Accuracy and potential usefulness of triplex real-time PCR for improving antibiotic treatment of patients with blood cultures showing clustered gram-positive cocci on direct smears

Rapid separation of bacteria from primary nasal samples using inertial microfluidics

Microbial populations play a crucial role in human health and the development of many diseases. These diseases often arise from the explosive proliferation of opportunistic bacteria, such as those in the nasal cavity. Recently, there have been increases in the prevalence of these opportunistic pathogens displaying antibiotic resistance. Thus, the study of the nasal microbiota and its bacterial diversity is critical in understanding pathogenesis and developing microbial-based therapies for well-known and emerging diseases. However, the isolation and analysis of these populations for clinical study complicates the already challenging task of identifying and profiling potentially harmful bacteria. Existing methods are limited by low sample throughput, expensive labeling, and low recovery of bacteria with ineffective removal of cells and debris. In this study, we propose a novel microfluidic channel with a zigzag configuration for enhanced isolation and detection of bacteria from human clinical nasal swabs. This microfluidic zigzag channel separates the bacteria from epithelial cells and debris by size differential focusing. As such, pure bacterial cell fractions devoid of large contaminating debris or epithelial cells are obtained. DNA sequencing performed on the separated bacteria defines the diversity and species present. This novel method of bacterial separation is simple, robust, rapid, and cost-effective and has the potential to be used for the rapid identification of bacterial cell populations from clinical samples.

Sankey diagrams can clarify 'evidence attrition': A systematic review and meta-analysis of the effectiveness of rapid diagnostic tests for antimicrobial resistance

OBJECTIVES

To demonstrate, using the example of a new systematic review of rapid diagnostic tests, how Sankey diagrams, alongside the PRISMA guidelines, can (i) facilitate reporting of the quality of the evidence base and (ii) help assess evidence syntheses when studies use heterogeneous outcomes.

METHODS

Systematic review and meta-analysis of experimental and observational studies which included at least one prescribing or clinical outcome of RDTs in hospital in-patients. Sub-group analysis was used to assess heterogeneity in summary effect estimates. A Sankey diagram was then used to show the pattern and quality of evidence on RDT outcomes.

RESULTS

57 studies from 14 countries were included. The introduction of RDTs did not significantly reduce in-hospital mortality (RR 0.83, 95% CI 0.60 - 1.15) or length of stay (weighted mean difference = -0.36, 95% CI -1.67 to 0.96). There was high heterogeneity in outcomes.

CONCLUSION

There is no clear evidence that the routine use of RDTs for bacterial identification and antibiotic susceptibility testing improves clinical outcomes in hospital in-patients. Sankey diagrams may be a useful further way succinctly to present the pattern and quality of evidence in systematic reviews, especially when it is heterogeneous and not easily amenable to meta-analysis.

The Effect of Ferula assa-foetida L and Carum copticum Hydroalcoholic Extract on the Expression Levels of Staphylococcus aureus Genes Involved in Quorum Sensing

Background

Quorum sensing is a microbial cell-to-cell communication process. Quorum sensing bacteria produce and release extracellular messenger molecules called autoinducers. Gram-positive and Gram-negative, homoserine lactones, and oligopeptides are autoinducers used to communicate and regulate gene expression.

Objectives

The goal of this study was to assess the impact of subinhibitory concentrations of Ferula assa-foetida l oleo-gum resin and Carum copticum fruit on the expression of tst and hld genes of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) strains.

Methods

This analytical study was performed using standard strains of MRSA (ATCC 33591) and MSSA (ATCC 29213). Suspensions of MRSA and MSSA bacteria were incubated at 37°C for 7 and 16 hours in the presence of ethanol extracts from F. assa-foetida and C. copticum. The expression of the hld and tst genes was then assessed using the real-time PCR protocol and SYBR Green Master Mix. The data analysis was carried out using the 2^-ΔΔCT method.

Results

The hld gene expression (RNAIII) of MRSA after 7 and 16 hours of exposure to the sMIC of the F. assa-foetida extract showed a fold change of -1 and 0.08, respectively, in comparison with controls. After 7 and 16 hours of exposure to the sMIC of the C. copticum extract, the fold change was -0.23 and -0.27, respectively. After exposure to the sMIC of the C. copticum extract for 16 hours, the fold change in the expression of the tst (TSST-1) MSSA gene was 0.37 lower than that of the control sample.

Conclusions

The results indicate that sMICs of ethanol extracts from F. assa-foetida and C. copticum can be used to control the expression of virulence genes in pathogenic bacteria, such as MRSA and MSSA.

Impact of a Rapid Blood Culture Assay for Gram-Positive Identification and Detection of Resistance Markers in a Pediatric Hospital

CONTEXT

Molecular diagnostics allow for rapid identification and detection of resistance markers of bloodstream infection, with a potential for accelerated antimicrobial optimization and improved patient outcomes. Although the impact of rapid diagnosis has been reported, studies in pediatric patients are scarce.

OBJECTIVE

To determine the impact of a molecular blood-culture assay that identifies a broad-spectrum of pathogens and resistance markers in pediatric patients with gram-positive bloodstream infections.

DESIGN

Data on the time to antimicrobial optimization, the length of hospitalization, and the hospital cost following implementation of a rapid assay were prospectively collected and compared with corresponding preimplementation data.

RESULTS

There were 440 episodes from 383 patients included, 221 preimplementation episodes and 219 postimplementation episodes. Overall time to antimicrobial optimization was shortened by 12.5 hours (P = .006), 11.9 hours (P = .005) for bloodstream infections of Staphylococcus aureus specifically. Duration of antibiotics for those with probable blood-culture contamination with coagulase-negative staphylococci was reduced by 36.9 hours (P < .001). Median length of stay for patients admitted to general pediatric units was 1.5 days shorter (P = .04), and median hospital cost was $3757 (P = .03) less after implementation. For S aureus bloodstream infections, median length of stay and hospital cost were decreased by 5.6 days (P = .01) and $13,341 (P = .03), respectively.

CONCLUSIONS

Implementation of molecular assay for the detection of gram-positive pathogens and resistance markers significantly reduced time to identification and resistance detection, resulting in accelerated optimization of therapy, shorter length of stay, and decreased health care cost.

