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Clinical Infectious Diseases : An... Jun 2024This meta-analysis examines the comparative diagnostic performance of polymerase chain reaction (PCR) for the diagnosis of Pneumocystis pneumonia (PCP) on different...
BACKGROUND
This meta-analysis examines the comparative diagnostic performance of polymerase chain reaction (PCR) for the diagnosis of Pneumocystis pneumonia (PCP) on different respiratory tract samples, in both human immunodeficiency virus (HIV) and non-HIV populations.
METHODS
A total of 55 articles met inclusion criteria, including 11 434 PCR assays on respiratory specimens from 7835 patients at risk of PCP. QUADAS-2 tool indicated low risk of bias across all studies. Using a bivariate and random-effects meta-regression analysis, the diagnostic performance of PCR against the European Organisation for Research and Treatment of Cancer-Mycoses Study Group definition of proven PCP was examined.
RESULTS
Quantitative PCR (qPCR) on bronchoalveolar lavage fluid provided the highest pooled sensitivity of 98.7% (95% confidence interval [CI], 96.8%-99.5%), adequate specificity of 89.3% (95% CI, 84.4%-92.7%), negative likelihood ratio (LR-) of 0.014, and positive likelihood ratio (LR+) of 9.19. qPCR on induced sputum provided similarly high sensitivity of 99.0% (95% CI, 94.4%-99.3%) but a reduced specificity of 81.5% (95% CI, 72.1%-88.3%), LR- of 0.024, and LR+ of 5.30. qPCR on upper respiratory tract samples provided lower sensitivity of 89.2% (95% CI, 71.0%-96.5%), high specificity of 90.5% (95% CI, 80.9%-95.5%), LR- of 0.120, and LR+ of 9.34. There was no significant difference in sensitivity and specificity of PCR according to HIV status of patients.
CONCLUSIONS
On deeper respiratory tract specimens, PCR negativity can be used to confidently exclude PCP, but PCR positivity will likely require clinical interpretation to distinguish between colonization and active infection, partially dependent on the strength of the PCR signal (indicative of fungal burden), the specimen type, and patient population tested.
PubMed: 38860786
DOI: 10.1093/cid/ciae239 -
Journal of the Egyptian National Cancer... Dec 2023The second most deadly gynecological cancer worldwide, cervical cancer is steadily on the rise in sub-Saharan Africa, while vaccination programs are struggling to get... (Review)
Review
INTRODUCTION
The second most deadly gynecological cancer worldwide, cervical cancer is steadily on the rise in sub-Saharan Africa, while vaccination programs are struggling to get off the ground. This systematic review's aim was to assess the prevalence and distribution of high- and low-risk HPV genotypes in West African women.
METHODS
Original studies were retrieved from PubMed/Medline, Embase, Scopus, Google Scholar, and Science Direct. In these studies, Human papillomavirus (HPV) DNA was assessed in cervical samples by polymerase chain reaction (PCR), Hybrid capture, and sequencing. The quality of the articles was assessed and the results were extracted and reviewed.
RESULTS
Thirty-nine studies from 10 West African countries were included for the systematic review including 30 for the pooled analysis. From an overall of 17358 participants, 5126 of whom were infected with at least one HPV genotype, the systematic review showed a prevalence varying from 8.9% to 81.8% in the general population. In contrast, the pooled prevalence of infection was 28.6% (n = 3890; 95% CI 27.85-29.38), and HPV-52 (13.3%), HPV-56 (9.3%), and HPV-35 (8.2) were the most frequent. Quadrivalent and nonavalent vaccines covered 18.2% and 55.8% of identified genotypes respectively.
CONCLUSION
Faced with this growing public health challenge in West Africa, it would be necessary for all its countries to have reliable data on HPV infection and to introduce the nonavalent vaccine. A study of the genotypic distribution of HPV in high-grade precancerous lesions and cervical cancer would be very useful in West Africa.
