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PloS One 2024Pleural empyema is a serious complication of pneumonia in children. Negative bacterial cultures commonly impede optimal antibiotic therapy. To improve bacterial... (Observational Study)
Observational Study
Pleural empyema is a serious complication of pneumonia in children. Negative bacterial cultures commonly impede optimal antibiotic therapy. To improve bacterial identification, we developed a molecular assay and evaluated its performance compared with bacterial culture. Our multiplex-quantitative PCR to detect Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus and Haemophilus influenzae was assessed using bacterial genomic DNA and laboratory-prepared samples (n = 267). To evaluate clinical performance, we conducted the Molecular Assessment of Thoracic Empyema (MATE) observational study, enrolling children hospitalised with empyema. Pleural fluids were tested by bacterial culture and multiplex-qPCR, and performance determined using a study gold standard. We determined clinical sensitivity and time-to-organism-identification to assess the potential of the multiplex-qPCR to reduce the duration of empiric untargeted antibiotic therapy. Using spiked samples, the multiplex-qPCR demonstrated 213/215 (99.1%) sensitivity and 52/52 (100%) specificity for all organisms. During May 2019-March 2023, 100 children were enrolled in the MATE study; median age was 3.9 years (IQR 2-5.6). A bacterial pathogen was identified in 90/100 (90%) specimens by multiplex-qPCR, and 24/100 (24%) by bacterial culture (P <0.001). Multiplex-qPCR identified a bacterial cause in 68/76 (90%) culture-negative specimens. S. pneumoniae was the most common pathogen, identified in 67/100 (67%) specimens. We estimate our multiplex-qPCR would have reduced the duration of untargeted antibiotic therapy in 61% of cases by a median 20 days (IQR 17.5-23, range 1-55). Multiplex-qPCR significantly increased pathogen detection compared with culture and may allow for reducing the duration of untargeted antibiotic therapy.
Topics: Humans; Child, Preschool; Empyema, Pleural; Male; Female; Multiplex Polymerase Chain Reaction; Child; Haemophilus influenzae; Staphylococcus aureus; Streptococcus pneumoniae; Streptococcus pyogenes; Infant; Hospitalization; Anti-Bacterial Agents; Sensitivity and Specificity; DNA, Bacterial
PubMed: 38917227
DOI: 10.1371/journal.pone.0304861 -
Microbiology Spectrum Jun 2024Metagenomic next-generation sequencing (mNGS) is an unbiased and rapid method for detecting pathogens. This study enrolled 145 suspected severe pneumonia patients who...
Metagenomic next-generation sequencing (mNGS) is an unbiased and rapid method for detecting pathogens. This study enrolled 145 suspected severe pneumonia patients who were admitted to the Affiliated Hospital of Jining Medical University. This study primarily aimed to determine the diagnostic performance of mNGS and conventional microbiological tests (CMTs) using bronchoalveolar lavage fluid samples for detecting pathogens. Our findings indicated that mNGS performed significantly higher sensitivity (97.54% vs 28.68%, < 0.001), coincidence (90.34% vs 35.17%, < 0.001), and negative predictive value (80.00% vs 13.21%, < 0.001) but performed lower specificity than CMTs (52.17% vs 87.5%, < 0.001). as the most common bacterial pathogen had the largest proportion (22.90%, 30/131) in this study. In addition to bacteria, fungi, and virus, mNGS can detect a variety of atypical pathogens such as and . Mixed infections were common in patients with severe pneumonia, and bacterial-fungal-viral-atypical pathogens were the most complicated infection. After adjustments of antibiotics based on mNGS and CMTs, the clinical manifestation improved in 139 (95.86%, 139/145) patients. Our data demonstrated that mNGS had significant advantage in diagnosing respiratory tract infections, especially atypical pathogens and fungal infections. Pathogens were detected timely and comprehensively, contributing to the adjustments of antibiotic treatments timely and accurately, improving patient prognosis and decreasing mortality potentially.IMPORTANCEMetagenomic next-generation sequencing using bronchoalveolar lavage fluid can provide more comprehensive and accurate pathogens for respiratory tract infections, especially when considering the previous usage of empirical antibiotics before admission or complicated clinical presentation. This technology is expected to play an important role in the precise application of antimicrobial drugs in the future.
