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The European Respiratory Journal Jan 2017Only 25% of multidrug-resistant tuberculosis (MDR-TB) cases are currently diagnosed. Line probe assays (LPAs) enable rapid drug-susceptibility testing for rifampicin... (Meta-Analysis)
Meta-Analysis Review
Only 25% of multidrug-resistant tuberculosis (MDR-TB) cases are currently diagnosed. Line probe assays (LPAs) enable rapid drug-susceptibility testing for rifampicin (RIF) and isoniazid (INH) resistance and Mycobacterium tuberculosis detection. Genotype MTBDRplusV1 was WHO-endorsed in 2008 but newer LPAs have since been developed.This systematic review evaluated three LPAs: Hain Genotype MTBDRplusV1, MTBDRplusV2 and Nipro NTM+MDRTB. Study quality was assessed with QUADAS-2. Bivariate random-effects meta-analyses were performed for direct and indirect testing. Results for RIF and INH resistance were compared to phenotypic and composite (incorporating sequencing) reference standards. M. tuberculosis detection results were compared to culture.74 unique studies were included. For RIF resistance (21 225 samples), pooled sensitivity and specificity (with 95% confidence intervals) were 96.7% (95.6-97.5%) and 98.8% (98.2-99.2%). For INH resistance (20 954 samples), pooled sensitivity and specificity were 90.2% (88.2-91.9%) and 99.2% (98.7-99.5%). Results were similar for direct and indirect testing and across LPAs. Using a composite reference standard, specificity increased marginally. For M. tuberculosis detection (3451 samples), pooled sensitivity was 94% (89.4-99.4%) for smear-positive specimens and 44% (20.2-71.7%) for smear-negative specimens.In patients with pulmonary TB, LPAs have high sensitivity and specificity for RIF resistance and high specificity and good sensitivity for INH resistance. This meta-analysis provides evidence for policy and practice.
Topics: Antitubercular Agents; DNA Probes; Drug Resistance, Multiple, Bacterial; Humans; Isoniazid; Microbial Sensitivity Tests; Mycobacterium tuberculosis; Nucleic Acid Amplification Techniques; Rifampin; Sensitivity and Specificity; Sputum; Tuberculosis, Multidrug-Resistant; Tuberculosis, Pulmonary
PubMed: 28100546
DOI: 10.1183/13993003.01075-2016 -
Health Technology Assessment... May 2015There is growing interest in the potential utility of real-time polymerase chain reaction (PCR) in diagnosing bloodstream infection by detecting pathogen... (Review)
Review
Rapid detection of health-care-associated bloodstream infection in critical care using multipathogen real-time polymerase chain reaction technology: a diagnostic accuracy study and systematic review.
BACKGROUND
There is growing interest in the potential utility of real-time polymerase chain reaction (PCR) in diagnosing bloodstream infection by detecting pathogen deoxyribonucleic acid (DNA) in blood samples within a few hours. SeptiFast (Roche Diagnostics GmBH, Mannheim, Germany) is a multipathogen probe-based system targeting ribosomal DNA sequences of bacteria and fungi. It detects and identifies the commonest pathogens causing bloodstream infection. As background to this study, we report a systematic review of Phase III diagnostic accuracy studies of SeptiFast, which reveals uncertainty about its likely clinical utility based on widespread evidence of deficiencies in study design and reporting with a high risk of bias.
OBJECTIVE
Determine the accuracy of SeptiFast real-time PCR for the detection of health-care-associated bloodstream infection, against standard microbiological culture.
DESIGN
Prospective multicentre Phase III clinical diagnostic accuracy study using the standards for the reporting of diagnostic accuracy studies criteria.
SETTING
Critical care departments within NHS hospitals in the north-west of England.
PARTICIPANTS
Adult patients requiring blood culture (BC) when developing new signs of systemic inflammation.
MAIN OUTCOME MEASURES
SeptiFast real-time PCR results at species/genus level compared with microbiological culture in association with independent adjudication of infection. Metrics of diagnostic accuracy were derived including sensitivity, specificity, likelihood ratios and predictive values, with their 95% confidence intervals (CIs). Latent class analysis was used to explore the diagnostic performance of culture as a reference standard.
