The profiling of microbiota in vaginal swab samples using 16S rRNA gene sequencing and IS-pro analysis.

BACKGROUND: 16S rRNA gene sequencing is currently the most common way of determining the composition of microbiota. This technique has enabled many new discoveries to be made regarding the relevance of microbiota to the health and disease of the host. However, compared to other diagnostic techniques, 16S rRNA gene sequencing is fairly costly and labor intensive, leaving room for other techniques to improve on these aspects. RESULTS: The current study aimed to compare the output of 16S rRNA gene sequencing to the output of the quick IS-pro analysis, using vaginal swab samples from 297 women of reproductive age. 16S rRNA gene sequencing and IS-pro analyses yielded very similar vaginal microbiome profiles, with a median Pearson's R2 of 0.97, indicating a high level of similarity between both techniques. CONCLUSIONS: We conclude that the results of 16S rRNA gene sequencing and IS-pro are highly comparable and that both can be used to accurately determine the vaginal microbiota composition, with the IS-pro analysis having the benefit of rapidity.

Clinical Microbiology in Underresourced Settings.

The article discusses the environment of laboratory diagnostic bacteriology testing in several underresourced settings experienced by the author. The major global infectious diseases are usually managed with government or donor-supported systems, whereas basic laboratory testing for bacterial infections has no formal global programs. The causes of many of those diseases can be detected using simple manual bacteriologic methods available in most resource-limited environments; however, the challenges of building laboratory capacity in those settings are many. Positive and negative aspects of developing such capacities in selected locations are presented.

Development and validation of external quality assessment panels for mycobacterial culture testing to diagnose tuberculosis in China.

Mycobacterial culture remains the gold standard for detection of Mycobacterium tuberculosis (MTB) in clinical samples. However, no external quality assessment (EQA) tools exist to validate results obtained using this sophisticated method. Therefore, we developed EQA panels to assess the quality of mycobacterial culture results produced by designated TB hospitals in China. Artificial sputum containing methylcellulose was used to supplement quantified mycobacterial solutions to simulate culture-negative and culture-positive clinical sputum samples of low or high mycobacterial concentration, respectively. After storage of the quantified simulated EQA panels for 4 weeks at 4 °C, experimental bacterial quantification of the panels was again conducted, with no impact of artificial sputum on mycobacterial culture results observed. Next, 47 tuberculosis (TB) hospitals were recruited for evaluation of the EQA panels. Overall, 29 hospitals (61.7%) produced mycobacterial culture test results matching expected results for the EQA panels, while the remaining 18 (38.3%) hospitals did not. False-negative results for the low mycobacterial concentration panel sample accounted for 33 (73.3%) diagnostic errors. Compared with hospitals using solid culture methods as a control group, hospitals using the liquid culture method were less likely to produce uncertified results (aOR 0.064, 95% CI 0.005-0.770). In conclusion, we first developed then evaluated EQA panels for validation of mycobacterial culture testing in China. Our data demonstrate that approximately one-third of TB hospitals failed to produce results that met criteria for classification as certified mycobacterial culture testing providers, emphasizing the importance of quality control and quality assurance in TB diagnostics.

Switching from expectorated to induced sputum cultures for tuberculosis diagnosis reduces cost without increasing risk.

Active pulmonary tuberculosis testing with 3 expectorated sputa can increase isolation days and expenditures compared with 1 induced sputum. Six-month retrospective and prospective chart reviews were conducted, and a screening algorithm was phased into 2 hospital sites. With induced sputum testing, isolation decreased from 7 to 4 days (interquartile range, 4-3, P = .0135), and there was a cost savings of $7,275 per case, with no added harm.

The 3-day rule for stool cultures: should all patients with haematological malignancies be excluded?

OBJECTIVES: The '3-day rule' for stool culture ordering suggests that only selected inpatients with nosocomial diarrhoea should have stool cultures for enteropathogenic bacteria (EPBs). Patients with haematological malignancies are not included in this group. We have analysed the ordering of stool cultures at Laikon Hospital to investigate whether all patients with haematological malignancies should be excluded from the 3-day rule. METHODS: We have retrospectively analysed all inpatient stool specimens sent to the microbiology laboratory for enteropathogenic bacteria culture at Laikon Hospital, Athens, Greece, between January 1, 2014 and December 31, 2014. We classified stool cultures sent after the third day as 'appropriate', 'excluded' with standard rule, 'excluded' with haematological malignancies, and 'inappropriate'. RESULTS: During the study period, 1101/1593 inpatient stool cultures (69.1%) had been ordered after the third day of hospitalization. The total yield for inpatient EPB stool cultures was 0.7% (11/1593). The yield for 'appropriate' cultures was significantly higher than the yield of all 'excluded' specimens (3.7% (3/81) versus 0.3% (2/585), p 0.018) and to 'inappropriate' orders (3.7% (3/81) versus 0.0% (0/485), p 0.0028). There was no difference in the yield between specimens 'excluded' with the standard rule and 'excluded' with haematological malignancies. CONCLUSIONS: In our hospital, the yield of stool cultures from patients with haematological malignancies is similar to that of patients 'excluded' from the standard 3-day rule. If patients with haematological malignancies were not excluded from the rule, we would reduce the inpatient stool cultures by 13.6% (217/1593) at the cost of missing one positive stool culture.