PubMed: 38916357
DOI: 10.1128/spectrum.00458-24 -
Clinical Kidney Journal Jun 2024vaccination effectiveness (VE) in individuals with reduced kidney function is unknown. We estimated pneumococcal conjugate vaccine (PCV13), pneumococcal polysaccharide...
BACKGROUND
vaccination effectiveness (VE) in individuals with reduced kidney function is unknown. We estimated pneumococcal conjugate vaccine (PCV13), pneumococcal polysaccharide vaccine (PPSV23), and combined PCV13 and PPSV23 effectiveness against pneumococcal disease in individuals with and without reduced estimated glomerular filtration rate (eGFR).
METHODS
All eligible individuals (case and controls) were adults (aged ≥18 years) hospitalized within the Geisinger Health System and required to have urinary antigen testing (i.e. test-negative design). Vaccination records were obtained from the electronic health record and statewide vaccination registry. After controlling for the probability of receiving a pneumococcal vaccine, we used multivariable logistic regression models to estimate the odds ratios (ORs) of vaccination between those who did and did not meet the case definition. VE was calculated as (1 - OR) × 100%.
RESULTS
There were 180 cases and 3889 controls (mean age 69 years, female 48%, white 97%, mean eGFR 71 mL/min/1.73 m). The adjusted population PCV13 VE was 39% (95% CI 13%-58%), and combination PCV13 and PPSV23 was 39% (95% CI 12%-58%). PPSV23 VE was -3.7% (95% CI -57% to 32%). Stratified by eGFR, adjusted PCV13 VE was consistent in eGFR ≥60 [VE 38% (95% CI 2.9%-61%)] and 30-59 [VE 61% (95% CI 24%-80%)] without significant interaction. VE was not calculable for eGFR <30 due to small sample size.
CONCLUSION
PCV13 vaccination was associated with reduced risk of hospitalization in individuals with a reduced eGFR (30-59 mL/min/1.73 m).
PubMed: 38915439
DOI: 10.1093/ckj/sfae145 -
Microbial Genomics Jun 2024Understanding how pathogens spread across geographical space is fundamental for control measures such as vaccination. (the pneumococcus) is a respiratory bacterium...
Understanding how pathogens spread across geographical space is fundamental for control measures such as vaccination. (the pneumococcus) is a respiratory bacterium responsible for a large proportion of infectious disease morbidity and mortality globally. Even in the post-vaccination era, the rates of invasive pneumococcal disease (IPD) remain stable in most countries, including Israel. To understand the geographical spread of the pneumococcus in Israel, we analysed 1174 pneumococcal genomes from patients with IPD across multiple regions. We included the evolutionary distance between pairs of isolates inferred using whole-genome data within a relative risk (RR) ratio framework to capture the geographical structure of . While we could not find geographical structure at the overall lineage level, the extra granularity provided by whole-genome sequence data showed that it takes approximately 5 years for invasive pneumococcal isolates to become fully mixed across the country.This article contains data hosted by Microreact.
Topics: Streptococcus pneumoniae; Israel; Humans; Pneumococcal Infections; Genome, Bacterial; Whole Genome Sequencing; Phylogeny; Genomics
PubMed: 38913413
DOI: 10.1099/mgen.0.001262 -
Open Forum Infectious Diseases Jun 2024In October 2013, Burkina Faso introduced 13-valent pneumococcal conjugate vaccine (PCV13) into the routine childhood immunization program using 3 primary doses with no...
BACKGROUND
In October 2013, Burkina Faso introduced 13-valent pneumococcal conjugate vaccine (PCV13) into the routine childhood immunization program using 3 primary doses with no booster. Previous pneumococcal carriage studies showed reductions in vaccine-type (VT) carriage in children aged <5 years but not in older age groups.
METHODS
We conducted a cross-sectional, age-stratified pneumococcal carriage study among healthy persons aged ≥1 month in Bobo-Dioulasso in March 2020. Pneumococci isolated by culture from nasopharyngeal swabs (all participants) and oropharyngeal swabs (participants aged ≥5 years) were serotyped by polymerase chain reaction; a subset was serotyped by Quellung. Using data from a study with the same design from March 2017, we examined changes in pneumococcal carriage by age group.
