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PloS One 2015Tuberculosis (TB) incidence and mortality are declining worldwide; however, poor detection of drug-resistant disease threatens to reverse current progress toward global... (Review)
Review
BACKGROUND
Tuberculosis (TB) incidence and mortality are declining worldwide; however, poor detection of drug-resistant disease threatens to reverse current progress toward global TB control. Multiple, rapid molecular diagnostic tests have recently been developed to detect genetic mutations in Mycobacterium tuberculosis (Mtb) genes known to confer first-line drug resistance. Their utility, though, depends on the frequency and distribution of the resistance associated mutations in the pathogen population. Mutations associated with rifampicin resistance, one of the two first-line drugs, are well understood and appear to occur in a single gene region in >95% of phenotypically resistant isolates. Mutations associated with isoniazid, the other first-line drug, are more complex and occur in multiple Mtb genes.
OBJECTIVES/METHODOLOGY
A systematic review of all published studies from January 2000 through August 2013 was conducted to quantify the frequency of the most common mutations associated with isoniazid resistance, to describe the frequency at which these mutations co-occur, and to identify the regional differences in the distribution of these mutations. Mutation data from 118 publications were extracted and analyzed for 11,411 Mtb isolates from 49 countries.
PRINCIPAL FINDINGS/CONCLUSIONS
Globally, 64% of all observed phenotypic isoniazid resistance was associated with the katG315 mutation. The second most frequently observed mutation, inhA-15, was reported among 19% of phenotypically resistant isolates. These two mutations, katG315 and inhA-15, combined with ten of the most commonly occurring mutations in the inhA promoter and the ahpC-oxyR intergenic region explain 84% of global phenotypic isoniazid resistance. Regional variation in the frequency of individual mutations may limit the sensitivity of molecular diagnostic tests. Well-designed systematic surveys and whole genome sequencing are needed to identify mutation frequencies in geographic regions where rapid molecular tests are currently being deployed, providing a context for interpretation of test results and the opportunity for improving the next generation of diagnostics.
Topics: Antitubercular Agents; Bacterial Proteins; Drug Resistance, Multiple, Bacterial; Humans; Isoniazid; Mutation; Mycobacterium tuberculosis; Oxidoreductases; Tuberculosis, Multidrug-Resistant
PubMed: 25799046
DOI: 10.1371/journal.pone.0119628 -
Journal of Clinical Microbiology Nov 2015Treponema pallidum PCR (Tp-PCR) testing now is recommended as a valid tool for the diagnosis of primary or secondary syphilis. The objectives were to systematically... (Comparative Study)
Comparative Study Meta-Analysis Review
Comparison of Diagnostic Accuracy of PCR Targeting the 47-Kilodalton Protein Membrane Gene of Treponema pallidum and PCR Targeting the DNA Polymerase I Gene: Systematic Review and Meta-analysis.
Treponema pallidum PCR (Tp-PCR) testing now is recommended as a valid tool for the diagnosis of primary or secondary syphilis. The objectives were to systematically review and determine the optimal specific target gene to be used for Tp-PCR. Comparisons of the performance of the two main targets are tpp47 and polA genes were done using meta-analysis. Three electronic bibliographic databases, representing abstract books from five conferences specialized in infectious diseases from January 1990 to March 2015, were searched. Search keywords included ("syphilis" OR "Treponema pallidum" OR "neurosyphilis") AND ("PCR" OR "PCR" OR "molecular amplification"). We included diagnostic studies assessing the performance of Tp-PCR targeting tpp47 (tpp47-Tp-PCR) or the polA gene (polA-Tp-PCR) in ulcers from early syphilis. All studies were assessed against quality criteria using the QUADAS-2 tool. Of 37 studies identified, 62.2% were judged at low risk of bias or applicability. Most used the U.S. Centers for Disease Control and Prevention (CDC) case definitions for primary or secondary (early) syphilis (89.2%; n = 33); 15 (40.5%) used darkfield microscopy (DFM). We did not find differences in sensitivity and specificity between the two Tp-PCR methods in the subgroup of studies using adequate reference tests. Among studies using DFM as the reference test, sensitivities were 79.8% (95% confidence intervals [CI], 72.7 to 85.4%) and 71.4% (46.0 to 88.0%) for tpp47-Tp-PCR and polA-Tp-PCR (P = 0.217), respectively; respective specificities were 95.3% (93.5 to 96.6%) and 93.7% (91.8 to 95.2%) (P = 0.304). Our findings suggest that the two Tp-PCR methods have similar accuracy and could be used interchangeably.
