Impact of pneumococcal conjugate vaccine 13 introduction on severe lower respiratory tract infections associated with respiratory syncytial virus or influenza virus in hospitalized children in Ulaanbaatar, Mongolia

Objectives

Limited data indicate a beneficial effect of pneumococcal conjugate vaccines (PCVs) on respiratory syncytial virus (RSV) and influenza infections in young children. We evaluated the impact of 13-valent PCV (PCV13) introduction on the incidence of severe lower respiratory tract infections (LRTIs) associated with RSV or influenza in hospitalized children.

Methods

Our study was restricted to children aged <2 years with arterial oxygen saturation <93% and children with radiologically confirmed pneumonia nested in a pneumonia surveillance project in four districts of Ulaanbaatar city, Mongolia. We tested nasopharyngeal swabs collected on admission for RSV and influenza using quantitative reverse transcription-polymerase chain reaction. The impact of PCV13 on the incidence of LRTI outcomes associated with RSV or with influenza for the period April 2015-March 2020 was estimated. Incidence rate ratios comparing pre- and post-vaccine periods were estimated for each outcome for each district using negative binomial models and for all districts combined with a mixed-effects negative binomial model. Adjusted models accounted for seasonality. Sensitivity analyses were conducted to assess the robustness of our findings.

Results

Among 5577 tested cases, the adjusted incidence rate ratios showed a trend toward a reduction in RSV-associated outcomes: all LRTIs (0.77, 95% confidence interval [CI] 0.44-1.36), severe LRTIs (0.88, 95% CI 0.48-1.62), very severe LRTIs (0.76, 95% CI 0.42-1.38), and radiologically confirmed pneumonia (0.66, 95% CI 0.32-1.38) but inconsistent trends in outcomes associated with influenza.

Conclusions

No significant reductions were observed in any outcomes associated with RSV and influenza after PCV introduction.

Microbial aetiology of community-acquired pneumonia in hospitalised adults: A prospective study utilising comprehensive molecular testing

OBJECTIVES

This study aimed to describe the microbial aetiology of community-acquired pneumonia (CAP) in adults admitted to a tertiary care hospital and assess the impact of syndromic polymerase chain reaction (PCR) panels on pathogen detection.

METHODS

Conducted at Haukeland University Hospital, Norway, from September 2020 to April 2023, this prospective study enrolled adults with suspected CAP. We analysed lower respiratory tract samples using both standard-of-care tests and the BIOFIRE® FILMARRAY® Pneumonia Plus Panel (FAP plus). The added value of FAP Plus in enhancing the detection of clinically relevant pathogens, alongside standard-of-care diagnostics, was assessed.

RESULTS

Of the 3238 patients screened, 640 met the inclusion criteria, with 384 confirmed to have CAP at discharge. In these patients, pathogens with proven or probable clinical significance were identified in 312 (81.3%) patients. Haemophilus influenzae was the most prevalent pathogen, found in 118 patients (30.7%), followed by SARS-CoV-2 in 74 (19.3%), and Streptococcus pneumoniae in 64 (16.7%). Respiratory viruses were detected in 186 (48.4%) patients. The use of FAP plus improved the pathogen detection rate from 62.8% with standard-of-care methods to 81.3%.

CONCLUSIONS

Pathogens were identified in 81% of CAP patients, with Haemophilus influenzae and respiratory viruses being the most frequently detected pathogens. The addition of the FAP plus panel, markedly improved pathogen detection rates compared to standard-of-care diagnostics alone.

Seasonal extreme temperatures and short-term fine particulate matter increases pediatric respiratory healthcare encounters in a sparsely populated region of the intermountain western United States

BACKGROUND

Western Montana, USA, experiences complex air pollution patterns with predominant exposure sources from summer wildfire smoke and winter wood smoke. In addition, climate change related temperatures events are becoming more extreme and expected to contribute to increases in hospital admissions for a range of health outcomes. Evaluating while accounting for these exposures (air pollution and temperature) that often occur simultaneously and may act synergistically on health is becoming more important.

METHODS

We explored short-term exposure to air pollution on children's respiratory health outcomes and how extreme temperature or seasonal period modify the risk of air pollution-associated healthcare events. The main outcome measure included individual-based address located respiratory-related healthcare visits for three categories: asthma, lower respiratory tract infections (LRTI), and upper respiratory tract infections (URTI) across western Montana for ages 0-17 from 2017-2020. We used a time-stratified, case-crossover analysis with distributed lag models to identify sensitive exposure windows of fine particulate matter (PM2.5) lagged from 0 (same-day) to 14 prior-days modified by temperature or season.

RESULTS

For asthma, increases of 1 µg/m3 in PM2.5 exposure 7-13 days prior a healthcare visit date was associated with increased odds that were magnified during median to colder temperatures and winter periods. For LRTIs, 1 µg/m3 increases during 12 days of cumulative PM2.5 with peak exposure periods between 6-12 days before healthcare visit date was associated with elevated LRTI events, also heightened in median to colder temperatures but no seasonal effect was observed. For URTIs, 1 unit increases during 13 days of cumulative PM2.5 with peak exposure periods between 4-10 days prior event date was associated with greater risk for URTIs visits that were intensified during median to hotter temperatures and spring to summer periods.

CONCLUSIONS

Delayed, short-term exposure increases of PM2.5 were associated with elevated odds of all three pediatric respiratory healthcare visit categories in a sparsely population area of the inter-Rocky Mountains, USA. PM2.5 in colder temperatures tended to increase instances of asthma and LRTIs, while PM2.5 during hotter periods increased URTIs.

Parental engagement in research on paediatric lower respiratory tract infections in Indonesia

BACKGROUND

Lower respiratory tract infections (LRTIs) in children are a major concern in Indonesia as it is the leading cause of morbidity and mortality. Therefore, research on LRTIs is crucial to improve children's health. However, clinical research in children is challenging due to parental concerns. This study aims to understand parental considerations for taking part in clinical studies on LRTI in the Indonesian context.