Comparative analysis of four commercial on-farm culture methods to identify bacteria associated with clinical mastitis in dairy cattle.

Several multiple-media culture systems have become commercially available for on-farm identification of mastitis-associated pathogens. However, the accuracy of these systems has not been thoroughly and independently validated against microbiological evaluations performed by referral laboratories. Therefore, the purpose of the present study was to evaluate the performance of commercially available culture plates (Accumast, Minnesota Easy System, SSGN and SSGNC Quad plates) to identify pathogens associated with clinical mastitis in dairy cows. Milk samples from the affected quarter with clinical mastitis were aerobically cultured with the on-farm culture systems and by two additional reference laboratories. Agreeing results from both standard laboratories were denoted as the reference standard (RS). Accuracy (Ac), sensitivity (Se), specificity (Sp), positive and negative predictive values (PPV and NPV, respectively) and Cohen's kappa coefficient (k) of on-farm plates were determined based on the RS culture of 211 milk samples. All four plate-systems correctly identified ≥ 84.9% of milk samples with no bacterial growth. Accumast had greater values for all overall predictive factors (Ac, Se, Sp, PPV and NPV) and a substantial agreement (k = 0.79) with RS. The inter-rater agreements of Minnesota, SSGN, and SSGNC with RS were moderate (0.45 ≤ k ≤ 0.55). The effectiveness to categorize bacterial colonies at the genus and species was numerically different amongst the commercial plates. Our findings suggest that Accumast was the most accurate on-farm culture system for identification of mastitis-associated pathogens of the four systems included in the analysis.

Novel cost-effective quality control approach for the Cepheid Xpert CT/NG assay for the detection of Chlamydia Trachomatis and Neisseria Gonorrhoeae.

The Xpert CT/NG is a rapid assay for detection of Neisseria gonorrhoeae and Chlamydia trachomatis. QC materials must be formulated to emulate human specimens, and are prohibitively expensive. A creative, cost-effective QC approach is proposed. The acceptable sample types for the Xpert CT/NG assay were extended to include eye swabs.

Using the mini-VIDAS(®) Easy Salmonella protocol to assess contamination in transitional and coastal waters.

Classical methodologies for Salmonella detection may be too long in time to assure public safety. Presently, one of the fastest assays for Salmonella detection using the mini-VIDAS(®) system is the Easy Salmonella protocol. This assay, developed for food matrixes analysis, was here assessed for the applicability on the detection of these bacteria in transitional and saltwaters. The presence of Salmonella was detected in 4.2 % of the samples studied. In these transitional waters, the proposed protocol presented an efficiency of 79.1 %, due to a high false positive rate (20.8 %), and a false negative rate of 0 %-implying reducing analysis time, the use of enrichment broths, and making it more cost effective. Despite the multitude of samples nature, the method here described revealed to be an efficient and promising tool for transitional waters analysis.

Multicenter Assessment of Gram Stain Error Rates.

Gram stains remain the cornerstone of diagnostic testing in the microbiology laboratory for the guidance of empirical treatment prior to availability of culture results. Incorrectly interpreted Gram stains may adversely impact patient care, and yet there are no comprehensive studies that have evaluated the reliability of the technique and there are no established standards for performance. In this study, clinical microbiology laboratories at four major tertiary medical care centers evaluated Gram stain error rates across all nonblood specimen types by using standardized criteria. The study focused on several factors that primarily contribute to errors in the process, including poor specimen quality, smear preparation, and interpretation of the smears. The number of specimens during the evaluation period ranged from 976 to 1,864 specimens per site, and there were a total of 6,115 specimens. Gram stain results were discrepant from culture for 5% of all specimens. Fifty-eight percent of discrepant results were specimens with no organisms reported on Gram stain but significant growth on culture, while 42% of discrepant results had reported organisms on Gram stain that were not recovered in culture. Upon review of available slides, 24% (63/263) of discrepant results were due to reader error, which varied significantly based on site (9% to 45%). The Gram stain error rate also varied between sites, ranging from 0.4% to 2.7%. The data demonstrate a significant variability between laboratories in Gram stain performance and affirm the need for ongoing quality assessment by laboratories. Standardized monitoring of Gram stains is an essential quality control tool for laboratories and is necessary for the establishment of a quality benchmark across laboratories.