Topics: Carrier Proteins; DNA Polymerase I; Humans; Lipoproteins; Polymerase Chain Reaction; Sensitivity and Specificity; Syphilis; Treponema pallidum
PubMed: 26311859
DOI: 10.1128/JCM.01619-15 -
Journal of Global Antimicrobial... Jun 2020Carbapenem-resistant Enterobacteriaceae (CRE) are a major public-health threat. The most important mechanism of carbapenem resistance in CRE is carbapenemase production.... (Meta-Analysis)
Meta-Analysis
OBJECTIVES
Carbapenem-resistant Enterobacteriaceae (CRE) are a major public-health threat. The most important mechanism of carbapenem resistance in CRE is carbapenemase production. Early identification of carbapenemase-producing Enterobacteriaceae (CPE) leads to improved clinical outcomes. This systematic review aimed to assess the accuracy and applicability of the modified Hodge test (MHT), the carbapenemase Nordmann-Poirel (Carba NP) test, the modified carbapenem inactivation method (mCIM) and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS) for CPE detection.
METHODS
The meta-analysis included pooled sensitivity, specificity, diagnostic odds ratio, and summary receiver operating characteristic (SROC) curve and area under the curve (AUC).
RESULTS
A total of 67 studies were included in the analysis. Pooled effect sizes (95% confidence interval) of the MHT, Carba NP, mCIM and MALDI-TOF/MS, respectively, were as follows: sensitivity, 92% (87-95%), 97% (94-98%), 99% (99-100%) and 99% (96-100%); specificity, 93% (86-97%), 100% (99-100%), 99% (96-100%) and 99% (96-100%); diagnostic odds ratio, 98.156 (48.175-199.995), 1277.710 (751.391-2172.692), 3597.352 (1287.575-10000) and 1781.360 (651.827-4868.228); and AUC, 0.97, 1, 1 and 1.
CONCLUSION
Carba NP, mCIM and MALDI-TOF/MS all demonstrated high accuracy in CPE detection, whereas the MHT is not recommended owing to some clear drawbacks. We recommend the selection of carbapenemase detection tests in the order of mCIM, Carba NP and MALDI-TOF/MS according to their simplicity, cost, and equipment and skills involved.
Topics: Bacterial Proteins; Bacteriological Techniques; Carbapenem-Resistant Enterobacteriaceae; Enterobacteriaceae Infections; Humans; Phenotype; Public Health; Sensitivity and Specificity; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; beta-Lactamases
PubMed: 31639543
DOI: 10.1016/j.jgar.2019.10.010 -
Pathogens and Disease Jul 2017Chlamydia trachomatis (hereafter CT) is Gram-negative, obligate intracellular pathogen. It causes the world's most common non-viral sexually transmitted disease. India... (Review)
Review
Chlamydia trachomatis (hereafter CT) is Gram-negative, obligate intracellular pathogen. It causes the world's most common non-viral sexually transmitted disease. India is home to the world's greatest burden of infectious diseases, yet information on prevalence rates of CT is scarce. This article systematically reviews the literature for the prevalence rates and testing methods in India. A total of 27 studies were included. Four main patients groups (symptomatic women, infertile women, pregnant women and asymptomatic population groups) could be identified with varying rates of CT (0.1%-32% using PCR, 2.4%-75% using ELISA serology). Most of the studies originated from urban settings, 11 of them from New Delhi. In-house PCR was the most common diagnostic technique used generating the following ranges in prevalence for the four group studies: symptomatic women 10%-50%, pregnant women 0.1%-2.5% and asymptomatic populations 0.9%-24.5%. The rates among infertile women were 9%-68% based on serology results. The prevalence rates featured in this paper are in line with other locations across the Indian subcontinent. This review highlights the extreme heterogeneity in the limited studies available in India on CT and the need for standardized guidelines for diagnosis and management of CT in India. The availability of resources should be considered in the formulation of recommendations.
