Emergence of Vancomycin-Resistant Enterococci in Australia: Phenotypic and Genotypic Characteristics of Isolates

Enterococci with resistance to glycopeptides have recently emerged in Australia. We developed multiplex PCR assays for vanA, vanB, vanC1, and vanC2 or vanC3 in order to examine the genetic basis for vancomycin resistance in Australian isolates of vancomycin-resistant Enterococcus faecium and E. faecalis (VRE). The predominant genotype from human clinical E. faecium isolates was vanB. The PCR van genotype was consistent with the resistance phenotype in all but six cases. One vanA E. faecalis isolate had a VanB phenotype, one vanB E. faecium isolate had a VanA phenotype, and four E. faecalis isolates were consistently negative for vanA, vanB, vanC1, and vanC2 or vanC3, even though they exhibited a VanB phenotype. These four isolates were subsequently examined for the presence of vanD by published methods and were found to be negative. No vancomycin-susceptible strains produced a PCR product. On the basis of our findings the epidemiology of VRE in Australia appears to be different from that in either the United States or Europe. Our multiplex PCR assays gave a rapid and accurate method for determining the genotype and confirming the identification of glycopeptide-resistant enterococci. Rapid and accurate methods are essential, because laboratory-based surveillance is critical in programs for the detection, control, and prevention of the transmission of glycopeptide-resistant enterococci.     

Characterization of Glycopeptide-Resistant Enterococci from a Swiss Hospital

Between August 1994 and September 1996, 28 glycopeptide-resistant enterococci (GRE) were isolated from 8 infected patients and 11 intestinal carriers hospitalized at the University Hospital of Geneva. Identification to the species was made by both phenotypic (API 20 STREP and Rapid ID 32 STREP systems, and Vitek Gram Positive Identification Card) and genotypic methods using a multiplex PCR assay developed also for the determination of the genotype of glycopeptide resistance (vanA, vanB, vanC1, and vanC2-C3 genes). Fifteen isolates were identified as Enterococcus faecium, 8 as E. gallinarum, 4 as E. faecalis, and 1 as E. hirae. All of the phenotypic identification methods failed to differentiate some isolates of E. gallinarum from E. faecium, or vice versa. Both vanA (n = 18) and vanB (n = 4) glycopeptide resistance genotypes were found. For the first time, the vanB determinant was found in two isolates of E. gallinarum. Two patients were colonized by two different species containing the vanA gene and one by two different species containing the vanB gene. All vanA isolates were highly resistant to both vancomycin and teicoplanin except for three isolates which were susceptible to teicoplanin. Molecular typing by pulsed-field gel electrophoresis showed identical or similar patterns among E. faecium isolates with the vanA gene in five patients for whom the epidemiological link could not be always elucidated. This study emphasizes the necessity of utilizing both phenotypic and genotypic methods to characterize GRE.     

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 (C_T) 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, C_T values of ≤25 acquired from enriched broths can be considered true positive. For broths with C_T values between 25 and 30, we recommend confirming the results by culture. C_T 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 C_T value is a useful and rapid tool for the detection of vanB VRE.     

Limitations of vitek GPS-418 cards in exact detection of vancomycin-resistant enterococci with the vanB genotype

The susceptibilities of 20 strains of vancomycin-resistant enterococci (VRE) with the vanB genotype obtained by using Vitek GPS-418 cards were compared with those obtained by the broth dilution method of the National Committee for Clinical Laboratory Standards (NCCLS) (approved standard M7-A4) and with those obtained by the agar screen method using bile esculin azide agar containing 6 microgram of vancomycin per ml. Although both the broth dilution and agar screen methods disclosed no discordance, Vitek GPS-418 cards yielded a very major error compared with the results obtained by the reference broth dilution method of the NCCLS. Vitek GPS-418 cards were therefore found to have considerable room for improvement for the accurate detection of vanB VRE strains.     

