Utility of direct, real-time PCR in the management of a nosocomial outbreak of vancomycin-resistant Enterococcus faecium (vanB genotype)

Monitoring of bacterial pathogens at workplaces in power plant using biochemical and molecular methods

Purpose

The aim of this study was to characterize the ways of spreading of the most common bacterial species isolated from workers as well as from the air and raw materials at the workplaces in power plant utilizing biomass sources. To monitor microbial transmission and identify the source of contamination in the working environment, a combination of molecular and biochemical methods was applied.

Methods

The study was carried out at workplaces in power plant utilizes biomass as a main fuel source. At each of the studied workplaces, bioaerosol particles were collected on sterile Teflon filters using personal conical inhalable samplers (CIS), and biomass samples (straw pellets and briquettes, corn briquettes, sunflower pellets and wood chips) were directly taken from their storage places. Simultaneously with that, the swab samples from the hands of ten workers and their used respiratory masks (of FFP2 class) were also collected after the work shift to evaluate individual workers’ microbial contamination. In all collected samples, total bacterial concentrations were assessed and the most common microbial isolates were identified to the species level using both biochemical (API tests) and molecular polymerase chain reaction (PCR), followed by random amplification of polymorphic DNA (RAPD) typing methods.

Results

The mean concentrations of culturable bacteria in the air and in biomass samples at the studied workplaces were high, i.e. 1.2 × 10⁶cfu/m³ and 3.8 × 10⁴cfu/g, respectively. The number of bacteria in the swab and mask samples also reached a high level of 1.4 × 10⁴ cfu/ml and 1.9 × 10³ cfu/cm², respectively. Among the most frequently isolated microorganisms from all types of samples were Gram-positive bacteria of the genus Bacillus and Staphylococcus xylosus. 37 bacterial strains belonging to the genus Bacillus (B. licheniformis 8, B. pumilus 15 and B. subtilis 4) and Staphylococcus (10) were genotyped by the RAPD-PCR method. Based on RAPD-PCR analyses, the genomic similarity among 19 Bacillus strains isolated from biomass, air, protective mask and hand samples as well as 6 S. xylosus strains isolated from air, mask and hand samples exceeded 80%.

Conclusion

This study demonstrated that biomass is the primary source of bacteria at power plant workplaces. These results also revealed that biomass-associated bacteria can be easily transferred to workers’ hands and mask during their routine activities. To improve health protection at the workplaces, adequate training courses on hand hygiene and how to use and remove respiratory masks correctly for workers should be introduced as a key element of the prevention strategy. From the occupational point of view, the PCR-based methods seem to be an efficient tool for a fast and precise typing of bacterial strains isolated from different sources in the occupational environment. Such methods may help to implement appropriate prophylactic procedures and minimize transmission of infectious agents at workplaces.

Outbreaks of Vancomycin-Resistant Enterococci in Hospital Settings: A Systematic Review and Calculation of the Basic Reproductive Number

BACKGROUND

Vancomycin-resistant enterococci (VRE) have spread worldwide.

OBJECTIVE

To systematically review VRE outbreaks and estimate the pooled basic reproductive rate (R0) of VRE.

METHODS

Eligible studies criteria were (1) published within 10 years, (2) report outbreak details, (3) involve 1 center, (4) estimate epidemic duration, and (5) concern adults. Descriptive analysis included number of index cases, secondary cases, and screened patients; infection control measures; and definition of contact patients. R0 was estimated by the equation R0=(ln2) D/td+1, with D as the generation time and td as the doubling time.

RESULTS

Thirteen VRE outbreaks were retained from 180 articles and, among them, 10 were kept for R0 calculation. The mean (range) number of index cases was 2.3 (1–8) and the mean (range) number of secondary cases was 15 (3–56). The mean (range) number of screened patients was 174 (32–509), with pooled VRE prevalence of 5.4% (95% CI, 4.5%–6.3%). Contact precautions were reported in 12 studies (92%), wards were closed in 7 (54%), with cohorting in 6 (46%). Two major screening policies were implemented: (1) a surveillance program in the unit or hospital (7 studies [54%]) and (2) screening of selected contact patients (6 studies [46%]). The pooled R0 of VRE was 1.32 (interquartile range, 1.03–1.46).

