Performance of the EUCAST disk diffusion method, the CLSI agar screen method, and the Vitek 2 automated antimicrobial susceptibility testing system for detection of clinical isolates of Enterococci with low- and medium-level VanB-type vancomycin resistance: a multicenter study

Emergence of vancomycin-resistant enterococci from vancomycin-susceptible enterococci in hospitalized patients under antimicrobial therapy

OBJECTIVES

Enterococci are opportunistic pathogens with plastic genomes that evolve, acquire, and transmit antimicrobial-resistant determinants such as vancomycin resistance clusters. While vancomycin-resistant enterococci (VRE) have emerged as successful nosocomial pathogens, the mechanism by which vancomycin-susceptible enterococci (VSE) transform to VRE in hospitalized patients remains understudied.

METHODS

Genomes of Enterococcus faecium from two critically ill hospitalized patients subjected to multiple antibiotic therapies, including broad-spectrum antibiotics, were investigated. To identify mechanisms of resistance evolution, genomes of vancomycin-susceptible and -resistant isolates were compared.

RESULTS

While VSE isolates were initially identified, VRE strains emerged post-vancomycin therapy. Comparative genomics revealed horizontal transmission of mobile genetic elements containing the Tn1549 transposon, which harbours the vanB-type vancomycin resistance gene cluster. This suggests that broad-spectrum antibiotic stress promoted the transfer of resistance-conferring elements, presumably from another gut inhabitant.

CONCLUSION

This is one of the first studies investigating VSE and VRE isolates from the same patient. The mechanism of transmission and the within-patient evolution of vancomycin resistance via mobile genetic elements under antibiotic stress is illustrated. Our findings serve as a foundation for future studies building on this knowledge which can further elucidate the dynamics of antibiotic stress, resistance determinant transmission, and interactions within the gut microbiota.

Performance of automated antimicrobial susceptibility testing for the detection of antimicrobial resistance in gram-negative bacteria: a NordicAST study

Automated testing of antimicrobial susceptibility is common in clinical microbiology laboratories but their ability to detect low-level resistance has been questioned. This Nordic multicentre study aimed to evaluate the performance of commercially available automated AST systems. A phenotypically well-characterised collection of gram-negative bacilli (Escherichia coli (n = 7), Klebsiella pneumoniae (n = 6) and Pseudomonas aeruginosa (n = 7)) with and without resistance mechanisms was examined by Danish (n = 1), Finnish (n = 6), Norwegian (n = 16) and Swedish (n = 5) laboratories. Minimum inhibitory concentrations (MICs) were determined for 12 antimicrobials with automated systems and compared with MICs obtained with gold standard broth microdilution. The automated systems used were VITEK 2 (n = 23), Phoenix (n = 4), MicroScan (n = 1), and ARIS (n = 1). Very major errors were identified for six antimicrobials; cefotaxime (6.9%), meropenem (0.4%), ciprofloxacin (0.7%), ertapenem (4.3%), amikacin (3.4%) and colistin (6.4%). Categorical agreement of MIC for the automated systems compared to broth microdilution ranged from 83% for imipenem to 100% for ampicillin and trimethoprim-sulfamethoxazole. The analysis revealed several important antimicrobials where resistance was underestimated, potentially with significant consequences in patient treatment. The results cast doubt on the use of automated AST in the management of patients with serious infections and suggests that more work is needed to define their limitations.

Molecular Epidemiology and Characterization of Multidrug-Resistant MRSA ST398 and ST239 in Himachal Pradesh, India

Aim

Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of severe and difficult-to-treat infections in humans and animals. We aimed to identify the predominant lineages of methicillin-resistant S. aureus in Himachal Pradesh, India, to understand the genomic epidemiology along with the genotypic and phenotypic characteristics.

Methods

We isolated 250 S. aureus from two district hospitals in Himachal Pradesh, India. Methicillin-Resistant S. aureus (MRSA) isolates were subjected to MLST, SCCmec typing, and resistance as well as virulence determinants were determined by PCR and sequencing. Bio-typing was also performed for source tracking.