Screening for vancomycin‐resistant enterococci: results of a survey in Stockholm

Fang H, Nord CE, Ullberg M. Screening for vancomycin‐resistant enterococci: results of a survey in Stockholm. APMIS 2010; 118: 413–7. Vancomycin‐resistant enterococci (VRE) are emerging in Stockholm hospitals. To rapidly screen for VRE from stool and rectal swab samples, a detection assay combining broth enrichment and real‐time PCR was set up. From September to December 2008, 6914 samples were screened for VRE using the broth‐PCR combined assay. Of them, 5463 samples were reported as negative the day after sampling. Among the 6914 samples, 47 was screened as vanA probable and 44 of them were confirmed as VRE; 1314 samples was screened as vanB probable and 93 of them were confirmed as VRE. The 44 vanA‐type VRE isolates, detected from 31 patients, were clustered into four genetic types by pulsed‐field gel electrophoresis (PFGE). The same PFGE type was observed in multiple isolates recovered from the same patient with vanA VRE. The 93 vanB‐type VRE isolates were detected from 60 patients, 59 of them harboring VRE with PFGE type 1. One patient with vanB VRE had two isolates of distinct PFGE types (types 1 and 5). PFGE type 1 and PFGE type 2 were predominant clones in vanB and vanA strains, respectively, represented by 98.3% (59/60) of patients with vanB VRE and 77.4% (24/31) of patients with vanA VRE.     

A new approach of real time polymerase chain reaction in detection of vancomycin-resistant enterococci and its comparison with other methods

Background: Vancomycin-resistant enterococci (VRE) are third leading cause of nosocomial infection. Therefore, an effective, accurate and early detection of VRE along with their minimum inhibitory concentrations (MICs) is required to initiate appropriate therapy and thus better patient outcome. Objective: To detect VRE by real time quantitative polymerase chain reaction (Q-PCR) and to compare the results with chrom ID (C-ID) VRE and PCR. Further the study also determined the fold change of vanA gene by Q-PCR in different groups of VRE isolates classified on the basis of glycopeptides MIC range. Subjects and Methods: A total of 145 (80 VRE and 65 vancomycin-susceptible enterococci) clinical isolates were included in the study. After the screening of VRE isolates MICs were determined by E-test and agar dilution method. Further VRE was confirmed by vanA and vanB specific PCR and Q-PCR. Results: The sensitivity and specificity of C-ID VRE was 100% and 95.38%. However, sensitivity and specificity of conventional and Q-PCR were found to be 100%. Conventional and Q-PCR confirmed that our all isolates were vanA type. Mean R value was significantly higher (P < 0.001) in group I (MIC> 1024 μg/ml) when compared to group II (MIC 512-1024 μg/ml) and group III (MIC < 512 μg/ml) isolates. The mean R was also significantly higher in group II when compared to group III isolates (P = 0.038). Conclusion: Q-PCR is a rapid technique to detect vanA in enterococci along with their MIC range, thus it might be helpful to decide the treatment modalities of infections caused by VRE.     

Comparison of testing methods for detection of decreased linezolid susceptibility due to G2576T mutation of the 23S rRNA gene in Enterococcus faecium and Enterococcus faecalis

E-test, Vitek 2, MicroScan, agar dilution, and disk diffusion were compared for detection of decreased linezolid susceptibility due to 23S rRNA gene G2576T mutation among 32 clinical Enterococcus strains initially reported as intermediate or resistant by E-test alone or Vitek 2 confirmed by E-test. Agar and broth dilution methods were in concordance with PCR detection of the mutation, and disk diffusion was somewhat less sensitive but equally specific.     

