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The Cochrane Database of Systematic... Nov 2020Prior to introducing pneumococcal conjugate vaccines (PCVs), Streptococcus pneumoniae was most commonly isolated from the middle ear fluid of children with acute otitis...
BACKGROUND
Prior to introducing pneumococcal conjugate vaccines (PCVs), Streptococcus pneumoniae was most commonly isolated from the middle ear fluid of children with acute otitis media (AOM). Reducing nasopharyngeal colonisation of this bacterium by PCVs may lead to a decline in AOM. The effects of PCVs deserve ongoing monitoring since studies from the post-PCV era report a shift in causative otopathogens towards non-vaccine serotypes and other bacteria. This updated Cochrane Review was first published in 2002 and updated in 2004, 2009, 2014, and 2019.
OBJECTIVES
To assess the effect of PCVs in preventing AOM in children up to 12 years of age.
SEARCH METHODS
We searched CENTRAL, MEDLINE, Embase, CINAHL, LILACS, Web of Science, and two trials registers, ClinicalTrials.gov and WHO ICTRP, to 11 June 2020.
SELECTION CRITERIA
Randomised controlled trials of PCV versus placebo or control vaccine.
DATA COLLECTION AND ANALYSIS
We used the standard methodological procedures expected by Cochrane. The primary outcomes were frequency of all-cause AOM and adverse effects. Secondary outcomes included frequency of pneumococcal AOM and frequency of recurrent AOM (defined as three or more AOM episodes in six months or four or more in one year). We used GRADE to assess the certainty of the evidence.
MAIN RESULTS
We included 15 publications of 11 trials (60,733 children, range 74 to 37,868 per trial) of 7- to 11-valent PCVs versus control vaccines (meningococcus type C vaccine in three trials, and hepatitis A or B vaccine in eight trials). We included one additional publication of a previously included trial for this 2020 update. We did not find any relevant trials with the newer 13-valent PCV. Most studies were funded by pharmaceutical companies. Overall, risk of bias was low. In seven trials (59,415 children), PCVs were administered in early infancy, whilst four trials (1318 children) included children aged one year and over who were either healthy or had a history of respiratory illness. There was considerable clinical heterogeneity across studies, therefore we reported results from individual studies. PCV administered in early infancy PCV7 The licenced 7-valent PCV with CRM197 as carrier protein (CRM197-PCV7) was associated with a 6% (95% confidence interval (CI) -4% to 16%; 1 trial; 1662 children) and 6% (95% CI 4% to 9%; 1 trial; 37,868 children) relative risk reduction (RRR) in low-risk infants (moderate-certainty evidence), but was not associated with a reduction in all-cause AOM in high-risk infants (RRR -5%, 95% CI -25% to 12%). PCV7 with the outer membrane protein complex of Neisseria meningitidis serogroup B as carrier protein (OMPC-PCV7) was not associated with a reduction in all-cause AOM (RRR -1%, 95% CI -12% to 10%; 1 trial; 1666 children; low-certainty evidence). CRM197-PCV7 and OMPC-PCV7 were associated with 20% (95% CI 7% to 31%) and 25% (95% CI 11% to 37%) RRR in pneumococcal AOM, respectively (2 trials; 3328 children; high-certainty evidence), and CRM197-PCV7 with 9% (95% CI -12% to 27%) and 10% (95% CI 7% to 13%) RRR in recurrent AOM (2 trials; 39,530 children; moderate-certainty evidence). PHiD-CV10/11 The effect of a licenced 10-valent PCV conjugated to protein D, a surface lipoprotein of Haemophilus influenzae, (PHiD-CV10) on all-cause AOM in healthy infants varied from 6% (95% CI -6% to 17%; 1 trial; 5095 children) to 15% (95% CI -1% to 28%; 1 trial; 7359 children) RRR (low-certainty evidence). PHiD-CV11 was associated with 34% (95% CI 21% to 44%) RRR in all-cause AOM (1 trial; 4968 children; moderate-certainty evidence). PHiD-CV10 and PHiD-CV11 were associated with 53% (95% CI 16% to 74%) and 52% (95% CI 37% to 63%) RRR in pneumococcal AOM (2 trials; 12,327 children; high-certainty evidence), and PHiD-CV11 with 56% (95% CI -2% to 80%) RRR in recurrent AOM (1 trial; 4968 children; low-certainty