Spread of ampicillin/vancomycin-resistant Enterococcus faecium of the epidemic-virulent clonal complex-17 carrying the genes esp and hyl in German hospitals

Milk-derived Lactobacillus with high production of short-chain fatty acids relieves antibiotic-induced diarrhea in mice

Antibiotic-associated diarrhea (AAD) is a common side effect during antibiotic treatment, and this has warranted research into alternative protocols. In this study, we investigated the potential therapeutic effects of three cohorts, Lactobacillus plantarum KLDS 1.0386, Lactobacillus acidophilus KLDS 1.0901 and a mixed strain of both, on intestinal inflammation, the intestinal mucosal barrier, and microbial community in mice with ampicillin-induced diarrhea. The results showed that Lactobacillus inhibited the activation of the TLR4/NF-κB signaling pathway, decreased the expression of pro-inflammatory cytokines, increased the expression of anti-inflammatory cytokines in the murine intestine, and alleviated the intestinal barrier damage and inflammation induced by ampicillin. In addition, Lactobacillus ameliorates intestinal epithelial barrier damage by increasing the expression of tight junction proteins and aquaporins. After Lactobacillus treatment, the diversity of gut microbiota increased significantly, and the composition and function of gut microbiota gradually recovered. In the gut microbiota, Bacteroidetes and Escherichia Shigella related to the synthesis of short-chain fatty acids (SCFAs) were significantly affected by ampicillin, while Lactobacillus regulates the cascade of the microbial-SCFA signaling pathway, which greatly promoted the generation of SCFAs. Collectively, Lactobacillus showed better results in treating AAD, especially in mixed strains.

Introduction and spread of vancomycin-resistant Enterococcus faecium (VREfm) at a German tertiary care medical center from 2004 until 2010: a retrospective whole-genome sequencing (WGS) study of the molecular epidemiology of VREfm

BACKGROUND

In most of Europe and especially in Germany, there is currently a concerning rise in the number of hospital-acquired infections due to vancomycin-resistant Enterococcus faecium (VREfm). Therefore, there is a need to improve our understanding of the way VREfm spreads in hospitals. In this study, we investigated the molecular epidemiology of VREfm isolates from the first appearance at our university hospital in 2004 until 2010. There is only very scarce information about the molecular epidemiology of VREfm from this early time in Germany.

METHODS

Our analysis includes all available first VREfm isolates of each patient at our tertiary care center collected during the years 2004-2010. If available, additional consecutive VREfm isolates from some patients were analyzed. We used multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) for the analysis and description of nosocomial transmission pathways as well as the detection of outbreaks.

RESULTS

VREfm isolates from 158 patients and 76 additional subsequent patient isolates were included in the analysis. Until 2006, detections of VREfm remained singular cases, followed by a peak in the number of VREfm cases in 2007 and 2008 with a subsequent decline to baseline in 2010. MLST and cgMLST analysis show significant changes in the dominant sequence types (STs) and complex types (CTs) over the study period, with ST192 and ST17 being responsible for the peak in VREfm cases in 2007 and 2008. The four largest clusters detected during the study period are comprised of these two STs. Cluster analysis shows a focus on specific wards and departments for each cluster. In the early years of this study (2004-2006), all analyzed VREfm stemmed from clinical specimens, whereas since 2007, approximately half of the VREfm were detected by screening. Of the 234 VREfm isolates analyzed, 96% had a vanB and only 4% had a vanA resistance genotype.

CONCLUSIONS

This retrospective study contributes significant knowledge about regional VREfm epidemiology from this early VREfm period in Germany. One remarkable finding is the striking dominance of vanB-positive VREfm isolates over the entire study period, which is in contrast with countrywide data. Analysis of cgMLST shows the transition from sporadic VRE cases at our institution to a sharp increase in VRE numbers triggered by oligoclonal spread and specific outbreak clusters with the dominance of ST192 and ST17.

Analysis of Antibiotic-Resistant and Virulence Genes of Enterococcus Detected in Calf Colostrum-One Health Perspective

Enterococci are considered among the most prevalent global multidrug-resistant microorganisms globally. Their dissemination is a global concern, particularly by food-producing animals for both animals and humans. The aim of this study was to identify the species and investigate the antibiotic resistance and virulence profile of Enterococcus in bovine colostrum. Out of 88 presumptive Enterococcus isolates, species identification and susceptibility to 14 antimicrobials were tested using the disk diffusion method. An analysis of the antibiotic resistance and virulence genes was performed on the most prevalent species, using specific PCR assays. Enterococcus faecalis (54.5%), E. faecium (14.8%) and E. gallinarum (6.8%) were the identified species. To the best of our knowledge, this is the first report of E. gallinarum in bovine colostrum. The majority of the isolates showed resistance to quinupristin-dalfopristin (95.9%), erythromycin (80.7%), tetracycline (80.7%) and streptomycin (58%). Ninety-two percent of isolates were classified as multidrug-resistant. The most frequently detected resistance genes were tet(K) (61.1%), tet(M) (75.9%), tet(L) (90.7%), erm(B) (55.6%) and ant(6)-Ia (46.3%). The most prevalent virulence factors were cpd, esp, agg and cylL_L. Enterococcus faecium showed a higher probability of carrying the erm(C), tet(M), ace and gel(E) genes (p < 0.05). These results demonstrated that colostrum can constitute an important reservoir and vehicle for the dissemination of antibiotic resistance and virulence genes to the three niches included in a One Health perspective (humans, animals and the environment), highlighting the importance of hygiene sanitary measures to mitigate colostrum microbial contamination.

Antimicrobial Resistance, Virulence Factors, and Genotypes of Enterococcus faecalis and Enterococcus faecium Clinical Isolates in Northern Japan: Identification of optrA in ST480 E. faecalis

Enterococcus faecalis and E. faecium are the major pathogens causing community- and healthcare-associated infections, with an ability to acquire resistance to multiple antimicrobials. The present study was conducted to determine the prevalence of virulence factors, drug resistance and its genetic determinants, and clonal lineages of E. faecalis and E. faecium clinical isolates in northern Japan. A total of 480 (426 E. faecalis and 54 E. faecium) isolates collected over a four-month period were analyzed. Three virulence factors promoting bacterial colonization (asa1, efaA, and ace) were more prevalent among E. faecalis (46-59%) than E. faecium, while a similar prevalence of enterococcal surface protein gene (esp) was found in these species. Between E. faecalis and E. faecium, an evident difference was noted for resistance to erythromycin, gentamicin, and levofloxacin and its responsible resistance determinants. Oxazolidinone resistance gene optrA and phenicol exporter gene fexA were identified in an isolate of E. faecalis belonging to ST480 and revealed to be located on a cluster similar to those of isolates reported in other Asian countries. The E. faecalis isolates analyzed were differentiated into 12 STs, among which ST179 and ST16 of clonal complex (CC) 16 were the major lineage. Nearly all the E. faecium isolates were assigned into CC17, which consisted of 10 different sequence types (STs), including a dominant ST17 containing multidrug resistant isolates and ST78 with isolates harboring the hyaluronidase gene (hyl). The present study revealed the genetic profiles of E. faecalis and E. faecium clinical isolates, with the first identification of optrA in ST480 E. faecalis in Japan.