Evaluation of GeneOhm VanR and Xpert vanA/vanB molecular assays for the rapid detection of vancomycin-resistant enterococci

Rapid diagnosis is critical for treating and preventing infections due to vancomycin-resistant enterococci (VRE). We assessed the performance of GeneOhm VanR and Xpert vanA/vanB assays that detect vanA and vanB, the two most important genes encoding vancomycin resistance, utilizing 50 stool samples from renal dialysis patients, as well as well-characterized VRE strains. Stool samples were screened for the presence of VRE by culture followed by polymerase chain reaction (PCR) for the detection of van genes in isolates. Furthermore, the direct detection of vanA/vanB from aerobically and anaerobically pre-enriched stools was performed by in-house PCR sequencing. GeneOhm was less sensitive (43.5% vs. 73.9%) and more specific (100% vs. 92.6%) than Xpert in detecting vanA from stool samples. vanB detection by GeneOhm was more sensitive than Xpert (100% vs. 87.5%), but equally non-specific (20.6% vs. 14.7%). A further estimation on log-serial dilutions of VRE strains showed that Xpert was more sensitive at detecting VRE at low concentrations (10–100 colony forming units [cfu]/ml).     

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

Background/PurposeTo evaluate the ability of quadruple Taqman probe real-time PCR to the detection of vanA, vanB and vanM in enterococcal isolates.MethodsA total of 343 strains, including 253 vancomycin-resistant enterococcus (VRE) strains and 90 non-VRE strains, were tested by both quadruple Taqman probe real-time PCR and gel-based PCR assay.ResultsWhen differentiating among three genotypes of vanA, vanB and vanM in VRE strains, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic accuracy and consistency of the quadruple Taqman probe real-time PCR were all 100%. Minimum.Inhibitory concentration (MIC) results showed that there was a wide MIC range of vancomycin and teicoplanin for the strains that harboring vanA/vanM gene respectively or harboring vanA and vanM genes simultaneously. However, the VRE strains with vanB genotype all were sensitive to teicoplanin.ConclusionConsidering the excellent PPV and low NPV, real-time PCR would be useful to monitor VRE-colonized or infected patients. However, further evaluation of the assay's performance in the clinical specimens is required, especially when considering that high level of PCR inhibitors present in these samples.     

Comparison of the new MicroScan Pos MIC Type 6 panel and AMS-Vitek Gram Positive Susceptibility Card (GPS-TA) for detection of high-level aminoglycoside resistance in Enterococcus species.

We compared the MicroScan Pos MIC Type 6 panel and AMS-Vitek Gram Positive Susceptibility Card (GPS-TA) to agar dilution screen plates for the detection of high-level aminoglycoside resistance in 182 enterococcal isolates. The specificity of the two commercial systems was 100%, with the exception of one susceptible isolate found to be streptomycin resistant by the Vitek system. The MicroScan and Vitek systems had comparable sensitivities for the detection of gentamicin resistance (90 and 95% respectively) and streptomycin resistance (85 and 78%, respectively). These results suggest that screening tests such as agar dilution screen plates, broth dilution, or disk diffusion should continue to be used to detect high-level gentamicin and streptomycin resistance.     

Factors influencing determination of high-level aminoglycoside resistance in Enterococcus faecalis.

The ability of seven methods to detect high-level gentamicin (58 strains) and streptomycin resistance (56 strains) among 107 Enterococcus faecalis isolates was investigated at the University of Chicago Medical Center and the University of Nebraska Medical Center. Methods included a standard agar screen plate, high-content disk diffusion, Remel (Lenexa, Kans.) EF Synergy Quad plates, standard microdilution panels prepared in house, Pasco MIC Gram-Positive panels (Difco Laboratories, Detroit, Mich.), MicroScan MIC Type 5 dry panels (Baxter Healthcare Corp., MicroScan Div., West Sacramento, Calif.), and Vitek GPS-TA cards (Vitek Systems Inc., Hazelwood, Mo.). Results indicating false resistance were not obtained by any method, and there was 100% agreement between the results of the disk diffusion and standard agar screen methods. Prolonging incubation from 24 to 48 h increased resistance detection for both agar and microdilution screens. EF Synergy Quad plates inoculated with micropipettes detected 100% of the streptomycin- and gentamicin-resistant isolates. Resistance detection for streptomycin and gentamicin, respectively, was 93 and 96% by standard microdilution, 93 and 98% by Pasco panels, 88 and 89% by MicroScan panels, and 88 and 91% by Vitek GPS-TA cards. False susceptibility occurred more frequently with streptomycin-resistant isolates than it did with gentamicin-resistant strains and appeared to be strain related in some instances. The use of an increased inoculum size enhanced resistance detection with these strains, but it complicated interpretation of results and led to the selection of streptomycin-resistant mutants. Until results of further studies delineate optimum test conditions, a delay in the final interpretation of agar and microdilution screen results until 48 h for isolates showing no or light growth at 24 h may help to minimize the occurrence of false susceptibility reporting.     