Rapid separation of bacteria from blood-review and outlook

The high morbidity and mortality rate of bloodstream infections involving antibiotic-resistant bacteria necessitate a rapid identification of the infectious organism and its resistance profile. Traditional methods based on culturing the blood typically require at least 24 h, and genetic amplification by PCR in the presence of blood components has been problematic. The rapid separation of bacteria from blood would facilitate their genetic identification by PCR or other methods so that the proper antibiotic regimen can quickly be selected for the septic patient. Microfluidic systems that separate bacteria from whole blood have been developed, but these are designed to process only microliter quantities of whole blood or only highly diluted blood. However, symptoms of clinical blood infections can be manifest with bacterial burdens perhaps as low as 10 CFU/mL, and thus milliliter quantities of blood must be processed to collect enough bacteria for reliable genetic analysis. This review considers the advantages and shortcomings of various methods to separate bacteria from blood, with emphasis on techniques that can be done in less than 10 min on milliliter-quantities of whole blood. These techniques include filtration, screening, centrifugation, sedimentation, hydrodynamic focusing, chemical capture on surfaces or beads, field-flow fractionation, and dielectrophoresis. Techniques with the most promise include screening, sedimentation, and magnetic bead capture, as they allow large quantities of blood to be processed quickly. Some microfluidic techniques can be scaled up. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:823-839, 2016.

Impact of the multiplex polymerase chain reaction in culture-positive samples on appropriate antibiotic use in patients with staphylococcal bacteremia

Rapid identification of the microorganisms in patients with bacteremia may be useful in clinical practice. We evaluated the impact of the multiplex polymerase chain reaction (PCR) on appropriate antibiotic use for patients with gram-positive cocci cluster (GPCC) bacteremia. We divided the GPCC bacteremia cases into a pre-PCR group (2010-2011) and a post-PCR group (2012-2013). A total 664 cases were included in the pre-PCR group; and 570, in the post-PCR group. In methicillin-susceptible Staphylococcus aureus (MSSA) cases, optimal antibiotics were administered earlier in the post-PCR group (77.4h versus 42.6h, P=0.035). Although the proportions of glycopeptide exposure did not differ (54.7% versus 56.7%, P=0.799), the duration of exposure decreased (69.6h versus 30.7h, P=0.004). In methicillin-resistant S. aureus cases, the time to optimal antibiotics administration did not differ (45.4h versus 43.7h, P=0.275). Multiplex PCR test significantly improved the early initiation of optimal antibiotics in MSSA bacteremia and reduced the unnecessary glycopeptide exposure.

Comparative dynamics of the emergence of fluoroquinolone resistance in staphylococci from the nasal microbiota of patients treated with fluoroquinolones according to their environment

Fluoroquinolone-resistant staphylococci (FQRS) are primarily selected in the nasal microbiota during fluoroquinolone (FQ) treatment. To gain insight into the dynamics of the emergence of FQRS, 49 hospitalised patients (HPs) and 62 community patients (CPs) treated with FQs were studied. Nasal swabs were collected before (T0), at the end of (T1) and 1 month after (T2) FQ treatment. FQRS were identified by mass spectrometry. Antibiotic resistance was determined. Pre- and post-exposure staphylococci populations were compared phenotypically and by MLST to determine the origin of FQRS. At T0, 33/49 HPs (67%) and 24/62 CPs (39%) carried FQRS (OR=3.3, 95% CI: 1.4-7.9; P<0.001). Among patients with no FQRS at T0, 15/16 HPs (94%) and 16/38 CPs (42%) had FQRS detected at T1 and/or T2 (OR=19.6, 95% CI: 2.5-902; P<0.001). Among FQRS having emerged, co-resistance to meticillin was detected in 87% and 82% of HPs and CPs, respectively. No selection of resistance emerging from the initial microbiota was evidenced. FQRS showed decreased species diversity in favour of Staphylococcus haemolyticus and Staphylococcus epidermidis. As a consequence of FQ treatment, acquisition of FQRS in the nasal microbiota is frequent in the community and almost inevitable in hospitals. Acquisition from extranasal sites prevails. A restriction in species diversity in favour of more pathogenic and resistant species occurs. This highlights the major impact of FQ treatment on nasal microbiota, the role of the ecological environment in the emergence of FQRS, and the high-risk of dissemination of resistant staphylococci.

Rapid amplification/detection of nucleic acid targets utilizing a HDA/thin film biosensor

Thin film biosensors exploit a flat, optically coated silicon-based surface whereupon formation of nucleic acid hybrids are enzymatically transduced in a molecular thin film that can be detected by the unaided human eye under white light. While the limit of sensitivity for detection of nucleic acid targets is at sub-attomole levels (60 000 copies) many clinical specimens containing bacterial pathogens have much lower levels of analyte present. Herein, we describe a platform, termed HDA/thin film biosensor, which performs helicase-dependant nucleic acid amplification on a thin film biosensor surface to improve the limit of sensitivity to 10 copies of the mecA gene present in methicillin-resistant strains of Staphylococcus. As double-stranded DNA is unwound by helicase it was either bound by solution-phase DNA primers to be copied by DNA polymerase or hybridized to surface immobilized probe on the thin film biosensor surface to be detected. Herein, we show that amplification reactions on the thin film biosensor are equivalent to in standard thin wall tubes, with detection at the limit of sensitivity of the assay occurring after 30 minutes of incubation time. Further we validate the approach by detecting the presence of the mecA gene in methicillin-resistant Staphylococcus aureus (MRSA) from positive blood culture aliquots with high specificity (signal/noise ratio of 105).

Molecular detection of antibiotic resistance genes from positive blood cultures

Rapid detection of the bacterial causative agent causing sepsis must be coupled with rapid identification of the antibiotic resistant mechanism that the pathogen might possess. Real-time PCR (qPCR)-based assays have been extensively utilized in the clinical microbiology field as diagnostic tools for the rapid detection of specific nucleic acid (NA) targets. In this chapter, we will discuss the technical aspects of using an internally controlled qPCR assay for the rapid detection of Klebsiella pneumoniae carbapenemase gene (bla KPC) in positive Bactec blood culture bottles. The multiplex qPCR (bla KPC/RNase P) utilizes specific primers and probes for the detection of the bacterial carbapenem resistance mechanism, bla KPC gene, and the internal control RNase P. The internal control of the qPCR assay is vital for detecting any inhibitors that are well known to be present in the blood culture bottles. Rapid detection of the antibiotic resistant mechanism present in the bacterial pathogen causing sepsis can help in better managing patients' infection.