RESULTS
Among 1005 (2017) and 1002 (2020) enrolled participants, VT carriage decreased (21.6% to 15.9%; adjusted prevalence ratio [aPR], 0.76 [95% confidence interval {CI}, .63-.92]). By age group, decline in VT carriage was significant among children aged 5-14 years (28.9% to 16.3%; aPR, 0.57 [95% CI, .39-.84]) but not among children aged <5 years (22.4% to 19.1%; aPR, 0.87 [95% CI, .70-1.09]) or adults aged ≥15 years (12.0% to 5.5%; aPR, 0.52 [95% CI, .26-1.05]).
CONCLUSIONS
Between 3 and 6 years after PCV13 introduction, significant declines in VT carriage were observed in older children, possibly reflecting indirect effects of PCV13 use. VT carriage in children aged <5 years remained stable with almost 1 in 5 carrying VT pneumococci, suggesting limitations to a PCV schedule without a booster dose.
PubMed: 38911949
DOI: 10.1093/ofid/ofae303 -
Journal of Oral Microbiology 2024Healthcare settings may amplify transmission of respiratory pathogens, however empirical evidence is lacking. We aimed to describe the spectrum and distribution of...
BACKGROUND
Healthcare settings may amplify transmission of respiratory pathogens, however empirical evidence is lacking. We aimed to describe the spectrum and distribution of respiratory pathogens among healthcare workers in eastern China.
METHODS
Healthcare workers were recruited from October 2020 to November 2021 in Jiangsu province. Participants were interviewed regarding demographic and hospital-based protective measures. Thirty-seven common respiratory pathogens were tested using real-time PCR/RT-PCR (Probe qPCR). The role of demographic and hospital-based protective measures on pathogens colonization using multivariable logistic regression models.
RESULTS
Among 316 enrolled healthcare workers, a total of 21 pathogens were detected. In total, 212 (67.1%) healthcare workers had at least one respiratory pathogen; 195 (61.7%) and 70 (22.2%) with a bacterial and viral pathogen. The most commonly detected pathogen was streptococcus pneumoniae (47.5%) followed by influenzae (21.2%). One hundred and five (33.2%) healthcare workers with copathogens had at least two respiratory pathogens. Both bacterial and viral colonization were more common in 2020 compared to 2021. A decreased risk of colonization was seen in participants with infection prevention and control training and suitable hand hygiene.
CONCLUSIONS
Colonization of respiratory pathogens in healthcare workers from eastern China was high. Differential risk was impacted only by hospital-based protective measures and not demographic factors.
PubMed: 38910869
DOI: 10.1080/20002297.2024.2365965 -
BMC Infectious Diseases Jun 2024Respiratory infections have long been recognized as a primary cause of acute exacerbation of chronic obstructive pulmonary disease (AE-COPD). Additionally, the emergence...
BACKGROUND
Respiratory infections have long been recognized as a primary cause of acute exacerbation of chronic obstructive pulmonary disease (AE-COPD). Additionally, the emergence of antimicrobial resistance has led to an urgent and critical situation in developing countries, including Vietnam. This study aimed to investigate the distribution and antimicrobial resistance of bacteria in patients with AE-COPD using both conventional culture and multiplex real-time PCR. Additionally, associations between clinical characteristics and indicators of pneumonia in these patients were examined.
METHODS
This cross-sectional prospective study included 92 AE-COPD patients with pneumonia and 46 without pneumonia. Sputum specimens were cultured and examined for bacterial identification, and antimicrobial susceptibility was determined for each isolate. Multiplex real-time PCR was also performed to detect ten bacteria and seven viruses.
RESULTS
The detection rates of pathogens in AE-COPD patients with pneumonia were 92.39%, compared to 86.96% in those without pneumonia. A total of 26 pathogenic species were identified, showing no significant difference in distribution between the two groups. The predominant bacteria included Klebsiella pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae, followed by Acinetobacter baumannii and Streptococcus mitis. There was a slight difference in antibiotic resistance between bacteria isolated from two groups. The frequency of H. influenzae was notably greater in AE-COPD patients who experienced respiratory failure (21.92%) than in those who did not (9.23%). S. pneumoniae was more common in patients with stage I (44.44%) or IV (36.36%) COPD than in patients with stage II (17.39%) or III (9.72%) disease. ROC curve analysis revealed that C-reactive protein (CRP) levels could distinguish patients with AE-COPD with and without pneumonia (AUC = 0.78).