Topics: Humans; Female; Uterine Cervical Neoplasms; Human Papillomavirus Viruses; Vaccination Coverage; Papillomavirus Infections; Papillomaviridae; Genotype; Prevalence
PubMed: 38060078
DOI: 10.1186/s43046-023-00196-x -
Survey of Ophthalmology 2024Acute retinal necrosis is a progressive intraocular inflammatory syndrome characterized by diffuse necrotizing retinitis that can lead to a poor visual outcome, mainly... (Meta-Analysis)
Meta-Analysis Review
Acute retinal necrosis is a progressive intraocular inflammatory syndrome characterized by diffuse necrotizing retinitis that can lead to a poor visual outcome, mainly from retinal detachment. The antiviral treatment approach for acute retinal necrosis varies as there are no established guidelines. We summarize the outcomes of acute retinal necrosis with available antiviral treatments. Electronic searches were conducted in PubMed/MEDLINE, EMBASE, Scopus, and Google Scholar for interventional and observational studies. Meta-analysis was performed to evaluate the pooled proportion of the predefined selected outcomes. This study was registered in PROSPERO (CRD42022320987). Thirty-four studies with a total of 963 participants and 1,090 eyes were included in the final analysis. The estimated varicella-zoster virus and herpes simplex virus polymerase chain reaction-positive cases were 63% (95% CI: 55-71%) and 35% (95% CI: 28-42%), respectively. The 3 main antiviral treatment approaches identified were oral antivirals alone, intravenous antivirals alone, and a combination of systemic (oral or intravenous) and intravitreal antivirals. The overall pooled estimated proportions of visual acuity improvement, recurrence, and retinal detachment were 37% (95% CI: 27-47%), 14% (95% CI: 8-21%), and 43% (95% CI: 38-50%), respectively. Patients treated with systemic and intravitreal antivirals showed a trend towards better visual outcomes than those treated with systemic antivirals (oral or intravenous) alone, even though this analysis was not statistically significant (test for subgroup differences P = 0.83).
Topics: Humans; Retinal Necrosis Syndrome, Acute; Antiviral Agents; Acyclovir; Eye Infections, Viral; Retinal Detachment; Retrospective Studies
PubMed: 37774799
DOI: 10.1016/j.survophthal.2023.09.004 -
Reviews in Medical Virology Jul 2024This systematic review and meta-analysis aimed to compare the effectiveness and safety of azvudine versus nirmatrelvir/ritonavir (Paxlovid) in treating coronavirus... (Meta-Analysis)
Meta-Analysis Review
This systematic review and meta-analysis aimed to compare the effectiveness and safety of azvudine versus nirmatrelvir/ritonavir (Paxlovid) in treating coronavirus disease 2019 (COVID-19). The researchers conducted searches on PubMed, Cochrane Library, Web of Science, medRxiv, and Google Scholar until January 2024. The Cochrane risk of bias tool was utilised to evaluate the quality of the included studies, and data analysis was performed using Comprehensive Meta-Analysis software. Thirteen studies, including 4949 patients, were analysed. The meta-analysis results showed no significant difference between the azvudine and Paxlovid groups in terms of mortality rate (odds rate [OR] = 0.84, 95% confidence interval [CI]: 0.59-1.21), negative polymerase chain reaction (PCR) conversion time (standard mean difference [SMD] = 1.52, 95% CI: -1.07-4.11), and hospital stay (SMD = -0.39, 95% CI: -1.12-0.33). However, a significant difference was observed between the two groups in terms of intensive care unit admission (OR = 0.42, 95% CI: 0.23-0.75) and the need for mechanical ventilation (OR = 0.61, 95% CI: 0.44-0.86) in favour of azvudine. The incidence of adverse events in the azvudine group was significantly lower (OR = 0.66, 95% CI: 0.43-0.99). The certainty of evidence was rated as low and moderate. Azvudine and Paxlovid demonstrated similar effectiveness in reducing mortality rates, negative PCR conversion time and hospital stay. However, azvudine showed better effectiveness in improving other outcomes. Regarding the level of certainty of evidence, further research is needed to validate or challenge these results.