Topics: Adult; Antigens, Bacterial; Asymptomatic Diseases; Chlamydia Infections; Chlamydia trachomatis; DNA, Bacterial; Enzyme-Linked Immunosorbent Assay; Female; Humans; India; Infertility, Female; Polymerase Chain Reaction; Pregnancy; Prevalence; Severity of Illness Index
PubMed: 28582495
DOI: 10.1093/femspd/ftx055 -
Antimicrobial Resistance and Infection... 2018Mupirocin is widely used for nasal decolonization of to prevent subsequent staphylococcal infection in patients and healthcare personnel. However, the prolonged and... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Mupirocin is widely used for nasal decolonization of to prevent subsequent staphylococcal infection in patients and healthcare personnel. However, the prolonged and unrestricted use has led to the emergence of mupirocin-resistant (mupR) . The aim of this systematic review was to investigate the prevalence, phenotypic and molecular characteristics, and geographic spread of mupR in Africa.
METHODS
We examined five electronic databases (EBSCOhost, Google Scholar, ISI Web of Science, MEDLINE, and Scopus) for relevant English articles on screening for mupR from various samples in Africa. In addition, we performed random effects meta-analysis of proportions to determine the pooled prevalence of mupR in Africa. The search was conducted until 3 August 2016.
RESULTS
We identified 43 eligible studies of which 11 (26%) were obtained only through Google Scholar. Most of the eligible studies (28/43; 65%) were conducted in Nigeria (10/43; 23%), Egypt (7/43; 16%), South Africa (6/43; 14%) and Tunisia (5/43; 12%). Overall, screening for mupR was described in only 12 of 54 (22%) African countries. The disk diffusion method was the widely used technique (67%; 29/43) for the detection of mupR in Africa. The -positive isolates were identified in five studies conducted in Egypt ( = 2), South Africa ( = 2), and Nigeria ( = 1). Low-level resistance (LmupR) and high-level resistance (HmupR) were both reported in six human studies from South Africa ( = 3), Egypt ( = 2) and Libya ( = 1). Data on mupR-MRSA was available in 11 studies from five countries, including Egypt, Ghana, Libya, Nigeria and South Africa. The pooled prevalence (based on 11 human studies) of mupR in Africa was 14% (95% CI =6.8 to 23.2%). The proportion of -positive in Africa ranged between 0.5 and 8%. Furthermore, the frequency of isolates that exhibited LmupR, HmupR and mupR-MRSA in Africa were 4 and 47%, 0.5 and 38%, 5 and 50%, respectively.
CONCLUSIONS
The prevalence of mupR in Africa (14%) is worrisome and there is a need for data on administration and use of mupirocin. The disk diffusion method which is widely utilized in Africa could be an important method for the screening and identification of mupR . Moreover, we advocate for surveillance studies with appropriate guidelines for screening mupR in Africa.
Topics: Africa; Animals; Anti-Bacterial Agents; Bacterial Proteins; Cattle; Cattle Diseases; Databases, Bibliographic; Drug Resistance, Bacterial; Humans; Mupirocin; Sheep; Sheep Diseases; Staphylococcal Infections; Staphylococcus aureus
PubMed: 30147868
DOI: 10.1186/s13756-018-0382-5 -
Acta Obstetricia Et Gynecologica... Jul 2020The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has exposed vulnerable populations to an unprecedented global health crisis. The...
INTRODUCTION
The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has exposed vulnerable populations to an unprecedented global health crisis. The knowledge gained from previous human coronavirus outbreaks suggests that pregnant women and their fetuses are particularly susceptible to poor outcomes. The objective of this study was to summarize the clinical manifestations and maternal and perinatal outcomes of COVID-19 during pregnancy.
MATERIAL AND METHODS
We searched databases for all case reports and series from 12 February to 4 April 2020. Multiple terms and combinations were used including COVID-19, pregnancy, maternal mortality, maternal morbidity, complications, clinical manifestations, neonatal morbidity, intrauterine fetal death, neonatal mortality and SARS-CoV-2. Eligibility criteria included peer-reviewed publications written in English or Chinese and quantitative real-time polymerase chain reaction (PCR) or dual fluorescence PCR-confirmed SARS-CoV-2 infection. Unpublished reports, unspecified date and location of the study or suspicion of duplicate reporting, cases with suspected COVID-19 that were not confirmed by a laboratory test, and unreported maternal or perinatal outcomes were excluded. Data on clinical manifestations, maternal and perinatal outcomes including vertical transmission were extracted and analyzed.