RESULTS
Of 1006 new patient episodes of systemic inflammation in 853 patients, 922 (92%) met the inclusion criteria and provided sufficient information for analysis. Index test assay failure occurred on 69 (7%) occasions. Adult patients had been exposed to a median of 8 days (interquartile range 4-16 days) of hospital care, had high levels of organ support activities and recent antibiotic exposure. SeptiFast real-time PCR, when compared with culture-proven bloodstream infection at species/genus level, had better specificity (85.8%, 95% CI 83.3% to 88.1%) than sensitivity (50%, 95% CI 39.1% to 60.8%). When compared with pooled diagnostic metrics derived from our systematic review, our clinical study revealed lower test accuracy of SeptiFast real-time PCR, mainly as a result of low diagnostic sensitivity. There was a low prevalence of BC-proven pathogens in these patients (9.2%, 95% CI 7.4% to 11.2%) such that the post-test probabilities of both a positive (26.3%, 95% CI 19.8% to 33.7%) and a negative SeptiFast test (5.6%, 95% CI 4.1% to 7.4%) indicate the potential limitations of this technology in the diagnosis of bloodstream infection. However, latent class analysis indicates that BC has a low sensitivity, questioning its relevance as a reference test in this setting. Using this analysis approach, the sensitivity of the SeptiFast test was low but also appeared significantly better than BC. Blood samples identified as positive by either culture or SeptiFast real-time PCR were associated with a high probability (> 95%) of infection, indicating higher diagnostic rule-in utility than was apparent using conventional analyses of diagnostic accuracy.
CONCLUSION
SeptiFast real-time PCR on blood samples may have rapid rule-in utility for the diagnosis of health-care-associated bloodstream infection but the lack of sensitivity is a significant limiting factor. Innovations aimed at improved diagnostic sensitivity of real-time PCR in this setting are urgently required. Future work recommendations include technology developments to improve the efficiency of pathogen DNA extraction and the capacity to detect a much broader range of pathogens and drug resistance genes and the application of new statistical approaches able to more reliably assess test performance in situation where the reference standard (e.g. blood culture in the setting of high antimicrobial use) is prone to error.
STUDY REGISTRATION
The systematic review is registered as PROSPERO CRD42011001289.
FUNDING
The National Institute for Health Research Health Technology Assessment programme. Professor Daniel McAuley and Professor Gavin D Perkins contributed to the systematic review through their funded roles as codirectors of the Intensive Care Foundation (UK).
Topics: Bacteremia; Critical Care; Cross Infection; England; False Negative Reactions; False Positive Reactions; Humans; Prospective Studies; Real-Time Polymerase Chain Reaction; Sensitivity and Specificity; State Medicine; Technology Assessment, Biomedical; Time Factors
PubMed: 25961752
DOI: 10.3310/hta19350 -
PloS One 2015The detection of mutations in the gyrA and gyrB genes in the Mycobacterium tuberculosis genome that have been demonstrated to confer phenotypic resistance to... (Review)
Review
Frequency and geographic distribution of gyrA and gyrB mutations associated with fluoroquinolone resistance in clinical Mycobacterium tuberculosis isolates: a systematic review.
BACKGROUND
The detection of mutations in the gyrA and gyrB genes in the Mycobacterium tuberculosis genome that have been demonstrated to confer phenotypic resistance to fluoroquinolones is the most promising technology for rapid diagnosis of fluoroquinolone resistance.
METHODS
In order to characterize the diversity and frequency of gyrA and gyrB mutations and to describe the global distribution of these mutations, we conducted a systematic review, from May 1996 to April 2013, of all published studies evaluating Mycobacterium tuberculosis mutations associated with resistance to fluoroquinolones. The overall goal of the study was to determine the potential utility and reliability of these mutations as diagnostic markers to detect phenotypic fluoroquinolone resistance in Mycobacterium tuberculosis and to describe their geographic distribution.