Association of targeted multiplex PCR with resequencing microarray for the detection of multiple respiratory pathogens

A large number of viral and bacterial organisms are responsible for community-acquired pneumonia (CAP) which contributes to substantial burden on health management. A new resequencing microarray (RPM-IVDC1) associated with targeted multiplex PCR was recently developed and validated for multiple respiratory viruses detection and discrimination. In this study, we evaluated the capability of RPM-IVDC1 for simultaneous identification of multiple viral and bacterial organisms. The nasopharyngeal aspirates (NPAs) of 110 consecutive CAP patients, aged from 1 month to 96 years old, were collected from five distinct general hospitals in Beijing during 1-year period. The samples were subjected to the RPM-IVDC1 established protocol as compared to a real-time PCR (qRT-PCR), which was used as standard. The results of virus detection were consistent with those previously described. A total of 37 of Streptococcus pneumoniae, 14 of Haemophilus influenzae, 10 of Mycoplasma pneumoniae, two of Klebsiella pneumoniae and one of Moraxella catarrhalis were detected by RPM-IVDC1. The sensitivities and specificities were compared with those of qRT-PCR for S. pneumoniae (100, 100%, respectively), H. influenzae (92.3, 97.9%, respectively), M. pneumoniae (69.2, 99.0%, respectively), K. pneumoniae (100, 100%, respectively), and M. catarrhalis (100, 100%, respectively). Additional 22 of Streptococcus spp., 24 of Haemophilus spp. and 16 of Neisseria spp. were identified. In addition, methicillin-resistant and carbapenemases allele were also found in nine of Staphylococcus spp. and one of K. pneumoniae, respectively. These results demonstrated the capability of RPM-IVDC1 for simultaneous detection of broad-spectrum respiratory pathogens in complex backgrounds and the advantage of accessing to the actual sequences, showing great potential use of epidemic outbreak investigation. The detection results should be carefully interpreted when introducing this technique in the clinical diagnostics.

Hemodialysis Catheter-related Infection: Prophylaxis, Diagnosis and Treatment

Purpose

Infectious complications associated with central venous catheters (CVCs) are a major source of morbidity and mortality among hemodialysis (HD) patients. This review aims to discuss prevention, diagnosis criteria and management of CVC-related infections in HD patients.

Methods

We searched Medline for articles published in the last 10 years, with the keywords “catheter,” “hemodialysis,” “infection,” “treatment,” “diagnosis,” “prophylaxis” and “adults.” Only English language articles were reviewed. We reviewed prophylaxis and surveillance protocols, diagnosis criteria, including new molecular tools, and the management of catheter-related infections, including antibiotic regimen, empiric and according to causal agents, lock therapy, catheter salvage or removal choice and treatment of complications.

Results

To prevent infectious complications, first of all we need to avoid using catheters. If we need CVC, adoption of prophylaxis and surveillance protocols, and antibiotic ointment at the exit site reduce infectious complications. The diagnosis of CVC-related infections should be made with drainage and/or blood cultures. Empiric systemic antibiotics should cover Gram-positive and -negative microorganisms, and final regimen should be based on culture results. In selected cases, salvage of site, by CVC exchange over wire, or salvage of catheter, using antibiotic lock, under the cover of systemic antibiotics, could be attempted.

Conclusions

The best approach to prevent CVC-related infection would be to avoid the use of CVC. However, in patients for whom it is impossible, the adoption of adequate prophylaxis protocols, early diagnosis and effective treatment of infectious complications are essential to improve outcomes.

The accuracy of Gram stain of respiratory specimens in excluding Staphylococcus aureus in ventilator-associated pneumonia

OBJECTIVE

To evaluate the Gram stain of deep tracheal aspirate as a tool to direct empiric antibiotic therapy, and more specifically as a tool to exclude the need for empiric antibiotic coverage against Staphylococcus aureus in ventilator-associated pneumonia (VAP).

DESIGN

A prospective, single-center, observational, cohort study.

SETTING

All wards at a community hospital.

PATIENTS

Adult patients requiring mechanical ventilation, identified as having VAP in a 54-month prospective surveillance database.

INTERVENTIONS

Sampling of lower airway secretions by deep endotracheal aspiration was taken from each patient who developed VAP. Samples were sent immediately for Gram stain and qualitative bacterial cultures. Demographic and relevant clinical data were collected; Gram stain, culture, and antibiotic susceptibility results were documented; and outcome was followed prospectively.

MEASUREMENTS AND MAIN RESULTS

The analysis included 114 consecutive patients with 115 episodes of VAP from June 2007 to January 2012. Sensitivity of Gram stain compared with culture was 90.47% for gram-positive cocci, 69.6% for gram-negative rods, and 50% for sterile cultures. Specificity was 82.5%, 77.8%, and 79%, respectively. Negative predictive value was high for gram-positive cocci (97%) and sterile cultures (96%) but low for gram-negative rods (20%). Acinetobacter baumanii (45%) and Pseudomonas aeruginosa (38 %) were the prevailing isolates. S aureus was found in 18.3% of the patients. Most isolates were multiresistant.

CONCLUSIONS

Absence of gram-positive bacteria on Gram stain had a high negative predictive value. These data can be used to narrow the initial empiric antibiotic regimen and to avoid unnecessary exposure of patients to vancomycin and other antistaphyloccocal agents.

Emergence of the European ST80 clone of community-associated methicillin-resistant Staphylococcus aureus as a cause of healthcare-associated infections in Eastern Algeria

AIMS

The authors had for aim to assess whether an in-hospital spread of the European community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) clone was on-going in Annaba, Eastern Algeria.

MATERIAL AND METHODS

We carried out a molecular epidemiological study of S. aureus strains causing infections in 4 hospitals located in Annaba, between February and October 2010.

RESULTS

Our study revealed a very low healthcare-associated MRSA (HCA-MRSA) infection incidence rate of 0.34 per 1000 patient-days. However, the rates of HCA-MRSA strains (85/119) and CA-MRSA (7/29) among S. aureus strains are much higher than those found in France. The European CA-MRSA clone (clonal complex 80, Staphylococcal Cassette Chromosome mec IVc, spa type t044, lukS/F-PV-positive) accounted for 14.1% of all healthcare-associated (HCA) MRSA infections.