evidence). PCV administered at a later age PCV7 We found no evidence of a beneficial effect on all-cause AOM of administering CRM197-PCV7 in children aged 1 to 7 years with a history of respiratory illness or frequent AOM (2 trials; 457 children; moderate-certainty evidence) and CRM197-PCV7 combined with a trivalent influenza vaccine in children aged 18 to 72 months with a history of respiratory tract infections (1 trial; 597 children; moderate-certainty evidence). CRM197-PCV9 In 1 trial including 264 healthy daycare attendees aged 1 to 3 years, CRM197-PCV9 was associated with 17% (95% CI -2% to 33%) RRR in parent-reported all-cause otitis media (very low-certainty evidence). Adverse events Nine trials reported on adverse effects (77,389 children; high-certainty evidence). Mild local reactions and fever were common in both groups, and occurred more frequently in PCV than in control vaccine groups: redness (< 2.5 cm): 5% to 20% versus 0% to 16%; swelling (< 2.5 cm): 5% to 12% versus 0% to 8%; and fever (< 39 °C): 15% to 44% versus 8% to 25%. More severe redness (> 2.5 cm), swelling (> 2.5 cm), and fever (> 39 °C) occurred less frequently (0% to 0.9%, 0.1% to 1.3%, and 0.4% to 2.5%, respectively) in children receiving PCV, and did not differ significantly between PCV and control vaccine groups. Pain or tenderness, or both, was reported more frequently in PCV than in control vaccine groups: 3% to 38% versus 0% to 8%. Serious adverse events judged to be causally related to vaccination were rare and did not differ significantly between groups, and no fatal serious adverse event judged causally related to vaccination was reported.
AUTHORS' CONCLUSIONS
Administration of the licenced CRM197-PCV7 and PHiD-CV10 during early infancy is associated with large relative risk reductions in pneumococcal AOM. However, the effects of these vaccines on all-cause AOM is far more uncertain based on low- to moderate-certainty evidence. We found no evidence of a beneficial effect on all-cause AOM of administering PCVs in high-risk infants, after early infancy, and in older children with a history of respiratory illness. Compared to control vaccines, PCVs were associated with an increase in mild local reactions (redness, swelling), fever, and pain and/or tenderness. There was no evidence of a difference in more severe local reactions, fever, or serious adverse events judged to be causally related to vaccination.
Topics: Acute Disease; Age Factors; Child; Child, Preschool; Female; Heptavalent Pneumococcal Conjugate Vaccine; Humans; Infant; Male; Otitis Media; Otitis Media with Effusion; Pneumococcal Vaccines; Randomized Controlled Trials as Topic; Vaccines, Conjugate
PubMed: 33231293
DOI: 10.1002/14651858.CD001480.pub6 -
BMC Pediatrics Nov 2019To summarize information about invasive pneumococcal disease (IPD) among children in mainland China. (Meta-Analysis)
Meta-Analysis
BACKGROUND
To summarize information about invasive pneumococcal disease (IPD) among children in mainland China.
METHODS
Sixteen eligible studies were included in this systematic review and the random effect model was used to estimate the pool prevalence of IPD.
RESULTS
The most predominant serotypes circulating in children were 19F (27.7, 95% confidence interval (95% CI): 17.7-37.6%), 19A (21.2%, 16.4-26.1%), 14 (16.5%, 12.8-20.1%), 6B (8.6%, 5.2-10.8%) and 23F (7.3%, 5.2-9.5%). The serotype coverage of the available pneumococcal conjugate vaccines PCV7, PCV10, and PCV13 was 60.8% (52.5-69.4%), 65.1% (57.7-72.4%), and 90.0% (87.1-92.8%), respectively. The pooled antibiotic resistance rates of Streptococcus pneumoniae revealed a resistance to penicillin prevalence rate of 32.0% (12.1-51.9%). Approximately 94.4% (90.7-98.1%) and 92.3% (87.4-97.3%) of isolates were resistant to erythromycin and clindamycin. eBURST analysis revealed great diversity among isolates, with 102 sequence types (STs) for 365 isolates. The major predominant clonal complexes (CCs) were CC271 (43.6%, 159/365), CC876 (13.4%, 49/365), CC81 (5.2%, 19/365), and CC90 (4.1%, 15/365). Long-term and regional surveillance of S. pneumoniae is necessary.