Antibiotic Resistance of Enterococcus spp. Isolated from the Urine of Patients Hospitalized in the University Hospital in North-Central Poland, 2016-2021

Urinary Tract Infections (UTIs) are common outpatient and inpatient infections, often treated with empirical therapy. Enterococcus spp. is responsible for about 10% of UTIs. This study aimed to determine the necessity of changing the empirical treatment of UTIs caused by Enterococcus spp. The evaluation was performed for 542 Enterococcus strains isolated from urine samples in the years 2016-2021. We identified three Enterococcus species that were found: E. faecalis (389, 71.8%), E. faecium (151, 27.8%) and E. gallinarum (2, 0.4%). E. faecalis was the dominant species every year. Among E. faecalis, the most prevalent was resistance to norfloxacin (51.4%). Almost all E. faecium strains (150, 99.3%) were resistant to beta-lactams and norfloxacin. Eighty-three strains (55.0%) were resistant to vancomycin and 72 (47.7%) to teicoplanin. E. faecium strains showed a significantly higher percentage of resistance mechanisms GRE (Glicopeptide-Resistant Enterococcus) (72, 48.7%) and VRE (Vancomycin-Resistant Enterococcus) (11, 7.3%), while only five strains of E. feacalis showed a VRE mechanism (1.3%). In the therapy of E. faecalis UTIs, ampicillin and imipenem still remain effective. However, the above-mentioned antibiotics, as well as fluoroquinolones, are not recommended in the treatment of UTIs of E. faecium etiology.

Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents

Enterococcus faecium is a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements (MGEs), which facilitate their transfer between lineages. Here, features including resistance determinants, virulence factors and MGEs were profiled in a set of 1273 E. faecium genomes from two disparate geographic locations (in the UK and Canada) from a range of agricultural, clinical and associated habitats. Neither lineages of E. faecium, type A and B, nor MGEs are constrained by geographic proximity, but our results show evidence of a strong association of many profiled genes and MGEs with habitat. Many features were associated with a group of clinical and municipal wastewater genomes that are likely forming a new human-associated ecotype within type A. The evolutionary dynamics of E. faecium make it a highly versatile emerging pathogen, and its ability to acquire, transmit and lose features presents a high risk for the emergence of new pathogenic variants and novel resistance combinations. This study provides a workflow for MGE-centric surveillance of AMR in Enterococcus that can be adapted to other pathogens.

Bifidobacterium animalis subsp. lactis XLTG11 improves antibiotic-related diarrhea by alleviating inflammation, enhancing intestinal barrier function and regulating intestinal flora

Antibiotic-associated diarrhea (AAD) is a common side effect during antibiotic treatment. In this study, we evaluated the regulatory effect of Bifidobacterium animalis subsp. lactis XLTG11 on mouse diarrhea caused by antibiotic-induced intestinal flora disturbance. Then, two strains of Bifidobacterium animalis subsp. lactis XLTG11 and Bifidobacterium animalis subsp. lactis BB-12 were administered to AAD mice. We found that the recovery effect of using B. lactis XLTG11 was better than that of B. lactis BB-12. B. lactis XLTG11 reduced the pathological characteristics of the intestinal tract, and significantly reduced the levels of lipopolysaccharide (LPS), D-lactic acid (D-LA) and diamine oxidase (DAO) to decrease intestinal permeability. In addition, these two strains significantly increased the expression of aquaporin and tight junction proteins, and inhibited toll-like receptor 4 (TLR4)/activation of the nuclear factor-κB (NF-κB) signaling pathway, significantly increased the levels of anti-inflammatory cytokines and decreased levels of pro-inflammatory cytokines. Moreover, after treatment with B. lactis XLTG11, the contents of acetic acid, propionic acid, butyric acid and total short-chain fatty acids were significantly increased. Compared with the MC group, B. lactis XLTG11 increased the abundance and diversity of the intestinal flora and changed the composition of the intestinal flora. We found that B. lactis XLTG11 can promote the recovery of intestinal flora and mucosal barrier function, thereby effectively improving AAD-related symptoms, providing a scientific basis for future clinical applications.

The changing molecular epidemiology of Enterococcus faecium harbouring the van operon at a teaching hospital in Western Australia: A fifteen-year retrospective study

INTRODUCTION

Enterococcus faecium is an opportunistic pathogen that has become one of the leading causes of hospital acquired infection that are resistant to multiple critically important antimicrobials.

AIM

The objective of the study was to describe the molecular characteristics and relationship between major strains of E. faecium harbouring the van operon and to determine if the strains had increasing virulence and antimicrobial resistance determinants over time.

METHODS

E. faecium harbouring the van operon detected using PCR from surveillance rectal swabs of patients that were admitted to high-risk units at a Perth teaching hospital from 2001 to 2015 were retrospectively analysed using a whole genome sequencing and bioinformatics approach.

RESULTS

ST18, ST78, ST80, ST173, ST203 and ST555 were identified as the major STs accounting for 93.7% of E. faecium isolates. Except for ST173, major STs identified at Royal Perth Hospital (RPH) have been reported across Australia and internationally. Isolates from each ST formed independently branched phylogenetic clusters with each harbouring unique virulence and antimicrobial resistance profiles. Depending on the ST, different genes conferring resistance to similar antimicrobial classes were identified. Except for ST80 which harboured the vanA type operon, all major strains harboured the vanB operon conferring only vancomycin resistance.

CONCLUSION

Major strains of E. faecium isolated over 15-years showed unique virulome and resistome profiles with no indication of increasing virulence or antimicrobial resistance determinants. Strains were distantly related and the acquisition of different genes encoding similar antimicrobial resistances suggest the independent evolution of each strain.

DATA SUMMARY

The whole genome sequences of all isolates from this study are accessible from the NCBI-SRA database under project number PRJNA575940 and PRJNA524213. Published reference sequence Aus0004 was obtained from NCBI-SRA under project number PRJNA86649 DOI:10.1128/JB.00259-12.

Determination of a Tentative Epidemiological Cut-Off Value (ECOFF) for Dalbavancin and Enterococcus faecium

Dalbavancin is a lipoglycopeptide antibiotic that shows potent activity against Gram-positive bacteria. It circumvents vanB-type glycopeptide resistance mechanisms; however, data on the in vitro activity of dalbavancin for Enterococcus faecium (E. faecium) are scarce, and thus, no breakpoints are provided. In recent years, there has been a continuing shift from vanA-type to vanB-type vancomycin-resistance in enterococci in Central Europe. Therefore, we aimed to investigate the in vitro activity of dalbavancin against different van-genotypes, with particular focus on vanB-type E. faecium. Dalbavancin susceptibility was determined for 25 van-negative, 50 vanA-positive, and 101 vanB-positive clinical E. faecium isolates (typed by cgMLST). Epidemiological Cut-Off Values (ECOFFs) were determined using ECOFFinder. For vanB-type E. faecium isolates, dalbavancin MICs were similar to those of vancomycin-susceptible isolates reaching values no higher than 0.125 mg/L. ECOFFs for van-negative and vanB-positive isolates were 0.5 mg/l and 0.25 mg/L respectively. In contrast, E. faecium possessing vanA predominantly showed dalbavancin MICs >8 mg/L, therefore preventing the determination of an ECOFF. We demonstrated the potent in vitro activity of dalbavancin against vancomycin-susceptible and vanB-type E. faecium. On the basis of the observed wildtype distribution, a dalbavancin MIC of 0.25 mg/L can be suggested as a tentative ECOFF for E. faecium.

Sequence type 17 is a predictor of subsequent bacteremia in vancomycin-resistant Enterococcus faecium-colonized patients: a retrospective cohort study

Background

Sequence type (ST) 17 vancomycin-resistant Enterococcus faecium (VREF) is frequently isolated in nosocomial settings. The aim of this study was to identify whether ST17 contributes to subsequent bacteremia more often than other STs among hospitalized patients carrying VREF.

Methods

A retrospective cohort study was conducted in patients carrying ST17 VREF and those with non-ST17 VREF. Rectal screening according to hospital policy was used to identify patients with VREF. Subsequent VREF bacteremia events within a year of detection of colonization were recorded. Cox regression analysis was used to adjust the covariates involved in determining the association between ST17 and subsequent bacteremia events.