Topics: Humans; COVID-19 Drug Treatment; Antiviral Agents; SARS-CoV-2; Ritonavir; Drug Combinations; COVID-19; Lopinavir; Treatment Outcome
PubMed: 38849982
DOI: 10.1002/rmv.2551 -
Public Health Aug 2023This systematic review was conducted to estimate the respective prevalence of gonorrhea among two high-risk populations in China and determine the epidemiological... (Meta-Analysis)
Meta-Analysis Review
OBJECTIVES
This systematic review was conducted to estimate the respective prevalence of gonorrhea among two high-risk populations in China and determine the epidemiological features of gonorrhea in them.
STUDY DESIGN
Systematic review.
METHODS
PubMed, Web of Science, China National Knowledge Infrastructure, and Wanfang databases were searched to identify studies published between January 1, 1990, and October 31, 2022, with gonorrhea prevalence tested by polymerase chain reaction among female sex workers (FSWs) and men who have sex with men (MSM). Meta-regression and subgroup analyses were used to investigate potential factors of heterogeneity across studies. Trend analysis of prevalence was conducted by the Jonckheere-Terpstra method.
RESULTS
We identified 88 prevalence data points from 49 studies in China, with 30,853 participants of FSWs and 5523 participants of MSM. Pooled prevalence of gonorrhea among FSWs and MSM were 6.9% (95% confidence interval: 4.6-9.7%) and 2.5% (95% confidence interval: 1.5-3.7%), respectively. The subgroup analyses showed there were period, regional, and specimen collection methods diversities among FSWs, and diversities of the regions and specimen collection anatomical sites were found among MSM, in which the prevalence of rectum and pharynx was significantly higher than the urethra. A decreasing trend in the prevalence of gonorrhea was seen among FSWs (z = -4.03) from 1999 to 2021, not found for MSM in China.
CONCLUSION
The prevalence of gonorrhea is high in two high-risk groups in China, with extragenital infections requiring particular attention. The findings of this study will provide evidence to formulate national policy and guidance for gonorrhea prevention and control.
Topics: Male; Humans; Female; Gonorrhea; Homosexuality, Male; Sex Workers; Chlamydia Infections; Prevalence; Sexual and Gender Minorities; China; HIV Infections
PubMed: 37441994
DOI: 10.1016/j.puhe.2023.06.010 -
Journal of Medical Virology Jan 2024Acute gastroenteritis outbreaks may be caused by the excretion of norovirus (NoV) from asymptomatic individuals. Despite numerous studies involving asymptomatic NoV... (Meta-Analysis)
Meta-Analysis
Acute gastroenteritis outbreaks may be caused by the excretion of norovirus (NoV) from asymptomatic individuals. Despite numerous studies involving asymptomatic NoV infection during outbreaks in China, a comprehensive assessment of its role has not been conducted, which is critical for emergency management. Our objective was to assess the prevalence of asymptomatic NoV infection during outbreaks in China. We conducted a comprehensive search of multiple databases, including PubMed, Web of Science, Cochrane Library, China National Knowledge Infrastructure, China Wanfang, and China Weipu, between January 1, 1997 and June 19, 2023. The retrieved articles and their references underwent screening, which utilized polymerase chain reaction-based assays for the detection of NoV in asymptomatic individuals during outbreaks that occurred in China. The primary summary data were the prevalence of asymptomatic NoV infection in outbreaks. We generated pooled estimates of asymptomatic prevalence in the population as a whole and in subgroups by using random-effect models. Of the 97 articles included, the pooled asymptomatic prevalence of NoV among 5117 individuals in outbreaks was 17.6% (95% confidence interval [CI]: 14.1-21.3). The asymptomatic prevalence of NoV GII (17.1%, 95% CI: 12.9-21.5) was similar to that of NoV GI (22.0%, 95% CI: 12.8-32.4). However, the proportion of asymptomatic individuals involved in NoV