METHODS

A cross-sectional study using a validated online questionnaire was conducted from November 2021 to March 2022. This study included parents from two public elementary schools and two private primary schools in Semarang, Indonesia. A total of 1236 responses were analysed.

RESULTS

There was a significant association between educational attainment and willingness to participate in general health and LRTI-related research requiring specimen collection; respondents with an advanced educational level were more likely to refuse participation in research. A similar pattern was observed among respondents with smaller families and younger children against participation in LRTI research. Most respondents who indicated not to participate explained that they did not perceive the necessity to take part and expressed their concerns about endangering their child's health as a consequence of the specimen collection. Most respondents expected a personal benefit and prioritized access to the study results for their child.

CONCLUSION

Parents' educational background and family composition are important determinants of parental engagement in research on LRTI in Indonesia. Notably, parents with a lower educational level, having large families, and older children were more inclined to participate. The emphasis on concerns about potential harm and personal benefit underscores the need for a targeted communication strategy.

Clinical recommendations for the inpatient management of lower respiratory tract infections in children and adolescents with severe neurological impairment in Germany

Children and adolescents with severe neurological impairment (SNI) require specialized care due to their complex medical needs. In particular, these patients are often affected by severe and recurrent lower respiratory tract infections (LRTIs). These infections, including viral and bacterial etiology, pose a significant risk to these patients, often resulting in respiratory insufficiency and long-term impairments. Using expert consensus, we developed clinical recommendations on the management of LRTIs in children and adolescents with SNI. These recommendations emphasize comprehensive multidisciplinary care and antibiotic stewardship. Initial treatment should involve symptomatic care, including hydration, antipyretics, oxygen therapy, and respiratory support. In bacterial LRTIs, antibiotic therapy is initiated based on the severity of the infection, with aminopenicillin plus a beta-lactamase inhibitor recommended for community-acquired LRTIs and piperacillin-tazobactam for patients with chronic lung disease or tracheostomy. Ongoing management includes regular evaluations, adjustments to antibiotic therapy based on pathogen identification, and optimization of supportive care. Implementation of these recommendations aims to improve the diagnosis and treatment of LRTIs in children and adolescents with SNI. What is Known: • Children and adolescents with severe neurological impairment are particularly affected by severe and recurrent lower respiratory tract infections (LRTIs). • The indication and choice of antibiotic therapy for bacterial LRTI is often difficult because there are no evidence-based treatment recommendations for this heterogeneous but vulnerable patient population; the frequent overuse of broad-spectrum or reserve antibiotics in this patient population increases selection pressure for multidrug-resistant pathogens. What is New: • The proposed recommendations provide a crucial framework for focused diagnostics and treatment of LRTIs in children and adolescents with severe neurological impairment. • Along with recommendations for comprehensive and multidisciplinary therapy and antibiotic stewardship, ethical and palliative care aspects are taken into account.

Risk factors associated with functional decline in older hospital survivors with acute lower respiratory tract infections: a prospective cohort study

OBJECTIVE

To evaluate the dynamics of basic activity of daily living (BADL) in older patients with acute lower respiratory tract infections (LRTIs) during acute phase and to investigate risk factors associated with decreased physical function at discharge.

METHODS

We conducted a prospective cohort study of patients aged 65 years and older who were hospitalized for acute LRTIs between April 15, 2020 and January 15, 2023. All patients received geriatric assessment at admission, including emotion, cognition, frailty, physical function status and so on. The BADL was also evaluated by the Barthel Index (BI) at two weeks before admission by recall (baseline status), at admission and at discharge. Based on the BI grades at baseline and at discharge, patients were classified into two groups: ADL decline and no ADL decline. Multivariable adjusted logistic regression models were used to evaluate the risk factors of decreased physical function.

RESULTS

A total of 364 older survivors with LRTIs were included in the analysis. The median age was 74 years (IQR 61.0-82.0), 231 (62.6%) were male, the median length of stay was 10 days. In the geriatric assessment, 139 patients (38.2%) were classified as frailty, 137 patients (37.6%) experienced insomnia, 60 patients (16.5%) exhibited cognitive impairments, and 37 patients (10.2%) were defined as malnutrition. Additionally, 30 patients (8.2%) dealt with emotional disorders. On average, patients were taking 3 medications, and Charlson Comorbidity Index score was 4. 72 patients (19.8%) had function decline at discharge. In the multivariable analysis, frailty status had an odds ratio of 4.25 (95% CI 1.31-19.26) for decreased physical function and cognitive impairment had an odds ratio of 2.58 (95% CI 1.27-5.19).

CONCLUSIONS

About 20% older patients with LRTIs experienced functional decline at discharge. Compared to age, severity of diseases and length of stay, frailty and cognitive impairment performed better at predicting the function decline. The apply of geriatric assessment may contribute to enhance the quality of management and treatment for patients with the older with LRTIs.

Pneumococcal colonization and coinfecting respiratory viruses in children under 5 years in Addis Ababa, Ethiopia: a prospective case-control study

A comprehensive understanding of the dynamics of Streptococcus pneumoniae colonization in conjunction with respiratory virus infections is essential for enhancing our knowledge of the pathogenesis and advancing the development of effective preventive strategies. Therefore, a case-control study was carried out in Addis Ababa, Ethiopia to investigate the colonization rate of S. pneumoniae and its coinfection dynamics with respiratory viruses among children under the age of 5 years. Samples from the nasopharyngeal and/or oropharyngeal, along with socio-demographic and clinical information, were collected from 420 children under 5 years old (210 cases with lower respiratory tract infections and 210 controls with conditions other than respiratory infections.). A one-step Multiplex real-time PCR using the Allplex Respiratory Panel Assays 1-4 was performed to identify respiratory viruses and bacteria. Data analysis was conducted using STATA software version 17. The overall colonization rate of S. pneumoniae in children aged less than 5 years was 51.2% (215/420). The colonization rates in cases and controls were 54.8% (115/210) and 47.6% (100/210), respectively (p = 0.14). Colonization rates were observed to commence at an early age in children, with a colonization rate of 48.9% and 52.7% among infants younger than 6 months controls and cases, respectively. The prevalence of AdV (OR, 3.11; 95% CI [1.31-8.19]), RSV B (OR, 2.53; 95% CI [1.01-6.78]) and HRV (OR, 1.7; 95% CI [1.04-2.78]) tends to be higher in children who tested positive for S. pneumoniae compared to those who tested negative for S. pneumoniae. Further longitudinal research is needed to understand and determine interaction mechanisms between pneumococci and viral pathogens and the clinical implications of this coinfection dynamics.

