enterococci selection/growth were tested.

RESULTS

All targeted van alleles (A, B, D and M) were correctly detected without cross-reactivity with other van genes (C, E, G, L and N) and no interference with the different routinely used culture media. A specificity and sensitivity of 100% and 99.7%, respectively, were determined, with limits of detection ranging from 21 to 238 cfu/reaction depending on the targets. The Bfast [VRE Panel] PCR kit worked equally well on the CFX and Chronos Dx platforms, with differences in multiplexing capacities (five and four optical channels, respectively) and in turnaround time (45 and 16 minutes, respectively).

CONCLUSIONS

The Bfast [VRE Panel] PCR kit is robust, easy to use, rapid and easily implementable in clinical microbiology laboratories for ultra-rapid confirmation of the four main acquired van genes. Its features, especially on Chronos Dx, seem to be unmatched compared to other tools for screening of VRE.

Vancomycin heteroresistance caused by unstable tandem amplifications of the vanM gene cluster on linear conjugative plasmids in a clinical Enterococcus faecium

Vancomycin heteroresistance is prone to missed detection and poses a risk of clinical treatment failure. We encountered one clinical Enterococcus faecium strain, SRR12, that carried a complete vanM gene cluster but was determined as susceptible to vancomycin using the broth microdilution method. However, distinct subcolonies appeared within the clear zone of inhibition in the E-test assay, one of which, named SRR12-v1, showed high-level resistance to vancomycin. SRR12 was confirmed as heteroresistant to vancomycin using population analysis profiling and displayed "revive" growth curves with a lengthy lag phase of over 13 hours when exposed to 2-32 mg/L vancomycin. The resistant subcolony SRR12-v1 was found to carry an identical vanM gene cluster to that of SRR12 but a significantly increased vanM copy number in the genome. Long-read whole genome sequencing revealed that a one-copy vanM gene cluster was located on a pELF1-like linear plasmid in SRR12. In comparison, tandem amplification of the vanM gene cluster jointed with IS1216E was seated on a linear plasmid in the genome of SRR12-v1. These amplifications of the vanM gene cluster were demonstrated as unstable and would decrease accompanied by fitness reversion after serial passaging for 50 generations under increasing vancomycin pressure or without antibiotic pressure but were relatively stable under constant vancomycin pressure. Further, vanM resistance in resistant variants was verified to be carried by conjugative plasmids with variable sizes using conjugation assays and S1-pulsed field gel electrophoresis blotting, suggesting the instability/flexibility of vanM cluster amplification in the genome and an increased risk of vanM resistance dissemination.

The prevalence and molecular epidemiology of vancomycin-resistant Enterococcus (VRE) carriage in patients admitted to intensive care units in Beijing, China

BACKGROUND

Vancomycin-resistant Enterococcus (VRE) can be carried in the gut for a long period and its carriage status is associated with subsequent infections. This study aimed to investigate the frequency of intestinal VRE carriage in intensive care patients in Beijing.

METHODS

A multicenter, retrospective cross-sectional study was conducted at six hospitals in Beijing, China. All patients admitted to intensive care units (ICUs) between April 2 and May 1, 2017, were enrolled, and their clinical data were gathered by reviewing electronic medical records. Rectal swabs collected from patients were stored at -80 °C in the Institute of Clinical Pharmacology, Peking University First Hospital, and they were selectively cultured for VRE, then the identified strains were analyzed by polymerase chain reaction (PCR) to detect the glycopeptide resistance gene and were characterized by multilocus sequence typing (MLST).

RESULTS

Of 148 patients recruited, 46 (31.1%) carried VRE, with the majority (n = 42) being Enterococcus faecium. In total, 78.3% of the VRE were vanA positive and 15.2% vanM positive, while 6.5% undetected glycopeptide resistance gene. The predominant ST was ST78 (47.6%) followed by ST192 (14.3%), ST555 (9.5%), and ST789 (9.5%). Multivariate analysis showed that factors associated VRE carriage were patients aged >65 years (odds ratio [OR], 3.786; 95% confidence interval [CI], 1.402-10.222) and recent third-generation cephalosporins use (OR, 6.360; 95% CI, 1.873-21.601).

CONCLUSIONS

The overall proportion of VRE carriage in patients admitted to ICUs was markedly high in Beijing, China. The vanM gene has been spread widely but vanA gene was the dominant resistance determinant in VRE in Beijing.

Check the melting temperature of the FilmArray BCID panel to avoid missed detection of vanM-type enterococci

PURPOSE

We aimed to evaluate whether the FilmArray blood culture identification (BCID) panel holds the ability to detect vanM-type vancomycin-resistant enterococci (VRE) clinical isolates effectively.

METHODS

Twenty VRE clinical strains, including 10 vanA-type VRE and 10 vanM-type VRE, were collected from patients in five tertiary hospitals, Shanghai, China. By conventional PCR and sequencing, the strains were identified and van genotypes were confirmed. All VRE strains were investigated using the FilmArray BCID panel. All results, including enterococcus assay, vanA/B assay, DNA melting curves and melting temperature (Tm), were recorded. We also compared these results with those obtained via the conventional PCR and sequencing.