Results

A 17.6% (44/250) of isolates were classified as MRSA by both the MRSA detection kit and disc diffusion methods. Antimicrobial Susceptibility Testing of MRSA isolates (n = 44) showed high resistance to oxacillin (77.27%), erythromycin (77.27%), tetracycline (75%), cefoxitin (65.9%), and gentamicin (61.36%), while low resistance was observed for teicoplanin (36.36%), vancomycin and levofloxacin (31.81%) and fusidic acid (18.18%). All isolates were sensitive to linezolid, quinupristin-dulfopristin, dalbavancin, and cefazoline. The SCCmec-II was observed in 20.45% of isolates, SCCmec-I in 11.36%, SCCmec-III in 9%, SCCmec-IV in 40.9% and SCCmec-V in 18.18%. The mecA gene was present in all isolates (n = 44) and 50% also had the vanA gene. 35% of isolates had the lukS-PV/lukf-PV toxin gene and 11.36% had the co-existence of mecA, vanA, and lukS-PV/lukf-PV. The major strain was ST398 (39%) followed by ST239 (27%), ST217 (16%), ST121 (11%), and ST338 (7%). The MRSA isolates produced staphylokinase and β-hemolysis but were negative for bovine plasma coagulation tests.

In Conclusion

The predominant MRSA clones in Himachal Pradesh, India, were hospital-associated multi-drug resistant-MRSA ST239 with PVL and community-associated MRSA ST398.

Antimicrobial Susceptibility Testing for Enterococci

Enterococci are major, recalcitrant nosocomial pathogens with a wide repertoire of intrinsic and acquired resistance determinants and the potential of developing resistance to all clinically available antimicrobials. As such, multidrug-resistant enterococci are considered a serious public health threat. Due to limited treatment options and rapid emergence of resistance to all novel agents, the clinical microbiology laboratory plays a critical role in deploying accurate, reproducible, and feasible antimicrobial susceptibility testing methods to guide appropriate treatment of patients with deep-seated enterococcal infections. In this review, we provide an overview of the advantages and disadvantages of existing manual and automated methods that test susceptibility of Enterococcus faecium and Enterococcus faecalis to β-lactams, aminoglycosides, vancomycin, lipoglycopeptides, oxazolidinones, novel tetracycline-derivatives, and daptomycin. We also identify unique problems and gaps with the performance and clinical utility of antimicrobial susceptibility testing for enterococci, provide recommendations for clinical laboratories to circumvent select problems, and address potential future innovations that can bridge major gaps in susceptibility testing.

A Simple and Rapid Low-Cost Procedure for Detection of Vancomycin-Resistance Genes in Enterococci Reveals an Outbreak of Vancomycin-Variable Enterococcus faecium

The detection of resistance to vancomycin in enterococci cultured from patients is important for the treatment of individual patients and for the prevention of hospital transmission. Phenotypic antimicrobial resistance tests may fail to detect potential vancomycin-resistant enterococci. We have developed and tested a PCR based procedure for routine screening for vancomycin-resistance genes in clinical samples with enterococci. Primary cultures from diagnostic samples reported with growth of Enterococcus faecium or E. facalis were tested for vanA and vanB genes by real-time PCR without the isolation of specific bacteria. Up to ten samples were pooled and tested in each real-time PCR reaction, with subsequent individual testing of cultures from positive pools. In a one-month test period in 2017 vanA gene was detected in one out of 340 urine samples with vancomycin-susceptible enterococci reported from diagnostic culture. A second test period in 2018 included 357 urine samples, and vanA gene was detected in samples from eight patients. Subsequently, all urine samples reported with growth of E. faecium during a period of one year were tested. Fifty-eight individuals were identified with enterococci, carrying the vanA gene not previously detected. Routine molecular testing of primary culture material from patient samples may improve the detection of hospitalized patients carrying E. faecium with resistance genes to vancomycin.

Evolution and antimicrobial resistance of enterococci isolated from Pecorino and goat cheese manufactured on-farm in an area facing constraints as per EU Regulation 1305/2013 in Umbria, Italy