Development and validation of multiplex real-time PCR for simultaneous detection of six bacterial pathogens causing lower respiratory tract infections and antimicrobial resistance genes

BACKGROUND

Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Streptococcus pneumoniae and Staphylococcus aureus are major bacterial causes of lower respiratory tract infections (LRTIs) globally, leading to substantial morbidity and mortality. The rapid increase of antimicrobial resistance (AMR) in these pathogens poses significant challenges for their effective antibiotic therapy. In low-resourced settings, patients with LRTIs are prescribed antibiotics empirically while awaiting several days for culture results. Rapid pathogen and AMR gene detection could prompt optimal antibiotic use and improve outcomes.

METHODS

Here, we developed multiplex quantitative real-time PCR using EvaGreen dye and melting curve analysis to rapidly identify six major pathogens and fourteen AMR genes directly from respiratory samples. The reproducibility, linearity, limit of detection (LOD) of real-time PCR assays for pathogen detection were evaluated using DNA control mixes and spiked tracheal aspirate. The performance of RT-PCR assays was subsequently compared with the gold standard, conventional culture on 50 tracheal aspirate and sputum specimens of ICU patients.

RESULTS

The sensitivity of RT-PCR assays was 100% for K. pneumoniae, A. baumannii, P. aeruginosa, E. coli and 63.6% for S. aureus and the specificity ranged from 87.5% to 97.6%. The kappa correlation values of all pathogens between the two methods varied from 0.63 to 0.95. The limit of detection of target bacteria was 1600 CFU/ml. The quantitative results from the PCR assays demonstrated 100% concordance with quantitative culture of tracheal aspirates. Compared to culture, PCR assays exhibited higher sensitivity in detecting mixed infections and S. pneumoniae. There was a high level of concordance between the detection of AMR gene and AMR phenotype in single infections.

CONCLUSIONS

Our multiplex quantitative RT-PCR assays are fast and simple, but sensitive and specific in detecting six bacterial pathogens of LRTIs and their antimicrobial resistance genes and should be further evaluated for clinical utility.

Metagenomic next generation sequencing of bronchoalveolar lavage samples for the diagnosis of lower respiratory tract infections: A systematic review and meta-analysis

Background

Lower respiratory tract infections (LRTI)are known to be diagnosed late or inaccurately. This has fueled the unscrupulous use of antibiotics, as they are often used empirically and clinically, leading to antibiotic abuse and multidrug resistance in patients. Metagenomic next-generation sequencing (mNGS), now widely used in clinical studies, could be a potential intervention to revolutionize microbiology by rapidly identifying unknown species.

Methods

This review and meta-analysis were conducted on eligible studies with respect to metagenomic sequencing on clinical LRTI diagnostics up to May 01, 2022. QUADAS-2 was employed to assess the methodological bias as well as applicability. After that, a meta-analysis was conducted to analyze the accuracy of mNGS, compared with the composite reference standard (CRS), among the enrolled studies.

Results

This work collected 1248 samples in 13/21 qualified articles to factor in the accuracy of the diagnostic test. Typically, methods like molecular testing, culture, composite measures, and clinical decision-making were adopted as the reference criteria. With regard to Bronchoalveolar Lavage Samples, their sensitivity was 89% (82-93%) while their specificity was 90% (66-98%), with obvious heterogeneities in these two factors as demonstrated by different studies. The summary receiver operating characteristic (SROC) curve was plotted for mNGS as a function of LRTI, and the area under the curve (AUC) was 0.94. A Funnel plot with a p-value greater than 0.05 indicated the absence of publication bias. Positive and negative likelihood ratios (PLR and NLR) were >10 and > 0.1, respectively. In this pre-test probability-post-probability-likelihood ratio relationship graph, the values were Prior prob (%) = 20, Post-prob-Pos (%) = 77 and Post-prob-Neg (%) = 4.

Conclusion

The AUC value of SROC suggested a high accuracy of mNGS in diagnosis, with no publication bias and high reliability. The application of mNGS exhibits notable diagnostic efficacy in discerning pathogens present in bronchoalveolar lavage fluid (BALF) among patients afflicted with LRTI. However, mNGS is more meaningful for the definitive diagnosis of the disease rather than the exclusion of the disease. This post-test probability is significantly higher than the pre-test probability.

Adjunct prednisone in community-acquired pneumonia: 180-day outcome of a multicentre, double-blind, randomized, placebo-controlled trial

BACKGROUND

Several trials and meta-analyses found a benefit of adjunct corticosteroids for community-acquired pneumonia with respect to short-term outcome, but there is uncertainty about longer-term health effects. Herein, we evaluated clinical outcomes at long term in patients participating in the STEP trial (Corticosteroid Treatment for Community-Acquired Pneumonia).

METHODS

This predefined secondary analysis investigated 180-day outcomes in 785 adult patients hospitalized with community-acquired pneumonia included in STEP, a randomised, placebo-controlled, double-blind trial. The primary endpoint was time to death from any cause at 180 days verified by telephone interview. Additional secondary endpoints included pneumonia-related death, readmission, recurrent pneumonia, secondary infections, new hypertension, and new insulin dependence.

