Distribution of insertion sequences associated with Tn1546-like elements among Enterococcus faecium isolates from patients in Korea

Prevalence and Molecular Characterization of Vancomycin Variable Enterococcus faecium Isolated From Clinical Specimens

Vancomycin variable Enterococcus (VVE) bacteria are phenotypically susceptible to vancomycin, but they harbor the vanA gene. We aimed to ascertain the prevalence of VVE among clinically isolated vancomycin-susceptible Enterococcus faecium (VSE) isolates, as well as elucidate the molecular characteristics of the vanA gene cluster within these isolates. Notably, we investigated the prevalence and structure of the vanA gene cluster of VVE. Between June 2021 and May 2022, we collected consecutive, non-duplicated vancomycin-susceptible Enterococcus faecium (VSE) samples. Real-time PCR was performed to detect the presence of vanA, vanB, and vanC. Overlapping PCR with sequencing and whole-genome sequencing were performed for structural analysis. Sequence types (STs) were determined by multilocus sequence typing. Exposure testing was performed to assess the ability of the isolates to acquire vancomycin resistance. Among 282 VSE isolates tested, 20 isolates (7.1%) were VVE. Among them, 17 isolates had partial deletions in the IS1216 or IS1542 sequences in vanS (N=10), vanR (N=5), or vanH (N=2). All VVE isolates belonged to the CC17 complex and comprised five STs, namely ST17 (40.0%), ST1421 (25.0%), ST80 (25.0%), ST787 (5.0%), and ST981 (5.0%). Most isolates were related to three hospital-associated clones (ST17, ST1421, and ST80). After vancomycin exposure, 18 of the 20 VVEs acquired vancomycin resistance. Considering the high reversion rate, detecting VVE by screening VSE for vanA is critical for appropriate treatment and infection control.

Potentially conjugative plasmids harboring Tn6636, a multidrug-resistant and composite mobile element, in Staphylococcus aureus

OBJECTIVES

This study aimed to provide detailed genetic characterization of Tn6636, a multidrug-resistant and composite mobile element, in clinical isolates of Staphylococcus aureus.

METHODS

A total of 112 ermB-positive methicillin-susceptible S. aureus (MSSA) and 224 ermB-positive methicillin-resistant S. aureus (MRSA) isolates collected from 2000 to 2015 were tested for the presence of Tn6636. Detection of the plasmids harboring Tn6636 was performed by S1 nuclease digestion pulsed-field gel electrophoresis (PFGE) analysis, conjugation test, and whole genome sequencing (WGS).

RESULTS

Prevalence of Tn6636 in MSSA is higher than that in MRSA. Ten MSSA isolates and 10 MRSA isolates carried Tn6636. The 10 MSSA isolates belonged to three sequence types (ST), including ST7 (n = 6), ST5 (n = 3), and ST59 (n = 1). The 10 MRSA isolates belonged to ST188 (n = 8) and ST965 (n = 2). Analysis of plasmid sequences revealed that Tn6636 was harbored by six different mosaic plasmids. In addition to resistance genes, some plasmids also harbored toxin genes.

CONCLUSION

The presence of multi-resistant Tn6636 in plasmids of both MSSA and MRSA with various STs suggests its broad dissemination. Results indicate that Tn6636 has existed for at least 16 years in Taiwan. The mosaic plasmids harboring Tn6636 can be transferred by conjugation. Ongoing surveillance of Tn6636 is essential to avoid continued spreading of resistant plasmids.

First characterization of Tn1546-like structures of vancomycin-resistant Enterococcus faecium Thai isolates

INTRODUCTION

Vancomycin-resistant Enterococcus faecium (VREfm) carrying vanA was first isolated from patient at Siriraj Hospital, Thailand in 2004. Since then, VREfm isolates have been detected increasingly in this 2500-bed university hospital. To understand the epidemiology of vanA VREfm in this setting, the isolates collected during 2004-2013 were characterized.

METHODS

A total of 49 vanA VREfm isolates previously confirmed by multiplex PCR were characterized by determining resistance phenotypes to vancomycin, teicoplanin, ampicillin and ciprofloxacin by broth microdilution method. Multilocus sequence typing (MLST) and virulence genes of those isolates were investigated. The Tn1546 structure diversity was studied by long-range overlapping PCR and primer walking sequencing.

RESULTS

Of all isolates studied, 9 sequence types (ST17, ST80, ST78, ST730, ST203, ST18, ST280, ST64, ST323) in clonal complex 17 and a novel ST1051 were revealed. The esp-positive isolates were 73.5%. Of all vanA operons characterized, at least 9 types of Tn1546-like structures were detected. All of vanA determinants contained 5'-end different from the Tn1546 prototype. Approximately 47% of them also carried the insertion sequence IS1251 at the intergenic region between vanS and vanH. Interestingly, another IS (ISEfa4) was found to be inside the sequence of IS1251 in ST17 isolate.

CONCLUSION

Heterogeneity of vanA VREfm was observed. Nearly all of isolates studied belonged to CC17. One novel ST1051 strain was detected. Isolates in the initial period carried vanA operon similar to the prototype. The diversity of vanA determinants has been increased in the recent isolates. A novel vanA operon structure was detected.