Results

The cohorts comprised 52 patients with ST17 and 169 patients with non-ST17 VREF. One-year VREF bacteremia-free rates were 85.9% and 90.2%, respectively. In multivariate analysis, ST17 was associated with subsequent bacteremia at an adjusted hazard risk (aHR) of 4.02 (95% confidence interval [CI], 1.32–12.29). Liver transplantation (aHR, 40.08; 95% CI, 4.87–329.76) and hematologic malignancy (aHR, 20.97; 95% CI, 4.87–87.82) were also significant. All cases of subsequent bacteremia in ST17 VREF carriers were caused by ST17; however, subsequent bacteremia in non-ST17 carriers was often caused by ST17 or another ST variant.

Conclusions

A specific genotype, ST17 is a predictor of subsequent bacteremia in hospitalized patients carrying VREF. Patients with a hematologic malignancy and those receiving a liver transplant are also at high risk. More targeted strategies may be needed to prevent VREF infection in hospitals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13756-021-00980-1.

Epidemiological typing of ST80 vancomycin-resistant Enterococcus faecium: core genome multilocus sequence typing versus single nucleotide polymorphism-based typing

OBJECTIVES

Vancomycin-resistant Enterococcus faecium (VRE) belonging to sequence type 80 (ST80) have been successfully disseminating in hospital settings. This study aimed to explore whole-genome sequencing (WGS)-based approaches in epidemiological typing of VRE by investigating a collection of ST80 strains.

METHODS

In total, 41 VRE ST80 isolates in three suspected transmission chains were subjected to WGS. The genetic relationship of the isolates was analysed by core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism (SNP)-based typing. The published genome sequence of a predominant ST80 clone in Copenhagen was also included in the analyses.

RESULTS

Group 1 isolates (n = 10) were recovered in the same geographic area, including two isolates from an outbreak of vanA genotype. Group 2 isolates (n = 4) were detected from another outbreak. Group 3 consisted of 3 non-outbreak isolates and 24 representative isolates from an outbreak of vanB genotype. Our findings indicated ≥24 allelic difference and >16 SNPs as the cut-off for excluding VRE strains from an outbreak. cgMLST identified >200 differing alleles between genomes of the Copenhagen clone and outbreak strains in this study. Our findings also demonstrated that SNP analysis was not suitable for typing samples from different groups, even with the same ST, owing to lack of an optimal reference genome.

CONCLUSION

cgMLST and SNPs provided comparable epidemiological discrimination for isolates with a suspected transmission chain. For diverse isolates, SNP analysis could be suboptimal. An approach applying cgMLST as the first-line typing method and SNPs as a complementary tool is suggested.

Characterization of bacteriocinogenic Enterococcus isolates from wild and laboratory rabbits for the selection of autochthonous probiotic strains in Tunisia

AIM

The objective of this study was to characterize lactic acid bacteria (LAB) from rabbits to be used as potential autochthonous probiotic.

METHODS AND RESULTS

Fifteen faecal samples were collected from wild and laboratory rabbits. One hundred and eight isolates were collected and tested for their inhibitory power against eight pathogenic bacteria. Among them, 43 Enterococcus isolates were able to inhibit at least one pathogen. Enterocine genes entA, entB and entP were detected in 14, 17 and 22 isolates, respectively. These isolates were tested for their antibiotic susceptibility and genes encoding virulence factors. Relevant phenotypes of antibiotic resistance were observed especially for ampicillin, vancomycin and linezolid. The following virulence genes were detected (number of positive isolates): hyl (5), esp (8), gelE (30), agg (2), ace (21), efa (6), CylL_L/s (5), cob (26), cpd (32) and ccf (33). Five isolates were considered as safe and showed tolerance to both acid and bile salt.

CONCLUSION

Bacteriocinogenic enterococci isolates from rabbits may show relevant resistance phenotypes and virulence factors. In addition, one Enterococcus durans isolate presents promising autochthonous probiotic candidate.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study reveals interesting properties for E. durans isolate and supports their utilization as autochthonous probiotic in rabbit husbandry.

Influence of Probiotics on the Salivary Microflora Oral Streptococci and Their Integration into Oral Biofilm

Probiotics’ ability to integrate into dental biofilms is not yet clarified. The aim of this trial was to detect probiotic bacteria from probiotic products in dental biofilm and saliva during and after intake. In this parallel, randomized clinical trial, 39 subjects wore customized appliances to build up intra-oral biofilms (72-h periods). The trial was divided into screening (S) to determine baseline biofilm flora, intervention (I), and wash out (WO). During I (28 days), subjects consumed a product containing (a) Enterococcus faecalis (b) Lactobacilluscasei, or (c) Lactobacillus rhamnosus GG. Probiotic bacteria and Streptococci spp. were detected in the biofilms and saliva of the 35 subjects that were included in the analysis. During I and WO, the ratio of probiotics in the biofilm was very low compared to total bacterial load, while saliva had slightly but not significantly higher values. No significant changes of probiotic bacteria (p > 0.05) were found at any visit during I or WO. The proportion of streptococci was significantly reduced (p < 0.05) during I and even lower in WO, compared to S. Probiotic bacteria could neither integrate nor persist in dental biofilm and saliva but did influence the growth of streptococci in biofilm and saliva.

Genomic analysis revealed distinct transmission clusters of vancomycin-resistant Enterococcus faecium ST80 in Stockholm, Sweden

Vancomycin-resistant Enterococcus faecium (VREfm) belonging to sequence type (ST)80 has become the predominant clonal lineage in Stockholm in the last three years. ST80 accounted for 75% and 46% of VRE cases in 2018 and 2019, respectively, and gave rise to both vanA-type and vanB-type outbreaks. Non-duplicate ST80-VREfm isolates (N = 188) were subjected to whole genome sequencing. Genomic analysis revealed three distinct transmission clusters. Our study indicated that difficulties in detecting low-grade vancomycin-resistant isolates by phenotypic testing might be one of the explanatory factors for the prolonged course of vanB-type outbreaks. Herein, we also report the first optrA-positive linezolid-resistant VRE isolate in Stockholm.

Thirty years of VRE in Germany - "expect the unexpected": The view from the National Reference Centre for Staphylococci and Enterococci

Enterococci are commensals of the intestinal tract of many animals and humans. Of the various known and still unnamed new enterococcal species, only isolates of Enterococcus faecium and Enterococcus faecalis have received increased medical and public health attention. According to textbook knowledge, the majority of infections are caused by E. faecalis. In recent decades, the number of enterococcal infections has increased, with the increase being exclusively associated with a rising number of nosocomial E. faecium infections. This increase has been accompanied by the dissemination of certain hospital-acquired strain variants and an alarming progress in the development of antibiotic resistance namely vancomycin resistance. With this review we focus on a description of the specific situation of vancomycin resistance among clinical E. faecium isolates in Germany over the past 30 years. The present review describes three VRE episodes in Germany, each of which is framed by the beginning and end of the respective decade. The first episode is specified by the first appearance of VRE in 1990 and a country-wide spread of specific vanA-type VRE strains (ST117/CT24) until the late 1990s. The second decade was initially marked by regional clusters and VRE outbreaks in hospitals in South-Western Germany in 2004 and 2005, mainly caused by vanA-type VRE of ST203. Against the background of a certain "basic level" of VRE prevalence throughout Germany, an early shift from the vanA genotype to the vanB genotype in clinical isolates already occurred at the end of the 2000s without much notice. With the beginning of the third decade in 2010, VRE rates in Germany have permanently increased, first in some federal states and soon after country-wide. Besides an increase in VRE prevalence, this decade was marked by a sharp increase in vanB-type resistance and a dominance of a few, novel strain variants like ST192 and later on ST117 (CT71, CT469) and ST80 (CT1065). The largest VRE outbreak, which involved about 2,900 patients and lasted over three years, was caused by a novel and until that time, unknown strain type of ST80/CT1013 (vanB). Across all periods, VRE outbreaks were mainly oligoclonal and strain types varied over space (hospital wards) and time. The spread of VRE strains obviously respects political borders; for instance, both vancomycin-variable enterococci which were highly prevalent in Denmark and ST796 VRE which successfully disseminated in Australia and Switzerland, were still completely absent among German hospital patients, until to date.