RESULTS
Forty-six studies, covering four continents and 18 countries, provided mutation data for 3,846 unique clinical isolates with phenotypic resistance profiles to fluoroquinolones. The gyrA mutations occurring most frequently in fluoroquinolone-resistant isolates, ranged from 21-32% for D94G and 13-20% for A90V, by drug. Eighty seven percent of all strains that were phenotypically resistant to moxifloxacin and 83% of ofloxacin resistant isolates contained mutations in gyrA. Additionally we found that 83% and 80% of moxifloxacin and ofloxacin resistant strains respectively, were observed to have mutations in the gyrA codons interrogated by the existing MTBDRsl line probe assay. In China and Russia, 83% and 84% of fluoroquinolone resistant strains respectively, were observed to have gyrA mutations in the gene regions covered by the MTBDRsl assay.
CONCLUSIONS
Molecular diagnostics, specifically the Genotype MTBDRsl assay, focusing on codons 88-94 should have moderate to high sensitivity in most countries. While we did observe geographic differences in the frequencies of single gyrA mutations across countries, molecular diagnostics based on detection of all gyrA mutations demonstrated to confer resistance should have broad and global utility.
Topics: Anti-Bacterial Agents; DNA Gyrase; Drug Resistance, Bacterial; Fluoroquinolones; Humans; Meta-Analysis as Topic; Mutation; Mycobacterium tuberculosis; Tuberculosis, Pulmonary
PubMed: 25816236
DOI: 10.1371/journal.pone.0120470 -
Gynecologic Oncology Mar 2014To systematically review the published literature in order to estimate the incidence and describe the variability of human papillomavirus (HPV) infection in women... (Review)
Review
OBJECTIVE
To systematically review the published literature in order to estimate the incidence and describe the variability of human papillomavirus (HPV) infection in women following treatment for cervical neoplasia.
METHODS
Several scientific literature databases (e.g. PubMed, ISI Web of Science) were searched through January 31, 2012. Eligible articles provided data on (i) baseline HPV infection status within 6 months prior to or at time of treatment (pre-treatment); and (ii) HPV test results for women's first visit after treatment occurring within 36 months (post-treatment). We abstracted and summarized the post-treatment incidence of newly detected HPV genotypes that were not present at pre-treatment, overall and stratified by study and other population characteristics.
RESULTS
A total of 25 studies were included, reporting post-treatment HPV incidence in nearly 2000 women. Mean patient age ranged from 31 to 43 years (median 36). Most studies used cervical exfoliated cell specimens to test for HPV DNA (n=20; 80%), using polymerase chain reaction (n=21; 84%). Cervical neoplasia treatment included loop electrical excision procedure (n=11; 44%); laser conization (n=2; 8%); laser ablation, surgical conization, cryotherapy, alpha-interferon (n=1; 4% each); or multiple treatment regimens (n=8; 32%). Follow-up times post-treatment ranged from 1.5 to 36 months (median 6). More than half of studies (n=17; 68%) estimated the incidence of any HPV type following treatment, while 7 (28%) focused specifically on high-risk (HR) HPV. HPV incidence after treatment varied widely, ranging from 0 to 47% (interquartile range: 0%-15%) in up to 3 years of follow-up after treatment. Lower HPV incidence was observed among studies that included relatively younger women, used laser conization, focused on HR-HPV rather than overall HPV infection, and had a lower proportion of recurrent cervical disease.
CONCLUSIONS
These modest summary incidence estimates from the published literature can guide clinicians, epidemiologists and health economists in developing best practices for post-treatment cervical cancer prevention.
Topics: Female; Humans; Incidence; Papillomaviridae; Papillomavirus Infections; Uterine Cervical Neoplasms; Uterine Cervical Dysplasia
PubMed: 24412508
DOI: 10.1016/j.ygyno.2013.12.040 -
Sao Paulo Medical Journal = Revista... 2012The age-stratified performance of the oncogenic HPV-DNA (human papillomavirus deoxyribonucleic acid) test for triage of low-grade squamous intraepithelial lesions (LSIL)... (Review)
Review
Colposcopic triage methods for detecting cervical intraepithelial neoplasia grade 3 after cytopathological diagnosis of low-grade squamous intraepithelial lesion: a systematic review on diagnostic tests.