RESULTS

From the originally included 785 patients, 727 were available for intention-to-treat analysis at day 180. There was no difference between groups with respect to time to death from any cause (HR for corticosteroid use 1.15, 95% CI 0.68 to 1.95, p = 0.601). Compared to placebo, corticosteroid-treated patients had significantly higher risks for recurrent pneumonia (OR 2.57, 95% CI 1.29 to 5.12, p = 0.007), secondary infections (OR 1.94, 95% CI 1.25 to 3.03, p = 0.003) and new insulin dependence (OR 8.73, 95% CI 1.10 to 69.62, p = 0.041). There was no difference regarding pneumonia-related death, readmission and new hypertension.

CONCLUSIONS

In patients with community-acquired pneumonia, corticosteroid use was associated with an increased risk for recurrent pneumonia, secondary infections and new insulin dependence at 180 days. Currently, it is uncertain whether these long-term adverse effects outweigh the short-term effects of corticosteroids in moderate CAP.

TRIAL REGISTRATION

This trial was registered with ClinicalTrials. gov, number NCT00973154 before the recruitment of the first patient. First posted: September 9, 2009. Last update posted: April 21, 2015.

Global burden of influenza lower respiratory tract infections in older people from 1990 to 2019

BACKGROUND

Infections with influenza viruses cause severe illness, substantial number of hospitalization and death, especially in older adults. However, few studies have focused on the burden of influenza lower respiratory tract infections (LRTIs) solely in older adults, particularly in low-resource settings.

AIMS

We aimed to estimate the mortality and DALYs of influenza LRTIs for people aged 55 years and older in 204 countries and territories from 1990 to 2019.

METHODS

The Global Burden of Disease (GBD) 2019 study was used to obtain data on mortality and DALYs of influenza LRTIs at the global, regional, and country levels.

RESULTS

In 2019, the global rates for mortality and DALYs of influenza LRTIs were 6.46 per 100,000 [95% uncertainty interval (UI): 2.37-12.62] and 97.39 per 100,000 (95% UI: 34.70-187.03). Although the rates for mortality and DALYs in people aged 55 years and older decreased from 1990 to 2019, the absolute numbers for both increased by 85.84% and 66.56%, respectively. Both the absolute numbers and rates of deaths and DALYs of influenza LRTIs were higher in male than in female in all age groups. Although low-socio-demographic index (SDI) regions experienced the largest declines for the rates of mortality and DALYs of influenza LRTIs over the past three decades, they still had the highest rates for mortality and DALYs in all age groups. Moreover, the absolute numbers and rates of deaths and DALYs of influenza LRTIs showed an increasing trend with age, reaching the peak in the people over 85 years old.

DISCUSSION

Burden of influenza LRTIs in older adults is still high and could continue to grow along with global aging.

CONCLUSION

Efforts to improve vaccination for influenza are needed for preparedness of another influenza pandemic, especially in low-SDI regions.

Use of antibiotics contrary to guidelines for children's lower respiratory tract infections in different health care settings

This study aimed to evaluate antibiotic prescriptions for children with lower respiratory tract infection (LRTI) in public and private primary care clinics and in a hospital's pediatric emergency department (PED) in 2012-2013 (pre-guideline) and in 2014-2015 (post-guideline). Special attention was paid to guideline compliance, especially regarding macrolide prescriptions, which the guidelines discourage. Retrospective data of 1431 children with LRTI in November-December 2012-2015 were collected from electronic registers and checked manually. Three diagnostic groups were analyzed: community-acquired pneumonia (CAP), wheezing bronchitis, and non-wheezing bronchitis. A comparison of the pre- and post-guideline periods revealed antibiotic prescription rates of 48.7% and 48.9% (p = 0.955) for all LRTIs, respectively, and 77.6% and 71.0% (p = 0.053) for non-wheezing bronchitis. The prescription rates for all LRTIs were 24.9% in PED and 45.9% in public (p < 0.001 vs. PED) and 75.4% in private clinics (p < 0.001 vs. PED and p < 0.001 vs. public clinics). During post-guideline periods, antibiotics were prescribed for CAP less often in private (56.3%) than in public clinics (84.6%; p = 0.037) or in PED (94.3%; p < 0.001 vs. private and p = 0.091 vs. public primary clinics). Macrolide prescriptions were highest in private clinics (42.8%), followed by public primary care clinics (28.5%; p < 0.05) and PED (0.8%; p < 0.05 vs. both public and private primary care). Amoxicillin was the predominant antibiotic in public primary care and PED and macrolides in private primary care.

CONCLUSION

 Antibiotic prescribing for children with LRTI differed significantly between healthcare providers. CAP was undertreated and bronchitis overtreated with antibiotics in primary care, especially in the private clinics.

WHAT IS KNOWN

• Clinical Treatment Guidelines tend to have modest effect on physicians' antibiotic prescribing habits. • Pediatric viral LRTIs are widely treated with unnecessary antibiotics.

WHAT IS NEW

• Remarkable differences in antibiotic prescriptions in pediatric LRTIs between Finnish private and public providers were observed. • Overuse of macrolides was common especially in private clinics.

Lower respiratory tract infections among newly diagnosed sleep apnea patients

BACKGROUND

Sleep apnea is associated with chronic comorbidities and acute complications. Existing data suggest that sleep apnea may predispose to an increased risk and severity of respiratory tract infections.

METHODS

We investigated the incidence of lower respiratory tract infections in the first and second year before and after diagnosis of sleep apnea in a Finnish nationwide, population-based, retrospective case-control study based on linking data from the national health care registers for primary and secondary care from 2015-2019. Controls were matched for age, sex, hospital district, and multimorbidity status. We furthermore analysed the independent effect of comorbidities and other patient characteristics on the risk of lower respiratory tract infections, and their recurrence.