Evaluation of commercial veterinary probiotics containing enterococci for transferrable vancomycin resistance genes

Objective

Vancomycin resistant enterococci (VRE) are of significant public health concern. The identification of VRE in livestock and food has increased. The objective of this study was to determine if the transferrable vancomycin resistance genes vanA and vanB were present in probiotics marketed for use in animals that claimed to contain Enterococcus spp.

Results

Of the 40 products selected, Enterococcus spp. DNA was successfully extracted from 36 products. Of these 36 products with enterococcal DNA, 2 (6%) had a PCR product consistent with vanA which was confirmed by sequencing. None of the products appeared to contain vanB.

Expression of VanA-type vancomycin resistance in a clinical isolate of Enterococcus faecium showing insertion of IS19 in the vanS gene

The characteristics of an unusual clinical isolate of Enterococcus faecium (CL-6729) showing insertion of IS19 (also known as ISEfm1) in the vanS gene while maintaining a constitutive VanA phenotype are described. This isolate was obtained from a hospital-acquired urinary tract infection, showed multidrug resistance by antimicrobial susceptibility testing, and belongs to ST78 based on multilocus sequence typing (MLST). Except for the vanS gene, all the other genes of the vanA gene cluster were intact according to conventional PCR, overlapping PCR and genome sequencing. By quantitative reverse transcription PCR (RT-qPCR), the isolate showed similar expression of the vanA, vanR and vanS genes in the presence and absence of vancomycin. The results suggest that insertion of IS19 in the vanS gene may be associated with constitutive expression of resistance to vancomycin in clinical isolate CL-6729, either by not impairing VanS activity or by inducing the emergence of another pathway that acts on vanA expression, which still needs to be fully investigated.

Phenotypic and genetic characteristics of vancomycin-resistant Enterococcus faecium

This study was based on 43 vancomycin-resistant Enterococcus faecium (VREfm) strains collected from clinical specimens. Susceptibility testing and resistance gene amplification revealed that these strains had multidrug resistance and all belonged to the VanA phenotype. Furthermore, there were seven ST types, and all belonged to the clonal complex (CC17); ST17 and ST78 were the main ST types. In particular, ST1392 and ST1394 are novel ST types first identified in this research. Genome analysis of SY1, LY19 and LY22 showed that tet(O)and tet(K) were the genes responsible for tetracycline resistance; acc(6')-Ie-aph(2')-Ia and aad(6) led to high-level gentamicin and high-level streptomycin resistance. At the same time, the genomic variation among the strains was large, which is of great significance for the prevention and control of the bacteria.

Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains

BACKGROUND

Enterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic differences responsible for probiotic, pathogenic and non-pathogenic properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains.

RESULTS

E. faecium 17OM39 was found to be closely related with marketed probiotic strain T110 based on core genome analysis. Strain 17OM39 was devoid of known vancomycin, tetracycline resistance and functional virulence genes. Moreover, E. faecium 17OM39 genome was found to be more stable due to the absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Genes associated with colonization and survival within gastrointestinal tract was also detected across all the strains.

CONCLUSIONS

Beyond shared genetic features; this study particularly identified genes that are responsible for imparting probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. Higher genomic stability, absence of known virulence factors and antibiotic resistance genes and close genomic relatedness with marketed probiotics makes E. faecium 17OM39 a potential probiotic candidate. The work presented here demonstrates that comparative genome analyses can be applied to large numbers of genomes, to find potential probiotic candidates.

Linezolid-resistant enterococci in Polish hospitals: species, clonality and determinants of linezolid resistance

The significant increase of the linezolid-resistant enterococci (LRE) has been observed in Polish hospitals since 2012 and our study aimed at elucidating the possible reasons for this phenomenon. Polish LRE isolates were analysed by multilocus-sequence typing (MLST) and multiple locus variable-number tandem repeat (VNTR) analysis (MLVA), polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP) to establish clonal relatedness and mechanism of linezolid resistance, respectively. Fifty analysed LRE (2008–2015) included mostly Enterococcus faecium (82%) and Enterococcus faecalis (16%). Enterococcus faecium belonged to the hospital-adapted lineages 17/18 and 78, while E. faecalis isolates represented ST6, a hospital-associated type, and ST116, found in both humans and food-production animals. The G2576T 23S rRNA mutation was the most frequent (94%) mechanism of linezolid/tedizolid resistance of LRE. None of the isolates carried the plasmid-associated gene of Cfr methyltransferase, whereas optrA, encoding the ABC-type drug transporter, was identified in two E. faecalis isolates. In these isolates, optrA was located on a plasmid, transferable to both E. faecium and E. faecalis, whose partial (36.3 kb) sequence was 100% identical to the pE394 plasmid, identified previously in China in both clinical and farm animal isolates. The optrA–E. faecium transconjugant displayed a significant growth deficiency, in contrast to the optrA–E. faecalis. Our study indicates the role of mutation acquisition by hospital-adapted clones of enterococci as a major driver of increasing resistance to linezolid and tedizolid. Transferability and apparent lack of a biological cost of resistance suggest that E. faecalis may be a natural reservoir of optrA, an emerging mechanism of oxazolidinone resistance.