GII (57.44%) was significantly higher than that of NoV GI (5.12%), and NoV GII (75.26%) was reported much more frequently than NoV GI (14.43%) in the included articles. Meta-regression analysis of 11 possible influencing factors (geographic region, setting, season, sample type, genotype, transmission route, occupation, age, per capita income, study quality, and cases definition) showed that the source of heterogeneity might be related to the outbreak settings, per capita income, and study quality (p = 0.037, 0.058, and 0.026, respectively). Of particular note was the asymptomatic prevalence peaked in preschoolers (27.8%), afterward, it fell into trough in elementary and junior school children (10.5%), before the second peak located in adults (17.8%), and the elderly (25.2%). Prevalent genotypes reported include GII.4, followed by GII.17, GII.2, GII.3, GII.6, and so forth. The estimated asymptomatic prevalence of NoV during outbreaks in China was as high as 17.6%, with NoV GII dominating. In addition, genetic subtypes of NoV in outbreaks should be detected whenever possible. The role of asymptomatic individuals in NoV outbreaks cannot be ignored. This knowledge will help governments develop public health policies and emergency response strategies for outbreaks, assess the burden, and develop vaccines.
Topics: Humans; Asymptomatic Infections; Caliciviridae Infections; China; Disease Outbreaks; Feces; Genotype; Norovirus; Phylogeny
PubMed: 38235934
DOI: 10.1002/jmv.29393 -
BMC Infectious Diseases Feb 2024Leptospirosis is an underdiagnosed infectious disease with non-specific clinical presentation that requires laboratory confirmation for diagnosis. The serologic... (Meta-Analysis)
Meta-Analysis
Diagnosis of human leptospirosis: systematic review and meta-analysis of the diagnostic accuracy of the Leptospira microscopic agglutination test, PCR targeting Lfb1, and IgM ELISA to Leptospira fainei serovar Hurstbridge.
BACKGROUND
Leptospirosis is an underdiagnosed infectious disease with non-specific clinical presentation that requires laboratory confirmation for diagnosis. The serologic reference standard remains the microscopic agglutination test (MAT) on paired serum samples. However, reported estimates of MAT's sensitivity vary. We evaluated the accuracy of four index tests, MAT on paired samples as well as alternative standards for leptospirosis diagnosis: MAT on single acute-phase samples, polymerase chain reaction (PCR) with the target gene Lfb1, and ELISA IgM with Leptospira fainei serovar Hurstbridge as an antigen.
METHODS
We performed a systematic review of studies reporting results of leptospirosis diagnostic tests. We searched eight electronic databases and selected studies that tested human blood samples and compared index tests with blood culture and/or PCR and/or MAT (comparator tests). For MAT selection criteria we defined a threshold for single acute-phase samples according to a national classification of leptospirosis endemicity. We used a Bayesian random-effect meta-analysis to estimate the sensitivity and specificity of MAT in single acute-phase and paired samples separately, and assessed risk of bias using the Quality Assessment of Studies of Diagnostic Accuracy Approach- 2 (QUADAS-2) tool.
RESULTS
For the MAT accuracy evaluation, 15 studies were included, 11 with single acute-phase serum, and 12 with paired sera. Two included studies used PCR targeting the Lfb1 gene, and one included study used IgM ELISA with Leptospira fainei serovar Hurstbridge as antigen. For MAT in single acute-phase samples, the pooled sensitivity and specificity were 14% (95% credible interval [CrI] 3-38%) and 86% (95% CrI 59-96%), respectively, and the predicted sensitivity and specificity were 14% (95% CrI 0-90%) and 86% (95% CrI 9-100%). Among paired MAT samples, the pooled sensitivity and specificity were 68% (95% CrI 32-92%) and 75% (95% CrI 45-93%) respectively, and the predicted sensitivity and specificity were 69% (95% CrI 2-100%) and 75% (2-100%).