CONCLUSIONS
Based on our pooled results showing that PCV13 coverage of the reported serotypes was 90% and that most serotypes contributed to the distribution of antibiotic-resistant isolates, implementation of PCV13 into the Chinese Expanded Program on Immunizations (EPI) would achieve health benefits in Chinese children.
Topics: Child; China; Drug Resistance, Bacterial; Humans; Microbial Sensitivity Tests; Pneumococcal Infections; Pneumococcal Vaccines; Prevalence; Serotyping; Streptococcus pneumoniae; Vaccines, Conjugate
PubMed: 31711442
DOI: 10.1186/s12887-019-1722-1 -
The Cochrane Database of Systematic... Jan 2020Chronic suppurative otitis media (CSOM), sometimes referred to as chronic otitis media (COM), is a chronic inflammation and infection of the middle ear and mastoid... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Chronic suppurative otitis media (CSOM), sometimes referred to as chronic otitis media (COM), is a chronic inflammation and infection of the middle ear and mastoid cavity, characterised by ear discharge (otorrhoea) through a perforated tympanic membrane. The predominant symptoms of CSOM are ear discharge and hearing loss. Antibiotics and antiseptics kill or inhibit the micro-organisms that may be responsible for the infection. Antibiotics can be applied topically or administered systemically via the oral or injection route. Antiseptics are always directly applied to the ear (topically).
OBJECTIVES
To assess the effectiveness of antibiotics versus antiseptics for people with chronic suppurative otitis media (CSOM).
SEARCH METHODS
The Cochrane ENT Information Specialist searched the Cochrane ENT Register; Central Register of Controlled Trials (CENTRAL; 2019, Issue 4, via the Cochrane Register of Studies); Ovid MEDLINE; Ovid Embase; CINAHL; Web of Science; ClinicalTrials.gov; ICTRP and additional sources for published and unpublished trials. The date of the search was 1 April 2019.
SELECTION CRITERIA
We included randomised controlled trials (RCTs) with at least a one-week follow-up involving patients (adults and children) who had chronic ear discharge of unknown cause or CSOM, where ear discharge had continued for more than two weeks. The intervention was any single, or combination of, antibiotic agent, whether applied topically (without steroids) or systemically. The comparison was any single, or combination of, topical antiseptic agent, applied as ear drops, powders or irrigations, or as part of an aural toileting procedure. Two comparisons were topical antiseptics compared to: a) topical antibiotics or b) systemic antibiotics. Within each comparison we separated where both groups of patients had received topical antibiotic a) alone or with aural toilet and b) on top of background treatment (such as systemic antibiotics).
DATA COLLECTION AND ANALYSIS
We used the standard Cochrane methodological procedures. We used GRADE to assess the certainty of the evidence for each outcome. Our primary outcomes were: resolution of ear discharge or 'dry ear' (whether otoscopically confirmed or not), measured at between one week and up to two weeks, two weeks to up to four weeks, and after four weeks; health-related quality of life using a validated instrument; and ear pain (otalgia) or discomfort or local irritation. Secondary outcomes included hearing, serious complications and ototoxicity measured in several ways.