RESULTS

According to the instructions of the FilmArray BCID panel, the Enterococcus assay is used to identify species and vanA/B assay is used to detect van genes. In all vanA-type VRE, the Enterococcus assay and vanA/B assay were positive. The results correctly showed that the tested strains were VRE. However, in 10 vanM-type VRE, the Enterococcus assay was positive and vanA/B assay were negative. The results mistakenly showed that the tested strains were vancomycin-sensitive enterococci (VSE). In the vanA/B assay, the melting curves of vanM-type VRE were similar to that of vanA-type VRE, but the Tm values were lower. The Tm values were then compared against the expected Tm range for the vanA/B assay. The Tm values of vanM-type VRE fall outside the assay-specific Tm range, resulting in negative reports. Thus, by adjusting the expected Tm range for the Enterococcus assay, the FilmArray BCID panel holds the ability to detect vanM-type VRE.

CONCLUSIONS

The vanM-type VRE isolates can be effectively detected by optimizing the expected Tm range for the vanA/B assay.

Vancomycin-variable enterococci in sheep and cattle isolates and whole-genome sequencing analysis of isolates harboring vanM and vanB genes

Background

Vancomycin resistance encoded by the vanA/B/M genes in enterococci is clinically important because of the transmission of these genes between bacteria. While vancomycin resistance is determined by detecting only vanA and vanB genes by routine analyses, failure to detect vanM resistance causes vancomycin resistance to be overlooked, and clinically appropriate treatment cannot be provided.

Aims

The study aimed to examine the presence of vanM-positive enterococcal isolates in Ankara, Turkey, and to have detailed information about them with sequence analyses.

Methods

Caecal samples were collected from sheep and cattle during slaughter at different slaughterhouses in Ankara, Turkey. Enterococci isolates were identified, confirmed, and analyzed for the presence of vanA/B/M genes. Antibiotic resistance profiles of isolates were determined by the broth microdilution method. A whole genome sequence analysis of the isolates harboring the vanM and vanB genes was performed.

Results

13.7% of enterococcal isolates were determined as Enterococcus faecium and Enterococcus faecalis. 15% of these isolates contained vanB, and 40% were vanM-positive. S98b and C32 isolates were determined to contain 16 CRISPR-Cas elements. 80% of the enterococci isolates were resistant to nitrofurantoin and 15% to ciprofloxacin. The first vanM-positive vancomycin-variable enterococci (VVE) isolates from food-producing animals were identified, and the S98b strain has been assigned to Genbank with the accession number CP104083.1.

Conclusion

Therefore, new studies are needed to facilitate the identification of vanM-resistant enterococci and VVE strains.

Novel Copper Oxide Bio-Nanocrystals to Target Outer Membrane Lectin of Vancomycin-Resistant Enterococcus faecium (VREfm): In Silico, Bioavailability, Antimicrobial, and Anticancer Potential

In present study, we used Olea europaea leaf extract to biosynthesize in situ Copper Oxide nanocrystals (CuO @OVLe NCs) with powerful antibacterial and anti-cancer capabilities. Physio-chemical analyses, such as UV/Vis, FTIR, XRD, EDX, SEM, and TEM, were applied to characterize CuO @OVLe NCs. The UV/Vis spectrum demonstrated a strong peak at 345 nm. Furthermore, FTIR, XRD, and EDX validated the coating operation's contact with colloidal CuO @OVLe NCs. According to TEM and SEM analyses, CuO @OVLe NCs exhibited a spherical shape and uniform distribution of size with aggregation, for an average size of ~75 nm. The nanoparticles demonstrated a considerable antibacterial effect against E. faecium bacterial growth, as well as an increased inhibition rate in a dose-dependent manner on the MCF-7, PC3, and HpeG2 cancer cell lines and a decreased inhibition rate on WRL-68. Molecular docking and MD simulation were used to demonstrate the high binding affinity of a ligand (Oleuropein) toward the lectin receptor complex of the outer membrane to vancomycin-resistant E. faecium (VREfm) via amino acids (Leu 195, Thr 288, His 165, and Ser 196). Hence, our results expand the accessibility of OVLe's bioactive components as a promising natural source for the manufacture of physiologically active components and the creation of green biosynthesis of metal nanocrystals.

New Mutations in cls Lead to Daptomycin Resistance in a Clinical Vancomycin- and Daptomycin-Resistant Enterococcus faecium Strain