CONCLUSION
Gram-negative bacteria still play a key role in the etiology of AE-COPD patients, regardless of the presence of pneumonia. This study provides updated evidence for the epidemiology of AE-COPD pathogens and the appropriate selection of antimicrobial agents in Vietnam.
Topics: Humans; Pulmonary Disease, Chronic Obstructive; Cross-Sectional Studies; Vietnam; Prospective Studies; Male; Female; Aged; Middle Aged; Anti-Bacterial Agents; Drug Resistance, Bacterial; Bacteria; Pneumonia, Bacterial; Microbial Sensitivity Tests; Sputum; Aged, 80 and over; Pneumonia
PubMed: 38910264
DOI: 10.1186/s12879-024-09515-6 -
Medicina 2024Despite improvements in health care, pneumonia-associated mortality remains high. The objective of this study was to analyze the factors associated with mortality in...
INTRODUCTION
Despite improvements in health care, pneumonia-associated mortality remains high. The objective of this study was to analyze the factors associated with mortality in bacteremic pneumonia caused by pneumococcus.
METHODS
Retrospective cohort study in adult patients with pneumonia diagnosis and isolation of pneumococcus in blood cultures, between January 2012 and May 2021, was carried out. Clinical and laboratory variables, radiological involvement, evolution and mortality during hospitalization were analyzed. The group of deceased patients was compared with that of survivors.
RESULTS
152 patients were included. Median age: 58 years; men: 58.9%; 33% presented a CURB-65 > than 2 at admission. Overall mortality: 34% (n=52). Deceased patients were more tachypneic on admission (respiratory rate 26 vs. 22; p=0.003), presented sensory alteration more frequently (58% vs. 14%; p< 0.001), PaO2/fraction of inspired oxygen ratio < 250 (58% vs. 22%; p<0.001), bilateral radiological compromise (50% vs. 32%; p=0.03), needed mechanical ventilation (50% vs 12%; p< 0.001), higher blood creatinine values (1.6 vs. 1.15; p=0.01), lower white blood cell count (10 900 vs 17 400; p=0.002), a lower glucose dosage (111 vs. 120; p=0.01), and fewer days of hospital stay (6 vs. 9; p=0.015). In logistic regression model, significant differences were maintained in the following factors associated with mortality: mechanical ventilation (OR=3.54), altered mental status (OR=5.95), chest X-ray with bilateral compromise (OR 3.20) and PAFI less than 250 (OR=3.62).
CONCLUSION
In our series, the factors related to mortality, despite the presence of bacteremia, do not differ from those published in the literature and which are part of the different prognostic scores used in routine practice.
Topics: Humans; Male; Retrospective Studies; Middle Aged; Female; Aged; Pneumonia, Pneumococcal; Risk Factors; Adult; Streptococcus pneumoniae; Hospital Mortality; Bacteremia
PubMed: 38907962
DOI: No ID Found -
PLoS Neglected Tropical Diseases Jun 2024Febrile illnesses that persist despite initial treatment are common clinical challenges in (sub)tropical low-resource settings. Our aim is to review infectious...
BACKGROUND
Febrile illnesses that persist despite initial treatment are common clinical challenges in (sub)tropical low-resource settings. Our aim is to review infectious etiologies of "prolonged fevers" (persistent febrile illnesses, PFI) and to quantify relative contributions of selected neglected target diseases with limited diagnostic options, often overlooked, causing inadequate antibiotic prescriptions, or requiring prolonged and potentially toxic treatments.
METHODS
We performed a systematic review of articles addressing the infectious etiologies of PFI in adults and children in sub-/tropical low- and middle-income countries (LMICs) using the PRISMA guidelines. A list of target diseases, including neglected parasites and zoonotic bacteria (e.g., Leishmania and Brucella), were identified by infectious diseases and tropical medicine specialists and prioritized in the search. Malaria and tuberculosis (TB) were not included as target diseases due to well-established epidemiology and diagnostic options. Four co-investigators independently extracted data from the identified articles while assessing for risk of bias.