The latest EU regulation on geographical indications (EU Regulation No. 1151/2012) has introduced a set of new tools for the protection and enhancement of food products in rural areas, under the group name of optional quality term (OQT). The Commission Delegated EU Regulation, No. 665/2014, regulated the conditions for the use of the optional quality term mountain product (MP), to support the implementation of a mountain value chain. This new tool is aimed at promoting local development, maintaining the economic activities in mountain areas, and redistributing wealth, whilst, at the same time, promoting the territory. Pecorino and goat cheeses are typical Italian cheeses made usually with whole raw ewe’s or raw goat’s milk, without starter culture addition. In an attempt to characterize these productions, the aim of this study was to investigate the evolution of enterococci during the production and ripening of Pecorino cheese made in three different farms, located in Umbria, Italy in areas facing natural or other specific constraints as stipulated by Regulation 1305/2013 on support for rural development by the European Agricultural Fund for Rural Development (EAFRD). Enterococci are enteric organisms which are commonly isolated from ewe and goat’s milk production in Umbria, Italy. Counts of enterococci in raw milk ranged from 1.75 for ovine milk to 3.62 for ewe milk and a marked reduction was observed after thermization especially in ovine milk. Out of 100 isolates, 69 were E. faecium, 23 E. durans, 8 E. faecalis and 2 E. casseliflavus and the distribution of species between farms and between samples showed a prevalence of E. faecium in ovine farms and E. durans in ewes farms, with an equal dis-tribution between samples. High percentages of susceptible isolates were found for amoxicil-lin/clavulanic acid, ampicillin, chloramphenicol, sulphamethoxazole, sulphamethoxazole/ trimethoprim, ticarcillin, vancomycin. A high prevalence of resistant strains (>30%) was ob-served for amikacin, ciprofloxacin, ceftriaxone, kanamycin, tetracycline. A comparison of this re-sults with those of previous works on similar dairy products revealed high levels of resistance to antimicrobials which needs to be addressed.

Phenotypic and genotypic detection methods for antimicrobial resistance in ESKAPE pathogens (Review)

Antimicrobial resistance (AMR) represents a growing public health problem worldwide. Infections with such bacteria lead to longer hospitalization times, higher healthcare costs and greater morbidity and mortality. Thus, there is a greater need for rapid detection methods in order to limit their spread. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) are a series of epidemiologically-important microorganisms of great concern due to their high levels of resistance. This review aimed to update the background information on the ESKAPE pathogens as well as to provide a summary of the numerous phenotypic and molecular methods used to detect their AMR mechanisms. While they are usually linked to hospital acquired infections, AMR is also spreading in the veterinary and the environmental sectors. Yet, the epidemiological loop closes with patients which, when infected with such pathogens, often lack therapeutic options. Thus, it was aimed to give the article a One Health perspective.

In vitro dissolution testing models of ocular implants for posterior segment drug delivery

The delivery of drugs to the posterior segment of the eye remains a tremendously difficult task. Prolonged treatment in conventional intravitreal therapy requires injections that are administered frequently due to the rapid clearance of the drug molecules. As an alternative, intraocular implants can offer drug release for long-term therapy. However, one of the several challenges in developing intraocular implants is selecting an appropriate in vitro dissolution testing model. In order to determine the efficacy of ocular implants in drug release, multiple in vitro test models were emerging. While these in vitro models may be used to analyse drug release profiles, the findings may not predict in vivo retinal drug exposure as this is influenced by metabolic and physiological factors. This review considers various types of in vitro test methods used to test drug release of ocular implants. Importantly, it discusses the challenges and factors that must be considered in the development and testing of the implants in an in vitro setup.

Failure of Vitek2 to reliably detect vanB-mediated vancomycin resistance in Enterococcus faecium

OBJECTIVES

The increasing prevalence of VRE necessitates their reliable detection, especially for low-level resistance mediated by vanB in Enterococcus faecium. In this prospective study we analysed if vanB-mediated vancomycin resistance can be reliably detected by Vitek2.

METHODS

One thousand, three hundred and forty-four enterococcal isolates from routine clinical specimens were tested by Vitek2 (bioMérieux, Nürtingen, Germany). Additionally, a bacterial suspension (with a turbidity equivalent to that of a 0.5 McFarland standard) was inoculated on chromID VRE screening agar (bioMérieux) and incubated for 48 h. If vancomycin tested susceptible by Vitek2 but growth was detected on the screening agar, PCR for vanA/vanB was performed (GeneXpert vanA/B test, Cepheid, Frankfurt, Germany). For isolates that tested susceptible to vancomycin by Vitek2 but were vanA/B positive, MICs were determined before and after cultivation in broth with increasing concentrations of vancomycin.

RESULTS

One hundred and fifty-six out of 491 E. faecium were VRE and were predominantly vanB positive (81.0%). Of these, Vitek2 did not identify 14 as VRE (sensitivity 91.0%). By broth microdilution 9/14 isolates demonstrated high MICs (≥32 mg/L) and 5/14 showed low vancomycin MICs, which did not increase despite vancomycin exposure. Three of the 14 isolates demonstrated growth on chromID VRE; after vancomycin exposure seven additional isolates were able to grow on chromID VRE.

CONCLUSIONS

Vitek2 fails to detect vanB-mediated vancomycin resistance consistently, especially, but not limited to, low-level resistance. As this may lead to treatment failure and further dissemination of vanB VRE, additional methods (e.g. culture on VRE screening agar or PCR) are necessary to reliably identify vanB-positive enterococci in clinical routine.