Daptomycin (DAP), a last-resort antibiotic for treating Gram-positive bacterial infection, has been widely used in the treatment of vancomycin-resistant enterococci (VRE). Resistance to both daptomycin and vancomycin leads to difficulties in controlling infections of enterococci. A clinical multidrug-resistant Enterococcus faecium EF332 strain that shows resistance to both daptomycin and vancomycin was identified, for which resistance mechanisms were investigated in this work. Whole-genome sequencing and comparative genomic analysis were performed by third-generation PacBio sequencing, showing that E. faecium EF332 contains four plasmids, including a new multidrug-resistant pEF332-2 plasmid. Two vancomycin resistance-conferring gene clusters vanA and vanM were found on this plasmid, making it the second reported vancomycin-resistant plasmid containing both clusters. New mutations in chromosomal genes cls and gdpD that, respectively, encode cardiolipin synthase and glycerophosphoryl diester phosphodiesterase were identified. Their potential roles in leading to daptomycin resistance were further investigated. Through molecular cloning and phenotypic screening, two-dimensional thin-layer chromatography, fluorescence surface charge test, and analysis of cardiolipin distribution patterns, we found that mutations in cls decrease surface negative charges of the cell membrane (CM) and led to redistribution of lipids of CM. Both events contribute to the DAP resistance of E. faecium EF332. Mutation in gdpD leads to changes in CM phospholipid compositions, but cannot confer DAP resistance. Neither mutation could result in changes in cellular septa. Therefore, we conclude that the daptomycin resistance of E. faecium EF332 is conferred by new cls mutations. This work reports the genetic basis for vancomycin and daptomycin resistance of a multidrug-resistant E. faecium strain, with the finding of new mutations of cls that leads to daptomycin resistance.

Regulation of Resistance in Vancomycin-Resistant Enterococci: The VanRS Two-Component System

Vancomycin-resistant enterococci (VRE) are a serious threat to human health, with few treatment options being available. New therapeutics are urgently needed to relieve the health and economic burdens presented by VRE. A potential target for new therapeutics is the VanRS two-component system, which regulates the expression of vancomycin resistance in VRE. VanS is a sensor histidine kinase that detects vancomycin and in turn activates VanR; VanR is a response regulator that, when activated, directs expression of vancomycin-resistance genes. This review of VanRS examines how the expression of vancomycin resistance is regulated, and provides an update on one of the field's most pressing questions: How does VanS sense vancomycin?

Highlights Regarding the Use of Metallic Nanoparticles against Pathogens Considered a Priority by the World Health Organization

The indiscriminate use of antibiotics has facilitated the growing resistance of bacteria, and this has become a serious public health problem worldwide. Several microorganisms are still resistant to multiple antibiotics and are particularly dangerous in the hospital and nursing home environment, and to patients whose care requires devices, such as ventilators and intravenous catheters. A list of twelve pathogenic genera, which especially included bacteria that were not affected by different antibiotics, was released by the World Health Organization (WHO) in 2017, and the research and development of new antibiotics against these genera has been considered a priority. The nanotechnology is a tool that offers an effective platform for altering the physicalchemical properties of different materials, thereby enabling the development of several biomedical applications. Owing to their large surface area and high reactivity, metallic particles on the nanometric scale have remarkable physical, chemical, and biological properties. Nanoparticles with sizes between 1 and 100 nm have several applications, mainly as new antimicrobial agents for the control of microorganisms. In the present review, more than 200 reports of various metallic nanoparticles, especially those containing copper, gold, platinum, silver, titanium, and zinc were analyzed with regard to their anti-bacterial activity. However, of these 200 studies, only 42 reported about trials conducted against the resistant bacteria considered a priority by the WHO. All studies are in the initial stage, and none are in the clinical phase of research.

Real-time PCR for the rapid detection of vanA, vanB and vanM genes

BACKGROUND/PURPOSE

To evaluate the ability of quadruple Taqman probe real-time PCR to the detection of vanA, vanB and vanM in enterococcal isolates.

METHODS

A total of 343 strains, including 253 vancomycin-resistant enterococcus (VRE) strains and 90 non-VRE strains, were tested by both quadruple Taqman probe real-time PCR and gel-based PCR assay.

RESULTS

When differentiating among three genotypes of vanA, vanB and vanM in VRE strains, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic accuracy and consistency of the quadruple Taqman probe real-time PCR were all 100%. Minimum. Inhibitory concentration (MIC) results showed that there was a wide MIC range of vancomycin and teicoplanin for the strains that harboring vanA/vanM gene respectively or harboring vanA and vanM genes simultaneously. However, the VRE strains with vanB genotype all were sensitive to teicoplanin.

CONCLUSION

Considering the excellent PPV and low NPV, real-time PCR would be useful to monitor VRE-colonized or infected patients. However, further evaluation of the assay's performance in the clinical specimens is required, especially when considering that high level of PCR inhibitors present in these samples.

Evaluation of Quadruple Real-Time PCR Method to Detect Enterococci Carrying Vancomycin-Resistant Genes vanA, vanB, vanM in Rectal Swabs

Purpose: To evaluate the sensitivity and accuracy of the quadruple real-time PCR method for the detection of enterococci carrying vancomycin-resistant genes vanA, vanB, and vanM in rectal swabs. Methods: Choosing PCR-sequenced DNA extracted directly from rectal swabs as the gold standard, the results of the quadruple real-time PCR method and the traditional method (screening culture combined PCR-sequencing method whose DNA extracted from single colony) were compared with the gold standard. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of the quadruple real-time PCR method and the traditional method were obtained. The time required for the three methods was calculated. Results: The results between gold standard and the quadruple real-time PCR method were similar. Compared to the traditional method, the quadruple real-time PCR method had a much higher sensitivity, specificity, PPV, NPV, and consistency. Our study found that the quadruple real-time PCR method is beneficial for detection of enterococci carrying vanM with vancomycin heteroresistance. The traditional method had high specificity and NPV, but its sensitivity and PPV were not ideal. The time needed for gold standard is a minimum of 28 h; the quadruple real-time PCR method takes 2-3 h while the traditional method consumes a minimum of 72 h. Conclusion: The quadruple real-time PCR method can provide a rapid and reliable result for the diagnosis of patients with colonized vancomycin-resistant enterococci. This new method is beneficial for the active screening, timely clinical treatment measures, epidemiological research, and hospital monitoring of the enterococci carrying vancomycin-resistant gene, especially for the enterococci with vancomycin heteroresistance carrying vanM.