CONCLUSIONS
Based on our analysis, the accuracy of MAT in paired samples was not high, but it remains the reference standard until a more accurate diagnostic test is developed. Future studies that include larger numbers of participants with paired samples will improve the certainty of accuracy estimates.
Topics: Humans; Serogroup; Bayes Theorem; Antibodies, Bacterial; Leptospira; Leptospirosis; Agglutination Tests; Sensitivity and Specificity; Enzyme-Linked Immunosorbent Assay; Immunoglobulin M; Polymerase Chain Reaction
PubMed: 38326762
DOI: 10.1186/s12879-023-08935-0 -
Clinical Microbiology and Infection :... Dec 2023Early identification of extended-spectrum ß-lactamase (ESBL) and carbapenemase-producing Enterobacterales (CP-CRE) is critical for timely therapy. Rapid phenotypic... (Meta-Analysis)
Meta-Analysis Review
Rapid phenotypic testing for detection of carbapenemase- or extended-spectrum ß-lactamase-producing Enterobacterales directly from blood cultures: a systematic review and meta-analysis.
BACKGROUND
Early identification of extended-spectrum ß-lactamase (ESBL) and carbapenemase-producing Enterobacterales (CP-CRE) is critical for timely therapy. Rapid phenotypic tests identifying these resistance mechanisms from pure bacterial colonies have been developed.
OBJECTIVES
To determine the operating characteristics of available rapid phenotypic tests when applied directly to positive blood cultures.
METHODS OF DATA SYNTHESIS
Bivariate random effects models were used unless convergence was not achieved where we used separate univariate models for sensitivity and specificity.
DATA SOURCES
MEDLINE, CENTRAL, Embase, BIOSIS, and Scopus from inception to 16 March 2021.
STUDY ELIGIBILITY CRITERIA
Studies using any rapid phenotypic assay for detection of ESBL or CP-CRE directly from blood cultures positive for Enterobacterales, including those utilizing spiked blood cultures. Case reports/series, posters, abstracts, review articles, those with ≤5 resistant isolates, and studies lacking data or without full text were excluded.
PARTICIPANTS
Consecutive patient samples (main analysis) or spiked blood cultures (sensitivity analysis).
TESTS
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assays (MALDI-TOF) and commercially available chromogenic or immunogenic assays.
REFERENCE STANDARD
Conventional laboratory methods and/or polymerase chain reaction (PCR).
ASSESSMENT OF RISK OF BIAS
Quality Assessment of Diagnostic Accuracy Studies Version 2 (QUADAS-2).
RESULTS
For detection of the ESBL phenotype the respective pooled sensitivities and specificities for consecutive clinical samples were as follows: 94% (95% CI 93-99%) and 97% (95% CI 95-100%) for MALDI-TOF/mass spectrometry (n = 1); and 98% (95% CI 92-100%) and 100% (95% CI 96-100%) for chromogenic assays (n = 7). For the CP-CRE phenotype the respective pooled sensitivity and specificities for consecutive clinical samples were as follows: 100% (95% CI 99-100%) and 100% (95% CI 100-100%) for MALDI-TOF (n = 2); 96% (95% CI 77-99%) and 100% (95% CI 81-100%) for chromogenic assays (n = 4); and 98% (95% CI 96-100%) and 100% (95% CI 100-100%) for immunogenic testing (n = 2).
CONCLUSIONS
Rapid phenotypic assays that can be directly applied to positive blood cultures to detect ESBL and carbapenemase production from Enterobacterales exist and, although clinical studies are limited, they appear to have high sensitivity and specificity. Their potential to facilitate patient care through timely identification of bacterial resistance should be further explored.