CONCLUSION

This study confirmed the emerging role of CA-MRSA as HCA pathogens in North-African Africa.

A cost-saving algorithm for rapid diagnosis of Staphylococcus aureus and susceptibility to oxacillin directly from positive blood culture bottles by combined testing with BinaxNOW® S. aureus and Xpert MRSA/SA Assay

We studied an algorithm combining 2 rapid methods to detect Staphylococcus aureus and its susceptibility to oxacillin directly from positive blood cultures; our goal was to reduce the cost of the procedure, while maintaining accuracy and a short turnaround time. A total of 581 blood cultures containing gram-positive cocci in clusters were tested by BinaxNOW® Staphylococcus aureus Test. Positive samples were further assessed by the Xpert MRSA/SA BC Assay. Phenotypic methods have identified coagulase-negative staphylococci in 505 samples and S. aureus in 76 samples, of which 51 were oxacillin sensitive and 25 were oxacillin resistant. Sensitivity and specificity of the BinaxNOW® Test were 92% and 99%, respectively, compared to the phenotypic method. The Xpert MRSA/SA BC Assay showed complete concordance with phenotypic identification and antimicrobial susceptibility results. The combined rapid assays produced results within 2 hours and reduced the cost by 75% compared with the Xpert MRSA/SA BC Assay if used alone on all blood bottles.

Bacteraemia due to meticillin-resistant Staphylococcus aureus carrying the mecC gene in a patient with urothelial carcinoma

We present a case of bacteraemia due to meticillin-resistant Staphylococcus aureus (MRSA) carrying the mecC gene. The susceptibility to meticillin of Staphylococcus aureus was investigated directly from one blood culture bottle using GenomEra MRSA/SA (Abacus Diagnostica Oy) test. This test identified S. aureus but the presence of the mecA gene result was negative, and the isolate was reported as meticillin-sensitive Staphylococcus aureus (MSSA). Susceptibility studies were done using VITEK 2 AST-P588 susceptibility cards (bioMérieux). The strain was identified as MRSA by the VITEK 2 system, although oxacillin MIC was low (0.5 µg ml(-1)). In view of these results, the isolate was tested for the presence of the mecC gene by a specific PCR and was verified as MRSA carrying mecC. The emergence of this new mecA homologue could have important consequences for the detection of MRSA when routine PCR methods are used as an identification method or provisional detection of MRSA, as in the case reported in this article, because S. aureus carrying the mecC gene will be wrongly diagnosed as meticillin susceptible. Negative results must be interpreted with caution and should be followed by conventional culture, and antimicrobial susceptibility testing or detection of mecC gene by a specific PCR.

Multiplex identification of gram-positive bacteria and resistance determinants directly from positive blood culture broths: evaluation of an automated microarray-based nucleic acid test

BACKGROUND

A multicenter study was conducted to evaluate the diagnostic accuracy (sensitivity and specificity) of the Verigene Gram-Positive Blood Culture Test (BC-GP) test to identify 12 Gram-positive bacterial gene targets and three genetic resistance determinants directly from positive blood culture broths containing Gram-positive bacteria.

METHODS AND FINDINGS

1,252 blood cultures containing Gram-positive bacteria were prospectively collected and tested at five clinical centers between April, 2011 and January, 2012. An additional 387 contrived blood cultures containing uncommon targets (e.g., Listeria spp., S. lugdunensis, vanB-positive Enterococci) were included to fully evaluate the performance of the BC-GP test. Sensitivity and specificity for the 12 specific genus or species targets identified by the BC-GP test ranged from 92.6%-100% and 95.4%-100%, respectively. Identification of the mecA gene in 599 cultures containing S. aureus or S. epidermidis was 98.6% sensitive and 94.3% specific compared to cefoxitin disk method. Identification of the vanA gene in 81 cultures containing Enterococcus faecium or E. faecalis was 100% sensitive and specific. Approximately 7.5% (87/1,157) of single-organism cultures contained Gram-positive bacteria not present on the BC-GP test panel. In 95 cultures containing multiple organisms the BC-GP test was in 71.6% (68/95) agreement with culture results. Retrospective analysis of 107 separate blood cultures demonstrated that identification of methicillin resistant S. aureus and vancomycin resistant Enterococcus spp. was completed an average of 41.8 to 42.4 h earlier using the BC-GP test compared to routine culture methods. The BC-GP test was unable to assign mecA to a specific organism in cultures containing more than one Staphylococcus isolate and does not identify common blood culture contaminants such as Micrococcus, Corynebacterium, and Bacillus.

CONCLUSIONS

The BC-GP test is a multiplex test capable of detecting most leading causes of Gram-positive bacterial blood stream infections as well as genetic markers of methicillin and vancomycin resistance directly from positive blood cultures.

Utility of PCR amplification and DNA microarray hybridization of 16S rDNA for rapid diagnosis of bacteremia associated with hematological diseases

OBJECTIVES

The rapid diagnosis of bacteremia is crucial for patient management including the choice of antimicrobial therapy, especially in cases of hematological disease, because neutropenia occurs frequently during antineoplastic chemotherapy or disease progression. We describe a rapid detection and identification system that uses universal PCR primers to amplify a variable region of bacterial 16S ribosomal DNA (rDNA), followed by DNA microarray hybridization.

METHODS

Probes for 72 microorganisms including most causal clinical pathogens were spotted onto a microarray plate. The DNA microarray and conventional methods of identification were applied to 335 cultures from patients with hematological diseases.

RESULTS

Forty-one samples (12.2%) tested positive by conventional blood culture test in a few days, while 40 cases (11.9%) were identified by the new method within 24 h. The sensitivity and specificity of this new method were 93% and 99%, respectively, compared with conventional blood culture testing.

CONCLUSIONS

PCR combined with a DNA microarray is useful for the management of febrile patients with hematological diseases.