A pilot evaluation of external quality assessment of GenoType MTBDRplus versions 1 and 2 using dried culture spot material.

Dried culture spots (DCS) of inactivated Mycobacteria strains designed as part of an external quality assessment (EQA) program for the GeneXpert system has applications to other molecular tuberculosis (TB) diagnostic platforms. DCS tested on the GenoType MTBDRplus and Mycobacterium CM assays performed well with MTBDRplus version 2 but require increased bacterial concentration for use with version 1.

Impact and cost-effectiveness of current and future tuberculosis diagnostics: the contribution of modelling.

The landscape of diagnostic testing for tuberculosis (TB) is changing rapidly, and stakeholders need urgent guidance on how to develop, deploy and optimize TB diagnostics in a way that maximizes impact and makes best use of available resources. When decisions must be made with only incomplete or preliminary data available, modelling is a useful tool for providing such guidance. Following a meeting of modelers and other key stakeholders organized by the TB Modelling and Analysis Consortium, we propose a conceptual framework for positioning models of TB diagnostics. We use that framework to describe modelling priorities in four key areas: Xpert(®) MTB/RIF scale-up, target product profiles for novel assays, drug susceptibility testing to support new drug regimens, and the improvement of future TB diagnostic models. If we are to maximize the impact and cost-effectiveness of TB diagnostics, these modelling priorities should figure prominently as targets for future research.

Application of microbiological quantitative methods for evaluation of changes in the amount of bacteria in patients with wounds and purulent fistulas subjected to phage therapy and for assessment of phage preparation effectiveness (in vitro studies).

PURPOSE: Quantitative microbiological studies may provide important information required for successful phage therapy (PT), however methods for PT monitoring of purulent wounds and fistulas has never been reported before. Therefore our goal was to determine and apply microbiological quantitative methods (MQMs) for monitoring experimental PT. METHODS: Samples from agar plates with growing bacteria were collected using dry and wet sterile compresses, or swabs. After shaking the sample in saline the amount of bacteria in suspension was determined. The method was standardized. The MQM using compress was applied for comparison of in vitro activity of phage preparations with other agents for wound rinsing. The usefulness of this swabbing method was tested in the Phage Therapy Unit for monitoring of experimental PT of patients with chronic wounds or purulent fistulas. RESULTS: Minimum, maximum and standard deviation values used for standardization of the studied method showed that data repeatability was good; thus the method was used for quantitation of bacteria taken both from plates in vitro and patients samples. Effectiveness of phage preparations was compared to gentamicin in vitro. Phages were as effective as antibiotics in reducing the amount of bacteria on agar plates, and this effect was not only due to simple mechanical removal of bacteria, but dependent on their antibacterial activity. We have also observed that the results of bacteria quantitation may correlate with the local status of a wound/fistula in a particular stage of PT. CONCLUSION: The standardized swabbing method of bacteria quantitation can be used for PT monitoring. Presented MQMs are simple and may help to monitor the therapy process and to decide on its duration, frequency and a kind of the phage applied. They can also be applied in other antibacterial treatment strategies.

An innovative pay-for-performance (P4P) strategy for improving malaria management in rural Kenya: protocol for a cluster randomized controlled trial.

BACKGROUND: In high-resource settings, 'pay-for-performance' (P4P) programs have generated interest as a potential mechanism to improve health service delivery and accountability. However, there has been little or no experimental evidence to guide the development or assess the effectiveness of P4P incentive programs in developing countries. In the developing world, P4P programs are likely to rely, at least initially, on external funding from donors. Under these circumstances, the sustainability of such programs is in doubt and needs assessment. METHODS/DESIGN: We describe a cluster-randomized controlled trial underway in 18 health centers in western Kenya that is testing an innovative incentive strategy to improve management of an epidemiologically and economically important problem--diagnosis and treatment of malaria. The incentive scheme in this trial promotes adherence to Ministry of Health guidelines for laboratory confirmation of malaria before treatment, a priority area for the Ministry of Health. There are three important innovations that are unique to this study among those from other resource-constrained settings: the behavior being incentivized is quality of care rather than volume of service delivery; the incentives are applied at the facility-level rather than the individual level, thus benefiting facility infrastructure and performance overall; and the incentives are designed to be budget-neutral if effective. DISCUSSION: Linking appropriate case management for malaria to financial incentives has the potential to improve patient care and reduce wastage of expensive antimalarials. In our study facilities, on average only 25% of reported malaria cases were confirmed by laboratory diagnosis prior to the intervention, and the total treatment courses of antimalarials dispensed did not correspond to the number of cases reported. This study will demonstrate whether facility rather than individual incentives are compelling enough to improve case management, and whether these incentives lead to offsetting cost-savings as a result of reduced drug consumption. TRIAL REGISTRATION: ClinicalTrials.gov Registration Number NCT01809873.