Enterococcus faecium: from microbiological insights to practical recommendations for infection control and diagnostics

Early in its evolution, Enterococcus faecium acquired traits that allowed it to become a successful nosocomial pathogen. E. faecium inherent tenacity to build resistance to antibiotics and environmental stressors that allows the species to thrive in hospital environments. The continual wide use of antibiotics in medicine has been an important driver in the evolution of E. faecium becoming a highly proficient hospital pathogen.For successful prevention and reduction of nosocomial infections with vancomycin resistant E. faecium (VREfm), it is essential to focus on reducing VREfm carriage and spread. The aim of this review is to incorporate microbiological insights of E. faecium into practical infection control recommendations, to reduce the spread of hospital-acquired VREfm (carriage and infections). The spread of VREfm can be controlled by intensified cleaning procedures, antibiotic stewardship, rapid screening of VREfm carriage focused on high-risk populations, and identification of transmission routes through accurate detection and typing methods in outbreak situations. Further, for successful management of E. faecium, continual innovation in the fields of diagnostics, treatment, and eradication is necessary.

Comparison of VITEK® 2, three different gradient strip tests and broth microdilution for detecting vanB-positive Enterococcus faecium isolates with low vancomycin MICs

OBJECTIVES

In 2018, EUCAST issued a warning regarding unreliable results of gradient strip tests for confirming vancomycin resistance in enterococci. We compared the performance of various diagnostic standard and confirmatory tests to identify and determine vanB-type vancomycin resistance.

METHODS

We analysed a collection of vanB-positive Enterococcus faecium isolates (n = 68) with low vancomycin MICs and compared the performance of VITEK® 2 (bioMérieux), broth microdilution and three gradient strip tests from different providers (Oxoid, Liofilchem and bioMérieux). For the latter we compared the standard procedure with a protocol with increased inoculum, a rich agar medium and a longer incubation time ('macromethod').

RESULTS

The sensitivity of VITEK® 2 was 81% compared with 72% for broth microdilution and 61%-63% for the three gradient strip tests using standard conditions. The macromethod substantially improved the performance of all strip tests resulting in a sensitivity of 89%-96% after 48 h of incubation.

CONCLUSIONS

We recommend that EUCAST changes the present warning against the general use of MIC strips. When MIC strips are used to either exclude or confirm suspected vancomycin resistance in E. faecium, and a PCR is not available, the macromethod should be employed. For clinically relevant enterococci, where a rapid therapeutic decision is needed, a molecular test (e.g. PCR) should be favoured in order to save time and to further increase sensitivity.

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.

Intra- and inter-laboratory agreement of the disc diffusion assay for assessing antimicrobial susceptibility of porcine Escherichia coli

Reliable assessment of the susceptibility of animal bacterial pathogens to antimicrobials is of paramount importance in the fight against antimicrobial resistance. This work aims to estimate the repeatability (intra-laboratory agreement) and reproducibility (inter-laboratory agreement) of the disc diffusion assay in veterinary laboratories to understand further if the assay has a role in the surveillance of antimicrobial resistance in animals. Seven major veterinary laboratories from all States in Australia participated, and each tested the same panel of isolates five times at three to four-week intervals, against six antimicrobial agents using Clinical and Laboratory Standards Institute protocols. The panel consisted of twenty different isolates from porcine Escherichia coli from clinical cases and a single reference strain (ATCC 25922). Laboratories were blinded to the identity of the isolates, replicates, and to each other. In total, 4200 inhibition zone diameters (mm) were collected, and analysed descriptively, graphically, and with linear mixed models. Regardless of the laboratories and isolate/antimicrobial combinations, the overall very major error rate (proportion of isolates classified as susceptible when actual status is resistant) was 1.6%; the major error rate (proportion of isolates classified as resistant when actual status is susceptible) was 1.6%; and the 'minor error' rate (proportion of isolates with intermediate susceptibility that measure fully susceptible or resistant or vice versa) was 2.4%. The variation between repeated measurements ranged between 4.4-7.2 mm depending on the antimicrobial agent assessed. The reproducibility was always more variable than the repeatability, which suggested some laboratory effects. The repeatability coefficient of disc diffusion was lowest for tetracycline (4.4 mm, 95% CI: 3.8-5.0 mm) and ampicillin (4.6 mm, 95% CI: 4.2-5.2 mm) and highest for trimethoprim-sulfamethoxazole (6.6 mm, 95% CI: 5.9-7.4 mm). The reproducibility coefficient of disc diffusion was lowest for gentamicin (5.4, 95% CI: 4.0-7.2) and highest for trimethoprim-sulfamethoxazole (7.2 mm, 95%CI: 4.5-11.7 mm). The precision of the disc diffusion assay was deemed satisfactory for use in a national surveillance program for clinical porcine E. coli isolates. However, measurement variation of the disc diffusion assay is of concern for isolates with marginal susceptibility or resistance due to increased risk of misclassification.