RESULTS
Eighteen articles reporting data from 108 pregnancies between 8 December 2019 and 1 April 2020 were included in the current study. Most reports described women presenting in the third trimester with fever (68%) and coughing (34%). Lymphocytopenia (59%) with elevated C-reactive protein (70%) was observed and 91% of the women were delivered by cesarean section. Three maternal intensive care unit admissions were noted but no maternal deaths. One neonatal death and one intrauterine death were also reported.
CONCLUSIONS
Although the majority of mothers were discharged without any major complications, severe maternal morbidity as a result of COVID-19 and perinatal deaths were reported. Vertical transmission of the COVID-19 could not be ruled out. Careful monitoring of pregnancies with COVID-19 and measures to prevent neonatal infection are warranted.
Topics: Betacoronavirus; COVID-19; Cesarean Section; Coronavirus Infections; Female; Humans; Infant; Infant, Newborn; Infectious Disease Transmission, Vertical; Maternal Mortality; Pandemics; Perinatal Mortality; Pneumonia, Viral; Pregnancy; Pregnancy Complications, Infectious; Pregnancy Outcome; SARS-CoV-2
PubMed: 32259279
DOI: 10.1111/aogs.13867 -
Annals of Internal Medicine Sep 2016Diagnosis of chronic hepatitis C virus (HCV) infection requires both a positive HCV antibody screen and confirmatory nucleic acid testing (NAT). Testing for hepatitis C... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Diagnosis of chronic hepatitis C virus (HCV) infection requires both a positive HCV antibody screen and confirmatory nucleic acid testing (NAT). Testing for hepatitis C virus core antigen (HCVcAg) is a potential alternative to NAT.
PURPOSE
To evaluate the accuracy of diagnosis of active HCV infection among adults and children for 5 HCVcAg tests compared with NAT.
DATA SOURCES
EMBASE, PubMed, Web of Science, Scopus, and Cochrane Database of Systematic Reviews from 1990 through 31 March 2016.
STUDY SELECTION
Case-control, cross-sectional, cohort, or randomized trials that compared any of 5 HCVcAg tests with an NAT reference standard.
DATA EXTRACTION
2 independent reviewers extracted data and assessed quality using an adapted QUADAS-2 (Quality Assessment of Diagnostic Accuracy Studies 2) tool.
DATA SYNTHESIS
44 studies evaluated 5 index tests. Studies for the Abbott ARCHITECT HCV Ag assay had the highest quality, whereas those for the Ortho HCV Ag enzyme-linked immunosorbent assay (ELISA) had the lowest quality. From bivariate analyses, the sensitivity and specificity of the assays were as follows: Abbott ARCHITECT, 93.4% (95% CI, 90.1% to 96.4%) and 98.8% (CI, 97.4% to 99.5%); Ortho ELISA, 93.2% (CI, 81.6% to 97.7%) and 99.2% (CI, 87.9% to 100%); and Hunan Jynda Bioengineering Group HCV Ag ELISA, 59.5% (CI, 46.0% to 71.7%) and 82.9% (CI, 58.6% to 94.3%). Insufficient data were available for a meta-analysis about the Fujirebio Lumipulse Ortho HCV Ag and Eiken Lumispot HCV Ag assays. In 3 quantitative studies using Abbott ARCHITECT, HCVcAg correlated closely with HCV RNA levels greater than 3000 IU/mL.
LIMITATIONS
Insufficient data were available on covariates, such as HIV or hepatitis B virus status, for subgroup analyses. Few studies reported genotypes of isolates, and data for genotypes 4, 5, and 6 were scant. Most studies were conducted in high-resource settings and reference laboratories.
CONCLUSION
The HCVcAg assays with signal amplification have high sensitivity, high specificity, and good correlation with HCV RNA levels greater than 3000 IU/mL and have the potential to replace NAT in settings with high HCV prevalence.
PRIMARY FUNDING SOURCE
National Institutes of Health.
Topics: Cross-Sectional Studies; Genotype; Hepacivirus; Hepatitis C; Hepatitis C Antigens; Humans; Nucleic Acid Amplification Techniques; RNA, Viral; Sensitivity and Specificity
PubMed: 27322622
DOI: 10.7326/M16-0065 -
Sexually Transmitted Infections Dec 2017Reducing HIV mother-to-child transmission (MTCT) is critical to ending the HIV pandemic. Reports suggest that herpes simplex virus-2 (HSV-2), a common coinfection in... (Review)
Review
BACKGROUND
Reducing HIV mother-to-child transmission (MTCT) is critical to ending the HIV pandemic. Reports suggest that herpes simplex virus-2 (HSV-2), a common coinfection in HIV-infected individuals, is associated with increased MTCT, but results have been conflicting. We conducted a systematic review of observational studies to quantify the magnitude of this relationship (PROSPERO no. CRD42016043315).