CONTEXT AND OBJECTIVE
The age-stratified performance of the oncogenic HPV-DNA (human papillomavirus deoxyribonucleic acid) test for triage of low-grade squamous intraepithelial lesions (LSIL) requires investigation. The objective of this study was to evaluate and compare the age-stratified performance (cutoff point: 35 years) of oncogenic HPV-DNA testing and repeated cytological tests, for detecting cervical intraepithelial neoplasia grade 3 (CIN3), in order to triage for LSIL.
DESIGN AND SETTING
Systematic review. Studies were identified in nine electronic databases and in the reference lists of the articles retrieved.
METHODS
The eligibility criteria consisted of initial cytological findings of LSIL; subsequent oncogenic HPV-DNA testing and repeated cytological tests; and CIN3 detection. The Quality Assessment of Diagnostic Accuracy Studies (QUADAS) guidelines were used for quality assessment. Qualitative information synthesis was performed.
RESULTS
Out of 7,776 studies, 284 were identified as pertinent and three fulfilled the eligibility criteria. The CIN3 prevalence ranged from 6% to 12%. The HPV-DNA positivity rate ranged from 64% to 83%; sensitivity for CIN3 detection ranged from 95.2% to 100%; and specificity was available in two studies (27% and 52%). The sensitivity of repeated cytological tests, in relation to the threshold for atypical squamous cells of undetermined significance (ASCUS), was available in two studies (33% and 90.8%); and specificity was available in one study (53%).
CONCLUSIONS
Currently, there is no scientific evidence available that would prove that colposcopic triage using oncogenic HPV-DNA testing to detect CIN3 performs better than repeated cytological tests, among women with LSIL aged 35 years and over.
Topics: Adult; Age Factors; Colposcopy; DNA Probes, HPV; Female; Humans; Papillomavirus Infections; Sensitivity and Specificity; Triage; Uterine Cervical Neoplasms; Uterine Cervical Dysplasia
PubMed: 22344359
DOI: 10.1590/s1516-31802012000100008 -
Revista de Salud Publica (Bogota,... 2009Avian mycobacteriosis is important for animal and human health; wild birds play an important role in mycobacterial species' ecology and movement. This review was aimed... (Review)
Review
Avian mycobacteriosis is important for animal and human health; wild birds play an important role in mycobacterial species' ecology and movement. This review was aimed at reporting the role of birds in the spread of avian mycobacteriosis in human and animal populations at risk and thus a systematic review was made of PubMed, Science Direct, Scielo and Scirus databases. Mycobacteria are classified into the Mycobacterium tuberculosis complex and non-tuberculous mycobacteria; the Mycobacterium avium complex represents the most important part of the latter because it is primarily responsible for mycobacterial infection in wild birds and is a potential pathogen for mammals, especially for immunocompromised patients. The clinical signs in birds are variable as it is a chronic and debilitating disease, involving emaciated carcasses, white nodules in different organs and microscopically it presents granulomatosous multifocal inflammation. Diagnosis begins by suspicion based on clinical signs and finishes with microbiological confirmation. New diagnostic techniques include testing with DNA-RNA probes. No effective treatment is currently available and chemoprophylaxis on suspicion of infection is not recommended at the start; these factors increase the potential risk of mycobacteriosis becoming one of the most frequently documented zoonotic diseases which is difficult to treat in birds and humans. Recent concern regarding mycobacterial infection lies in the increased frequency of these opportunistic infections occurring in immunocompromised individuals and these infections' potential impact on bird conservation, this being increased by greater contact between humans and wild and captive birds.
Topics: Animals; Birds; Humans; Risk Factors; Tuberculosis, Avian
PubMed: 19721987
DOI: 10.1590/s0124-00642009000100014