Impact of vanA-Positive Enterococcus faecium Exhibiting Diverse Susceptibility Phenotypes to Glycopeptides on 30-Day Mortality of Patients with a Bloodstream Infection

This study was performed to evaluate the impacts of vanA positivity of Enterococcus faecium exhibiting diverse susceptibility phenotypes to glycopeptides on clinical outcomes in patients with a bloodstream infection (BSI) through a prospective, multicenter, observational study. A total of 509 patients with E. faecium BSI from eight sentinel hospitals in South Korea during a 2-year period were enrolled in this study. Risk factors of the hosts and causative E. faecium isolates were assessed to determine associations with the 30-day mortality of E. faecium BSI patients via multivariable logistic regression analyses. The vanA gene was detected in 35.2% (179/509) of E. faecium isolates; 131 E. faecium isolates exhibited typical VanA phenotypes (group vanA-VanA), while the remaining 48 E. faecium isolates exhibited atypical phenotypes (group vanA-atypical), which included VanD (n = 43) and vancomycin-variable phenotypes (n = 5). A multivariable logistic regression indicated that vanA positivity of causative pathogens was independently associated with the increased 30-day mortality rate in the patients with E. faecium BSI; however, there was no significant difference in survival rates between the patients of the vanA-VanA and vanA-atypical groups (log rank test, P = 0.904). A high 30-day mortality rate was observed in patients with vanA-positive E. faecium BSIs, and vanA positivity of causative E. faecium isolates was an independent risk factor for early mortality irrespective of the susceptibility phenotypes to glycopeptides; thus, intensified antimicrobial stewardship is needed to improve the clinical outcomes of patients with vanA-positive E. faecium BSI.

Characterization of clinical enterococci isolates, focusing on the vancomycin-resistant enterococci in a tertiary hospital in China: based on the data from 2013 to 2018

Background

Vancomycin-resistant Enterococcus spp. (VRE) have spread all over the world. The present study aims to investigate the species distribution, specimen type and susceptibilities of Enterococcal species collected from Nanjing Drum Tower Hospital from 2013 to 2018. Additionally, distribution of VRE and prevalence of van gene among VRE isolates were also analyzed.

Methods

The susceptibilities of 3913 Enterococcus isolates were retrospectively investigated. Among these strains, 60 VRE strains were further anazlyed in this study. The minimum inhibitory concentrations (MICs) of the VRE strains towards vancomycin, teicoplanin and linezolid were determined by E-test. Polymerase chain reaction (PCR) and DNA sequencing were used to investigate the prevalence of van genes among VRE. Furthermore, the sequence types (STs) of VRE strains were explored by multi-locus sequence typing (MLST).

Results

Among the 3913 enterococci isolates, Enterococcus faecalis (n = 1870, 47.8%) and Enterococcus faecium (1738, 44.4%) were the main isolates. These Enterococcus strains were mainly isolated from urine (n = 1673, 42.8%), followed by secretions (n = 583, 14.9%) and ascites (n = 554, 14.2%). VRE displayed a decreasing trend year by year. Molecular analysis revealed that 49 out of 60 VRE isolates carried vanA gene, 10 carried vanM, and 1 carried both vanA and vanM genes. Sixteen distinct STs were identified among the 58 VREM, with ST78 (n = 16), ST192 (n = 8) and ST570 (n = 7) being the most dominant ones.

Conclusions

E. faecalis and E. faecium were the major enterococci strains which are the main pathogens of urinary traction infections; vanA and vanM were the main determinants conferring resistance to vancomycin; ST78, ST192 and ST570 were the leading STs of VREM which displayed a decreasing trend of prevalence year by year.

Vancomycin-resistant Enterococcus faecium pneumonia in a uremic patient on hemodialysis: a case report and review of the literature

Background

Even though enterococci can cause serious infections in multiple sites, they are a rare cause of pneumonia. We reported a uremic patient with vancomycin-resistant E. faecium (VRE-fm) pneumonia, possibly related to epileptic seizures.

Case presentation

A 57-year old man with uremia on hemodialysis was admitted to the hospital with complaint of recurrent epileptic seizures, followed by a two-week history of recurrent fever and cough with purulent sputum. Chest CT demonstrated multiple exudation of both lungs. He was diagnosed as community acquired pneumonia. Despite antibiotic combination therapy, abnormal chest shadows aggravated. Sputum and blood cultures were initially negative, but later blood culture grew VRE-fm. We suspected aspiration of gastrointestinal content induced by epilepsy as the most likely mechanism. The patient was successfully treated with a four-week course of linezolid according to the antibiotic susceptibility testing.