RESULTS

Sleep apnea patients had a higher incidence of lower respiratory tract infections than their matched controls within one year before (hazard ratio 1.35, 95% confidence interval 1.16-1.57) and one year after (hazard ratio1.39, 95% confidence interval1.22-1.58) diagnosis of sleep apnea. However, we found no difference in the incidence of lower respiratory tract infections within the second year before or after diagnosis of sleep apnea in comparison with matched controls. In sleep apnea, history of lower respiratory tract infection prior to sleep apnea, multimorbidity, COPD, asthma, and age greater than 65 years increased the risk of incident and recurrent lower respiratory tract infections.

CONCLUSIONS

Sleep apnea patients are at increased risk of being diagnosed with a lower respiratory tract infection within but not beyond one year before and after diagnosis of sleep apnea. Among sleep apnea patients, chronic comorbidities had a significant impact on the risk of lower respiratory tract infections and their recurrence.

Viral etiologies of lower respiratory tract infections in children < 5 years of age in Addis Ababa, Ethiopia: a prospective case-control study

BACKGROUND

Lower respiratory tract infections (LRTIs) are a major cause of morbidity and mortality in children worldwide and disproportionally affect Sub-Saharan Africa. Despite the heaviest burden of LRIs in Ethiopia, to date, no published studies have reported a comprehensive viral etiology of LRTIs among children in Ethiopia. The objective of this study was to determine and estimate the etiological contribution of respiratory viruses to LRTIs in < 5 years children in Ethiopia.

METHODS

A prospective case-control study was conducted from September 2019 to May 2022 in two major governmental hospitals, St. Paul Hospital Millennium Medical College and ALERT Hospital in Addis Ababa, Ethiopia. Nasopharyngeal/oropharyngeal samples and socio-demographic and clinical information were collected from children under 5 years. A one-step Multiplex real-time PCR (Allplex™ Respiratory Panel Assays 1-3) was done to detect respiratory viruses. STATA software version 17 was used for the data analysis. We computed the odds ratio (OR), the attributable fraction among exposed (AFE) and the population attributable fraction (PAF) to measure the association of the detected viruses with LRTIs.

RESULTS

Overall, 210 LRTIs cases and 210 non-LRTI controls were included in the study. The likelihood of detecting one or more viruses from NP/OP was higher among cases than controls (83.8% vs. 50.3%, p = 0.004). The multivariate logistic regression showed a significantly higher detection rate for RSV A (OR: 14.6, 95% CI 4.1-52.3), RSV B (OR: 8.1, 95% CI 2.3-29.1), influenza A virus (OR: 5.8, 95% CI 1.5-22.9), and PIV 1 (OR: 4.3, 95% CI 1.1-16.4), among cases when compared with controls. The overall AFE and PAF for RSV A were (93.2% and 17.3%), RSV B (87.7% and 10.4%) and Influenza A virus (82.8% and 6.3%), respectively. The mean CT values were significantly lower for only RSV B detected in the case groups as compared with the mean CT values of RSV B detected in the control group (p = 0.01).

CONCLUSIONS

RSV, Influenza A and PIV 1 viruses were significantly associated with LRTIs in < 5 years children in Addis Ababa, Ethiopia. Therefore, we underscore the importance of developing prevention strategies for these viruses in Ethiopia and support the importance of developing and introducing an effective vaccine against these viruses.

Procalcitonin as a biomarker to guide treatments for patients with lower respiratory tract infections

INTRODUCTION

Lower respiratory tract infections are amongst the main causes for hospital/intensive care unit admissions and antimicrobial prescriptions. In order to reduce antimicrobial pressure, antibiotic administration could be optimized through procalcitonin-based algorithms.

AREAS COVERED

In this review, we discuss the performances of procalcitonin for the diagnosis and the management of community-acquired and ventilator-associated pneumonia. We provide up-to-date evidence and deliver clear messages regarding the purpose of procalcitonin to reduce unnecessary antimicrobial exposure.

EXPERT OPINION

Antimicrobial pressure and resulting antimicrobial resistances are a major public health issue as well as a daily struggle in the management of patients with severe infectious diseases, especially in intensive care units where antibiotic exposure is high. Procalcitonin-guided antibiotic administration has proven its efficacy in reducing unnecessary antibiotic use in lower respiratory tract infections without excess in mortality, hospital length of stay or disease relapse. Procalcitonin-guided algorithms should be implemented in wards taking care of patients with severe infections. However, procalcitonin performances are different regarding the setting of the infection (community versus hospital-acquired infections) the antibiotic management (start or termination of antibiotic) as well as patient's condition (immunosuppressed or in shock) and we encourage the physicians to be aware of these limitations.

Pathogenic bacteria recovered from Gene X-pert tuberculosis-negative adult patients in Gondar, Northwest Ethiopia

INTRODUCTION

Lower respiratory tract infections (LRTIs) caused by drug-resistant pathogenic bacteria is a major problem in developing countries including Ethiopia. Therefore, this study aimed to determine the pathogenic bacteria and their antimicrobial susceptibility patterns among Gene X-pert tuberculosis-negative adult patients with clinically suspected LRTIs at the University of Gondar Comprehensive Specialized Referral Hospital, Gondar, Northwest Ethiopia.

METHODS

This institutional-based cross-sectional study was conducted from February 01 to March 15, 2020. Socio-demographic data were collected by using a structured questionnaire. A total of 254 sputum specimens were collected from Gene X-pert tuberculosis-negative patients. Bacterial recovery was performed using blood, chocolate, and MacConkey agar plates. Bacterial isolates were identified based on Gram staining, colony characteristics, and biochemical reactions. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method. Methicillin resistance of S. aureus was confirmed using cefoxitin (30 µg). Descriptive statistics were calculated for each variable and results are shown in tables and figures.