Topics: Humans; Anti-Bacterial Agents; Blood Culture; beta-Lactamases; Bacterial Proteins; Phenotype; Microbial Sensitivity Tests
PubMed: 37722531
DOI: 10.1016/j.cmi.2023.09.007 -
Diagnostics (Basel, Switzerland) Feb 2024Giardiasis, caused by the protozoan , affects around 400 million people worldwide, emphasizing the critical need for accurate diagnosis to enhance human health,... (Review)
Review
Giardiasis, caused by the protozoan , affects around 400 million people worldwide, emphasizing the critical need for accurate diagnosis to enhance human health, especially in children. Prolonged giardiasis in childhood can lead to intellectual deficits and other complications. A variety of diagnostic tools, including microscopic, immunological, and molecular methods, are available for detecting infection. Choosing the most suitable method can be challenging due to the abundance of options. This systematic review assesses the reliability and applicability of these diagnostic modalities. Utilizing the Dimensions and Wordart platforms for data analysis, we focus on relevant literature addressing diagnostic methods for human giardiasis. Microscopic techniques, particularly Ritchie's method, emerge as the primary choice, followed by enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR). PCR's limited use is attributed to its high cost and infrastructure challenges in developing nations. In conclusion, our analysis supports microscopic methods as the gold standard for giardiasis diagnosis. However, in cases where symptoms persist despite a negative diagnosis, employing more sensitive diagnostic approaches is advisable.
PubMed: 38396402
DOI: 10.3390/diagnostics14040364 -
Veterinary Parasitology, Regional... Jan 2024The role of ixodid ticks especially Rhipicephalus sanguineus and Heamaphysalis elliptica in the epidemiology of several diseases of veterinary and public health... (Review)
Review
The role of ixodid ticks especially Rhipicephalus sanguineus and Heamaphysalis elliptica in the epidemiology of several diseases of veterinary and public health importance have been documented. This study conducted a systematic review focusing on the distribution of R. sanguineus and H. elliptica, as well as the common tick-borne pathogens they harbour. The Scopus, ScienceDirect, PubMed, and Web of Science databases were used to search for English journal articles published between January 1990 and June 2021. The articles were assessed by following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. This systematic review was registered on PROSPERO [(ID no: CRD42022327372). Of the studies included in the systematic review, 247 and 19 articles had identified R. sanguineus and H. elliptica respectively, whereas 15 articles had identified both tick species. There is a reported worldwide distribution of R. sanguineus from 64 countries, whereas H. elliptica was only reported in the African continent from 6 countries. In total, 120 articles that were included in this systematic review reported detection of tick-borne pathogens from R. sanguineus (n = 118 articles) and/or H. elliptica (n = 2 articles) ticks. According to the studies tick-borne pathogens harboured by R. sanguineus included protozoa such as Babesia spp., Hepatozoon spp., Leishmania spp., and Theileria spp., as well as bacteria such as Acinetobacter spp. Anaplasma spp., Bacillus spp., Borrelia spp., Brucella spp., Coxiella spp., and Staphylococcus spp. The H. elliptica was reported to be harbouring Babesia spp., Ehrlichia spp. and Rickettsia spp. Most of the studies (50%) used the conventional polymerase chain reaction (PCR) technique for the detection of tick-borne pathogens, followed by real-time PCR (qPCR) (n = 26), and nested PCR (n = 22). This systematic review has shed light on the distribution of two common dog ticks as well as the tick-borne pathogens of veterinary and zoonotic importance they are harbouring. This data will enable surveillance studies that can report whether the distribution of these ticks and their associated tick-borne pathogens is expanding or shrinking or is stable.
Topics: Dogs; Animals; Rhipicephalus sanguineus; Ixodidae; Anaplasma; Babesia; Borrelia
PubMed: 38199685
DOI: 10.1016/j.vprsr.2023.100969