MAIN RESULTS
We identified seven studies (935 participants) across four comparisons with antibiotics compared against acetic acid, aluminium acetate, boric acid and povidone-iodine. None of the included studies reported the outcomes of quality of life or serious complications. A. Topical antiseptic (acetic acid) versus topical antibiotics (quinolones or aminoglycosides) It is very uncertain if there is a difference in resolution of ear discharge with acetic acid compared with aminoglycosides at one to two weeks (risk ratio (RR) 0.88, 95% confidence interval (CI) 0.72 to 1.08; 1 study; 100 participants; very low-certainty evidence). No study reported results for ear discharge after four weeks. It was very uncertain if there was more ear pain, discomfort or local irritation with acetic acid or topical antibiotics due to the low numbers of participants reporting events (RR 0.16, 95% CI 0.02 to 1.34; 2 RCTs; 189 participants; very low-certainty evidence). No differences between groups were reported narratively for hearing (quinolones) or suspected ototoxicity (aminoglycosides) (very low-certainty evidence). B. Topical antiseptic (aluminium acetate) versus topical antibiotics No results for the one study comparing topical antibiotics with aluminium acetate could be used in the review. C. Topical antiseptic (boric acid) versus topical antibiotics (quinolones) One study reported more participants with resolution of ear discharge when using topical antibiotics (quinolones) compared with boric acid ear drops at between one to two weeks (risk ratio (RR) 1.56, 95% confidence interval (CI) 1.27 to 1.92; 1 study; 409 participants; moderate-certainty evidence). This means that one additional person will have resolution of ear discharge for every five people receiving topical antibiotics (compared with boric acid) at two weeks. No study reported results for ear discharge after four weeks. There was a bigger improvement in hearing in the topical antibiotic group compared to the topical antiseptic group (mean difference (MD) 2.79 decibels (dB), 95% CI 0.48 to 5.10; 1 study; 390 participants; low-certainty evidence) but this difference may not be clinically significant. There may be more ear pain, discomfort or irritation with boric acid compared with quinolones (RR 0.56, 95% CI 0.32 to 0.98; 2 studies; 510 participants; low-certainty evidence). Suspected ototoxicity was not reported. D. Topical antiseptic (povidone-iodine) versus topical antibiotics (quinolones) It is uncertain if there is a difference between quinolones and povidone-iodine with respect to resolution of ear discharge at one to two weeks (RR 1.02, 95% CI 0.82 to 1.26; 1 RCT, 39 participants; very low-certainty evidence). The study reported qualitatively that there were no differences between the groups for hearing and no patients developed ototoxic effects (very low-certainty evidence). No results for resolution of ear discharge beyond four weeks, or ear pain, discomfort or irritation, were reported. E. Topical antiseptic (acetic acid) + aural toileting versus topical + systemic antibiotics (quinolones) One study reported that participants receiving topical and oral antibiotics had less resolution of ear discharge compared with acetic acid ear drops and aural toileting (suction clearance every two days) at one month (RR 0.69, 95% CI 0.53 to 0.90; 100 participants). The study did not report results for resolution of ear discharge at between one to two weeks, ear pain, discomfort or irritation, hearing or suspected ototoxicity.
AUTHORS' CONCLUSIONS
Treatment of CSOM with topical antibiotics (quinolones) probably results in an increase in resolution of ear discharge compared with boric acid at up to two weeks. There was limited evidence for the efficacy of other topical antibiotics or topical antiseptics and so we are unable to draw conclusions. Adverse events were not well reported.
Topics: Administration, Topical; Anti-Bacterial Agents; Anti-Infective Agents, Local; Humans; Otitis Media, Suppurative; Quinolones; Randomized Controlled Trials as Topic
PubMed: 31902139
DOI: 10.1002/14651858.CD013056.pub2 -
Human Vaccines & Immunotherapeutics Dec 2022In 2010, a 10-valent pneumococcal non-typeable protein D conjugate vaccine (PHiD-CV) was introduced in the Brazilian national immunization program; the 3 + 1 dose...