Evaluation of Screening and Commercial Methods for Detection of Methicillin Resistance in Coagulase-Negative Staphylococci

The National Committee for Clinical Laboratory Standards recommends 48 h of incubation by the oxacillin salt agar screen (OSAS) method for the detection of methicillin-resistant coagulase-negative staphylococci (CoNS). An earlier identification of methicillin resistance is desirable. The time to detection of the mecA gene by PCR was compared with the times to detection by OSAS, by the oxacillin disk diffusion (ODD) method, and with MicroScan Gram Positive Combo type 6 panels (MicroScan Inc. Sacramento, Calif.) and Vitek GPS-SA cards (bioMérieux Vitek Inc., Hazelwood, Mo.). The combination of the Vitek card and the ODD method detected 92 of 99 methicillin-resistant strains of CoNS at 24 h; however, 6 mecA-positive strains were phenotypically methicillin susceptible. We conclude that most methicillin-resistant CoNS can be detected and the results can be reported after overnight incubation by a combination of methods.     

Performance of eight methods, including two new rapid methods, for detection of oxacillin resistance in a challenge set of Staphylococcus aureus organisms

Using a set of 55 Staphylococcus aureus challenge organisms, we evaluated six routine methods (broth microdilution, disk diffusion, oxacillin agar screen, MicroScan conventional panels, MicroScan rapid panels, and Vitek cards) currently used in many clinical laboratories and two new rapid methods, Velogene and the MRSA-Screen, that require less than a day to determine the susceptibility of S. aureus to oxacillin. The methods were evaluated by using the presence of the mecA gene, as detected by PCR, as the "gold standard." The strains included 19 mecA-positive heterogeneously resistant strains of expression class 1 or 2 (demonstrating oxacillin MICs of 4 to >16 microg/ml) and 36 mecA-negative strains. The oxacillin MICs of the latter strains were 0.25 to 4 microg/ml when tested by broth microdilution with 2% NaCl-supplemented cation-adjusted Mueller-Hinton broth as specified by the NCCLS. However, when tested by agar dilution with 4% salt (the conditions used in the oxacillin agar screen method), the oxacillin MICs of 16 of the mecA-negative strains increased to 4 to 8 microg/ml. On initial testing, the percentages of correct results (% sensitivity/% specificity) were as follows: broth microdilution, 100/100; Velogene, 100/100; Vitek, 95/97; oxacillin agar screen, 90/92; disk diffusion, 100/89; MicroScan rapid panels, 90/86; MRSA-Screen, 90/100; and MicroScan conventional, 74/97. The MRSA-Screen sensitivity improved to 100% if agglutination reactions were read at 15 min. Repeat testing improved the performance of some but not all of the systems.     