Rapid disc diffusion antibiotic susceptibility testing for Pseudomonas aeruginosa, Acinetobacter baumannii and Enterococcus spp

Background

We investigated the feasibility of rapid disc diffusion antibiotic susceptibility testing (rAST) with reading of inhibition zones after 6 and/or 8 h of incubation for Enterococcus faecalis, Enterococcus faecium, Pseudomonas aeruginosa and Acinetobacter baumannii. In addition, we evaluated discrimination of resistant populations from the WT populations at early timepoints and the requirement for clinical breakpoint adaptations for proper interpretation of rAST data.

Methods

In total, 815 clinical strains [E. faecalis (n = 135), E. faecium (n = 227), P. aeruginosa (n = 295) and A. baumannii (n = 158)] were included in this study. Disc diffusion plates were streaked, incubated and imaged using the WASPLab^TM automation system. WT populations and non-WT populations were defined using epidemiological cut-offs.

Results and conclusions

rAST at 6 and 8 h was possible for A. baumannii and enterococci with readability of inhibition zones >90%. Overall categorical agreement of rAST at 6 h with AST at 18 h was 97.2%, 97.4% and 95.3% for E. faecalis, E. faecium and A. baumannii, respectively. With few exceptions, major categorization error rates were <1% for A. baumannii, and vancomycin-resistant E. faecium were clearly separated from the WT at 6 h. For P. aeruginosa the average readability of inhibition zones was 68.9% at 8 h and we found an overall categorical agreement of 94.8%. Adaptations of clinical breakpoints and/or introduction of technical buffer zones, preferably based on aggregated population data from various epidemiological settings, are required for proper interpretation of rAST.

Dissemination and genetic analysis of the stealthy vanB gene clusters of Enterococcus faecium clinical isolates in Japan

Background

VanB-type vancomycin (VAN) resistance gene clusters confer VAN resistances on Enterococcus spp. over a wide range of MIC levels (MIC = 4–1000 mg/L). However, the epidemiology and the molecular characteristics of the VAN susceptible VanB-type Enterococcus still remain unclear.

Results

We characterized 19 isolates of VanB-type Enterococcus faecium that might colonize in the gut and were not phenotypically resistant to VAN (MIC = 3 mg/L). They were obtained from two hospitals in Japan between 2009 and 2010. These isolates had the identical vanB gene cluster and showed same multilocus sequence typing (MLST) (ST78) and the highly related profiles in pulsed-field gel electrophoresis (PFGE). The vanB gene cluster was located on a plasmid, and was transferable to E. faecium and E. faecalis. Notably, from these VanB-type VREs, VAN resistant (MIC≥16 mg/L) mutants could appear at a frequency of 10^− 6–10^− 7/parent cell in vitro. Most of these revertants acquired mutations in the vanS_B gene, while the remainder of the revertants might have other mutations outside of the vanB gene cluster. All of the revertants we tested showed increases in the VAN-dependent expression of the vanB gene cluster, suggesting that the mutations affected the transcriptional activity and increased the VAN resistance. Targeted mutagenesis revealed that three unique nucleotide substitutions in the vanB gene cluster of these strains attenuated VAN resistance.

Conclusions

In summary, this study indicated that stealthy VanB-type E. faecium strains that have the potential ability to become resistance to VAN could exist in clinical settings.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1342-1) contains supplementary material, which is available to authorized users.

Continuous increase of vancomycin resistance in enterococci causing nosocomial infections in Germany - 10 years of surveillance

Background

Enterococci are frequent pathogens causing nosocomial infections in Germany. Infections due to strains with vancomycin resistance are high when compared with other European states. Therefore, the study aimed to describe the recent progression of nosocomial infections due to vancomycin-resistant enterococci (VRE) in Germany.