Conclusions

Physicians should consider multi-drug resistant organisms such as VRE in uremic patients with pneumonia that fails to resolve with broad-spectrum antibiotics, especially in the cases with aspiration induced by epilepsy, immunocompromised conditions, and repeated or prolonged hospitalizations.

Tandem amplification of the vanM gene cluster drives vancomycin resistance in vancomycin-variable enterococci

BACKGROUND

Vancomycin-variable enterococci (VVE) are a potential risk factor for vancomycin resistance gene dissemination and clinical treatment failure. vanM has emerged as a new prevalent resistance determinant among clinical enterococci in China. A total of 54 vancomycin-susceptible enterococci (VSE) isolates carrying incomplete vanM gene clusters were isolated in our previous study.

OBJECTIVES

To determine the potential of vanM-carrying VSE to develop vancomycin resistance and investigate the mechanism of alteration of the resistance phenotype.

METHODS

Fifty-four vanM-positive VSE strains were induced in vitro by culturing in increasing concentrations of vancomycin. Genetic changes between three parent VVE strains and their resistant variants were analysed using Illumina and long-read sequencing technologies, quantitative PCR and Southern blot hybridization. Changes in expression level were determined by quantitative RT-PCR.

RESULTS

Twenty-five of the 54 VSE strains carrying vanM became resistant upon vancomycin exposure. A significant increase in vanM copy number was observed ranging from 5.28 to 127.64 copies per cell in induced resistant VVE strains. The vanM transposon was identified as tandem repeats with IS1216E between them, and occurred in either the plasmid or the chromosome of resistant VVE cells. In addition, an increase in vanM expression was observed after resistance conversion in VVE.

CONCLUSIONS

This study identified tandem amplification of the vanM gene cluster as a new mechanism for vancomycin resistance in VVE strains, offering a competitive advantage for VVE under antibiotic pressure.

Novel Multidrug-Resistant Enterococcal Mobile Linear Plasmid pELF1 Encoding vanA and vanM Gene Clusters From a Japanese Vancomycin-Resistant Enterococci Isolate

Vancomycin-resistant enterococci are troublesome pathogens in clinical settings because of few treatment options. A VanA/VanM-type vancomycin-resistant Enterococcus faecium clinical isolate was identified in Japan. This strain, named AA708, harbored five plasmids, one of which migrated during agarose gel electrophoresis without S1 nuclease treatment, which is indicative of a linear topology. We named this plasmid pELF1. Whole genome sequencing (WGS) analysis of the AA708 strain revealed that the complete sequence of pELF1 was 143,316 bp long and harbored both the vanA and vanM gene clusters. Furthermore, mfold analysis and WGS data show that the left end of pELF1 presumably forms a hairpin structure, unlike its right end. The pELF1 plasmid was not digested by lambda exonuclease, indicating that terminal proteins were bound to the 5′ end of the plasmid, similar to the Streptomyces linear plasmids. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis results were also consistent with the exonuclease assay results. In retardation assays, DNAs containing the right end of proteinase K-untreated pELF1 did not appear to move as well as the proteinase K-treated pELF1, suggesting that terminal proteins might be attached to the right end of pELF1. Palindromic sequences formed hairpin structures at the right terminal sequence of pELF1; however, sequence similarity with the well-known linear plasmids of Streptomyces spp. was not high. pELF1 was unique as it possessed two different terminal structures. Conjugation experiments revealed that pELF1 could be transferred to E. faecalis, E. faecium, E. casseliflavus, and E. hirae. These transconjugants exhibited not only high resistance levels to vancomycin, but also resistance to streptomycin, kanamycin, and erythromycin. These results indicate that pELF1 has the ability to confer multidrug resistance to Enterococcus spp. simultaneously, which might lead to clinical hazards.

Epidemiology and risk factors of methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci infections in Zhejiang China from 2015 to 2017

Background

Gram-positive bacteria are dangerous and challenging agents of infection due to their increasing resistance to antibiotics. We aim to analyse the epidemiology and risk factors of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) in Zhejiang China.

Methods

Gram-positive bacteria (including S. aureus, Enterococcus faecalis and Enterococcus faecium) were collected from eighty-six hospitals of eleven cities in Zhejiang China from 2015 to 2017. The detection rates of MRSA and VRE infection were calculated for the non-duplicated isolate according to year, region, hospital level, patient age, specimen type and patient category. Meanwhile, the detected resistances of MRSA, E. faecalis and E. faecium to different antibiotics from 2015 to 2017 were compared. The risk factors and the differences in MRSA and VRE detection rates were compared using odds ratio (OR) with 95% confidence interval (95% CI) and Chi-square test respectively.

Results

From 2015 to 2017, the detection rates of MRSA and VRE decreased gradually. The cities with the highest MRSA and VRE detection rates tended to be adjacent; for example, the neighbouring cities Hangzhou and Quzhou had simultaneously high rates of MRSA and VRE infection. Patients from IIIA hospital who were older than 75 years and in the intensive care unit (ICU) were most at risk. No vancomycin-resistant isolate was found in MRSA. Resistance of E. faecalis and E. faecium to vancomycin and linezolid decreased slightly and then maintained a low level.