In 2010, a 10-valent pneumococcal non-typeable protein D conjugate vaccine (PHiD-CV) was introduced in the Brazilian national immunization program; the 3 + 1 dose schedule was replaced by a 2 + 1 dose schedule in 2016. This systematic review presents the latest published evidence (2015-2020) on the impact after 10-year use of PHiD-CV in Brazil from a total of 29 publications. Overall, the PHiD-CV program had a positive impact on the morbidity and mortality associated with invasive pneumococcal disease (IPD), pneumonia and acute otitis media (AOM) in children <5 years-old. A reduction in the vaccine-type invasive disease was observed in all-ages; suggesting indirect protection unvaccinated older children and adults. The occurrence of non-vaccine type disease was evidenced in some studies. Higher vaccination coverage is required at national and state level for sustained population impact. Given the change in the vaccination schedule and the dynamics of pneumococcal disease epidemiology, continuous surveillance is warranted.GSK Study identifier: HO-18-19438.
Topics: Adolescent; Brazil; Child; Child, Preschool; Humans; Infant; Otitis Media; Pneumococcal Infections; Pneumococcal Vaccines; Vaccination; Vaccines, Conjugate
PubMed: 33735585
DOI: 10.1080/21645515.2021.1879578 -
Clinical Infectious Diseases : An... Nov 2022Patient exposure to antibiotics promotes the emergence of drug-resistant pathogens. The aim of this study was to identify whether the temporal dynamics of resistance... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Patient exposure to antibiotics promotes the emergence of drug-resistant pathogens. The aim of this study was to identify whether the temporal dynamics of resistance emergence at the individual-patient level were predictable for specific pathogen-drug classes.
METHODS
Following a systematic review, a novel robust error meta-regression method for dose-response meta-analysis was used to estimate the odds ratio (OR) for carrying resistant bacteria during and following treatment compared to baseline. Probability density functions fitted to the resulting dose-response curves were then used to optimize the period during and/or after treatment when resistant pathogens were most likely to be identified.
RESULTS
Studies of Streptococcus pneumoniae treatment with β-lactam antibiotics demonstrated a peak in resistance prevalence among patients 4 days after completing treatment with a 3.32-fold increase in odds (95% confidence interval [CI], 1.71-6.46). Resistance waned more gradually than it emerged, returning to preexposure levels 1 month after treatment (OR, 0.98 [95% CI, .55-1.75]). Patient isolation during the peak dose-response period would be expected to reduce the risk that a transmitted pathogen is resistant equivalently to a 50% longer isolation window timed from the first day of treatment.
CONCLUSIONS
Predictable temporal dynamics of resistance levels have implications both for surveillance and control.
Topics: Humans; Streptococcus pneumoniae; beta-Lactams; Pneumococcal Infections; Microbial Sensitivity Tests; Anti-Bacterial Agents
PubMed: 35438765
DOI: 10.1093/cid/ciac293 -
Vaccine Apr 2024Streptococcus pneumoniae (Spn) is a commensal pathogen that usually colonizes the upper respiratory tract of children. Likewise, Spn colonization has been considered a... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Streptococcus pneumoniae (Spn) is a commensal pathogen that usually colonizes the upper respiratory tract of children. Likewise, Spn colonization has been considered a critical factor in the development of pneumococcal invasive disease. However, Spn prevalence in adults remains unclear. This study performs a systematic review and meta-analysis to explore the prevalence of Spn Nasopharynx - Oropharynx Colonization (NOC) in adults.
METHODS
A Systematic review of scientific databases was utilized to identify eligible studies that follow strict selection criteria. Subsequently, a meta-analysis was conducted to establish NOC prevalence in adults (≥18 years old). The heterogeneity and sensitivity analyses were assessed using the microorganism identification technique, sample type, and age subgroups.
RESULTS
Initial selection includes 69 studies, with 37 selected for the meta-analysis, involving 23,724 individuals. The overall prevalence (95 % CI) of Spn NOC among adults was 6 % (5-9). The subgroup analysis revealed that young adults (YA), 18-64 years old, had a prevalence of 10 %, whereas older adults (OA), ≥65 years old, had a prevalence of 2 %. The identification of Spn NOC may vary depending on the method of diagnosis used. High heterogeneity (I2 > 90 %) was observed but diminished to 70 % when the analysis was restricted to oropharyngeal swabs as an identification method. Furthermore, heterogeneity decreased to 58 % when exclusively employing traditional culture as the identification method.