Methods

We analyzed data from two components of the German national nosocomial infection surveillance system for the period 2007–2016. For primary bloodstream infections (BSIs) and urinary tract infections (UTIs) we used data from intensive care units and for surgical site infections (SSIs) data from surgical departments. In a sensitivity analysis, we considered only data from participants that participated continuously from 2007 to 2016 (“core group”). We calculated proportions of VRE among all nosocomial enterococcal infections with 95% confidence intervals (95% CIs) and trends over time. A multivariable logistic regression was used to compare occurrence of VRE proportions among German federal states.

Results

Enterococcal infections from 857 ICUs and 1119 surgical departments were analyzed. On ICUs, the proportion of vancomycin resistance in enterococci causing nosocomial infections significantly increased for BSIs from 5.9 to 16.7% and for UTIs from 2.9 to 9.9%; for surgical site infections, the proportion of VRE increased from 0.9 to 5.2% (P < 0.001 for all). In the core group, the increase of VRE was more pronounced in ICUs (BSIs: 5.5 to 21.6%; UTIs: 2 to 11.2%) but was not seen in surgical departments (SSIs: 1.5 to 2.8%). Compared with the most populous German federal state North Rhine Westphalia, enterococcal infections in Hesse (Odds Ratio (OR) 2.3, 95% CI 1.7–3.1), Saxony (OR 2.5, 95% CI 1.8–3.5) and Thuringia (OR 1.9, 95% CI 1.4–2.6) were more likely to be caused by vancomycin-resistant strains.

Conclusion

In Germany, the proportion of VRE in nosocomial infection due to enterococci is still increasing. It remains unclear, why a large variation in the proportion of VRE exists between German federal states.

Diagnostic Evasion of Highly-Resistant Microorganisms: A Critical Factor in Nosocomial Outbreaks

Highly resistant microorganisms (HRMOs) may evade screening strategies used in routine diagnostics. Bacteria that have evolved to evade diagnostic tests may have a selective advantage in the nosocomial environment. Evasion of resistance detection can result from the following mechanisms: low-level expression of resistance genes not resulting in detectable resistance, slow growing variants, mimicry of wild-type-resistance, and resistance mechanisms that are only detected if induced by antibiotic pressure. We reviewed reports on hospital outbreaks in the Netherlands over the past 5 years. Remarkably, many outbreaks including major nation-wide outbreaks were caused by microorganisms able to evade resistance detection by diagnostic screening tests. We describe various examples of diagnostic evasion by several HRMOs and discuss this in a broad and international perspective. The epidemiology of hospital-associated bacteria may strongly be affected by diagnostic screening strategies. This may result in an increasing reservoir of resistance genes in hospital populations that is unnoticed. The resistance elements may horizontally transfer to hosts with systems for high-level expression, resulting in a clinically significant resistance problem. We advise to communicate the identification of HRMOs that evade diagnostics within national and regional networks. Such signaling networks may prevent inter-hospital outbreaks, and allow collaborative development of adapted diagnostic tests.

Evaluation of the novel artus C. difficile QS-RGQ, VanR QS-RGQ and MRSA/SA QS-RGQ assays for the laboratory diagnosis of Clostridium difficile infection (CDI), and for vancomycin-resistant enterococci (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) screening

Clostridium difficile, methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) are worldwide prevalent healthcare-associated pathogens. We have evaluated three Qiagen artus QS-RGQ assays for the detection of these pathogens. We examined 200 stool samples previously tested for C. difficile infection (CDI), 94 rectal swabs previously screened for VRE and 200 MRSA screening nasal swabs. With the routine diagnostic laboratory results being adopted as the gold standard, the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the artus C. difficile assay were 100%, for the artus VanR QS-RGQ assay, 95, 68, 44 and 98%, and for the artus MRSA/SA assay, 80, 94, 93 and 83%, respectively. The artus VanR assay detected the vanA and/or vanB genes in 32% of culture-negative VRE screens; in 71% of these cases, only vanB was detected. An over-estimation of the rate of faecal VRE colonisation could be due to a patient population with high rates of faecal carriage of non-enterococcal species carrying vanB. Based on our findings, we conclude that all three artus QS-RGQ assays could be a useful addition to a diagnostic laboratory, and that the optimal choice of assay should be determined according to user needs.