Comparative genome analysis of multiple vancomycin-resistant Enterococcus faecium isolated from two fatal cases

Enterococcus faecium is both a commensal of the human intestinal tract and an opportunistic pathogen. The increasing incidence of enterococcal infections is mainly due to the ability of this organism to develop resistance to multiple antibiotics, including vancomycin. The aim of this study was to perform comparative genome analyses on four vancomycin-resistant Enterococcus faecium (VRE_fm) strains isolated from two fatal cases in a tertiary hospital in Malaysia. Two sequence types, ST80 and ST203, were identified which belong to the clinically important clonal complex (CC) 17. This is the first report on the emergence of ST80 strains in Malaysia. Three of the studied strains (VREr5, VREr6, VREr7) were each isolated from different body sites of a single patient (patient Y) and had different PFGE patterns. While VREr6 and VREr7 were phenotypically and genotypically similar, the initial isolate, VREr5, was found to be more similar to VRE2 isolated from another patient (patient X), in terms of the genome contents, sequence types and phylogenomic relationship. Both the clinical records and genome sequence data suggested that patient Y was infected by multiple strains from different clones and the strain that infected patient Y could have derived from the same clone from patient X. These multidrug resistant strains harbored a number of virulence genes such as the epa locus and pilus-associated genes which could enhance their persistence. Apart from that, a homolog of E. faecalis bee locus was identified in VREr5 which might be involved in biofilm formation. Overall, our comparative genomic analyses had provided insight into the genetic relatedness, as well as the virulence potential, of the four clinical strains.

Role of Horizontal Transfer of the Transposon Tn1546in the Nosocomial Spread ofvanAVancomycin-Resistant Enterococci at a Tertiary Care Hospital in Korea

Objective:

To investigate the epidemiologic characteristics of vancomycin-resistant enterococci (VRE) infection.

Design.

An epidemiologic description by means of chromosomal DNA fingerprinting and transposon typing.

Setting.

A 2,200-bed tertiary care hospital in Korea.

Patients.

First VRE isolates were obtained from patients hospitalized from April 1997 to December 2001.

Interventions.

Thevangenotypes of isolates were identified by means of multiplex polymerase chain reaction (PCR). The macro-restriction patterns of chromosomal DNA were determined by pulsed-field gel electrophoresis (PFGE). The transposon Tn1546was typed by means of 2 sets of long PCR restriction fragment-length polymorphism analysis, which wereClaI restriction of a 10.4-kb region fromorf1tovanZandDdeI restriction of a 4.4-kb region fromvanRtovanX.

Results.

VRE isolates were recovered from 215 patients. All werevanAgenotype. PFGE analysis of the 215 isolates showed 172 types, including 21 clusters composed of 64 isolates and 151 types of as many isolates. Each type was composed of 2-10 isolates; the isolates within each PFGE cluster were detected within a 10-month period and mostly shared a transposon type. Transposon typing classified 169 strains into 15 types and 158 strains belonged to 4 major transposon clusters. Each of these 4 transposon clusters was isolated from patients treated in 5-22 different wards during a 31-52 month period and consisted of 9-80 PFGE types. Each of the other 11 types were found in only one strain.

Conclusions.

Our findings suggest that the horizontal transfer of Tn1546has a major role in the nosocomial spread ofvanAVRE. Clonal spread of VRE seemed to contribute to short-term dissemination in limited areas.

Vancomycin-resistance phenotypes, vancomycin-resistance genes, and resistance to antibiotics of enterococci isolated from food of animal origin

In the present study, 500 raw beef, pork, and chicken meat samples and 100 pooled egg samples were analyzed for the presence of vancomycin-resistant enterococci, vancomycin-resistance phenotypes, and resistance genes. Of 141 isolates of enterococci, 88 strains of Enterococcus faecium and 53 strains of E. faecalis were identified. The most prevalent species was E. faecium. Resistance to ampicillin (n = 93, 66%), ciprofloxacin (n = 74, 52.5%), erythromycin (n = 73, 51.8%), penicillin (n = 59, 41.8%) and tetracycline (n = 52, 36.9%) was observed, while 53.2% (n = 75) of the isolates were multiresistant and 15.6% (n = 22) were susceptible to all antibiotics. Resistance to vancomycin was exhibited in 34.1% (n = 30) of the E. faecium isolates (n = 88) and 1.9% (n = 1) of the E. faecalis isolates (n = 53) using the disc-diffusion test and the E-test. All isolates were tested for vanA and vanB using real-time polymerase chain reaction (PCR) and multiplex PCR, and for vanC, vanD, vanE, vanG genes using multiplex PCR only. Among E. faecalis isolates, no resistance genes were identified. Among the E. faecium isolates, 28 carried the vanA gene when tested by multiplex PCR and 29 when tested with real-time PCR. No isolate carrying the vanC, vanD, vanE, or vanG genes was identified. Melting-curve analysis of the positive real-time PCR E. faecium isolates showed that 22 isolates carried the vanA gene only, 2 isolates the vanB2,3 genes only, and seven isolates carried both the vanA and vanB2,3 genes. Enterococci should be considered a significant zoonotic pathogen and a possible reservoir of genes encoding resistance potentially transferred to other bacterial species.