Rapid monitoring of Campylobacter in high-shedding flocks for targeted disease control.

Broilers excreting Campylobacter spp. at high levels (>7 log CFU/g of feces) were described in the Dutch Campylobacter Risk Management and Assessment project as an important source of carcass contamination. The researchers concluded that the risk of infection to humans could be economically and efficiently minimized by eliminating these flocks from fresh poultry meat chains. In the present study, we evaluated a simple and rapid gold-labeled immunosorbent assay (GLISA) for the identification of Campylobacter spp. in flocks shedding high levels of the pathogen. Results were obtained within 2 h. Pooled samples from 102 of the 114 Campylobacter-positive flocks produced positive results, resulting in a test sensitivity of 89.5% (95% confidence interval, 82.6 to 94.2%) and a test specificity of 94.5% (86.7 to 98.2%). Given a GLISA detection limit of 7.3 log CFU/g of feces, nearly all Campylobacter-positive flocks were identified as "high shedders." Therefore, reduction of the incidence of Campylobacter infections by elimination of high-shedding flocks from fresh meat production is an unrealistic approach. Under the constraints given, a reduction in the incidence of Campylobacter spp. in Austria will require either improved hygiene or an intensive carcass decontamination strategy in fresh meat production facilities.

Pathology consultation on detection of Clostridium difficile.

Laboratory methods for detecting Clostridium difficile have undergone considerable evolution since the organism's etiologic association with antibiotic-associated diarrhea and colitis was established. Clearly, familiarity with the advantages and shortcomings of the various assays is essential for the laboratory director when choosing among these tests. For the consulting pathologist, furthermore, an understanding of the laboratory's role in securing a diagnosis of C difficile infection (CDI) is also required to identify requests for unnecessary testing that may be costly and potentially misleading. The purpose of this article is to highlight the major differences in laboratory test methods for CDI and to review a few commonly encountered provider ordering scenarios.

Evaluation of tuberculosis diagnostics: establishing an evidence base around the public health impact.

The limitations of existing tuberculosis diagnostic tools are significantly hampering tuberculosis control efforts, most noticeably in areas with high prevalence of human immunodeficiency virus (HIV) infection and antituberculosis drug resistance. However, renewed global interest in tuberculosis research has begun to bear fruit, with several new diagnostic technologies progressing through the development pipeline. There are significant challenges in building a sound evidence base to inform public health policies because most diagnostic research focuses on the accuracy of individual tests, with often significant limitations in the design, conduct, and reporting of diagnostic accuracy studies. Diagnostic accuracy studies may not be appropriate to guide public health policies, and clinical trials may increasingly be required to determine the incremental value and cost-effectiveness of new tools. The urgent need for new diagnostics should not distract from pursuing rigorous scientific evaluation focused on public health impact.

Proficiency panel testing--a reliable tool in external quality assessment of sputum smear microscopy services in Gujarat, India.

OBJECTIVE: To assess the proficiency of Senior TB Laboratory Supervisors (STLSs) and district level Laboratory Technicians (LTs) in sputum smear microscopy. METHOD: Intermediate Reference Laboratory (IRL), Ahmedabad had manufactured and validated Proficiency Panel Testing slides from sputum samples, made On Site Evaluation (OSE) visits of District TB Centres (DTCs) in two rounds, and conducted Proficiency Panel Testing of STLSs & DTC-LTs from January 2005 to June 2009. RESULTS: High level of concordance in Z-N smear grading was found between Microbiologist and district laboratory staff. DTC readers reported overall consistency level of more than 98% in Z-N grade agreement during both the IRL, EQA, OSE visits. The tendency to over-grade the panel slides was much higher (more than 22%) as compared to under-grade (less than 2%) them in "correct slides". High False Positive (HFP) error was not observed in the present study. CONCLUSION: Laboratory supervisor's proficiency can be quickly assessed by Proficiency Panel Testing, under multi-level quality assurance network system of sputum smear microscopy in public health programmes like the RNTCP. Proficiency Panel Testing is highly replicable and reproducible tool for quick and reliable assessment of proficiency of the staff and it can be made more effective by raising the proportion of lower grade positive slides in panel set of each reader. DTC readers' overall agreement level of more than 98% in Z-N grade suggests high level of precision and excellent consistency during both the IRL, EQA, OSE rounds. It is concluded that even for a large network of sputum smear microscopy centres under public health programmes like the RNTCP in order to take corrective action, Proficiency Panel Testing can be effectively used for quick identification of suboptimal- technical performance of the supervisory staff.