A Silenced vanA Gene Cluster on a Transferable Plasmid Caused an Outbreak of Vancomycin-Variable Enterococci

We report an outbreak of vancomycin-variable vanA(+) enterococci (VVE) able to escape phenotypic detection by current guidelines and demonstrate the molecular mechanisms for in vivo switching into vancomycin resistance and horizontal spread of the vanA cluster. Forty-eight vanA(+) Enterococcus faecium isolates and one Enterococcus faecalis isolate were analyzed for clonality with pulsed-field gel electrophoresis (PFGE), and their vanA gene cluster compositions were assessed by PCR and whole-genome sequencing of six isolates. The susceptible VVE strains were cultivated in brain heart infusion broth containing vancomycin at 8 μg/ml for in vitro development of resistant VVE. The transcription profiles of susceptible VVE and their resistant revertants were assessed using quantitative reverse transcription-PCR. Plasmid content was analyzed with S1 nuclease PFGE and hybridizations. Conjugative transfer of vanA was assessed by filter mating. The only genetic difference between the vanA clusters of susceptible and resistant VVE was an ISL3-family element upstream of vanHAX, which silenced vanHAX gene transcription in susceptible VVE. Furthermore, the VVE had an insertion of IS1542 between orf2 and vanR that attenuated the expression of vanHAX Growth of susceptible VVE occurred after 24 to 72 h of exposure to vancomycin due to excision of the ISL3-family element. The vanA gene cluster was located on a transferable broad-host-range plasmid also detected in outbreak isolates with different pulsotypes, including one E. faecalis isolate. Horizontally transferable silenced vanA able to escape detection and revert into resistance during vancomycin therapy represents a new challenge in the clinic. Genotypic testing of invasive vancomycin-susceptible enterococci by vanA-PCR is advised.

Prevalence of Virulence Factors and Vancomycin-resistant Genes among Enterococcus faecalis and E. faecium Isolated from Clinical Specimens

BACKGROUND

The aim of this study was to determine the occurrence of virulence determinants and vancomycin-resistant genes among Enterococcus faecalis and E. faecium obtained from various clinical sources.

METHODS

The study was performed on the 280 enterococcal isolated from clinical specimens in Hamadan hospitals, western Iran in 2012-14. Antibiotic susceptibility testing was performed using disk diffusion and Minimal Inhibitory Concentration (MIC) methods. The presence of vancomycin-resistant genes and virulence genes was investigated using PCR.

RESULTS

Totally 280 enterococcal isolates were identified as follows: E. faecalis (62.5%), E. faecium (24%) and Enterococcus spp (13.5%). The results of antibiotic susceptibility testing showed that resistance rates to vancomycin and teicoplanin in E. faecalis and E. faecium isolates were 5% and 73%, respectively. Of Sixty vancomycin-resistant Enterococci strains, fifty-one isolates were identified as E. faecium (VREfm) and nine as E. faecalis (VREfs). Prevalence of esp, hyl, and asa1 genes were determined as 82%, 71.6%, and 100%, respectively in E. faecium strains; and 78%, 56/6%, and 97%, respectively in E. faecalis strains.

CONCLUSION

The increased frequency of VREF, as seen with rapid rise in the number of vanA isolates should be considered in infection control practices.

Evaluation of the Xpert vanA/vanB assay using enriched inoculated broths for direct detection of vanB vancomycin-resistant Enterococci

Rapid and accurate detection of VRE (vancomycin-resistant enterococci) is required for adequate antimicrobial treatment and infection prevention measures. Previous studies using PCR for the detection of VRE, including Cepheid's Xpert vanA/vanB assay, reported accurate detection of vanA VRE; however, many false-positive results were found for vanB VRE. This is mainly due to nonenterococcal vanB genes, which can be found in the gut flora. Our goal was to optimize the rapid and accurate detection of vanB VRE and to improve the positive predictive value (PPV) by limiting false-positive results. We evaluated the use of the Xpert vanA/vanB assay on rectal swabs and on enriched inoculated broths for the detection of vanB VRE. By adjusting the cycle threshold (CT) cutoff value to ≤ 25 for positivity by PCR on enriched broths, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 96.9%, 100%, 100%, and 99.5% for vanB VRE, respectively. As shown in this study, CT values of ≤ 25 acquired from enriched broths can be considered true positive. For broths with CT values between 25 and 30, we recommend confirming the results by culture. CT values of >30 appeared to be true negative. In conclusion, this study shows that the Cepheid's Xpert vanA/vanB assay performed on enriched inoculated broths with an adjusted cutoff CT value is a useful and rapid tool for the detection of vanB VRE.

Controlling the spread of vancomycin-resistant enterococci. Is active screening worthwhile?