Conclusions

The detection rates of MRSA and VRE stayed at moderate and low levels during the three year period of this study, while local dissemination was found in MRSA and VRE isolates. Sustained surveillance is necessary to prevent the spread or clonal dissemination of drug-resistant strains in Zhejiang China.

Horizontal transfer of vanA between probiotic Enterococcus faecium and Enterococcus faecalis in fermented soybean meal and in digestive tract of growing pigs

Background

The aim of this study was to investigate the intergeneric transfer of vancomycin resistance gene vanA between probiotic enterococci in the fermentation progress of soybean meal and in the digestive tract of growing pigs. One vanA genotype vancomycin resistant E. faecium strain, Efm4, and one chloramphenicol-resistant E. faecalis strain, Efs2, were isolated from twenty-nine probiotic basis feed material / additive samples. For in vitro conjugation, Efm4 and Efs2 were used as starter to ferment soybean meal. For in vivo conjugation, thirty growing pigs were randomly assigned to five groups (n = 6), treated with a basic diet, or supplemented with 10% fermented soybean meal, 1% Efm4, 5% Efs2 or a combination of 1% Efm4 + 5% Efs2 for 7 d, respectively. Fecal samples of pigs in each group were collected daily for the isolation and dynamic analysis of Efm4, Efs2 and transconjugants. The sequence types (STs) of Efm4, Efs2 and transconjugants were analyzed by multilocus sequence typing (MLST). The vanA harboring plasmid in Efm4 and transconjugants was analyzed by S1-pulsed field gel electrophoresis (PFGE) and further verified by multiple alignments.

Results

The results showed that, in FSBM, transconjugants were detected 1 h after the fermentation, with a conjugation frequency of ~ 10^- 3 transconjugants / recipient. Transconjugants proliferated with Efm4 and Efs2 in the first 8 h and maintained steadily for 10 d till the end of the experiment. Additionally, in vivo experiment showed that transcojugants were recovered in one of six pigs in both FSBM and Efm4 + Efs2 groups, with conjugation frequency of ~ 10^- 5 and ~ 10^- 4, respectively. MLST revealed the ST of Efm4, Efs2 and transconjugants was ST1014, ST69 and ST69, respectively. S1-PFGE confirmed the existence of the vanA-harboring, 142,988-bp plasmid, which was also a multi-drug resistant plasmid containing Tn1546-like transposon.

Conclusions

The findings revealed the potential safety hazard existing in the commercial probiotic enterococci in China, because the horizontal transfer from farm to fork could potentially pose a safety risk to the public.

Characterization of vanM carrying clinical Enterococcus isolates and diversity of the suppressed vanM gene cluster

Here we report the prevalence of the suppressed vanM gene cluster as a reservoir of vancomycin resistance genes. Among 1284 clinical isolates of enterococci from four hospitals in Hangzhou, China, 55 isolates of Enterococcus faecium and one isolate of Enterococcus faecalis were screened positive for the vanM genotype. Antimicrobial susceptibility testing showed that 55 of the 56 vanM-positive isolates were susceptible to vancomycin and teicoplanin. Most of them (54/56) belonged to the main epidemic lineage CC17, mostly the ST78 type. The vanM gene clusters in the 55 vancomycin-susceptible isolates showed sequence diversity owing to different insertion locations of IS1216E. The vanM transposons could be classified into five types and they all carried two or more IS1216E elements, leading to complete or partial deletions of vanR, vanS, or vanX. Quantitative reverse transcription polymerase chain reaction showed that the expression level of vanM was significantly lower in the vancomycin-susceptible isolates than in the vancomycin-resistant isolate. Considering the prevalence of the vanM genotype and the potential for conversion to a resistant phenotype, vanM might act as an important determinant of glycopeptide resistance in the future. It is essential to strengthen the surveillance of vanM-containing enterococci to control the dissemination of vancomycin resistance.

Nanodelivery strategies for the treatment of multidrug-resistant bacterial infections

One of the most important health concerns in society is the development of nosocomial infections caused by multidrug-resistant pathogens. The purpose of this review is to discuss the issues in current antibiotic therapies and the ongoing progress of developing new strategies for the treatment of ESKAPE pathogen infections, which is acronymized for Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species. We not only examine the current issues caused by multidrug resistance but we also examine the barrier effects such as biofilm and intracellular localization exploited by these pathogens to avoid antibiotic exposure. Recent innovations in nanomedicine approaches and antibody antibiotic conjugates are reviewed as potential novel approaches for the treatment of bacterial infection, which ultimately may expand the useful life span of current antibiotics.

Antimicrobial-resistant CC17 Enterococcus faecium: The past, the present and the future

Enterococcus faecium is a robust opportunistic pathogen that is most commonly found as a commensal of the human and animal gut but can also survive in the environment. Since the introduction and use of antimicrobials, E. faecium has been found to rapidly acquire resistance genes that, when expressed, can effectively circumvent the effects of most antimicrobials. The rapid acquisition of multiple antimicrobial resistances has led to the adaptation of specific E. faecium clones in the hospital environment, collectively known as clonal complex 17 (CC17). CC17 E. faecium are responsible for a significant proportion of hospital-associated infections, which can cause severe morbidity and mortality. Here we review the history of E. faecium from commensal to a significant hospital-associated pathogen, its robust phenotypic characteristics, commonly used laboratory typing schemes, and antimicrobial resistances with a focus on vancomycin and its associated mechanism of resistance. Finally, we review the global epidemiology of vancomycin-resistant E. faecium and potential solutions to problems faced in public health.