Elucidating vancomycin-resistant Enterococcus faecium outbreaks: the role of clonal spread and movement of mobile genetic elements

Background

Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a nosocomial pathogen worldwide. The dissemination of VREfm is due to both clonal spread and spread of mobile genetic elements (MGEs) such as transposons.

Objectives

We aimed to combine vanB-carrying transposon data with core-genome MLST (cgMLST) typing and epidemiological data to understand the pathways of transmission in nosocomial outbreaks.

Methods

Retrospectively, 36 VREfm isolates obtained from 34 patients from seven VREfm outbreak investigations in 2014 were analysed. Isolates were sequenced on a MiSeq and a MinION instrument. De novo assembly was performed in CLC Genomics Workbench and the hybrid assemblies were obtained through Unicycler v0.4.1. Ridom SeqSphere+ was used to extract MLST and cgMLST data. Detailed analysis of each transposon and their integration points was performed using the Artemis Comparison Tool (ACT) and multiple blast analyses.

Results

Four different vanB transposons were found among the isolates. cgMLST divided ST80 isolates into three cluster types (CTs); CT16, CT104 and CT106. ST117 isolates were divided into CT24, CT103 and CT105. Within VREfm isolates belonging to CT103, two different vanB transposons were found. In contrast, VREfm isolates belonging to CT104 and CT106 harboured an identical vanB transposon.

Conclusions

cgMLST provides a high discriminatory power for the epidemiological analysis of VREfm. However, additional transposon analysis is needed to detect horizontal gene transfer. Combining these two methods allows investigation of both clonal spread as well as the spread of MGEs. This leads to new insights and thereby better understanding of the complex transmission routes in VREfm outbreaks.

Study on the therapeutic index and synergistic effect of Chitosan-zinc oxide nanomicellar composites for drug-resistant bacterial biofilm inhibition

The synergistic effectiveness of chitosan with zinc oxide nanomicelles (CZNPs) on broad spectrum of multidrug resistance (MDR) was previously evidenced in our labs, requiring elucidation of the therapeutic index (TI) for safe in vivo use. This in vitro assessment estimated the effective dose (ED₅₀) of micellar CZNPs for eradication of the MDR Enterococcus faecium 1449 model and the corresponding cytotoxic dose (LD₅₀) against rat small intestinal epithelial cells as functions of TI. In order to visually determine the mechanistic effects of micellar CZNPs on bacterial biofilm size reduction, LIVE/DEAD viability assay was used in conjunction with advanced fluorescence imaging and 3D confocal microscopy. Biofilm quantification was performed through the measure of the fluorescence intensity, using the Biotek Synergy Neo2 for calculating the ED₅₀. To generate the LD₅₀, the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) cytotoxicity assay was implemented. Quantification results revealed, at the same concentration (200 µg/mL), micellar CZNPs had average biofilm reduction of approximately 50.22% at 24 h (ED₅₀ = 199.13 µg/mL, LD₅₀ = 240.20 µg/mL, TI = 1.2062), compared to chitosan (15.66%) and ZnO (13.94%) alone. Conclusively, the ED₅₀ of micellar CZNPs on MDR bacterial biofilms (199.13 µg/mL) as a function of TI reveals a promising nanotherapeutic agent in comparison to either Chitosan or ZnO alone.

Temporal and Geographic Variation in Antimicrobial Susceptibility and Resistance Patterns of Enterococci: Results From the SENTRY Antimicrobial Surveillance Program, 1997-2016

Background

The SENTRY Antimicrobial Surveillance Program was established in 1997 and presently encompasses more than 750 000 bacterial isolates from over 400 medical centers worldwide. Among these pathogens, enterococci represents a prominent cause of bloodstream (BSIs), intra-abdominal (IAIs), skin and skin structure, and urinary tract infections (UTIs). In the present study, we reviewed geographic and temporal trends in Enterococcus species and resistant phenotypes identified throughout the SENTRY Program.

Methods

From 1997 to 2016, a total of 49 491 clinically significant enterococci isolates (15 species) were submitted from 298 medical centers representing the Asia-Pacific (APAC), European, Latin American (LATAM), and North American (NA) regions. Bacteria were identified by standard algorithms and matrix-assisted laser desorption ionization–time of flight mass spectrometry. Susceptibility (S) testing was performed by reference broth microdilution methods and interpreted using Clinical and Laboratory Standards Institute/US Food and Drug Administration and European Committee on Antimicrobial Susceptibility Testing criteria.

Results

The most common Enterococcus species in all 4 regions were Enterococcus faecalis (64.7%) and E. faecium (EFM; 29.0%). Enterococci accounted for 10.7% of BSIs in NA and was most prominent as a cause of IAIs (24.0%) in APAC and of UTIs (19.8%) in LATAM. A steady decrease in the susceptibility to ampicillin and vancomycin was observed in all regions over the 20-year interval. Vancomycin-resistant enterococci (VRE) accounted for more than 8% of enterococcal isolates in all regions and was most common in NA (21.6%). Among the 7615 VRE isolates detected, 89.1% were the VanA phenotype (91.0% EFM) and 10.9% were VanB. Several newer antimicrobial agents demonstrated promising activity against VRE, including daptomycin (99.6–100.0% S), linezolid (98.0%–99.6% S), oritavancin (92.2%–98.3% S), tedizolid (99.5%–100.0% S), and tigecycline (99.4%–100.0% S).

Conclusions

Enterococci remained a prominent gram-positive pathogen in the SENTRY Program from 1997 through 2016. The overall frequency of VRE was 15.4% and increased over time in all monitored regions. Newly released agents with novel mechanisms of action show promising activity against VRE.

Rapid and sensitive detection of the vanA resistance gene from clinical Enterococcus faecium and Enterococcus faecalis isolates by loop-mediated isothermal amplification

OBJECTIVES

Vancomycin resistance in Enterococcus spp., mediated mainly by the vanA resistance gene, has become a major health concern as it has spread worldwide. Therefore, a rapid method is urgently required to detect the vanA gene for timely and appropriate antimicrobial control of resistant Enterococcus infections.

METHODS

The loop-mediated isothermal amplification (LAMP) assay was optimised for vanA detection in Enterococcus spp. isolates.

RESULTS

The LAMP primer set designed in this study could reliably recognise seven distinct regions of the vanA gene and amplify the gene within 25min at an isothermal temperature of 65°C with high specificity. The sensitivity of the optimised assay was high, with a detection limit for vanA as low as 100pg/μL, which is 100-fold more sensitive than the PCR assay. A special advantage of this optimised LAMP method is that the vanA gene could be detected directly from clinical specimens.

CONCLUSION

This optimised LAMP assay has great application potential for efficient detection of vanA in clinical diagnosis and epidemiological studies.

First molecular characterization of related cases of healthcare-associated infections involving multidrug-resistant Enterococcus faecium vanA in Algeria

Purpose

Vancomycin-resistant Enterococcus (VRE) faecium (VREfm) are highly resistant bacteria emerging worldwide and rarely studied using molecular tools in Algeria since their first report in 2006. The aim of the study was to investigate healthcare-associated infections (HAIs) involving the first VRE in Batna University Hospital, Algeria, and characterize isolates using molecular tools.

Patients and methods

Medical charts were reviewed for patients with VREfm. van genes were detected by multiplex polymerase chain reaction (PCR), and strains were characterized by automated repetitive sequence-based PCR (rep-PCR), multiplex rep-PCR, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST).