Direct mecA polymerase chain reaction testing of blood culture bottles growing Gram-positive cocci and the clinical potential in optimizing antibiotic therapy for staphylococcal bacteremia

This study evaluated the performance of direct mecA polymerase chain reaction (PCR) from blood culture bottles growing Gram-positive cocci in clusters and its role in optimization of antibiotic therapy. A total of 266 blood cultures including 121 methicillin-resistant and 122 methicillin-susceptible Staphylococci were tested for mecA. Compared to phenotypic testing, the overall performance of direct mecA PCR was 99% for sensitivity, specificity, positive predictive value, and negative predictive value, respectively. Assessment of antibiotic therapy upon microbiology reporting of direct mecA PCR results from 38 patients prior to (phase I) and 48 patients after implementation of testing and reporting (phase II) showed that the mean time to antibiotic optimization in phase II (0.9 ± 0.9 day) was significantly shorter than that in phase I (2.2 ± 3.2 days) (P < 0.05). Methicillin-susceptible staphylococcal bacteremias had significantly higher frequency of antibiotic adjustment upon direct mecA reporting, compared to methicillin-resistant staphylococcal bacteremias. Our study indicated that direct mecA PCR improved timely antibiotic optimization.

In silico analyses of primers used to detect the pathogenicity genes of Vibrio cholerae

In Vibrio cholerae, the etiological agent of cholera, most of the virulence genes are located in two pathogenicity islands, named TCP (Toxin-Co-regulated Pilus) and CTX (Cholera ToXins). For each V. cholerae pathogenicity gene, we retrieved every primer published since 1990 and every known allele in order to perform a complete in silico survey and assess the quality of the PCR primers used for amplification of these genes. Primers with a melting temperature in the range 55–60°C against any target sequence were considered valid. Our survey clearly revealed that two thirds of the published primers are not able to properly detect every genetic variant of the target genes. Moreover, the quality of primers did not improve with time. Their lifetime, i.e. the number of times they were cited in the literature, is also not a factor allowing the selection of valid primers. We were able to improve some primers or design new primers for the few cases where no valid primer was found. In conclusion, many published primers should be avoided or improved for use in molecular detection tests, in order to improve and perfect specificity and coverage. This study suggests that bioinformatic analyses are important to validate the choice of primers.

Impact of results of a rapid Staphylococcus aureus diagnostic test on prescribing of antibiotics for patients with clustered gram-positive cocci in blood cultures

In tropical northern Australia, approximately 20% of Staphylococcus aureus bacteremia is caused by methicillin-resistant Staphylococcus aureus (MRSA). We prospectively evaluated the impact on clinician antibiotic prescribing of the results obtained from performing the GeneXpert MRSA/SA test on 151 positive blood cultures with clustered gram-positive cocci. The GeneXpert result led to earlier appropriate prescription of vancomycin for 54% of patients with MRSA; 25% of patients avoided vancomycin, and 16% of patients had all antibiotics ceased.

Quantitative PCR for Etiologic Diagnosis of Methicillin-Resistant Staphylococcus aureus Pneumonia in Intensive Care Unit

Background

Ventilator-associated pneumonia (VAP) requires prompt and appropriate treatment. Since methicillin-resistant Staphylococcus aureus (MRSA) is a frequent pathogen in VAP, rapid identification of it, is pivotal. Our aim was to evaluate the utility of quantitative polymerase chain reaction (qPCR) as a useful method for etiologic diagnoses of MRSA pneumonia.

Methods

We performed qPCR for mecA, S. aureus-specific femA-SA, and S. epidermidis-specific femA-SE genes from bronchoalveolar lavage or bronchial washing samples obtained from clinically-suspected VAP. Molecular identification of MRSA was based on the presence of the mecA and femA-SA gene, with the absence of the femA-SE gene. To compensate for the experimental and clinical conditions, we spiked an internal control in the course of DNA extraction. We estimated number of colony-forming units per mL (CFU/mL) of MRSA samples through a standard curve of a serially-diluted reference MRSA strain. We compared the threshold cycle (Ct) value with the microbiologic results of MRSA.

Results

We obtained the mecA gene standard curve, which showed the detection limit of the mecA gene to be 100 fg, which corresponds to a copy number of 30. We chose cut-off Ct values of 27.94 (equivalent to 1×10⁴ CFU/mL) and 21.78 (equivalent to 1×10⁵ CFU/mL). The sensitivity and specificity of our assay were 88.9% and 88.9% respectively, when compared with quantitative cultures.

Conclusion

Our results were valuable for diagnosing and identifying pathogens involved in VAP. We believe our modified qPCR is an appropriate tool for the rapid diagnosis of clinical pathogens regarding patients in the intensive care unit.

Clinical impact of a real-time PCR assay for rapid identification of staphylococcal bacteremia

The purpose of this study was to evaluate the impact of real-time PCR reporting both on timely identification of clustered Gram-positive cocci (GPC) in blood cultures and on appropriate antibiotic treatment. This retrospective, interventional cohort study evaluated inpatients with blood cultures positive for GPC in the pre-PCR (15 January 2009 to 14 January 2010) and post-PCR (15 January 2010 to 14 January 2011) periods. Post-PCR implementation, laboratory services completed batched PCR; results other than methicillin-resistant Staphylococcus aureus (MRSA) were reported in the electronic medical record without additional interventions. The assay's sensitivity and specificity, time to identification of staphylococcal bacteremia, and clinically relevant outcomes, including time to optimal antibiotic therapy, were evaluated. Demographic information was also collected and analyzed. Sixty-eight and 58 patients with Staphylococcus aureus bacteremia from the pre- and post-PCR periods, respectively, met inclusion criteria. Similar numbers of consecutive patients with coagulase-negative staphylococci were analyzed for comparison. The time to identification was significantly reduced post-PCR implementation (mean, 13.2 h; 95% confidence interval [95% CI], 10.5 to 15.9 h; P < 0.0001). However, the time to optimal antibiotic therapy was not significantly reduced. We conclude that implementation of a PCR assay demonstrated the potential to improve appropriate antibiotic use based on clinically meaningful and statistically significant reductions in the time to microbiologic identification. However, in order to realize this potential benefit, processes must be optimized and additional interventions initiated to facilitate providers' use of the PCR result.