Draft Genome Sequence of a Vibrio parahaemolyticus Strain, KS17.S5-1, with Multiple Antibiotic Resistance Genes, Which Causes Acute Hepatopancreatic Necrosis Disease in Penaeus monodon in the West Coast of Peninsular Malaysia

We report the first draft genome sequence of a Vibrio parahaemolyticus strain (Vp_AHPND), which causes acute hepatopancreatic necrosis disease (AHPND) in Penaeus monodon. The strain has a pVA1-like plasmid carrying pirA_vp and pirB_vp genes.

We report the first draft genome sequence of a Vibrio parahaemolyticus strain (Vp_AHPND), which causes acute hepatopancreatic necrosis disease (AHPND) in Penaeus monodon. The strain has a pVA1-like plasmid carrying pirA_vp and pirB_vp genes. Whole-genome comparisons revealed >98% similarity to Vp_AHPND isolates from Thailand, Mexico, and Vietnam.

Characteristics of clinical and environmental vanM-carrying vancomycin-resistant enterococci isolates from an infected patient

vanM, an uncommon glycopeptide resistance gene, was first identified in an Enterococcus faecium isolate (Efm-HS0661) from Shanghai, China, in 2006 and has been predominant in this city since 2011. A vanM-carrying E. faecium was isolated from the bloodstream of a patient in an intensive care unit (ICU) in Hangzhou, China, in 2014. Further surveillance screening of a rectal swab and environmental surfaces of the patient yielded a large number of vanM-positive E. faecium. These isolates (including 1 from the bloodstream, 1 from the rectal swab and 43 representative isolates from environmental samples) were classified into four pulsed-field gel electrophoresis (PFGE) patterns and two sequence types (ST78 and ST564). PCR amplification and sequence analysis indicated that the genetic structure surrounding the vanM gene of these isolates was similar to that of the original vanM-carrying isolate Efm-HS0661. This study highlights the emergence of infections and environmental contamination caused by vanM-carrying E. faecium in an ICU of another Chinese city outside of Shanghai.

Susceptibility of vancomycin-resistant and -sensitive Enterococcus faecium obtained from Danish hospitals to benzalkonium chloride, chlorhexidine and hydrogen peroxide biocides

PURPOSE

In Danish hospitals, the number of infections caused by vancomycin-resistant Enterococcus faecium (VRE faecium) has dramatically increased in recent years. Hospital disinfectants are essential in eliminating pathogenic microorganisms, and reduced susceptibility may contribute to hospital-associated infections. We have addressed whether clinical VRE faecium display decreased biocide susceptibility when compared to vancomycin-sensitive Enterococcus faecium (VSE faecium) isolates.

METHODOLOGY

In total 12 VSE faecium and 37 VRE faecium isolates obtained from Danish hospitals over an extended time period were tested for susceptibility towards three commonly applied biocides, namely benzalkonium chloride, chlorhexidine and hydrogen peroxide.

RESULTS

For benzalkonium chloride, 89 % of VRE faecium strains had a minimal inhibitory concentration (MIC) of 8 mg l^-1, whereas for VSE faecium, only 25 % of the strains had an MIC of 8 mg l^-1. For chlorhexidine, the MIC of 95 % of VRE faecium strains was 4 mg l^-1 or higher, while only 33 % of VSE faecium strains displayed MIC values at the same level. In contrast, both VRE and VSE faecium displayed equal susceptibility to hydrogen peroxide, but a higher minimal bactericidal concentration (MBC) was found for the former. The efflux activity was also assessed, and this was generally higher for the VRE faecium strains compared to VSE faecium.

CONCLUSION

VRE faecium from Danish hospitals demonstrated decreased susceptibility towards benzalkonium chloride and chlorhexidine compared to VSE faecium, where the use of chlorhexidine is particularly heavy in the hospital environment. These findings suggest that biocide tolerance may characterize VRE faecium isolated in Danish hospitals.

Progress in Pharmacological Sciences in China

Pharmacology is the science that investigates the interactions between organisms and drugs and their mechanisms. Pharmacology plays a translational role in modern medicine, bridging basic research and the clinic. With its economy booming, China has invested an enormous amount of financial and human resources in pharmacological research in the recent decade. As a result, major breakthroughs have been achieved in both basic and clinical research, with the discovery of many potential drug targets and biomarkers that has made a sizable contribution to the overall advancement of pharmacological sciences. In this article, we review recent research efforts and representative scientific achievements and discuss future challenges and directions for the pharmacological sciences in China.