CONCLUSIONS
This study found a low prevalence of Spn NOC in adults. Notably, the prevalence of Spn NOC was higher in younger adults than in older adults. It is essential to highlight a significant heterogeneity among studies, which indicates there is no standardized method of Spn NOC identification.
Topics: Child; Humans; Infant; Aged; Adolescent; Young Adult; Adult; Middle Aged; Streptococcus pneumoniae; Nasopharynx; Pneumococcal Infections; Oropharynx; Nose; Carrier State
PubMed: 38514352
DOI: 10.1016/j.vaccine.2024.03.041 -
International Journal of Infectious... Mar 2020Geographic region can be an important source of variation in the immune response to pneumococcal conjugate vaccines (PCV). The aim of this study was to collate data from... (Meta-Analysis)
Meta-Analysis
OBJECTIVE
Geographic region can be an important source of variation in the immune response to pneumococcal conjugate vaccines (PCV). The aim of this study was to collate data from available PCV clinical trials in order to characterize the differences in antibody responses in different countries.
METHODS
A systematic review and meta-analysis was conducted to examine the difference in antibody responses after primary series of PCVs in infants, associated with geographic regions, compared with each other and with the different PCVs using random-effects models.
RESULTS
A total of 69 trials were included. Studies conducted in the Western Pacific Region (WPR) showed higher geometric mean concentrations (GMC) compared to studies conducted in Europe. The pooled GMC for serotype 4 after three doses of PCV7 in the WPR was 5.19 μg/ml (95% confidence interval 4.85-5.53 μg/ml), while for studies conducted in Europe this was 2.01 μg/ml (95% confidence interval 1.88-2.14 μg/ml). The IgG GMC ratios among the WPR versus European regions ranged from 1.51 to 2.87 for PCV7, 1.69 to 3.22 for PCV10, and 1.49 to 3.08 for PCV13.
CONCLUSIONS
Studies conducted in the WPR generally showed greater antibody responses than the studies conducted in Europe. Indications of differences among geographic regions highlight the fact that further research is needed to compare the biological factors contributing to immune responses, which may affect vaccination schedules.
Topics: Antibody Formation; Australasia; Clinical Trials as Topic; Asia, Eastern; Female; Heptavalent Pneumococcal Conjugate Vaccine; Humans; Immunization Schedule; Infant; Male; Pneumococcal Infections; Pneumococcal Vaccines; Serogroup; Streptococcus pneumoniae
PubMed: 32147023
DOI: 10.1016/j.ijid.2019.12.021 -
F1000Research 2020: This study aimed to summarise the evidence on the impact of routine administration of 10-valent and 13-valent pneumococcal conjugate vaccines on pneumonia in children...
: This study aimed to summarise the evidence on the impact of routine administration of 10-valent and 13-valent pneumococcal conjugate vaccines on pneumonia in children under five years of age in sub-Saharan Africa. A systematic search of the literature was conducted including primary research reporting on the impact of 10- or 13-valent pneumococcal vaccines on childhood pneumonia in a sub-Saharan African country. Case-control, cohort, pre-post and time-series study designs were eligible for inclusion. Thematic narrative synthesis was carried out to summarise the findings. Eight records were included in the final analysis, 6 records were pre-post or time-series studies, 1 was a case-control study and 1 report combined pre-post and case-control studies. Vaccine impact on clinical pneumonia measured as percentage reduction in risk (%RR) was mostly non-significant. The reduction in risk was more consistent in radiological and pneumococcal pneumonia. Evidence of the positive impact of routine infant pneumococcal vaccination on clinical pneumonia incidence in sub-Saharan Africa is inconclusive. Ongoing surveillance and further research is required to establish the long term trend in pneumonia epidemiology and aetiology after PCV introduction. : CRD42019142369 30/09/19.