Evolution of nasal carriage of methicillin-resistant coagulase-negative staphylococci in a remote population

Nasal carriage of methicillin-resistant coagulase-negative staphylococci (MR-CoNS) is highly prevalent in community subjects, but its dynamic has been little investigated. Nasal swabbing was performed in 2006 and 2008 in 154 Amerindians living isolated in French Guiana. MR-CoNS strains were identified and characterized by non-β-lactam susceptibility testing and staphylococcal cassette chromosome mec element (SCCmec) typing, characterizing the associations of ccr and mec gene complex allotypes, and for MR Staphylococcus epidermidis (MRSE), multilocus variable number of tandem repeats analysis (MLVA) was used. The impact of sociodemographic and medical characteristics on the persistence of MR-CoNS carriage was assessed by bivariate analysis. Prevalence of MR-CoNS carriage was 50.6% in 2006 and 46.8% in 2008. The 274 MR-CoNS isolates, including S. epidermidis (n = 89, 62 MLVA patterns), Staphylococcus haemolyticus (n = 78), and Staphylococcus hominis (n = 72), exhibited 41 distinct ccr and mec gene complex associations. Persistent carriage (in 2006 and 2008), intermittent carriage (either in 2006 or 2008), and noncarriage were documented in 25.3, 47.4, and 27.3% of the participants, respectively. Persistent carriage of a given MRSE isolate was rarely observed (n = 8 isolates). Furthermore, no epidemiological factor, including antibiotic exposure, was associated with persistent carriage. The high diversity of MRSE clones and their ccr and mec gene complex associations contrasted with the high carriage rates in this isolated community, which might reflect the occurrence of SCCmec rearrangement and the generation of new MR-CoNS strains.

Clinical impact of a real-time PCR assay for rapid identification of Staphylococcus aureus and determination of methicillin resistance from positive blood cultures

The full identification and susceptibility profile of staphylococci from positive blood cultures (BCs) generally takes 24-48 h using phenotypic methods. The aim of this prospective study was to evaluate the clinical impact of a real-time PCR strategy for rapid identification of staphylococci and determination of methicillin resistance directly from positive BCs. During a 12-month period, 250 episodes of positive BCs with organism morphology resembling staphylococci were enrolled. Two strategies were compared: conventional (n = 128) using standard phenotypic methods or rapid (n = 122) using a real-time PCR assay that is able to detect specific genes of Staphylococcus aureus (nuc and sa442) and the encoding gene for methicillin resistance (mecA). Overall, 97 episodes (39%) were clinical-significant bloodstream infections. The prevalence of methicillin resistance of S. aureus was 24%. A favorable outcome (defined as clinical cure with resolution of signs and no evidence of recurrence or relapse at 12 weeks follow-up) was observed in similar proportions of episodes with (58%) or without (60%) PCR testing (p 0.8). In multivariate analyses, age and infection due to methicillin-susceptible S. aureus (adjusted OR 0.96, 95% CI 0.93-0.99; and adjusted OR 3.11, 95% CI 1.12-8.65, respectively) were the unique factors independently associated with a favorable outcome. Among the 153 episodes of contaminated BCs, similar proportions received unjustified antibiotic therapy (PCR strategy: 17%, conventional testing: 10%; p 0.33). In a setting with a moderate level of methicillin-resistant S. aureus and relatively high contamination of BCs, real-time PCR testing was not beneficial compared to conventional methods.

Rapid detection of blaKPC carbapenemase genes by internally controlled real-time PCR assay using bactec blood culture bottles

Rapid detection of drug-resistant bacteria in clinical samples plays an instrumental role in patients' infection management and in implementing effective infection control policies. In the study described in this report, we validated a multiplex TaqMan real-time quantitative PCR (qPCR) assay for the detection of bla(KPC) genes and the human RNase P gene in Bactec blood culture bottles. The MagNA Pure LC (version 2.0) instrument was utilized to extract nucleic acids from the inoculated broth, while bovine serum albumin (BSA) was utilized as the PCR inhibitor reliever. The multiplex assay, which was specific for the detection of bla(KPC) genes, had a limit of detection of 19 CFU per reaction mixture with human blood-spiked Bactec bottles. Of the 323 Bactec blood culture sets evaluated, the same 55 (17%) blood cultures positive for carbapenem-resistant bacteria by culture were also positive by the validated qPCR assay. Thus, the sensitivity, specificity, positive predictive value, and negative predictive value of the qPCR assay compared to the results of culture were all 100%. bla(KPC) genes were also detected from the same Bactec bottle broth after manual extraction with a QIAamp DNA minikit; however, there was an average 3-threshold-cycle delay in the qPCR readings. With the limited therapeutic options available, the accurate and rapid detection of bla(KPC)-possessing bacteria by the described bla(KPC)/RNase P assay will be a crucial first step in ensuring optimal clinical outcomes and infection control.

New molecular and surrogate biomarker-based tests in the diagnosis of bacterial and fungal infection in febrile neutropenic patients

PURPOSE OF REVIEW

Prompt diagnosis of infection in febrile neutropenia hosts with hematological malignancy is essential in directing therapy. We highlight experience using modern molecular and biomarker-based methods to diagnose bacterial and fungal bloodstream infections and invasive aspergillosis in these patients.

RECENT FINDINGS

Nucleic acid amplification-based strategies are used to detect and identify pathogens from blood cultures or from blood/clinical specimens; the latter are more likely to influence clinical management. Advances in DNA extraction include standardization of isolation of Aspergillus DNA from blood. Broad-range and/or multiplex PCR generally have greater clinical utility than pathogen-specific assays. However, Aspergillus-PCR assays are useful in confirming/excluding disease and monitoring high-risk patients for invasive aspergillosis. Commercial real-time PCR/peptide nucleic acid fluorescent in-situ hybridization systems, used as adjuncts to blood cultures, to detect bacteria and fungi in blood cultures (or blood), are as sensitive as culture and enable earlier institution of targeted therapy. Yet there are no data indicating that molecular detection of bacterial/fungal pathogens influences patient outcomes. Positive serum Aspergillus galactomannan and 1,3-β-D-glucan tests are useful biomarkers in the diagnosis/screening of fungal infection, and have potential as measures of response to antifungal therapy. Serum procalcitonin levels can help differentiate infectious, from noninfectious, fever. Combined molecular and nonmolecular testing likely offers optimal diagnostic accuracy.

SUMMARY

Numerous PCR-based and biomarker tools are available for the diagnosis and screening of infection in febrile neutropenia hosts. The optimal approach remains to be resolved by prospective studies examining the impact of one or more of tests on patient outcomes.