RESULTS

In this study, the overall sputum culture positivity rate was 145/254 (57.1%). Gram-negative bacteria 111 (64.9%) were predominant compared to Gram-positive bacteria 60 (35.1%). Of the 145 culture-positive cases, 26 (14.8%) had poly-bacterial infections. S. aureus 40 (66.7%) was the predominant Gram-positive bacterium whereas K. pneumoniae 33 (29.7%), was the most isolated Gram-negative bacterium. Bacterial species, such as S. aureus were sensitive to ciprofloxacin 38/40 (95.0%), gentamicin 37/40 (92.5%), cefoxitin 36/40 (90.0%), and clindamycin 34/40 (85.0%). The proportion of Methicillin-resistant S. aureus was low, 4(10.0%). S. pneumoniae was sensitive to chloramphenicol 8/9 (88.9%) and resistant to ciprofloxacin 6/9 (66.7%). K pneumoniae, P. aeruginosa, E. coli, Serratia species, and H. influenzae also demonstrated high levels of resistance to ampicillin at rates of 21/33 (63.6%), 8/8 (100.0%), 15/17 (88.2%), 7/10 (70.0%), and 6/6 (100.0%), respectively.

CONCLUSION

This study revealed a higher burden of Gram-negative and Gram-positive pathogenic bacterial agents, which is responsible for LRTs. Therefore, routine sputum culture identification and antibiotic susceptibility testing should be performed in Gene X-pert tuberculosis-negative patients.

Childhood lower respiratory tract infections linked to residential airborne bacterial and fungal microbiota

Residential microbial composition likely contributes to the development of lower respiratory tract infections (LRTI) among children, but the association is poorly understood. We aimed to study the relationship between the indoor airborne dust bacterial and fungal microbiota and childhood LRTI in Ibadan, Nigeria. Ninety-eight children under the age of five years hospitalized with LRTI were recruited and matched by age (±3 months), sex, and geographical location to 99 community-based controls without LRTI. Participants' homes were visited and sampled over a 14-day period for airborne house dust using electrostatic dustfall collectors (EDC). In airborne dust samples, the composition of bacterial and fungal communities was characterized by a meta-barcoding approach using amplicons targeting simultaneously the bacterial 16S rRNA gene and the internal-transcribed-spacer (ITS) region-1 of fungi in association with the SILVA and UNITE database respectively. A 100-unit change in house dust bacterial, but not fungal, richness (OR 1.06; 95%CI 1.03-1.10) and a 1-unit change in Shannon diversity (OR 1.92; 95%CI 1.28-3.01) were both independently associated with childhood LRTI after adjusting for other indoor environmental risk factors. Beta-diversity analysis showed that bacterial (PERMANOVA p < 0.001, R² = 0.036) and fungal (PERMANOVA p < 0.001, R² = 0.028) community composition differed significantly between homes of cases and controls. Pair-wise differential abundance analysis using both DESEq2 and MaAsLin2 consistently identified the bacterial phyla Deinococcota (Benjamini-Hochberg (BH) adjusted p-value <0.001) and Bacteriodota (BH-adjusted p-value = 0.004) to be negatively associated with LRTI. Within the fungal microbiota, phylum Ascomycota abundance (BH adjusted p-value <0.001) was observed to be directly associated with LRTI, while Basidiomycota abundance (BH adjusted p-value <0.001) was negatively associated with LRTI. Our study suggests that early-life exposure to certain airborne bacterial and fungal communities is associated with LRTI among children under the age of five years.

Estimating the economic burden of respiratory syncytial virus infections in infants in Vietnam: a cohort study

BACKGROUND

Little information is available on the costs of respiratory syncytial virus (RSV) in Vietnam or other low- and middle-income countries. Our study estimated the costs of LRTIs associated with RSV infection among children in southern Vietnam.

METHODS

We conducted a prospective cohort study evaluating household and societal costs associated with LRTIs stratified by RSV status and severity among children under 2 years old who sought care at a major pediatric referral hospital in southern Vietnam. Enrollment periods were September 2019-December 2019, October 2020-June 2021 and October 2021-December 2021. RSV status was confirmed by a validated RT-PCR assay. RSV rapid detection antigen (RDA) test performance was also evaluated. Data on resource utilization, direct medical and non-medical costs, and indirect costs were collected from billing records and supplemented by patient-level questionnaires. All costs are reported in 2022 US dollars.

RESULTS

536 children were enrolled in the study, with a median age of 7 months (interquartile range [IQR] 3-12). This included 210 (39.2%) children from the outpatient department, 318 children (59.3%) from the inpatient respiratory department (RD), and 8 children (1.5%) from the intensive care unit (ICU). Nearly 20% (105/536) were RSV positive: 3.9 percent (21/536) from the outpatient department, 15.7% (84/536) from the RD, and none from the ICU. The median total cost associated with LRTI per patient was US$52 (IQR 32-86) for outpatients and US$184 (IQR 109-287) for RD inpatients. For RSV-associated LRTIs, the median total cost per infection episode per patient was US$52 (IQR 32-85) for outpatients and US$165 (IQR 95-249) for RD inpatients. Total out-of-pocket costs of one non-ICU admission of RSV-associated LRTI ranged from 32%-70% of the monthly minimum wage per person (US$160) in Ho Chi Minh City. The sensitivity and the specificity of RSV RDA test were 88.2% (95% CI 63.6-98.5%) and 100% (95% CI 93.3-100%), respectively.

CONCLUSION

These are the first data reporting the substantial economic burden of RSV-associated illness in young children in Vietnam. This study informs policymakers in planning health care resources and highlights the urgency of RSV disease prevention.

Tea consumption and risk of lower respiratory tract infections: a two-sample mendelian randomization study

BACKGROUND

Observational studies have reported the association between tea consumption and the risk of lower respiratory tract infections (LRTIs). However, a consensus has yet to be reached, and whether the observed association is driven by confounding factors or reverse causality remains unclear.

METHOD

A two-sample Mendelian randomization (MR) analysis was conducted to determine whether genetically predicted tea intake is causally associated with the risk of common LRTI subtypes. Genome-wide association study (GWAS) from UK Biobank was used to identify single-nucleotide polymorphisms (SNPs) associated with an extra cup of tea intake each day. The summary statistics for acute bronchitis, acute bronchiolitis, bronchiectasis, pneumonia, and influenza and pneumonia were derived from the FinnGen project.