Results

During a 6-month period, VREfm infections occurred in four patients hospitalized in three wards. The four isolates were E. faecium vanA belonging to the hospital-adapted clonal complex 17. PCR-based methods did not discriminate the isolates but MLST and PFGE delineated a subgroup of three VREfm of identical pulsotype and sequence type (ST) 80 (yet identified for five isolates in the international PubMLST database) while the fourth isolate was of ST789 (not previously identified for a VREfm) and displayed an unrelated pulsotype. The three genotypically related isolates were recovered in patients who underwent surgery in the same department, suggesting an outbreak for which the source and route of transmission remained unidentified.

Conclusion

This first molecular epidemiology study of VRE in Algeria was useful in delimiting an outbreak involving three of the four HAI cases and revealed rarely encountered genotypes. Considering the threat and burden of VRE infections worldwide, particularly in the USA, and the late emergence in Algeria, our study supports the urgent need for improved and early adequate infection control measures to avoid VRE spread in North African hospitals.

Structural and Functional Alterations in the Microbial Community and Immunological Consequences in a Mouse Model of Antibiotic-Induced Dysbiosis

The aim of this study was to establish continuous therapeutic-dose ampicillin (CTDA)-induced dysbiosis in a mouse model, mimicking typical adult exposure, with a view to using this to assess its impact on gut microbiota, intestinal metabolites and host immune responses. Mice were exposed to ampicillin for 14 days and antibiotic-induced dysbiosis was evaluated by alteration of microbiota and gut permeability. The cecal index was increased in the CTDA group, and the gut permeability indicated by fluorescent dextran, endotoxin and D-Lactate in the serum was significantly increased after antibiotic use. The tight-junction proteins ZO-1 and occludin in the colon were reduced to half the control level in CTDA. We found that alpha-diversity was significantly decreased in mice receiving CTDA, and microbial community structure was altered compared with the control. Key taxa were identified as CTDA-specific, and the relative abundance of Enterococcus and Klebsiella was particularly enriched while Lachnospiraceae, Coprobacillus and Dorea were depleted after antibiotic treatment. In particular, a significant increase in succinate and a reduction in butyrate was detected in CTDA mice, and the triggering of NF-κB enhancement reflected that the host immune response was influenced by ampicillin use. The observed perturbation of the microbiota was accompanied by modulation of inflammatory state; this included increase in interferon-γ and RegIIIγ, and a decrease in secretory IgA in the colon mucosa. This study allowed us to identify the key taxa associated with an ampicillin-induced state of dysbiosis in mice and to characterize the microbial communities via molecular profiling. Thus, this work describes the bacterial ecology of antibiotic exposure model in combination with host physiological characteristics at a detailed level of microbial taxa.

The changing epidemiology of VanB Enterococcus faecium in Poland

Increasing prevalence of VanB Enterococcus faecium in Polish hospitals reported to National Reference Centre for Susceptibility Testing (NRCST) prompted us to investigate the basis of this phenomenon. Two-hundred seventy-eight E. faecium isolates of VanB phenotype from the period 1999 to 2010 obtained by NRCST were investigated by multilocus sequence typing (MLST) and multilocus VNTR analysis (MLVA). Localization, transferability, and partial structure of the vanB-carrying Tn1549 transposon were studied by hybridization, PCR mapping, sequencing, and conjugation. VanB isolates almost exclusively represented hospital-associated E. faecium, with a significant shift from representatives of 17/18 lineage to 78 lineage after 2005. The vanB determinant, initially located mostly on transferable plasmids of the pRUM-, pLG1-, and pRE25-replicon types, later on was found almost exclusively on the host chromosome. Fifteen different plasmid and chromosomal insertion sites were identified, typically associated with single transposon coupling sequences, mostly not observed before. Our study demonstrates the significant change in the epidemiology of VanB-E. faecium in Poland, associated with the introduction and spread of the lineage 78 of the hospital-adapted E. faecium. These data point to the importance of the lineage 78 for the spread of vancomycin-resistance, determined by the vanB gene cluster, resulting in an increasing VRE prevalence in hospitals. This study also supports the scenario, in which representatives of the hospital-associated E. faecium independently acquire the vanB determinant de novo and spread within and among hospitals, concomitantly undergoing differentiation.

Double-Serine Fluoroquinolone Resistance Mutations Advance Major International Clones and Lineages of Various Multi-Drug Resistant Bacteria

The major international sequence types/lineages of methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae and ESBL-producing E. coli were demonstrated to have been advanced by favorable fitness balance associated with high-level resistance to fluoroquinolones. The paper shows that favorable fitness in the major STs/lineages of these pathogens was principally attained by the capacity of evolving mutations in the fluoroquinolone-binding serine residues of both the DNA gyrase and topoisomerase IV enzymes. The available information on fitness balance incurred by individual and various combinations of mutations in the enzymes is reviewed in multiple species. Moreover, strong circumstantial evidence is presented that major STs/lineages of other multi-drug resistant bacteria, primarily vancomycin-resistant Enterococcus faecium (VRE), emerged by a similar mechanism. The reason(s) why the major ST/lineage strains of various pathogens proved more adept at evolving favorable mutations than most isolates of the same species remains to be elucidated.

The emerging problem of linezolid-resistant enterococci

Enterococcus is a significant pathogen in numerous infections, particularly in nosocomial infections, and is thus a great challenge to clinicians. Linezolid (LNZ), an oxazolidinone antibiotic, is an important therapeutic option for infections caused by Gram-positive bacterial pathogens, especially vancomycin-resistant enterococci. A systematic review was performed of the available literature on LNZ-resistant enterococci (LRE) to characterise these infections with respect to epidemiological, microbiological and clinical features. The results validated the potency of LNZ against enterococcal infections, with a sustained susceptibility rate of 99.8% in ZAAPS and 99.2% in LEADER surveillance programmes. Patients with LRE had been predominantly exposed to LNZ prior to isolation of LRE, with a mean treatment duration of 29.8±48.8days for Enterococcus faecalis and 23.1±21.4days for Enterococcus faecium. Paradoxically, LRE could also develop in patients without prior LNZ exposure. LNZ resistance was attributed to 23S rRNA (G2576T) mutations (51.2% of E. faecalis and 80.5% of E. faecium) as well as presence of the cfr gene (4.7% and 4.8%, respectively), which could transfer horizontally among the strains. In addition to the cfr gene, 32 cases of optrA-positive LRE were identified. Further study is required to determine the prevalence of novel resistance genes. The emergence of LRE thus hampers the treatment of such infections, which warrants worldwide surveillance.

Characterization of Enterococcus Isolates Colonizing the Intestinal Tract of Intensive Care Unit Patients Receiving Selective Digestive Decontamination

Enterococci have emerged as important opportunistic pathogens in intensive care units (ICUs). In this study, enterococcal population size and Enterococcus isolates colonizing the intestinal tract of ICU patients receiving Selective Digestive Decontamination (SDD) were investigated. All nine patients included in the study showed substantial shifts in the enterococcal 16S rRNA gene copy number in the gut microbiota during the hospitalization period. Furthermore, 41 Enterococcus spp. strains were isolated and characterized from these patients at different time points during and after ICU hospitalization, including E. faecalis (n = 13), E. faecium (n = 23), and five isolates that could not unequivocally assigned to a specific species (E. sp. n = 5) Multi locus sequence typing revealed a high prevalence of ST 6 in E. faecalis isolates (46%) and ST 117 in E. faecium (52%). Furthermore, antibiotic resistance phenotypes, including macrolide and vancomycin resistance, as well as virulence factor-encoding genes [asa1, esp-fm, esp-fs, hyl, and cyl (B)] were investigated in all isolates. Resistance to ampicillin and tetracycline was observed in 25 (61%) and 19 (46%) isolates, respectively. Furthermore, 30 out of 41 isolates harbored the erm (B) gene, mainly present in E. faecium isolates (78%). The most prevalent virulence genes were asa1 in E. faecalis (54%) and esp (esp-fm, 74%; esp-fs, 39%). Six out of nine patients developed nosocomial enterococcal infections, however, corresponding clinical isolates were unfortunately not available for further analysis. Our results show that multiple Enterococcus species, carrying several antibiotic resistance and virulence genes, occurred simultaneously in patients receiving SDD therapy, with varying prevalence dynamics over time. Furthermore, simultaneous presence and/or replacement of E. faecium STs was observed-, reinforcing the importance of screening multiple isolates to comprehensively characterize enterococcal diversity in ICU patients.