[Interest of real-time PCR Xpert MRSA/SA on GeneXpert(®) DX System in the investigation of staphylococcal bacteremia]

AIM OF THE STUDY

Recently, a rapid, fully automated real-time PCR test has become available for detection of Staphylococcus aureus in positive blood cultures, Xpert MRSA/SA blood culture. This study was defined to evaluate the use of this product in our hospital setting to assist in optimizing antibiotic treatment.

MATERIALS AND METHODS

Over a period of 18months (from February 2008 to July 2009), 51 positive blood cultures were examined for Staphylococcus using the Xpert MRSA/SA assay on the GeneXpert(®) System. The PCR results were transferred to the clinician as soon as available. The presence of empirical antibiotic therapy was noted and modified if necessary after discussions between the clinician and the infectious disease specialist.

RESULTS

Twenty-three blood bottles were positive for S. aureus, two were resistant to methicillin. Twenty-eight were coagulase negative staphylococci. No discrepancy between identification (S. aureus) and methicillin resistance was observed. Thirty-two samples had clinically significant bacteremia (23 S. aureus and nine coagulase negative staphylococci). Sixteen (50%) of these patients had received inappropriate antibiotic therapy (11 without antibiotic therapy, five with betalactam antibiotics). For these patients, an appropriate antibiotic therapy was prescribed according to these results. Sixteen patients had adequate empirical antibiotic therapy at the time of receiving the PCR result. Among these 16 patients, eight switches were performed from broad-spectrum treatment to a more restrictive antistaphylococcal treatment. Of the 19 patients with a nonclinically relevant coagulase negative staphylococci infection, four were already on antibiotics for other infections and these treatments were not modified. Empirical treatment could be avoided in 13 patients who had a clinical presentation consistent with staphylococcal bacteremia (multiple sores, history of carrying methicllin-resistant or susceptible S. aureus infection, presence of intravascular material or prosthesis).

CONCLUSION

The real-time PCR Cepheid Xpert MRSA/SA on GeneXpert(®) DX System has become an essential tool in our laboratory enhancing the reports of positive blood cultures for staphylococci. This test is fast (50min) and reliable. It allows optimization of antibiotic therapy in hospital.

Real-time identification of bacteria and Candida species in positive blood culture broths by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Delays in the identification of microorganisms are a barrier to the establishment of adequate empirical antibiotic therapy of bacteremia. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) allows the identification of microorganisms directly from colonies within minutes. In this study, we have adapted and tested this technology for use with blood culture broths, thus allowing identification in less than 30 min once the blood culture is detected as positive. Our method is based on the selective recovery of bacteria by adding a detergent that solubilizes blood cells but not microbial membranes. Microorganisms are then extracted by centrifugation and analyzed by MALDI-TOF-MS. This strategy was first tested by inoculating various bacterial and fungal species into negative blood culture bottles. We then tested positive patient blood or fluid samples grown in blood culture bottles, and the results obtained by MALDI-TOF-MS were compared with those obtained using conventional strategies. Three hundred twelve spiked bottles and 434 positive cultures from patients were analyzed. Among monomicrobial fluids, MALDI-TOF-MS allowed a reliable identification at the species, group, and genus/family level in 91%, 5%, and 2% of cases, respectively, in 20 min. In only 2% of these samples, MALDI-TOF MS did not yield any result. When blood cultures were multibacterial, identification was improved by using specific databases based on the Gram staining results. MALDI-TOF-MS is currently the fastest technique to accurately identify microorganisms grown in positive blood culture broths.

Clinical review: the role of biomarkers in the diagnosis and management of community-acquired pneumonia

In patients with community-acquired pneumonia, traditional criteria of infection based on clinical signs and symptoms, clinical scoring systems, and general inflammatory indicators (for example, leukocytosis, fever, C-reactive protein and blood cultures) are often of limited clinical value and remain an unreliable guide to etiology, optimal therapy and prognosis. Procalcitonin is superior to other commonly used markers in its specificity for bacterial infection (allowing alternative diagnoses to be excluded), as an indicator of disease severity and risk of death, and mainly as a guide to the necessity for antibiotic therapy. It can therefore be viewed as a diagnostic, prognostic, and perhaps even theragnostic test. It more closely matches the criteria for usefulness than other candidate biomarkers such as C-reactive protein, which is rather a nonspecific marker of acute phase inflammation, and proinflammatory cytokines such as plasma IL-6 levels that are highly variable, cumbersome to measure, and lack specificity for systemic infection. Elevated levels of pro-adrenomedullin, copeptin (which is produced in equimolar amounts to vasopressin), natriuretic peptides and cortisol are significantly related to mortality in community-acquired pneumonia, as are other prohormones such as pro-atrial natriuretic peptide, coagulation markers, and other combinations of inflammatory cytokine profiles. However, all biomarkers have weaknesses as well as strengths. None should be used on its own; and none is anything more than an aid in the exercise of clinical judgment based upon a synthesis of available clinical, physiologic and laboratory features in each patient.

Accelerated identification of Staphylococcus aureus from blood cultures by a modified fluorescence in situ hybridization procedure

This study evaluated fluorescence in situ hybridization (FISH) for rapid identification of Staphylococcus aureus and coagulase-negative staphylococci (CoNS) directly from blood cultures. Initially, 360 blood cultures containing Gram-positive cocci were investigated by a previously described microwave-FISH procedure: 44/49 (89.8 %) S. aureus and 298/299 (99.7 %) CoNS were correctly identified. Because FISH proved useful and reliable but handling was found to be inconvenient, the method was modified by employing a recently developed slide chamber. This reduced the time required from 60 to 30 min. The simplified execution allowed integration of the method into the workflow of a routine laboratory without difficulty. The modified method proved to be highly reliable, identifying 37/37 (100 %) S. aureus and 169/172 (98.2 %) CoNS directly from blood cultures.

DNA microarray-based identification of bacterial and fungal pathogens in bloodstream infections

The accurate and rapid identification of pathogens in blood is a major challenge in clinical pathogen diagnostics because of the high mortality of sepsis. Here we report the development of DNA microarray for the identification of pathogens causing bloodstream infections. Species-specific and bacteria- and fungi-broad-ranged probes were designed to identify 50 bacteria and 7 fungi. The specificities and sensitivities of the selected probes were successfully validated by applying reference strains. To assess the performance of the DNA microarray in a clinical setting, blind tests were performed using 112 blood culture specimens that showed preliminary presence of pathogenic microorganisms by culture-based method, resulting in the correct identification of pathogens in 104 samples showing the sensitivity of 93%. In addition, closely-related species could be discriminated by the distinct hybridization patterns. This DNA microarray-based pathogen diagnosis takes approximately 10 h starting from a positive blood culture, considerably reducing time required to sufficiently identify pathogens by subsequent agar-culture and biochemical tests which requires altogether at least 1-3 days. Also, the amount of sample required for the identification of pathogens is much less than that required for biochemical assays. Thus, the DNA microarray reported here should be useful for the effective identification of microbial pathogens in blood cultures from septicemic patients.