RESULTS

We found that genetically predicted an extra daily cup of tea intake was causally associated with the decreased risk of bronchiectasis [odds ratio (OR) = 0.61, 95% confidence interval (CI) = 0.47-0.78, P < 0.001], pneumonia (OR = 0.90, 95% CI = 0.85-0.96, P = 0.002), influenza and pneumonia (OR = 0.91, 95% CI = 0.85-0.97, P = 0.002), but not with acute bronchitis (OR = 0.91, 95% CI = 0.82-1.01, P = 0.067) and acute bronchiolitis (OR = 0.79, 95% CI = 0.60-1.05, P = 0.100). Sensitivity analyses showed that no heterogeneity and pleiotropy could bias the results.

CONCLUSIONS

Our findings provided new evidence that genetically predicted an extra daily cup of tea intake may causally associated with a decreased risk of bronchiectasis, pneumonia, and influenza and pneumonia.

Adults with symptoms of pneumonia: a prospective comparison of patients with and without infiltrates on chest radiography

OBJECTIVE

Most studies on patients hospitalized with community-acquired pneumonia (CAP) require confirmation of an infiltrate by chest radiography, but in practice admissions are common among patients with symptoms of pneumonia without an infiltrate (SPWI). The aim of this research was to compare clinical characteristics, microbial etiology, and outcomes among patients with CAP and SPWI.

METHODS

Adults suspected of CAP were prospectively recruited at Landspitali University Hospital over a 1-year period, 2018 to 2019. The study was population based. Those admitted with two or more of the following symptoms were invited to participate: temperature ≥38°C or ≤36°C, sweating, shaking/chills, chest pain, a new cough, or new onset of dyspnea. Primary outcome was mortality at 30 days and one year.

RESULTS

Six hundred twenty-five cases were included, 409 with CAP and 216 with SPWI; median age was 75 (interquartile range [IQR] 64-84) and 315 (50.4%) were females. Patients with CAP were more likely to have fever (≥38.0°C) (66.9% [273/408]) vs. 49.3% (106/215), p < 0.001), a higher CRP (median 103 [IQR 34-205] vs. 55 (IQR 17-103), p < 0.001), identification of Streptococcus pneumoniae (18.0% [64/355]) vs. 6.3% (10/159) of tested, p = 0.002) and to receive antibacterial treatment (99.5% [407/409]) vs. 87.5% (189/216), p < 0.001) but less likely to have a respiratory virus detected (25.4% [33/130]) vs. 51.2% (43/84) of tested, p < 0.001). The adjusted odds ratios for 30-day and 1 year mortality of SPWI compared to CAP were 0.86 (95% CI 0.40-1.86) and 1.46 (95% CI 0.92-2.32), respectively.

DISCUSSION

SPWI is a common cause of hospitalization and despite having fever less frequently, lower inflammatory markers, and lower detection rate of pneumococci than patients with CAP, mortality is not significantly different.

Indoor bacterial and fungal aerosols as predictors of lower respiratory tract infections among under-five children in Ibadan, Nigeria

BACKGROUND

This study aimed to investigate the association between exposure to diverse indoor microbial aerosols and lower respiratory tract infections (LRTI) among children aged 1 to 59 months in Ibadan, Nigeria.

METHODS

One hundred and seventy-eight (178) hospital-based LRTI cases among under-five children were matched for age (± 3 months), sex and geographical location with 180 community-based controls (under-five children without LRTI). Following consent from caregivers of eligible participants, a child's health questionnaire, clinical proforma and standardized home-walkthrough checklist were used to collect data. Participant homes were visited and sampled for indoor microbial exposures using active sampling approach by Anderson sampler. Indoor microbial count (IMC), total bacterial count (TBC), and total fungal count (TFC) were estimated and dichotomized into high (> median) and low (≤ median) exposures. Alpha diversity measures including richness (R), Shannon (H) and Simpson (D) indices were also estimated. Conditional logistic regression models were used to test association between exposure to indoor microbial aerosols and LRTI risk among under-five children.

RESULTS

Significantly higher bacterial and fungal diversities were found in homes of cases (R = 3.00; H = 1.04; D = 2.67 and R = 2.56; H = 0.82; D = 2.33) than homes of controls (R = 2.00; H = 0.64; D = 1.80 and R = 1.89; H = 0.55; D = 1.88) p < 0.001, respectively. In the multivariate models, higher categories of exposure to IMC (aOR = 2.67, 95% CI 1.44-4.97), TBC (aOR = 2.51, 95% CI 1.36-4.65), TFC (aOR = 2.75, 95% CI 1.54-4.89), bacterial diversity (aOR = 1.87, 95% CI 1.08-3.24) and fungal diversity (aOR = 3.00, 95% CI 1.55-5.79) were independently associated with LRTI risk among under-five children.

CONCLUSIONS

This study suggests an increased risk of LRTI when children under the age of five years are exposed to high levels of indoor microbial aerosols.

Association between early viral lower respiratory tract infections and subsequent asthma development

BACKGROUND

The association between hospitalization for human respiratory syncytial virus (HRSV) bronchiolitis in early childhood and subsequent asthma is well established. The long-term prognosis for non-bronchiolitis lower respiratory tract infections (LRTI) caused by viruses different from HRSV and rhinovirus, on the other hand, has received less interest.

AIM

To investigate the relationship between infant LRTI and later asthma and examine the influence of confounding factors.

METHODS

The PubMed and Global Index Medicus bibliographic databases were used to search for articles published up to October 2021 for this systematic review. We included cohort studies comparing the incidence of asthma between patients with and without LRTI at ≤ 2 years regardless of the virus responsible. The meta-analysis was performed using the random effects model. Sources of heterogeneity were assessed by stratified analyses.