CONCLUSION

We discerned considerable heterogeneity in screening policies during VRE outbreaks. Pooled R0 was higher than 1, confirming the epidemic nature of VRE.

Infect. Control Hosp. Epidemiol. 2016;37(3):289–394

Rapid identification of pathogens using molecular techniques

Real-time PCR is the traditional face of nucleic acid detection in the diagnostic microbiology laboratory and is now generally regarded as robust enough to be widely adopted. Methods based on nucleic acid detection of this type are bringing increased accuracy to diagnosis in areas where culture is difficult and/or expensive, and these methods are often effective partners to other rapid molecular diagnostic tools such as matrix-assisted laser desorption ionisation-time of flight mass spectrometry (MALDI-TOF MS). This change in practice has particularly affected the recognition of viruses and fastidious or antibiotic-exposed bacteria, but has been also shown to be effective in the recognition of troublesome or specialised phenotypes such as antiviral resistance and transmissible antibiotic resistance in the Enterobacteriaceae. Quantitation and high-intensity sequencing (of multiple whole genomes) has brought new opportunities as well as new challenges to the microbiology community. Diagnostic microbiologists currently training might be expected to deal less with the culture-based techniques of the last half-century than with the high-volume data and complex analyses of the next.

French recommendations for the prevention of 'emerging extensively drug-resistant bacteria' (eXDR) cross-transmission

Controlling the spread of multi- or extensively drug-resistant bacteria (MDR or XDR) includes a dual strategy for reducing antibiotic prescriptions and preventing their spread from patient carriers. Standard precautions are applicable to all health professionals caring for any patients; additional barrier precautions (isolation) are recommended for patients carrying transmissible infectious diseases or MDR bacteria in sporadic or epidemic situations. Moreover, additional precautions may be required for populations at particular risk of infection or colonization by emerging XDR (eXDR), defined in our country as carbapenemase-producing Enterobacteriaceae and vancomycin-resistant enterococci. Our ability to detect and identify eXDR carriers early and ensure their follow-up, through effective communication between all those involved, is a significant challenge for controlling their spread. Thus, the French High Committee for Public Health has updated and standardized all French existing recommendations concerning the prevention of the cross-transmission of these bacteria, and these recommendations are summarized in this review. The recommendations are based on scientific and operational knowledge up to 2013. Different preventive strategies are recommended for patients found to be carrying eXDR and those who are considered to be at risk of having eXDR because of a history of contact. The local context, the experience of the infection control team, the different times at which detection of eXDR takes place (during admission, hospitalization, etc.) and the epidemiological situation (sporadic cases, clusters, outbreaks, widespread epidemic) must be included in risk assessments that in turn inform the control measures that should be applied in each clinical circumstance.

Zero prevalence of vancomycin-resistant enterococci among Swedish preschool children

OBJECTIVES

Enterococci are a natural part of the bacterial flora of humans, animals, and insects and are frequently found in the community. Vancomycin-resistant enterococci (VRE) have emerged as a growing problem, associated with high morbidity and mortality. The aim of this study was to investigate the prevalence of VRE among healthy Swedish preschool children and ascertain whether they constitute a reservoir for the bacteria.

METHODS

In total, 313 individual diapers were collected from preschools in Uppsala, Sweden. Fecal samples were screened by analyzing the color change in a broth followed by polymerase chain reaction for vanA and vanB genes, which are associated with vancomycin resistance.

RESULTS

Neither vanA nor vanB genes could be detected from the samples.

CONCLUSIONS

Preschool children in Uppsala do not constitute a reservoir for VRE. The zero prevalence is consistent with the overall decline in VRE prevalence in Sweden during the last years.