METHODS
We searched Medline (1981 to June week 3, 2016), EMBASE (1981 to week 26, 2016), relevant conferences (2013-2016) and bibliographies of identified studies for cohort and case-control studies enrolling HIV-positive women during pregnancy or peripartum that quantified the effect of HSV-2 infection on MTCT. The primary outcome was the risk of perinatal HIV transmission associated with maternal HSV-2 status. Risk of bias was evaluated using a standardised tool, and results were meta-analysed where appropriate using a random-effects model, with studies weighted using the inverse variance method.
RESULTS
From 2103 hits, 112 studies were considered for inclusion, and 10 were ultimately included. Of the included studies, three used a case-control design, three were retrospective cohorts and four were prospective cohorts. Risk of bias was low in three studies, moderate in six and high in one. The median sample size was 278.5 mother-infant pairs (range: 48-1513). The most common strategy for classifying maternal HSV-2 status was type-specific serology (n=6), followed by genital shedding (n=3) or genital culture (n=3), clinical diagnosis of herpes (n=2) or genital ulcer disease (n=1). Results from five studies that provided quantitative estimates of the association between HSV-2 seropositivity and MTCT were meta-analysed, yielding a pooled unadjusted OR=1.17 (95% CI=0.69 to 1.96, I=58%). Three of these studies further considered key confounding variables, specifically antiretroviral use and/or viral load (n=3), and mode of delivery (n=2), yielding a pooled adjusted OR=1.57 (95% CI=1.17 to 2.11, I=0).
CONCLUSIONS
Maternal HSV-2 coinfection appears to be associated with increased perinatal HIV transmission. Further study of the effect of HSV-2 treatment on MTCT is warranted.
Topics: Antibodies, Viral; Coinfection; Female; HIV Infections; Herpes Genitalis; Herpesvirus 2, Human; Humans; Infectious Disease Transmission, Vertical; Observational Studies as Topic; Pregnancy; Pregnancy Complications, Infectious; Prevalence; Risk Factors; Seroepidemiologic Studies; Viral Load
PubMed: 28600331
DOI: 10.1136/sextrans-2016-052921 -
Parasitology Jul 2020Reliable diagnosis of human helminth infection(s) is essential for ongoing disease surveillance and disease elimination. Current WHO-recommended diagnostic assays are... (Review)
Review
Reliable diagnosis of human helminth infection(s) is essential for ongoing disease surveillance and disease elimination. Current WHO-recommended diagnostic assays are unreliable in low-endemic near-elimination settings and typically involve the invasive, onerous and potentially hazardous sampling of bodily fluids such as stool and blood, as well as tissue via biopsy. In contrast, diagnosis by use of non-invasive urine sampling is generally painless, more convenient and low risk. It negates the need for specialist staff, can usually be obtained immediately upon request and is better accepted by patients. In some instances, urine-based diagnostic assays have also been shown to provide a more reliable diagnosis of infection when compared to traditional methods that require alternative and more invasive bodily samples, particularly in low-endemicity settings. Given these relative benefits, we identify and review current research literature to evaluate whether non-invasive urine sampling is currently exploited to its full potential in the development of diagnostic tools for human helminthiases. Though further development, assessment and validation are needed before their routine use in control programmes, low-cost, rapid and reliable assays capable of detecting transrenal helminth-derived antigens and cell-free DNA show excellent promise for future use at the point-of-care in high-, medium- and even low-endemicity elimination settings.
Topics: Animals; Antigens, Helminth; Biomarkers; DNA, Helminth; Eosinophil Cationic Protein; Feces; Helminthiasis; Helminths; Humans; Schistosomiasis; Urine
PubMed: 31831084
DOI: 10.1017/S0031182019001732 -
Annals of Allergy, Asthma & Immunology... Sep 2017
Review
Topics: Allergens; Bacterial Proteins; Crops, Agricultural; Food Hypersensitivity; Food, Genetically Modified; Humans; Immune Sera; Immunoglobulin E; Plants, Genetically Modified; Risk Assessment; Transgenes; Uncertainty
PubMed: 28890018
DOI: 10.1016/j.anai.2017.07.010