The Risk of Some Veterinary Antimicrobial Agents on Public Health Associated with Antimicrobial Resistance and their Molecular Basis

The risk of antimicrobial agents used in food-producing animals on public health associated with antimicrobial resistance continues to be a current topic of discussion as related to animal and human public health. In the present review, resistance monitoring data, and risk assessment results of some important antimicrobial agents were cited to elucidate the possible association of antimicrobial use in food animals and antimicrobial resistance in humans. From the selected examples, it was apparent from reviewing the published scientific literature that the ban on use of some antimicrobial agents (e.g., avoparcin, fluoroquinolone, tetracyclines) did not change drug resistance patterns and did not mitigate the intended goal of minimizing antimicrobial resistance. The use of some antimicrobial agents (e.g., virginiamycin, macrolides, and cephalosporins) in food animals may have an impact on the antimicrobial resistance in humans, but it was largely depended on the pattern of drug usage in different geographical regions. The epidemiological characteristics of resistant bacteria were closely related to molecular mechanisms involved in the development, fitness, and transmission of antimicrobial resistance.

Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones?

Enterococci are Gram-positive bacteria that are found in plants, soil and as commensals of the gastrointestinal tract of humans, mammals, and insects. Despite their commensal nature, they have also become globally important nosocomial pathogens. Within the genus Enterococcus, Enterococcus faecium, and Enterococcus faecalis are clinically most relevant. In this review, we will discuss how E. faecium and E. faecalis have evolved to become a globally disseminated nosocomial pathogen. E. faecium has a defined sub-population that is associated with hospitalized patients and is rarely encountered in community settings. These hospital-associated clones are characterized by the acquisition of adaptive genetic elements, including genes involved in metabolism, biofilm formation, and antibiotic resistance. In contrast to E. faecium, clones of E. faecalis isolated from hospitalized patients, including strains causing clinical infections, are not exclusively found in hospitals but are also present in healthy individuals and animals. This observation suggests that the division between commensals and hospital-adapted lineages is less clear for E. faecalis than for E. faecium. In addition, genes that are reported to be associated with virulence of E. faecalis are often not unique to clinical isolates, but are also found in strains that originate from commensal niches. As a reflection of more ancient association of E. faecalis with different hosts, these determinants Thus, they may not represent genuine virulence genes but may act as host-adaptive functions that are useful in a variety of intestinal environments. The scope of the review is to summarize recent trends in the emergence of antibiotic resistance and explore recent developments in the molecular epidemiology, population structure and mechanisms of adaptation of E. faecium and E. faecalis.

Prevalence, Antimicrobial Resistance, and Genotypic Characterization of Vancomycin-Resistant Enterococci in Meat Preparations

A total of 160 samples of poultry (80), pork (40), and beef (40) preparations (red sausages, white sausages, hamburgers, meatballs, nuggets, minced meat, escalope, and crepes) were tested in northwestern Spain to determine the prevalence of vancomycin-resistant enterococci (VRE). VRE were detected in 38 (23.8%) samples (37.5% of poultry, 15.0% of pork, and 5.0% of beef samples). One strain per food sample was further characterized. Isolates were identified as Enterococcus faecium (14 strains), E. durans (10), E. hirae (7), E. gallinarum (5), and E. casseliflavus-E. flavescens (2). All strains showed resistance or intermediate susceptibility to three or more antimicrobials of clinical significance, in addition to vancomycin. High rates of resistance or intermediate susceptibility were observed for teicoplanin (81.6% of isolates), chloramphenicol (81.6%), erythromycin (100%), quinupristin-dalfopristin (89.5%), and ciprofloxacin (81.6%). A moderate rate of resistance or intermediate susceptibility emerged for ampicillin (34.2%) and tetracycline (36.8%). Genes encoding antimicrobial resistance and virulence were studied by PCR. The vanA, vanB, vanC-1, and vanC-2/3 genes were identified in 27, 1, 5, and 2 isolates, respectively. Other resistance genes or transposon sequences found were tet(L), tet(M), Tn5397 (tetracycline), erm(A), erm(B) (erythromycin), vat(D), and vat(E) (quinupristin-dalfopristin). Most isolates were free of virulence determinants (agg, hyl, and efaAfm genes were detected in one, one, and five strains, respectively). Strains were classified as not biofilm producers (crystal violet assay; 4 isolates) or weak biofilm producers (34 isolates). Cluster analysis (EcoRI ribotyping) suggested a strong genetic relationship among isolates from different types of meat preparations, animal species, and retail outlets. Meat preparations might play a role in the spread through the food chain of VRE with several resistance and virulence genes.

Characterization of Enterococcus faecium bacteriophage IME-EFm5 and its endolysin LysEFm5

Due to the worldwide prevalence of antibiotic resistant strains, phages therapy has been revitalized recently. In this study, an Enterococcus faecium phage named IME-EFm5 was isolated from hospital sewage. Whole genomic sequence analysis demonstrated that IME-EFm5 belong to the Siphoviridae family, and has a double-stranded genome of 42,265bp (with a 35.51% G+C content) which contains 70 putative coding sequences. LysEFm5, the endolysin of IME-EFm5, contains an amidase domain in its N-terminal and has a wider bactericidal spectrum than its parental phage IME-EFm5, including 7 strains of vancomycin-resistant E. faecium. The mutagenesis analysis revealed that the zinc ion binding residues (H27, H132, and C140), E90, and T138 are required for the catalysis of LysEFm5. However, the antibacterial activity of LysEFm5 is zinc ion independent, which is inconsistent with most of other amidase members. The phage lysin LysEFm5 might be an alternative treatment strategy for infections caused by multidrug-resistant E. faecium.