Characterization of antimicrobial resistance and quinolone resistance factors in high-level ciprofloxacin-resistant Enterococcus faecalis and Enterococcus faecium isolates obtained from fresh produce and fecal samples of patients

BACKGROUND

The emergence of fluoroquinolone-resistant enterococci is worldwide. Antimicrobial resistance was characterized and the effect of quinolone-resistance factors was analyzed in high-level ciprofloxacin-resistant (HLCR) Enterococcus faecalis and Enterococcus faecium isolated from fresh produce and fecal samples of patients.

RESULTS

Among the 81 ciprofloxacin-resistant Enterococcus isolates, 46 showed high levels of ciprofloxacin resistance, resistance to other quinolone antibiotics, and multidrug resistance profiles. The virulence factors esp and hyl were identified in 27 (58.7%) and 25 (54.3%) of isolates, respectively. Sequence type analysis showed that 35 strains of HLCR E. faecium were clonal complex 17. Eleven strains of HLCR E. faecalis were confirmed as sequence type (ST) 28, ST 64 and ST 125. Quinolone resistance-determining region mutation was identified in HLCR Enterococcus isolates; with serine being changed in gyrA83, gyrA87 and parC80. This result shows that gyrA and parC mutations could be important factors for high-level resistance to fluoroquinolones.

CONCLUSION

No significant differences were observed in antimicrobial resistance patterns and genetic characteristics among the isolates from fresh produce and fecal samples. Therefore, good agricultural practices in farming and continuous monitoring of patients, food and the environment for Enterococcus spp. should be performed to prevent antimicrobial resistance and enable reduction of resistance rates. © 2016 Society of Chemical Industry.

Nursing staff fluctuation and pathogenic burden in the NICU - effective outbreak management and the underestimated relevance of non-resistant strains

In the course of a hospital management takeover, a microbial outbreak took place in a tertiary neonatal intensive care unit (NICU). Here, we characterize the outbreak and its management. About 4 months prior to takeover, there was a sharp increase in positive isolates for MSSA and multidrug-resistant organisms (MDROs). Simultaneously, the nursing staff sick leave rate increased dramatically which directly correlated with the number of infection/colonization per week (r2 = 0.95, p = 0.02). During the following months we observed several peaks in positive isolates of methicillin-sensitive staphylococcus aureus (MSSA), MDROs and subsequently a vancomycin-resistant enterococcus (VRE) outbreak. Interventional outbreak management measures were only successful after substantial recruitment of additional nursing staff. None of the VRE, but 44% (n = 4) of MDRO and 32% (n = 23) of MSSA colonized infants developed symptomatic infections (p = 0.02). Among the latter, 35% suffered from serious consequences such as osteomyelitis. The most important risk factors for colonization-to-infection progression were low gestational age and birth weight. Nursing staff fluctuation poses a substantial risk for both bacterial colonization and infection in neonates. Comprehensive outbreak management measures are only successful if adequate nursing staff is available. Non resistant strains account for most neonatal infections - possibly due to their limited perception as being harmful.

Safety assessment of commensal enterococci from dogs

Enterococci form a complex, diverse, and very important group of bacteria from the technological and food safety aspect, or from the health-improving aspect as probiotics. Generally, enterococci are considered to be of low pathogenic potential, which is associated mostly with clinical strains. In these strains, production of virulence factors as well as resistance to many antimicrobial drugs could complicate treatment of nosocomial infections. Because there is a lack of information on incidence of these attributes in animal commensal enterococci, we screened 160 strains originating from feces of clinically healthy dogs in Eastern Slovakia (n = 105). The predominant species were Enterococcus faecium (57.5%) followed by Enterococcus faecalis (21.9%), and Enterococcus hirae (17.5%), while Enterococcus casseliflavus (1.9%) and Enterococcus mundtii (1.2%) rarely occurred. Among the tested antibiotics, gentamicin (high level) was the most effective drug against canine enterococci (95% of isolates were sensitive). In contrast, the highest resistance recorded (71.9%) was to teicoplanin. PCR screening showed the highest incidence of virulence genes in E. faecalis species. The most frequently detected were genes encoding adhesins efa _Afm and efa _Afs and sex pheromone cpd. IS16 gene, a marker specific for hospital strains, appeared in nine E. faecium strains. No strain was positive for DNase activity, 8.8% of the isolated strains showed gelatinase activity, and almost 100% strains produced tyramine. It seems commensal-derived enterococci from dogs could also to some extent be potential reservoir of risk factors for other microbiota or organisms.

Dispersion of the Vancomycin Resistance Genes vanA and vanC of Enterococcus Isolated from Nile Tilapia on Retail Sale: A Public Health Hazard

Although normally regarded harmless commensals, enterococci may cause a range of different infections in humans, including urinary tract infections, sepsis, and endocarditis. The acquisition of vancomycin resistance by enterococci (VRE) has seriously affected the treatment and infection control of these organisms. VRE are frequently resistant to all antibiotics that are effective treatment for vancomycin-susceptible enterococci, which leaves clinicians treating VRE infections with limited therapeutic options. With VRE emerging as a global threat to public health, we aimed to isolate, identify enterococci species from tilapia and their resistance to van-mediated glycopeptide (vanA and vanC) as well as the presence of enterococcal surface protein (esp) using conventional and molecular methods. The cultural, biochemical (Vitek 2 system) and polymerase chain reaction results revealed eight Enterococcus isolates from the 80 fish samples (10%) to be further identified as E. faecalis (6/8, 75%) and E gallinarum (2/8, 25%). Intraperitoneal injection of healthy Nile tilapia with the eight Enterococcus isolates caused significant morbidity (70%) within 3 days and 100% mortality at 6 days post-injection with general signs of septicemia. All of the eight Enterococcus isolates were found to be resistant to tetracycline. The 6/6 E. faecalis isolates were susceptible for penicillin, nitrofurantoin, gentamicin, and streptomycin. On the other hand 5/6 were susceptible for ampicillin, vancomycin, chloramphenicol, and ciprofloxacin. The two isolates of E. gallinarum were sensitive to rifampicin and ciprofloxacin and resistant to vancomycin, chloramphenicol, and erythromycin. Molecular characterization proved that they all presented the prototypic vanC element. On the whole, one of the two vancomycin resistance gene was present in 3/8 of the enterococci isolates, while the esp virulence gene was present in 1/8 of the enterococci isolates. The results in this study emphasize the potential role that aquatic environments are correlated to proximity to anthropogenic activities in determining the antimicrobial resistance patterns of Enterococcus spp. recovered from fish in the river Nile in Giza, Elmounib, Egypt as a continuation of our larger study on the reservoirs of antibiotic resistance in the environment.