Molecular analysis of vanA outbreak of Enterococcus faecium in two Warsaw hospitals: the importance of mobile genetic elements

Vancomycin-resistant Enterococcus faecium represents a growing threat in hospital-acquired infections. Two outbreaks of this pathogen from neighboring Warsaw hospitals have been analyzed in this study. Pulsed-field gel electrophoresis (PFGE) of SmaI-digested DNA, multilocus VNTR analysis (MLVA), and multilocus sequence typing (MLST) revealed a clonal variability of isolates which belonged to three main lineages (17, 18, and 78) of nosocomial E. faecium. All isolates were multidrug resistant and carried several resistance, virulence, and plasmid-specific genes. Almost all isolates shared the same variant of Tn1546 transposon, characterized by the presence of insertion sequence ISEf1 and a point mutation in the vanA gene. In the majority of cases, this transposon was located on 50 kb or 100 kb pRUM-related plasmids, which lacked, however, the axe-txe toxin-antitoxin genes. 100 kb plasmid was easily transferred by conjugation and was found in various clonal backgrounds in both institutions, while 50 kb plasmid was not transferable and occurred solely in MT159/ST78 strains that disseminated clonally in one institution. Although molecular data indicated the spread of VRE between two institutions or a potential common source of this alert pathogen, epidemiological investigations did not reveal the possible route by which outbreak strains disseminated.

Outbreak of vancomycin-susceptible Enterococcus faecium containing the wild-type vanA gene

Accurate detection of vancomycin-resistant enterococci (VRE) is essential in preventing transmission in health care settings. Chromogenic media are widely used for screening VRE because of fast turnaround times (TAT) and high sensitivity. We report an outbreak of Enterococcus faecium bearing vanA yet susceptible to vancomycin (vancomycin-variable Enterococcus [VVE]). Between October 2009 to March 2011, clinical and screening specimens (n=14,747) were screened for VRE using VRE-selective medium and/or PCR. VVE isolates were genotyped to determine relatedness. Plasmids from these isolates were characterized by sequencing. Overall, 52 VVE isolates were identified, comprising 15% of all VRE isolates identified. Isolates demonstrated growth on Brilliance VRE agar (Oxoid) at 24 h of incubation but did not grow on brain heart infusion agar with 6 μg/ml vancomycin (Oxoid) or bile esculin azide agar with 6 μg/ml vancomycin (Oxoid) and were susceptible to vancomycin. Genotyping of 20 randomly selected VVE isolates revealed that 15/20 were identical, while 5 were highly related. PCR of the VVE transposon confirmed the presence of vanHAXY gene cluster; however, vanS (sensor) and vanR (regulator) genes were absent. The outbreak was controlled through routine infection control measures. We report an emergence of a fit strain of E. faecium containing vanA yet susceptible to vancomycin. Whether this new strain represents VRE has yet to be determined; however, unique testing procedures are required for reliable identification of VVE.

Comparison of genetic epidemiology of vancomycin-resistant Enterococcus faecium isolates from humans and poultry

This study was conducted to investigate the molecular characteristics and genetic relatedness of vancomycin-resistant Enterococcus faecium (VREF) isolates obtained from humans and poultry in Korea. A total of 147 VREF isolates from humans (71 clinical isolates) and poultry (76 isolates) in Korea were compared with respect to their antibiotic susceptibilities, organization of the Tn1546 transposon element, detection of virulence genes (esp and hyl), pulsed-field gel electrophoresis (PFGE) typing and multilocus sequence typing (MLST). All of the human and poultry isolates had the vanA gene and 11.3% (8/71) of the clinical isolates showed the VanB phenotype/vanA genotype. PCR mapping of the Tn1546 elements was different for isolates of the two groups: human isolates were classified into five transposon types, whereas all poultry isolates were identical to Tn1546 of E. faecium strain BM4147. The esp gene was detected in both human (93.0%, 66/71) and poultry (26.3%, 20/76) isolates, as was the hyl gene (human isolates: 80.3%, 57/71; poultry isolates: 26.3%, 20/76). Using MLST, the 71 human isolates could be divided into ten sequence types (STs) belonging to clonal complex (CC) 17 (except for one singleton). The 76 poultry isolates were categorized into 14 STs and 88.2% (67/76) of the poultry isolates belonged to CC26. PFGE typing of the human isolates demonstrated diverse PFGE profiles among the strains. However, the PFGE patterns of the poultry isolates were possibly related to the strains collected from individual farms. These data suggest that epidemic clonal groups of human and poultry VREFs in Korea have evolved through different evolutionary processes.