Prevalence of Vancomycin-Resistant Enterococci in Europe

 The aim of the present study was to determine the prevalence of vancomycin-resistant enterococci (VRE) in Europe. Overall, 49 laboratories in 27 countries collected 4,208 clinical isolates of enterococci. Species identification, susceptibility testing, and van gene determination by polymerase chain reaction were performed in a central laboratory. Overall, 18 vanA and 5 vanB isolates of VRE were found. The prevalence of vanA VRE was highest in the UK (2.7%), while the prevalence of vanB VRE was highest in Slovenia (2%). Most vanA and vanB VRE were identified as Enterococcus faecium. Most VRE isolates originated from the patient's urogenital tract, skin, or digestive tract. VRE were equally distributed among clinical departments, with no clear preponderance in any single patient group. A total of 71 isolates containing the vanC gene were identified. The prevalence of vanC VRE was highest in Latvia and Turkey, where rates were 14.3 and 11.7%, respectively. Two-thirds of these isolates were identified as Enterococcus gallinarum and one-third as Enterococcus casseliflavus; the majority of these isolates were cultured from feces. Almost all isolates were obtained from hospitalized patients, mostly children. The highest prevalence of high-level gentamicin-resistant enterococci was seen in Turkey and Greece. In general, the distribution of this resistance type seemed unrelated to the occurrence of VRE. The prevalence of vanA/vanB VRE in Europe is still low; the majority of the VRE isolates exhibit the vanC genotype and colonize the gastrointestinal tract of hospitalized children.     

Comparative study of selective chromogenic (chromID VRE) and bile esculin agars for isolation and identification of vanB-containing vancomycin-resistant enterococci from feces and rectal swabs

The new chromogenic agar chromID VRE (cIDVRE; bioMérieux) was compared with bile esculin agar (BD) containing 6 mg/liter vancomycin for the detection of colonization with vanB-containing vancomycin-resistant enterococci (VRE). At 48 h of incubation, the results obtained with both media were comparable. However, cIDVRE detected significantly more VRE at 24 h (39.3% versus 21.3%, P = 0.003), and its use may facilitate the timely implementation of infection control procedures.     

Performance Characteristics of the Cepheid Xpert vanA Assay for Rapid Identification of Patients at High Risk for Carriage of Vancomycin-Resistant Enterococci

We compared the performance characteristics of culture and the Cepheid Xpert vanA assay for routine surveillance of vancomycin-resistant enterococci (VRE) from rectal swabs in patients at high risk for VRE carriage. The Cepheid Xpert vanA assay had a limit of detection of 100 CFU/ml and correctly detected 101 well-characterized clinical VRE isolates with no cross-reactivity in 27 non-VRE and related culture isolates. The clinical sensitivity, specificity, positive predictive value, and negative predictive value of the Xpert vanA PCR assay were 100%, 96.9%, 91.3%, and 100%, respectively, when tested on 300 consecutively collected rectal swabs. This assay provides excellent predictive values for prompt identification of VRE-colonized patients in hospitals with relatively high rates of VRE carriage.     

Characterization of an Enterococcus gallinarum Isolate Carrying a Dual vanA and vanB Cassette

The ability of vancomycin resistance determinants to be horizontally transferred within enterococci species is a concern. Identification and characterization of vancomycin-resistant enterococci (VRE) in a clinical isolate have a significant impact on infection control practices. In this study, we describe a clinical isolate of Enterococcus gallinarum exhibiting high-level resistance to vancomycin and teicoplanin. The genetic characterization of this isolate showed the presence of vanA and vanB genes in addition to the naturally carried vanC gene. vanA was identified on pA6981, a 35,608-bp circular plasmid with significant homology to plasmid pS177. The vanB operon was integrated into the bacterial chromosome and showed a high level of homology to previously reported Tn1549 and Tn5382. To the best of our knowledge, this is the first report of E. gallinarum carrying both vanA and vanB operons, indicating the importance of identifying the vancomycin resistance mechanism in non-E. faecium and non-E. faecalis enterococcal species.     