Penicillin-Binding Protein 5 Sequence Alteration and Levels of plp5 mRNA Expression in Clinical Isolates of Enterococcus faecium with Different Levels of Ampicillin Resistance

Eighty-two nonduplicated ampicillin-resistant Enterococcus faecium (AREF) isolates from clinical infections at the Charles Nicolle Hospital of Tunisia were investigated. They were collected from January 2001 to December 2009. Genetic relationship between them was studied using pulsed-field gel electrophoresis. The amino acid sequence difference variations of the C-terminal part of penicillin-binding protein 5 (PBP5) versus levels of expressed mRNA were investigated by polymerase chain reaction (PCR), sequencing, and real-time PCR quantification of (PBP5), respectively. No β-lactamase activity was detected and none of our strains showed resistance to glycopeptides, which retain their therapeutic efficiency against enterococcal infections in our hospital. Pattern analysis of the strains revealed six main clones disseminating in different wards. Sequence data revealed the existence of 19 different plp5 alleles with a difference in 16 amino acid positions spanning from residue 414 to 632. Each allele presented at least five amino acid substitutions (His-470→Gln, Asn-496→Lys, Ala-499→Thr, Glu-525→Asp, and Glu-629→Val). No correlation between amino acid sequence polymorphism of PBP5 and levels of ampicillin resistance was detected. The levels of plp5 mRNA expression varied between strains and did not always correlate with levels of ampicillin resistance in clinical AREF.

Epidemiology and molecular typing of VRE bloodstream isolates in an Irish tertiary care hospital

OBJECTIVES

Ireland has the highest rate of vancomycin-resistant Enterococcus faecium (VREfm) isolated from blood of nosocomial patients in Europe, which rose from 33% (110/330) in 2007 to 45% (178/392) in 2012. No other European country had a VREfm rate from blood cultures of >25%. Our aim was to elucidate the reasons for this significantly higher rate in Ireland.

METHODS

The epidemiology and molecular typing of VRE from bloodstream infections (BSIs) was examined in a tertiary care referral hospital and isolates were compared with those from other tertiary care referral centres in the region.

RESULTS

The most common source of VRE BSIs was intra-abdominal sepsis, followed by line-related infection and febrile neutropenia. Most of the isolates were positive for vanA; 52% (43/83) possessed the esp gene and 12% (10/83) possessed the hyl gene. Genotyping by SmaI macrorestriction analysis (PFGE) of isolates revealed clonal relatedness between bloodstream isolates and environmental isolates. VRE BSI isolates from two other tertiary care hospitals in the Dublin region showed relatedness by PFGE analysis. MLST revealed four STs (ST17, ST18, ST78 and ST203), all belonging to the clonal complex of hospital-associated strains.

CONCLUSIONS

Irish VRE BSI isolates have virulence factor profiles as previously reported from Europe. Typing analysis shows the spread of individual clones within the hospital and between regional tertiary care hospitals. Apart from transmission of VRE within the hospital and transfer of colonized patients between Irish hospitals, no other explanation for the persistently high VREfm BSI rate in Ireland has been found.

Recent recombination events in the core genome are associated with adaptive evolution in Enterococcus faecium

Reasons for the rising clinical impact of the bacterium Enterococcus faecium include the species' rapid acquisition of adaptive genetic elements. Here, we focused on the impact of recombination on the evolution of E. faecium. We used the recently developed BratNextGen algorithm to detect recombinant regions in the core genome of 34 E. faecium strains, including three newly sequenced clinical strains. Recombination was found to have a significant impact on the E. faecium genome: of the original 1.2 million positions in the core genome, 0.5 million were predicted to have been affected by recombination in at least one strain. Importantly, strains in one of the two major E. faecium clades (clade B), which contains most of the E. faecium human gut commensals, formed the most important reservoir for donating foreign DNA to the second major E. faecium clade (clade A), which contains most of the clinical isolates. Also, several genomic regions were found to mainly recombine in specific hospital-associated E. faecium strains. One of these regions (the epa-like locus) likely encodes the biosynthesis of cell wall polysaccharides. These findings suggest a crucial role for recombination in the emergence of E. faecium as a successful hospital-associated pathogen.

[Vancomycin-resistant enterococci (VRE). Recent results and trends in development of antibiotic resistance]

Enterococci (mainly E. faecalis, E. faecium) are important nosocomial pathogens predominantly affecting older and/or immunocompromised patients. The bacteria possess a broad spectrum of intrinsic and acquired antibiotic resistance properties. Among these, the transferrable glycopeptide resistance of the vanA and vanB genotypes in vancomycin-resistant enterococci (VRE; reservoir: E. faecium) as well as resistance to last resort antibiotics (e.g. linezolid and tigecycline) are of special concern. Enterococci (including VRE) are easily transferred in hospitals; however, colonizations are far more frequent than infections. Resistance frequencies for vancomycin in clinical E. faecium isolates have remained at a relatively constant level of 8-15% (but with local or regional variations) in recent years whereas frequencies for teicoplanin resistance have shown a slight decrease. Glycopeptide resistance trends correlate with a spread of hospital-associated E. faecium strains carrying the vanA and, with rising frequency in recent years, the vanB gene cluster, the latter being associated with teicoplanin susceptibility. This increased occurrence of vanB-positive E. faecium strains may be caused by an increased use of antibiotics selecting enterococci and VRE as well as due to methodological reasons (e.g. reduced EUCAST MIC-breakpoints for glycopeptides; increased use and sensitive performance of chromogenic VRE agars, increased use of molecular diagnostic assays).

American crows as carriers of vancomycin-resistant enterococci with vanA gene

We studied the vanA-carrying vancomycin-resistant enterococci (VRE) isolated from American crows in the United States during the winter 2011/2012. Faecal samples from crows were cultured selectively for VRE and characterized. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to examine epidemiological relationships of vanA-containing VRE. Isolates were tested in vitro for their ability to horizontally transfer the vancomycin resistance trait. VRE with the vanA gene were found in 15 (2.5%) of 590 crows samples, from which we obtained 22 different isolates. Enterococcal species were Enterococcus faecium (14) and E. faecalis (8). One, two and 19 isolates originated from Kansas, New York State and Massachusetts, respectively. Based on MLST analysis, E. faecium isolates were grouped as ST18 (6 isolates), ST555 (2), and novel types ST749 (1), ST750 (3), ST751 (1), ST752 (1). Enterococcus faecalis isolates belonged to ST6 (1), ST16 (3) and ST179 (4). All isolates were able to transfer the vancomycin resistance trait via filter mating with very high transfer range. Clinically important enterococci with the vanA gene occur in faeces of wild American crows throughout the United States. These migrating birds may contribute to the dissemination of VRE in environment over large distances. [Correction added after first online publication on 06 August 2013: The number of E. faecium ST752 isolate is now amended to '1', consistent with that shown in the 'Results' section and Figure 2.].

Detection of antibiotic resistant enterococci and Escherichia coli in free range Iberian Lynx (Lynx pardinus)

Thirty fecal samples from wild specimens of Iberian lynx were collected and analyzed for Enterococcus spp. (27 isolates) and Escherichia coli (18 isolates) recovery. The 45 isolates obtained were tested for antimicrobial resistance, molecular mechanisms of resistance, and presence of virulence genes. Among the enterococci, Enterococcus faecium and Enterococcus hirae were the most prevalent species (11 isolates each), followed by Enterococcus faecalis (5 isolates). High percentages of resistance to tetracycline and erythromycin (33% and 30%, respectively) were detected among enterococcal isolates. The tet(M) and/or tet(L), erm(B), aac(6')-Ie-aph(2″)-Ia, ant(6)-Ia, or aph(3')-IIIa genes were detected among resistant enterococci. Virulence genes were detected in one E. faecalis isolate (cpd, cylB, and cylL) and one E. hirae isolate (cylL). High percentages of resistance were detected in E. coli isolates to tetracycline (33%), streptomycin (28%), nalidixic acid (28%), and sulfamethoxazole-trimethoprim (SXT, 22%). Additionally, the blaTEM, tet(A), aadA, cmlA, and different combinations of sul genes were detected among most ampicillin, tetracycline, streptomycin, chloramphenicol and SXT-resistant isolates, respectively. Two isolates contained a class 1 integron with the gene cassette arrays dfrA1 + aadA1 and dfrA12 + aadA2. The E. coli isolates were ascribed to phylo-groups A (n=5); B1 (n=4); B2 (n=6), and D (n=3), with the virulence gene fimA present in all E. coli isolates. This study found resistance genes in wild specimens of Iberian lynx. Thus, it is important to notice that multiresistant bacteria have reached species as rare and completely non-synanthropic as the Iberian lynx. Furthermore, the susceptibility of this endangered species to bacterial infection may be affected by the presence of these virulence and resistance genes.