Comparisons between geographically diverse samples of carried Staphylococcus aureus

Approximately one-third of the human population is asymptomatically colonized by Staphylococcus aureus. However, much of the global diversity within the carriage populations remains uncharacterized, and it is unclear to what degree the variation is geographically partitioned. We isolated 300 carriage isolates from 1,531 adults contemporaneously in four countries: France, Algeria, Moldova, and Cambodia. All strains were characterized by multilocus sequence typing. Six clonal complexes (CCs) were present in all four samples (CC30, -45, -121, -15, -5, and -8). Analyses based on the genotype frequencies revealed the French and Algerian samples to be most similar and the Cambodian sample to be most distinct. While this pattern is consistent with likely rates of human migration and geographic distance, stochastic clonal expansion also contributes to regional differences. Phylogenetic analysis revealed a highly divergent and uncharacterized genotype (ST1223) within Cambodia. This lineage is related to CC75, which has previously been observed only in remote aboriginal populations in northern Australia.

Evaluation of the BD GeneOhm StaphSR assay for detection of methicillin-resistant and methicillin-susceptible Staphylococcus aureus isolates from spiked positive blood culture bottles

To improve the clinical outcome of Staphylococcus aureus septicemia, the early selection of appropriate antibiotic treatment is crucial. Molecular diagnostics represents an attractive approach for the rapid identification of S. aureus and the determination of its methicillin (meticillin) resistance. In direct comparison to other molecular assays (sa442 and mecA real-time PCRs) and standard laboratory procedures, we evaluated the BD GeneOhm StaphSR assay for its use in the detection of S. aureus and methicillin-resistant S. aureus (MRSA) from spiked blood culture bottles (n = 134). In the case of detecting S. aureus (n = 90; for methicillin-susceptible S. aureus, n = 45; for MRSA, n = 45), the BD GeneOhm StaphSR assay had a sensitivity and a specificity of 100% each (95% confidence intervals [CIs], 96.0 to 100% and 82.4 to 100%, respectively). For MRSA (n = 45), the test was 95.6% (95% CI, 84.9 to 99.5%) sensitive and 95.3% (95% CI, 86.9 to 99.0%) specific. Overall, five discrepant results arose with this assay due to the presence of methicillin-susceptible, revertant MRSA strains (3/45) and MRSA strains that were not detected by the BD GeneOhm StaphSR assay (2/45). Compared to other real-time PCR-based molecular approaches and to conventional standard laboratory methods, the BD GeneOhm StaphSR turned out to be an appropriate diagnostic tool for a rapid (approximately 1.5 h), preliminary identification of S. aureus and MRSA from blood cultures.

Future diagnostic and therapeutic approaches in surgical infections

Despite ongoing efforts to standardize therapy and improve management, the morbidity and mortality associated with surgical infections remain high. Continued innovation is required to improve outcomes further, particularly in the face of the increasing prevalence of multidrug resistant organisms. Although they remain in the experimental stages, a number of recent advances have the potential to have significant impact on the management and outcomes of surgical infections. These include novel diagnostic strategies, antimicrobials targeting microbial virulence factors, novel vaccines, and risk stratification based on genetic profiling.

Diversity of staphylococcal cassette chromosome mec structures in methicillin-resistant Staphylococcus epidermidis and Staphylococcus haemolyticus strains among outpatients from four countries

In staphylococci, methicillin (meticillin) resistance (MR) is mediated by the acquisition of the mecA gene, which is carried on the size and composition variable staphylococcal cassette chromosome mec (SCCmec). MR has been extensively studied in Staphylococcus aureus, but little is known about MR coagulase-negative staphylococci (MR-CoNS). Here, we describe the diversity of SCCmec structures in MR-CoNS from outpatients living in countries with contrasting environments: Algeria, Mali, Moldova, and Cambodia. Their MR-CoNS nasal carriage rates were 29, 17, 11, and 31%, respectively. Ninety-six MR-CoNS strains, comprising 75 (78%) Staphylococcus epidermidis strains, 19 (20%) Staphylococcus haemolyticus strains, 1 (1%) Staphylococcus hominis strain, and 1 (1%) Staphylococcus cohnii strain, were analyzed. Eighteen different SCCmec types were observed, with 28 identified as type IV (29%), 25 as type V (26%), and 1 as type III (1%). Fifteen strains (44%) were untypeable for their SCCmec. Thirty-four percent of MR-CoNS strains contained multiple ccr copies. Type IV and V SCCmec were preferentially associated with S. epidermidis and S. haemolyticus, respectively. MR-CoNS constitute a widespread and highly diversified MR reservoir in the community.

The carriage population of Staphylococcus aureus from Mali is composed of a combination of pandemic clones and the divergent Panton-Valentine leukocidin-positive genotype ST152

Staphylococcus aureus is an important human pathogen, but it appears more commonly in asymptomatic colonization of the nasopharynx than in cases of invasive disease. Evidence concerning the global population structure of S. aureus is limited by the overrepresentation in the multilocus sequence testing database of disease isolates recovered from Western Europe, the Americas, Australia, and Japan. We address this by presenting data from the S. aureus carriage population in Mali, the first detailed characterization of asymptomatic carriage from an African population. These data confirm the pandemic spread of many of the common S. aureus clones in the carriage population. We also note the high frequency (approximately 24%) of a single divergent genotype, sequence type 152 (ST152), which has not previously been recovered from nasal carriage isolates but corresponds to a sporadic Panton-Valentine leukocidin (PVL)-positive, community-acquired methicillin-resistant S. aureus clone noted mostly in Central Europe. We show that 100% of the ST152 isolates recovered from nasal carriage samples in Mali are PVL positive and discuss implications relating to the emergence and spread of this virulent genotype.