Novel vancomycin-resistance transposon, plasmid replicon types, and virulence factors of vancomycin-resistant Enterococci in Zhejiang, China

Forty-seven vancomycin-resistant Enterococcus (VRE) strains were isolated from clinical samples in 13 Zhejiang hospitals and fecal samples from ICU patients in a large teaching hospital in China. No VRE isolates were detected in healthy human subjects. CC17 was the main clonal complex in clinical Enterococcus faecium isolates but not in isolates from healthy human subjects. Novel vancomycin-resistance transposons were detected among VRE strains. This is the first report demonstrating insertion of tnpA and fosB genes in the vanRS-vanH intergenic region of Tn1546 leading to coresistance to vancomycin and fosfomycin. The four plasmid replicon types (pRUM, pRE25, pEF418, and pB82) were more common in VRE isolates, suggesting their association with vancomycin resistance and nosocomial transmission. The prevalence rate of vancomycin-resistant Staphylococcus aureus-related Inc18-like plasmid, pIP501, in VRE was 21.3%. The prevalence of the esp gene among VRE isolates was high (76.6%). In several VRE strains, the esp and hyl genes were cotransferred with the vanA gene by conjugation. Although the frequency of VRE is low in Chinese hospitals, its association with virulence determinants, the vancomycin-resistance transposon with other resistance gene insertions or plasmids may lead to multidrug resistance and the evolution of pathogenic VRE.

Mobile genetic elements and their contribution to the emergence of antimicrobial resistant Enterococcus faecalis and Enterococcus faecium

Mobile genetic elements (MGEs) including plasmids and transposons are pivotal in the dissemination and persistence of antimicrobial resistance in Enterococcus faecalis and Enterococcus faecium. Enterococcal MGEs have also been shown to be able to transfer resistance determinants to more pathogenic bacteria such as Staphylococcus aureus. Despite their importance, we have a limited knowledge about the prevalence, distribution and genetic content of specific MGEs in enterococcal populations. Molecular epidemiological studies of enterococcal MGEs have been hampered by the lack of standardized molecular typing methods and relevant genome information. This review focuses on recent developments in the detection of MGEs and their contribution to the spread of antimicrobial resistance in clinically relevant enterococci.

Molecular epidemiology of vancomycin-resistant Enterococcus faecium bloodstream infections among patients with neutropenia over a 6-year period in South Korea

Over a 6-year period (March 2000-February 2006), there were 60 vancomycin-resistant Enterococcus faecium (VREF) bloodstream infections (BSIs) in a hematology unit, accounting for 83.3% of all VREF BSIs in the hospital. We investigated 49 VREF isolates causing BSIs in patients with neutropenia to understand the molecular epidemiology at this unit. All isolates had the vanA genotype. Pulsed-field gel electrophoresis typing revealed high clonal diversity (23 types with nine clusters comprising 35 isolates) and 1 predominant type, type A (14/49, 28.6%), persisted at this unit throughout the study period, suggesting the clonal spread of this endemic strain by cross-contamination. Tn1546 types were less heterogeneous, with five main Tn1546 types, two of which (types I and IV) accounted for 67.4% of isolates. This indicates that in addition to clonal spread, the horizontal transfer of Tn1546 played a major role in the nosocomial dissemination of vancomycin resistance. The genetic diversity of VREF increased over time, implying an increasing influx of new strains into the unit and genetic changes, possibly attributable to the horizontal transfer of diverse Tn1546 types. Despite such diversity, all the isolates belonged to clonal complex 17, which is the epidemic clone worldwide, enriched with the esp (35/49, 71.4%) and hyl (24/49, 48.9%) virulence genes. This hospital-adapted clone has become endemic and is well suited to causing BSIs in patients with neutropenia in this unit.

Distribution of insertion sequences associated with Tn1546 and clonal diversity of vancomycin-resistant enterococci isolated from patients in Tehran, Iran

BACKGROUND AND OBJECTIVES

Infection with vancomycin-resistant enterococci (VRE) has caused a therapeutic problem. VanA and VanB resistant types are the predominant phenotypes among vancomycin resistant enetrococci. Transposon 1546 (Tn1546) harboring the vanA gene cluster, plays an important role in the horizontal transfer of vanA gene. In this study, we examined the phenotypic and genotypic diversity of a number of clinical VRE.

MATERIALS AND METHODS

Twenty-four clinical VRE isolated from two university hospitals in Tehran were examined based on their antimicrobial susceptibility, Tn1546 related element organization and pulsed-field gel electrophoresis (PFGE) patterns. Integration of well-studied insertion sequence elements IS1216V, IS1542 and IS1251 was examined by PCR mapping and sequencing.

RESULTS

From 24 isolates, 15 isolates with VanA phenotype and 9 isolates with VanB phenotype were identified which both groups interestingly possessed the vanA gene. According to PCR mapping, our isolates were assigned to 6 main groups. In 14 (58.3%) isolates, IS1216V was inserted in vanX-vanY region and/or in truncated left-hand of Tn1546-like elements. In 11 (45.8%) isolates, both IS1216V and IS1542 were inserted in vanX-vanY and orf2-vanR regions, respectively and none of them harbored IS1251. Interestingly, PFGE of the isolates showed a high degree of diversity.

CONCLUSION

PCR mapping revealed that VanA elements in our isolates were highly heterogeneous. Overall, we found no correlation between transposon type and PFGE pattern. Genetic diversity of VRE provides practical information for epidemiological studies and our data showed horizontal transfer of VRE in this region.