Vancomycin-resistant Enterococcus faecium and the emergence of new sequence types associated with hospital infection

Enterococcus faecium is a major species in infections by vancomycin-resistant enterococci (VRE). New variants of the pathogen have emerged and become dominant in healthcare settings. Two such examples, vanB ST796 and vanA ST1421 sequence types, originally arose in Australia and proceeded to cause VRE outbreaks in other countries. Of concern is the detection in Europe of vancomycin variable enterococci (VVE) belonging to ST1421 that exhibit a vancomycin-susceptible phenotype but can revert to resistant in the presence of vancomycin. The recent application of genome sequencing for increasing our understanding of the evolution and spread of VRE is also explored here.     

Comparison of Agar Dilution, Disk Diffusion, MicroScan, and Vitek Antimicrobial Susceptibility Testing Methods to Broth Microdilution for Detection of Fluoroquinolone-Resistant Isolates of the Family Enterobacteriaceae

Fluoroquinolone resistance appears to be increasing in many species of bacteria, particularly in those causing nosocomial infections. However, the accuracy of some antimicrobial susceptibility testing methods for detecting fluoroquinolone resistance remains uncertain. Therefore, we compared the accuracy of the results of agar dilution, disk diffusion, MicroScan Walk Away Neg Combo 15 conventional panels, and Vitek GNS-F7 cards to the accuracy of the results of the broth microdilution reference method for detection of ciprofloxacin and ofloxacin resistance in 195 clinical isolates of the family Enterobacteriaceae collected from six U.S. hospitals for a national surveillance project (Project ICARE [Intensive Care Antimicrobial Resistance Epidemiology]). For ciprofloxacin, very major error rates were 0% (disk diffusion and MicroScan), 0.9% (agar dilution), and 2.7% (Vitek), while major error rates ranged from 0% (agar dilution) to 3.7% (MicroScan and Vitek). Minor error rates ranged from 12.3% (agar dilution) to 20.5% (MicroScan). For ofloxacin, no very major errors were observed, and major errors were noted only with MicroScan (3.7% major error rate). Minor error rates ranged from 8.2% (agar dilution) to 18.5% (Vitek). Minor errors for all methods were substantially reduced when results with MICs within ±1 dilution of the broth microdilution reference MIC were excluded from analysis. However, the high number of minor errors by all test systems remains a concern.     

Molecular characterization of vancomycin-resistant enterococci isolated from a hospital in Beijing,China

ObjectiveTo investigate the occurrence of vancomycin-resistant enterococci (VRE) isolated from patients in Peking Union Medical College Hospital, Beijing, China from 2011 to 2017, and to evaluate their resistance mechanisms and genetic relatedness.MethodsAll isolates were identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). Antibiotic susceptibility testing was performed using the broth microdilution method. Molecular characterization were detected by PCR and sequencing. Genotyping of VRE isolates was performed by multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) analysis. Virulence genes were detected by multiplex PCR.ResultsA total of 87 consecutive VRE were collected, including 84 isolates of vancomycin resistant Enterococcus faecium (VREfm) and 3 isolates of Enterococcus faecalis (VREfs). Urine (40.2%, 35/87) and blood (17.2%, 15/87) were the most commonly specimens. All VREfm isolates were resistant to ampicillin, and were susceptible to daptomycin, linezolid and tigecycline. The resistant rate of teicoplanin was 47.6%. All of the VREfm isolates carried the vanA gene, no isolates carried vanB. 11.9% (10/84) VREfm isolates carried both vanA and vanM. Among them, 76.2% (64/84) and 66.7% (56/84) carried esp and hyl, respectively. The 3 vancomycin resistant E. faecalis (VREfs) isolates were varied, and only one carried vanB. A total of 3 and 18 STs were detected among VREfs and VREfm strains, respectively. PFGE results indicated a genetic diversity among VREfm isolates.ConclusionThis study confirms that VREfm isolates associated with ST78 were the main epidemic lineage responsible for nosocomial infections in China, as were also observed in other nations worldwide.