Ciprofloxacin Resistance in Enterococcus faecalis Strains Isolated From Male Patients With Complicated Urinary Tract Infection

PURPOSE

Urinary tract infection (UTI) is one of the most prevalent bacterial infections, and fluoroquinolone therapy is a well-known standard regimen for UTI. The prevalence and risk factor analysis of fluoroquinolone resistance in enterococcal UTIs are not well documented. The aim of this study was to evaluate the antimicrobial susceptibility and risk factors for ciprofloxacin resistance in Enterococcus faecalis strains isolated from patients with complicated UTI.

MATERIALS AND METHODS

We evaluated 81 E. faecalis strains isolated from 81 male patients at a single teaching hospital over 3 years. The Vitek 2 automatic system was used for antimicrobial susceptibility analysis.

RESULTS

Antimicrobial resistance rates were rare for ampicillin/sulbactam, imipenem, and vancomycin in E. faecalis. Forty-six percent of the E. faecalis strains were resistant to levofloxacin, 47% were resistant to ciprofloxacin, and 58% were resistant to norfloxacin. E. faecalis strains were highly resistant to erythromycin (92%) and ftetracycline (96%). The risk factor analysis revealed that age intervals, the underlying diseases, catheterization, and the number of admissions did not increase the risk of ciprofloxacin resistance, whereas patients with hospital-acquired infection (odds ratio [OR], 18.15; 95% confidence interval [CI], 3.46 to 95.13; p=0.001), patients who were treated in a urological department (OR, 6.15; 95% CI, 1.5 to 25.41; p=0.012), and patients who were transferred from health care centers (OR, 7.393; 95% CI, 1.32 to 41.22; p=0.023) had an increased risk of ciprofloxacin resistance compared with the matched controls.

CONCLUSIONS

Ciprofloxacin is no longer a recommended therapy for E. faecalis from complicated UTI in men with risk factors. We suggest that ampicillin/sulbactam can be recommended as alternatives for treating ciprofloxacin-resistant E. faecalis strains associated with UTI in Korea.

High abundance and diversity of antimicrobial resistance determinants among early vancomycin-resistant Enterococcus faecium in Poland

The purpose of this study was to investigate the clonal structure, antimicrobial resistance phenotypes and their determinants among early vancomycin-resistant Enterococcus faecium (VREm) isolates in Poland. Two hundred and eighty-one VREm isolates collected between 1997 and 2005 were studied. VREm isolates were characterised by multilocus sequence typing (MLST). The presence of antimicrobial resistance determinants, transposon-specific genes, IS16 and esp Efm was checked by polymerase chain reaction (PCR). Ciprofloxacin and ampicillin resistance determinants were investigated by sequencing. Two hundred and twenty-two (79 %) and 59 (21 %) VREm isolates were vanA- and vanB-positive, respectively. Among 135 representative isolates, MLST yielded 33 different sequence types (STs), of which 29 were characteristic of hospital-associated E. faecium; 128 (94.8 %) and 123 (91.1 %) isolates harboured the IS16 and esp Efm genes, and all 135 isolates were resistant to ciprofloxacin and ampicillin. Resistance to tetracycline (71.1 % isolates) was mostly associated with tetM (75.0 %) and the concomitant presence of the Tn916 integrase gene. High-level resistance to streptomycin (93.3 % of isolates) and high-level resistance to gentamicin (94.1 % of isolates) were due to ant(6')-Ia and aac(6')-Ie-aph(2″) genes, respectively, the latter of which is known to be located on various Tn4001-type transposons. Fifteen combinations of mutations in the quinolone-determining regions of GyrA and ParC were identified, including changes not previously reported, such as S83F and A84P in GyrA. Twenty-three variants of the penicillin-binding protein PBP5 occurred in the studied group, and novel insertions at amino acid positions 433 and 568 were identified. This analysis revealed the predominance of hospital-associated strains of E. faecium, carrying an abundant and divergent range of resistance determinants among early VREm isolates in Poland.

Antimicrobial activity, antibiotic susceptibility and virulence factors of Lactic Acid Bacteria of aquatic origin intended for use as probiotics in aquaculture

Background

The microorganisms intended for use as probiotics in aquaculture should exert antimicrobial activity and be regarded as safe not only for the aquatic hosts but also for their surrounding environments and humans. The objective of this work was to investigate the antimicrobial/bacteriocin activity against fish pathogens, the antibiotic susceptibility, and the prevalence of virulence factors and detrimental enzymatic activities in 99 Lactic Acid Bacteria (LAB) (59 enterococci and 40 non-enterococci) isolated from aquatic animals regarded as human food.

Results

These LAB displayed a broad antimicrobial/bacteriocin activity against the main Gram-positive and Gram-negative fish pathogens. However, particular safety concerns based on antibiotic resistance and virulence factors were identified in the genus Enterococcus (86%) (Enterococcus faecalis, 100%; E. faecium, 79%). Antibiotic resistance was also found in the genera Weissella (60%), Pediococcus (44%), Lactobacillus (33%), but not in leuconostocs and lactococci. Antibiotic resistance genes were found in 7.5% of the non-enterococci, including the genera Pediococcus (12.5%) and Weissella (6.7%). One strain of both Pediococcus pentosaceus and Weissella cibaria carried the erythromycin resistance gene mef(A/E), and another two P. pentosaceus strains harboured lnu(A) conferring resistance to lincosamides. Gelatinase activity was found in E. faecalis and E. faecium (71 and 11%, respectively), while a low number of E. faecalis (5%) and none E. faecium exerted hemolytic activity. None enterococci and non-enterococci showed bile deconjugation and mucin degradation abilities, or other detrimental enzymatic activities.

Conclusions

To our knowledge, this is the first description of mef(A/E) in the genera Pediococcus and Weissella, and lnu(A) in the genus Pediococcus. The in vitro subtractive screening presented in this work constitutes a valuable strategy for the large-scale preliminary selection of putatively safe LAB intended for use as probiotics in aquaculture.

Performance of three chromogenic VRE screening agars, two Etest(®) vancomycin protocols, and different microdilution methods in detecting vanB genotype Enterococcus faecium with varying vancomycin MICs

Frequencies of vanB-type Enterococcus faecium increased in Europe during the last years. VanB enterococci show various levels of vancomycin MICs even below the susceptible breakpoint challenging a reliable diagnostics. The performance of 3 chromogenic vancomycin-resistant enterococci (VRE) screening agars, 2 Etest® vancomycin protocols, and different microdilution methods to detect 129 clinical vanB E. faecium strains was investigated. Altogether, 112 (87%) were correctly identified as VanB-type Enterococcus by microdilution MICs. An Etest® macromethod protocol was more sensitive than the standard protocol while keeping sufficient specificity in identifying 15 vanA/vanB-negative strains. Three chromogenic VRE agars performed similarly with 121 (94%), 123 (95%), and 124 (96%) vanB isolates that grew on Brilliance™ VRE Agar, CHROMagar™ VRE, and chromID™ VRE agar, respectively. Using identical media and conditions, we did not identify different growth behaviour on agar and in broth. A few vanB strains showed growth of microcolonies inside the Etest® vancomycin inhibition zones, suggesting a VanB heteroresistance phenotype.