Molecular epidemiology of vancomycin-resistant enterococci in Singapore

AIMS

To characterise the mechanism of glycopeptide resistance, genetic relatedness, and pathogenicity factors in isolates of vancomycin-resistant enterococci (VRE) in Singapore.

METHODS

A total of 292 Enterococcus faecium and 17 Enterococcus faecalis were isolated from humans, and five E. faecium, two Enterococcus durans, two Enterococcus flavescens, one Enterococcus casseliflavus, and one Enterococcus gallinarum from chickens. The mechanism of glycopeptide resistance and pathogenicity factors were studied by PCR and the genetic relatedness determined by pulsed-field gel electrophoresis (PFGE), multi-locus variable number tandem repeat analysis (MLVA), and Tn1546 analysis.

RESULTS

There were five outbreak clones among the vancomycin-resistant E. faecium with one clone predominant. Four of the clones were vanB positive, and only one clone carried vanA. All outbreak clones were esp gene positive. Sporadic human isolates and chicken isolates were vanA positive and did not contain any pathogenicity genes. The situation was reversed in vancomycin-resistant E. faecalis where almost all isolates were vanA positive.

CONCLUSIONS

Most VRE in Singapore is hospital associated with a small number of clones of esp-positive vanB E. faecium responsible for the majority of isolates.

Relapse and reacquisition of rectal colonization by vancomycin-resistantEnterococcus faeciumafter decolonization

To better understand the epidemiology of colonization of vancomycin-resistant enterococci (VRE), we performed an 8-year retrospective study of all hospitalized patients with recurrent VRE colonization after they were documented as being clear of VRE and compared the primary colonization isolates and recolonization isolates by pulsed-field gel electrophoresis and Tn1546typing. Review of the medical records of all patients showed that of the 15 patients with recurrent colonization, six continued to be hospitalized on the same floor. Five were discharged home and then readmitted. Four were moved to another floor. Patients who remained on the same floor were recolonized with a strain that was indistinguishable from the original colonizing strain. Patients who were moved or were discharged hadde novoVRE colonization with strains distinct from the original colonizing strain.

Spread of vancomycin-resistant Enterococcus faecium in two haematological centres in Russia

This paper describes the clonal diversity of vancomycin-resistant Enterococcus faecium isolated from patients with haematological malignancies in Russia. Pulsed-field gel electrophoresis (PFGE) typing of 129 vanA-positive E. faecium strains revealed 23 independent restriction profiles with two predominant clonal types. Multilocus sequence typing (MLST) of 16 strains selected from two predominant PFGE types showed that they belong to the epidemic clonal complex (CC) 17. Tn1546-like elements of isolates were compared with the prototype element from E. faecium BM4147 by polymerase chain reaction (PCR). Four different Tn1546 types were distinguished according to structural alternations. Polymorphism in the orf1 and vanSH genes was detected. However, a significant prevalence of the prototype Tn1546 was revealed. Tn1546-like elements with the same structures were observed in strains of different PFGE types. The virulence genes esp, gelE and hyl were detected by PCR in 118 isolates (91%), 87 isolates (67%) and 35 isolates (27%), respectively. In contrast, agg and cylA genes were not found. The detection frequency of esp was higher in epidemic strains than in sporadic ones (100% vs. 56%; P<0.05). This study describes a genetically variable population of vancomycin-resistant E. faecium in two Russian haematological centres. The spread of vancomycin resistance was mostly due to the distribution of the two subclones of E. faecium CC17, enriched with the virulence marker esp. At the same time, dissemination of an altered Tn1546 also occurred.

VanB phenotype-vanA genotype Enterococcus faecium with heterogeneous expression of teicoplanin resistance

Six VanB phenotype-vanA genotype isolates of Enterococcus faecium with heterogeneous expression of teicoplanin resistance which gave rise to an outbreak at a Korean tertiary care teaching hospital have IS1216V in the coding region of vanS. This could be the underlying cause of the VanB phenotype-vanA genotype with heterogeneous expression of teicoplanin resistance.

Molecular structure and transferability of Tn1546-like elements in Enterococcus faecium isolates from clinical, sewage, and surface water samples in Iran

The molecular structure and transferability of Tn1546 in 143 vancomycin-resistant Enterococcus faecium (VREF) isolates obtained from patients (n = 49), surface water (n = 28), and urban and hospital sewage (n = 66) in Tehran, Iran, were investigated. Molecular characterization of Tn1546 elements in vanA VREF was performed using a combination of restriction fragment length polymorphism analysis and DNA sequencing of the internal PCR fragments of vanA transposons. Long-PCR amplification showed that the molecular size of Tn1546 elements varied from 10.8 to 12.8 kb. The molecular analysis of Tn1546 showed that 45 isolates (31.5%) harbored a deletion/mutation upstream from nucleotide 170. No horizontal transfer of Tn1546 was observed following filter-mating conjugation with these isolates. Nevertheless, the rates of transferability for other isolates were 10(-5) to 10(-6) per donor. Insertion sequences IS1216V and IS1542 were present in 103 (72%) and 138 (96.5%) of the isolates, respectively. The molecular analysis of Tn1546 elements resulted in three genomic organizations. The genomic organization lineage 1 was dominated by the isolates from clinical samples (3.4%), lineage 2 was dominated mostly by sewage isolates (24.5%), and lineage 3 contained isolates obtained from all sources (72.1%). The genetic diversity determined using pulsed-field gel electrophoresis (PFGE) revealed a single E. faecium clone, designated 44, which was common to the samples obtained from clinical specimens and hospital and municipal sewage. Furthermore, the results suggest that lineage 3 Tn1546 was highly disseminated among our enterococcal isolates in different PFGE patterns.