Real-time PCR as a diagnostic tool for bacterial diseases

In recent years, quantitative real-time PCR tests have been extensively developed in clinical microbiology laboratories for routine diagnosis of infectious diseases, particularly bacterial diseases. This molecular tool is well-suited for the rapid detection of bacteria directly in clinical specimens, allowing early, sensitive and specific laboratory confirmation of related diseases. It is particularly suitable for the diagnosis of infections caused by fastidious growth species, and the number of these pathogens has increased recently. This method also allows a rapid assessment of the presence of antibiotic resistance genes or gene mutations. Although this genetic approach is not always predictive of phenotypic resistances, in specific situations it may help to optimize the therapeutic management of patients. Finally, an approach combining the detection of pathogens, their mechanisms of antibiotic resistance, their virulence factors and bacterial load in clinical samples could lead to profound changes in the care of these infected patients.

Comparison of real-time PCR and a microimmunofluorescence serological assay for detection of chlamydophila pneumoniae infection in an outbreak investigation

We assessed the performance of a recently validated real-time PCR assay and a commercially available microimmunofluorescence serologic test for the detection of Chlamydophila pneumoniae infection during an outbreak. Evaluation of specimens from 137 individuals suggests that real-time PCR holds greater utility as a diagnostic tool for early C. pneumoniae detection.

Diagnostic accuracy of the Cepheid GeneXpert vanA/vanB assay ver. 1.0 to detect the vanA and vanB vancomycin resistance genes in Enterococcus from perianal specimens

Rapid detection of vancomycin-resistant enterococci (VRE) carriers could be useful to health care facilities to minimize transmission. To that end, we compared the performance of the Cepheid GeneXpert vanA/vanB assay with that of direct and broth-enriched culture methods for detection of VRE from perianal swabs. Enterococci were cultivated on Enterococcosel™ agar with 8 μg/mL vancomycin, Bile Esculin Azide Agar with 6 μg/mL vancomycin, and Bile Esculin Azide Enterococcosel Broth. Compared to the reference standard (combination of direct agar plating, broth-enriched culture, and clinical chart review), the sensitivity, specificity, positive predictive value, and negative predictive value of the vanA/vanB assay were 96.4%, 93.0%, 92.0%, and 96.9%, respectively (n=184). The 95% limit of detection was 100 colony-forming units (CFU)/mL for vanA and 114 CFU/mL for vanB. In summary, the GeneXpert vanA/vanB assay is a rapid and accurate method to identify vanA/vanB-colonized patients for VRE screening programs that use perianal swab specimens.

Real time PCR for the rapid detection of vanA gene in surface waters and aquatic macrophyte by molecular beacon probe

Enterococci serve as an "indicator" of fecal contamination for recreational water quality. The vancomycin-resistant-enterococci (VRE) are emerging environmental contaminants in the surface waters. The aim ofthis study wasto develop a rapid and specific molecular beacon probe (MBP)-based real-time PCR assay for detection of vanA gene in surface waters and aquatic macrophyte. The limit of detection (LOD) of the MBP assay was 1 CFU/mL of VRE [r = 0.943; PCR efficiency = 99.7%] in 2-fold dilution format within 2.5 h and demonstrated high specificityfor environmental enterococci isolates exhibiting VanA phenotype (n=25). VRE were detected from downstream surface waters of the rivers impacted by point sources of pollution and recreational activities.The probe detected vanA gene in rootmat associated microbiota of E. crassipes (Mart) Solms. an aquatic nuisance weed, at eutrophic sites of the surface waters (ANOVA p < 0.001). In addition, the assay enabled detection of otherwise nondetectable vanA gene concentration in the upstream sites of two Indian rivers (Student's ttest p < 0.001). The MBP assay developed can be used for sensitive and rapid detection of VRE in surface waters and identification of nonpoint sources of pollution for implementation of preventive measures to protect human health.