RESULTS
196 articles from 52 countries were included, 117 from Africa (33 countries), 71 from Asia (16 countries), and 8 from Central and -South America (3 countries). Target diseases were reported as the cause of PFI in almost half of the articles, most frequently rickettsioses (including scrub typhus), relapsing fever borreliosis (RF-borreliosis), brucellosis, enteric fever, leptospirosis, Q fever and leishmaniasis. Among those, RF-borreliosis was by far the most frequently reported disease in Africa, particularly in Eastern Africa. Rickettsioses (including scrub typhus) were often described in both Africa and Asia. Leishmaniasis, toxoplasmosis and amoebiasis were the most frequent parasitic etiologies. Non-target diseases and non-tropical organisms (Streptococcus pneumoniae, Escherichia coli, and non-typhoidal Salmonella spp) were documented in a fifth of articles.
CONCLUSIONS
Clinicians faced with PFI in sub-/tropical LMICs should consider a wide differential diagnosis including enteric fever and zoonotic bacterial diseases (e.g., rickettsiosis, RF-borreliosis and brucellosis), or parasite infections (e.g., leishmaniasis) depending on geography and syndromes. In the absence of adequate diagnostic capacity, a trial of antibiotics targeting relevant intra-cellular bacteria, such as doxycycline or azithromycin, may be considered.
PubMed: 38905305
DOI: 10.1371/journal.pntd.0011978 -
Microbiology Spectrum Jun 2024Outbreaks of influenza A viruses are generally seasonal and cause annual epidemics worldwide. Due to their frequent reassortment and evolution, annual surveillance is of...
Outbreaks of influenza A viruses are generally seasonal and cause annual epidemics worldwide. Due to their frequent reassortment and evolution, annual surveillance is of paramount importance to guide vaccine strategies. The aim of this study was to explore the molecular epidemiology of influenza A virus and nasopharyngeal microbiota composition in infected patients in Saudi Arabia. A total of 103 nasopharyngeal samples from 2015 and 12 samples from 2022 were collected from patients positive for influenza A. Sequencing of influenza A as well as metatranscriptomic analysis of the nasopharyngeal microbiota was conducted using Oxford Nanopore sequencing. Phylogenetic analysis of hemagglutinin, neuraminidase segments, and concatenated influenza A genomes was performed using MEGA7. Whole-genome sequencing analysis revealed changing clades of influenza A virus: from 6B.1 in 2015 to 5a.2a in 2022. One sample containing the antiviral resistance-mediating mutation S247N toward oseltamivir and zanamivir was found. Phylogenetic analysis showed the clustering of influenza A strains with the corresponding vaccine strains in each period, thus suggesting vaccine effectiveness. Principal component analysis and alpha diversity revealed the absence of a relationship between hospital admission status, age, or gender of infected patients and the nasopharyngeal microbial composition, except for the infecting clade 5a.2a. The opportunistic pathogens , , and were the most common species detected. The molecular epidemiology appears to be changing in Saudi Arabia after the COVID-19 pandemic. Antiviral resistance should be carefully monitored in future studies. In addition, the disease severity of patients as well as the composition of the nasopharyngeal microbiota in patients infected with different clades should also be assessed.IMPORTANCEIn this work, we have found that the clade of influenza A virus circulating in Riyadh, KSA, has changed over the last few years from 6B.1 to 5a.2a. Influenza strains clustered with the corresponding vaccine strains in our population, thus emphasizing vaccine effectiveness. Metatranscriptomic analysis showed no correlation between the nasopharyngeal microbiome and the clinical and/or demographic characteristics of infected patients. This is except for the 5a.2a strains isolated post-COVID-19 pandemic. The influenza virus is among the continuously evolving viruses that can cause severe respiratory infections. Continuous surveillance of its molecular diversity and the monitoring of anti-viral-resistant strains are thus of vital importance. Furthermore, exploring potential microbial markers and/or dysbiosis of the nasopharyngeal microbiota during infection could assist in the better management of patients in severe cases.
PubMed: 38904365
DOI: 10.1128/spectrum.00665-24