Diversity of Tn1546 and its role in the dissemination of vancomycin-resistant enterococci in Portugal

We characterized the molecular diversity of vanA vancomycin-resistant enterococci (VRE; 176 isolates/87 pulsed-field gel electrophoresis types) from different sources and cities in Portugal (1996 to 2004): (i) food animals (FA; n = 38 isolates out of 31 samples), hospitalized humans (HH; n = 101/101), healthy human volunteers (HV; n = 7/4), and environmental sources (n = 30/10). Some strains were isolated from different hosts and persistently recovered for years. Twenty-four Tn1546 variants were identified, all located on plasmids (30 to 250 kb). Some Tn1546 variants were associated with specific sources such as FA (3 types), HH (11 types), or HV (1 type), while others were recovered from isolates of different origins (8 types). Polymorphisms in the central vanRSHA region of Tn1546 were scarcely detected, while alterations upstream of vanR and downstream of vanA were frequently identified involving mutations (vanS and vanX), deletions (vanY), insertions (IS1216V, ISEf1, and IS19; sequences with or without homology with others available in GenBank databases), and different genetic rearrangements. Most Tn1546 variants contained IS1216V (14 types) or ISEf1 (6 types). IS1216V was found alone or associated with an IS3-like element at different orientations and positions in Tn1546 from human, animal, and environmental samples. ISEf1 was located within vanX-vanY region at nucleotide 9044 of Tn1546 variants mostly associated with clinical isolates, suggesting a common genetic platform. IS19 was observed within the vanX-vanY region in one Tn1546 variant from poultry. Recent spread of VRE in Portugal reflects a complex epidemiology involving both clonal spread and plasmid dissemination containing a variety of Tn1546 types. Apparent Tn1546 heterogeneity among enterococci from human, animal, and environmental sources might reflect frequent genetic exchange events and evolution of particular widely disseminated genetic elements.

Genetic rearrangements of TN1546-like elements in vancomycin-resistant Enterococcus faecium isolates collected from hospitalized patients over a seven-year period

The heterogeneity of Tn1546 results from point mutations, deletions, and the integration of insertion sequence (IS) elements. Among these variations, the presence of IS elements accounts for much of the heterogeneity. Such a rearrangement could play a key role in the evolution of the vanA gene cluster, and hence, it may modify its transferability. In this study, we characterized the consequence of Tn1546 in vanA-containing Enterococcus faecium isolates collected from patients over time. From 1998 to 2004, 57 vanA-containing E. faecium isolates were collected from hospitalized patients at Ajou University Hospital in Korea. PCR amplification of internal regions of Tn1546 was performed, and both DNA strands were directly sequenced by the dideoxy termination method. All isolates were divided into three main types, including the prototype, according to the distribution of IS elements integrated into Tn1546 elements. Type I was characterized by an IS1542 insertion in the orf2-vanR intergenic region and an IS1216V insertion in the vanX-vanY intergenic region. Type II was represented by the presence of two copies of IS1216V at the 3' end of IS1542 and in the vanX-vanY intergenic region, as well as IS1542 in the orf2-vanR intergenic region. Seventeen strains isolated from 1998 to 2000 represented type I, and 38 strains isolated from 2000 to 2004 represented type II. The remaining two isolates were the prototype. The tendency for the rearrangement of Tn1546 was that the sequences were shortened as time passed, especially at the left or the right end, and hence, this could gradually modulate their transferability.

The first molecular analysis of clinical isolates of VanA-type vancomycin-resistant Enterococcus faecium strains in Mainland China

AIMS

The aim of this study was to examine two VanA-type vancomycin-resistant Enterococcus faecium (VRE) strains that had been isolated from patients resident in mainland China. This is the first molecular analysis of clinical VRE strains being isolated in mainland China.

METHODS AND RESULTS

Two VanA-type VRE isolates were isolated from in-patients at hospitals located in the Chinese cities Beijing and Dalian and were designated C264 and I125. The plasmids pC264V (40 kbp) and pI125V (370 kbp) that were isolated from C264 and I125, respectively, carried a Tn1546-like element encoding VanA resistance. The vancomycin-resistant plasmids pC264V and pI125V were transferred by filter mating at frequencies of 10(-7) and 10(-4) respectively. Sequence analysis of pC264V revealed that two IS1216V sequences and an IS1542 sequence were present within the Tn1546-like element. pI125V had two IS1216V insertions in the Tn1546-like element.

CONCLUSIONS

The two VanA-type vancomycin-resistant E. faecium (VRE) strains C264 and I125 were isolated from in-patients in Chinese hospitals. The vancomycin-resistant conjugative plasmids pC264V and pI125V plasmids isolated from these strains carried the Tn1546-like element. The Tn1546-like element was found to contain the insertion sequences IS1216V and IS1542.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first molecular analysis of VanA-type VRE strains from patients resident in mainland China.