Topics: Africa South of the Sahara; Case-Control Studies; Child, Preschool; Humans; Infant; Pneumococcal Infections; Pneumococcal Vaccines; Pneumonia; Vaccines, Conjugate
PubMed: 33335713
DOI: 10.12688/f1000research.25227.2 -
Infectious Diseases and Therapy Apr 2024Estimating the burden of lower respiratory tract infections (LRTIs) increasingly relies on administrative databases using International Classification of Diseases (ICD)... (Review)
Review
INTRODUCTION
Estimating the burden of lower respiratory tract infections (LRTIs) increasingly relies on administrative databases using International Classification of Diseases (ICD) codes, but no standard methodology exists. We defined best practices for ICD-based algorithms that estimate LRTI incidence in adults.
METHODS
We conducted a systematic review of validation studies assessing the use of ICD code-based algorithms to identify hospitalized LRTIs in adults, published in Medline, EMBASE, and LILACS between January 1996 and January 2022, according to PRISMA guidelines. We assessed sensitivity, specificity, and other accuracy measures of different algorithms.
RESULTS
We included 26 publications that used a variety of ICD code-based algorithms and gold standard criteria, and 18 reported sensitivity and/or specificity. Sensitivity was below 80% in 72% (38/53) of algorithms and specificity exceeded 90% in 77% (37/48). Algorithms for all-cause LRTI (n = 18) that included only pneumonia codes in primary position (n = 3) had specificity greater than 90% but low sensitivity (55-72%). Sensitivity increased by 5-15%, with minimal loss in specificity, with the addition of primary codes for severe pneumonia (e.g. sepsis) while pneumonia codes were in secondary position, and by 13% with codes from LRTI-related infections (e.g. viral) or other respiratory diseases (e.g. empyema). Sensitivity increased by 8% when pneumonia codes were in any position, but specificity was not reported. In hospital-acquired pneumonia and pneumococcal-specific pneumonia, algorithms containing only nosocomial- or pathogen-specific ICD codes had poor sensitivity, which improved when broader pneumonia codes were added, in particular codes for unspecified organisms.
CONCLUSION
Our systematic review highlights that most ICD code-based algorithms are relatively specific, but miss a substantial number of hospitalized LRTI adult cases. Best practices to estimate LRTI incidence in this population include the use of all pneumonia ICD codes for any LRTI outcome and, to a lesser extent, those for other LRTI-related infections or respiratory diseases.
PubMed: 38498108
DOI: 10.1007/s40121-024-00949-8 -
BMC Medical Research Methodology May 2024Systematic literature reviews (SLRs) are critical for life-science research. However, the manual selection and retrieval of relevant publications can be a time-consuming...
OBJECTIVE
Systematic literature reviews (SLRs) are critical for life-science research. However, the manual selection and retrieval of relevant publications can be a time-consuming process. This study aims to (1) develop two disease-specific annotated corpora, one for human papillomavirus (HPV) associated diseases and the other for pneumococcal-associated pediatric diseases (PAPD), and (2) optimize machine- and deep-learning models to facilitate automation of the SLR abstract screening.
METHODS
This study constructed two disease-specific SLR screening corpora for HPV and PAPD, which contained citation metadata and corresponding abstracts. Performance was evaluated using precision, recall, accuracy, and F1-score of multiple combinations of machine- and deep-learning algorithms and features such as keywords and MeSH terms.
RESULTS AND CONCLUSIONS
The HPV corpus contained 1697 entries, with 538 relevant and 1159 irrelevant articles. The PAPD corpus included 2865 entries, with 711 relevant and 2154 irrelevant articles. Adding additional features beyond title and abstract improved the performance (measured in Accuracy) of machine learning models by 3% for HPV corpus and 2% for PAPD corpus. Transformer-based deep learning models that consistently outperformed conventional machine learning algorithms, highlighting the strength of domain-specific pre-trained language models for SLR abstract screening. This study provides a foundation for the development of more intelligent SLR systems.
Topics: Humans; Machine Learning; Papillomavirus Infections; Economics, Medical; Algorithms; Outcome Assessment, Health Care; Deep Learning; Abstracting and Indexing
PubMed: 38724903
DOI: 10.1186/s12874-024-02224-3