Vancomycin-resistant enterococci (VRE) are significant causes of healthcare-acquired infections. Active screening, i.e. the use of rectal swabs or faeces to detect carriage in at-risk patients, has been described as contributing to prevention by identifying previously unrecognized cases. The aim of this review was to determine the impact of screening for VRE on prevention and control, its cost-effectiveness and recent approaches to laboratory detection. A review of published studies in English from 2000 was undertaken. Whereas various guidelines were accessed and reviewed, the emphasis was on original reports and studies. It was determined that the patient groups who may need screening are those admitted to critical care units, haematology/oncology and transplant wards, patients on chronic dialysis and patients admitted to acute hospitals from long-stay units. Active screening is associated with reduced VRE colonization and infection and cost savings in some studies, even if these fall short of randomized trials. Selective media increase sensitivity and reduce the time to detection but the role of molecular methods remains to be determined. In conclusion, active screening contributes to VRE prevention probably by heightening awareness of control measures, including isolation. However, further studies are required to: better define high-risk groups that warrant screening; quantify the clinical and economic benefit; and determine the optimal laboratory methods in a range of different patient populations.

A multicentre hospital outbreak in Sweden caused by introduction of a vanB2 transposon into a stably maintained pRUM-plasmid in an Enterococcus faecium ST192 clone

The clonal dissemination of VanB-type vancomycin-resistant Enterococcus faecium (VREfm) strains in three Swedish hospitals between 2007 and 2011 prompted further analysis to reveal the possible origin and molecular characteristics of the outbreak strain. A representative subset of VREfm isolates (n = 18) and vancomycin-susceptible E. faecium (VSEfm, n = 2) reflecting the spread in time and location was approached by an array of methods including: selective whole genome sequencing (WGS; n = 3), multi locus sequence typing (MLST), antimicrobial susceptibility testing, virulence gene profiling, identification of mobile genetic elements conferring glycopeptide resistance and their ability to support glycopeptide resistance transfer. In addition, a single VREfm strain with an unrelated PFGE pattern collected prior to the outbreak was examined by WGS. MLST revealed a predominance of ST192, belonging to a hospital adapted high-risk lineage harbouring several known virulence determinants (n≥10). The VREfm outbreak strain was resistant to ampicillin, gentamicin, ciprofloxacin and vancomycin, and susceptible to teicoplanin. Consistently, a vanB2-subtype as part of Tn1549/Tn5382 with a unique genetic signature was identified in the VREfm outbreak strains. Moreover, Southern blot hybridisation analyses of PFGE separated S1 nuclease-restricted total DNAs and filter mating experiments showed that vanB2-Tn1549/Tn5382 was located in a 70-kb sized rep17/pRUM plasmid readily transferable between E. faecium. This plasmid contained an axe-txe toxin-antitoxin module associated with stable maintenance. The two clonally related VSEfm harboured a 40 kb rep17/pRUM plasmid absent of the 30 kb vanB2-Tn1549/Tn5382 gene complex. Otherwise, these two isolates were similar to the VREfm outbreak strain in virulence- and resistance profile. In conclusion, our observations support that the origin of the multicentre outbreak was caused by an introduction of vanB2-Tn1549/Tn5382 into a rep17/pRUM plasmid harboured in a pre-existing high-risk E. faecium ST192 clone. The subsequent dissemination of VREfm to other centres was primarily caused by clonal spread rather than plasmid transfer to pre-existing high-risk clones.

Low vancomycin MICs and fecal densities reduce the sensitivity of screening methods for vancomycin resistance in Enterococci

Active surveillance is part of a multifaceted approach used to prevent the spread of vancomycin-resistant enterococci (VRE). The impact of fecal density, the vancomycin MIC of the isolate, and the vancomycin concentration in liquid medium on test performance are uncertain. Using fecal specimens spiked with a collection of 18 VRE (predominantly vanB) with a wide vancomycin MIC range, we compared the performances of commercial chromogenic agars (CHROMagar VRE, chromID VRE, Brilliance VRE, and VRE Select) and 1 liquid medium (Enterococcosel enrichment broth) for VRE detection. The specificity of solid media was excellent; however, the sensitivity at 48 h varied from 78 to 94%. Screening using liquid medium was less sensitive than screening with solid media, particularly as the vancomycin content increased. Sensitivity declined (i) as the fecal VRE density decreased, (ii) when the media were assessed at 24 h (versus 48 h), and (iii) for isolates with a low vancomycin MIC (sensitivity, 25 to 75% versus 100% for isolates with vancomycin MIC of <16 mg/liter versus >32 mg/liter on solid medium using 10(6) CFU/ml of feces). Depending on local epidemiology and in particular VRE vancomycin MICs, the sensitivity of culture-based methods for VRE screening of stool or rectal specimens may be suboptimal, potentially facilitating secondary transmission.