Molecular characterization of vancomycin-resistant enterococcus faecium isolates from mainland China

Little is known about vancomycin-resistant enterococci in China. Thirteen pulsed-field gel electrophoresis-confirmed heterogeneous VanA-type vancomycin-resistant Enterococcus faecium (VRE) isolates were obtained from five Chinese hospitals from 2001 to 2005. The isolates were typed by multilocus sequence typing into nine different sequence types (STs), including five new STs (ST18, ST25, ST78, ST203, ST320, ST321, ST322, ST323, and ST335). Vancomycin resistance in each isolate was encoded on conjugative plasmids; two of the plasmids, pZB18 (67 kbp) and pZB22 (200 kbp), were highly conjugative and were able to transfer at high frequencies of around 10(-4) and 10(-7) per donor cell in broth mating, respectively. None of the plasmids identified in these isolates carried traA, which is usually conserved in the pMG1-like highly conjugative plasmid for E. faecium, implying that pZB18 and pZB22 were novel types of a highly conjugative plasmid in enterococci. Thirteen Tn1546-like elements encoding VanA-type VRE on the conjugative plasmids were classified into six types (types I to VI), and most of them contained both IS1216V and IS1542 insertions. The isolates carrying the type II element were predominant. The six type elements were different from that of a VanA-type Enterococcus faecalis strain isolated from Chinese chicken meat. The results suggested that the disseminations of VRE in these areas were by Tn1546-like elements being acquired by the conjugative plasmids and transferred among E. faecium strains.

High frequency of vancomycin-resistant Enterococcus faecium isolates with VanB phenotype and vanA genotype in Korean hospitals

A total of 59 vancomycin-resistant Enterococcus faecium (VREF) clinical isolates were collected from 8 Korean hospitals for 2 months in 2004. They were investigated by genotyping for glycopeptide resistance, multilocus sequence typing (MLST), esp repeat profiling, and structural analysis of Tn1546-like element. Nine of 59 VREF isolates (15.3%) from 5 hospitals in Korea showed VanB phenotype, but they contained vanA gene. MLST and esp repeat profiling indicated that E. faecium isolates with VanB phenotype and vanA genotype occurred from independent genetic background except 3 isolates from 1 hospital. Structural analysis of Tn1546 also showed that these isolates were not clonally related. Data showed a relatively high frequency of VREF isolates with incongruence between phenotype and genotype for glycopeptide resistance in Korean hospitals.

Phenotypic and genetic characterization of vancomycin-resistant enterococci from hospitalized humans and from poultry in Korea

Vancomycin resistant enterococci (VRE) isolates from humans (23 isolates) and poultry (20 isolates) were characterized by antibiotic susceptibility, vancomycin resistance transferability, pulsed-field gel electrophoresis (PFGE), and structural analysis of Tn1546-like elements. VRE isolates from humans and poultry showed different resistance patterns, transferability, and transfer rate. In addition to these phenotypic differences between humans and poultry VRE, PFGE and the structure of Tn1546-like elements were also distinct. Most poultry isolates (16/20) were identical to the prototype vanA transposon, Tn1546, while most human isolates (21/23) had multiple integrations of insertion sequence. The transmission of VRE and vancomycin resistance determinant between humans and poultry could not be demonstrated in this study.

First nosocomial outbreak of vancomycin-resistant Enterococcus faecium expressing a VanD-like phenotype associated with a vanA genotype

Although enterococci expressing acquired vancomycin resistance phenotype have been reported increasingly worldwide, they have been rarely reported in France. From August to December 2004 we faced an outbreak of vancomycin-resistant Enterococcus faecium (VRE) isolates in the nephrology department at Bicêtre Hospital (K.-Bicêtre, France). The expression of the glycopeptide resistance varied among the 26 VRE isolates, with vancomycin MICs ranging from 12 to >256 microg/ml, whereas teicoplanin MICs ranged from 4 to 48 microg/ml. However, several strains appeared to be susceptible to glycopeptides according to disk diffusion testing and expressed resistance only after subculture with glycopeptides. In addition, a heterogeneous expression of glycopeptide resistance was also observed. This so-called VanD-like phenotype of resistance (low-level resistance to vancomycin and mostly susceptibility to teicoplanin) was surprisingly associated with a vanA gene. Plasmid extraction and mating-out experiments indicated that the vanA gene was located on a 200-kb self-transferable plasmid. Pulsed-field gel electrophoresis identified mostly dissemination of a single clone, whereas diffusion of the VanA-positive plasmid in different genomic backgrounds had also occurred. The vanA gene was part of a vanA-type operon for expression of resistance located on a Tn1546-like transposon. Sequencing of this transposon identified insertion of insertion sequence IS16 in the vanY gene that encodes a d,d-carboxypeptidase that might explain in part the peculiar VanD-type phenotype of resistance. This report is the first description of a VRE outbreak in France and underlines the difficulty in detecting this organism due to variability on the expression of the glycopeptide resistance trait, if any.