RESULTS

This review included 15 articles (18 unique studies) that met the inclusion criteria. LRTIs at ≤ 2 years were associated with an increased risk of subsequent asthma up to 20 years [odds ratio (OR) = 5.0, 95%CI: 3.3-7.5], with doctor-diagnosed asthma (OR = 5.3, 95%CI: 3.3-8.6), current asthma (OR = 5.4, 95%CI: 2.7-10.6), and current medication for asthma (OR = 1.2, 95%CI: 0.7-3.9). Our overall estimates were not affected by publication bias (P = 0.671), but there was significant heterogeneity [I² = 58.8% (30.6-75.5)]. Compared to studies with hospitalized controls without LRTI, those with ambulatory controls had a significantly higher strength of association between LRTIs and subsequent asthma. The strength of the association between LRTIs and later asthma varied significantly by country and age at the time of the interview. The sensitivity analyses including only studies with similar proportions of confounding factors (gender, age at LRTI development, age at interview, gestational age, birth weight, weight, height, smoking exposure, crowding, family history of atopy, and family history of asthma) between cases and controls did not alter the overall estimates.

CONCLUSION

Regardless of the causative virus and confounding factors, viral LRTIs in children < 2 years are associated with an increased risk of developing a subsequent asthma. Parents and pediatricians should be informed of this risk.

Preparation and evaluation of a new combined conjugated vaccine against Klebsiella pneumonia and Pseudomonas aeruginosa

AIMS

Lower respiratory tract infections (LRTIs) have been identified by the WHO as the most deadly infectious diseases and a pervasive public health problem, causing increased hospital admissions, mortality, and antibiotic use. This study aims to determine the most common and resistant bacteria that cause LRTIs and prepare an appropriate vaccine to reduce and prevent potential future infections.

METHODS AND RESULTS

Our survey was conducted by collecting respiratory exudate specimens. The most predominant and resistant types were Klebsiella pneumonia and Pseudomonas aeruginosa. The lipopolysaccharides (LPS) were extracted using a modified hot phenol method to prepare the vaccine. The LPS were then activated and conjugated. The immunogenicity of the prepared singles and combined vaccines was determined through an in- vivo assay using BALB/c mice. The prepared vaccine provided high protection against the lethal dose of both bacteria in mice. The combined vaccine shows a significant value in achieving high immunization.

CONCLUSION

These findings demonstrate the potential of the bacterial LPS molecules to be used as effective vaccines.

SIGNIFICANCE AND IMPACT OF STUDY

developing an effective single and combined vaccine against Pseudomonas aeruginosa and Klebsiella pneumonia can protect and reduce LRTI incidence.

Pediatric Lower Respiratory Tract Infections: Imaging Guidelines and Recommendations

Lower respiratory tract infection (LRTI) remains a major cause of morbidity and mortality in children. Various organisms cause LRTI, including viruses, bacteria, fungi, and parasites, among others. Infections caused by 2 or more organisms also occur, sometimes enhancing the severity of the infection. Medical imaging helps confirm a diagnosis but also plays a role in the evaluation of acute and chronic sequelae. Medical imaging tests help evaluate underlying pathology in pediatric patients with recurrent or long-standing symptoms as well as the immunocompromised.

A LAMP-based system for rapid detection of eight common pathogens causing lower respiratory tract infections

Lower respiratory tract infections (LRTIs) are a leading cause of morbidity and mortality worldwide and lack a rapid diagnostic method. To improve the diagnosis of LRTIs, we established an available loop-mediated isothermal amplification (LAMP) assay for the detection of eight common lower respiratory pathogens, including Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, Escherichia coli, Haemophilus influenzae, Streptococcus pneumoniae, and Moraxella catarrhalis. The whole process can be achieved within 1 h (sample to results read out). We established an extraction free isothermal system. 528 sputum samples collected from patients suspected to have LRTIs were analyzed by the system (8 tests in each sample, a total of 4224 tests) and compared with the standard culture method (SCM). The samples with inconsistent results were further verified by Sanger sequencing and High-throughput sequencing (NGS). The detection limits of the LAMP assay for the 8 pathogens ranged from 10³ to 10⁴ CFU/mL. Upon testing 528 samples, the Kappa coefficients of all pathogens ranged between 0.5 and 0.7 indicated a moderate agreement between the LAMP assay and the SCM. All inconsistent samples were further verified by Sanger sequencing, we found that the developed LAMP assay had a higher consistency level with Sanger sequencing than the SCM for all pathogens. Additionally, when the NGS was set to a diagnostic gold standard, the specificity and sensitivity of the LAMP assay for LRTIs were 94.49% and 75.00%. The present study demonstrated that the developed LAMP has high consistency with the sequencing methods. Meanwhile, the LAMP assay has a higher detection rate compared to the SCM. It may be a powerful tool for rapid and reliable clinical diagnosis of LRTIs in primary hospitals.

The incidence of lower respiratory tract infections and pneumococcal vaccination status in adults in flemish primary care

Pneumococcal vaccination coverage of adults at risk for pneumococcal disease is below recommended levels. There is no observational data on pneumococcal vaccination and the incidence of lower respiratory tract infections in a general adult population. The current study had the objective to explore the incidence of lower respiratory tract infections and the pneumococcal vaccine coverage in function of age, influenza vaccination status and risk status, in Flanders, Belgium. We used data from Intego, ageneral practice-based morbidity registration network in Flanders (Belgium). We gathered data on pneumococcal vaccinations, influenza vaccination (in 2014) and ICPC2-coded diagnoses of pneumonia and acute bronchitis (2015). First, we divided the population into three groups along the risk status for developing apneumococcal infection according to the recommendations for pneumococcal vaccination in adults by the Belgian High Council of Health. 28.6% from our total adult study population are considered the target group for vaccination. Second, we found that the average pneumococcal vaccination coverage in this targeted population was 18.7%. Third, we found asignificantly higher incidence of LRTI in patients previously vaccinated against pneumococcal disease and/or influenza across the majority of subgroups. Pneumococcal vaccination coverage in Flanders is quantitatively low but observed to be qualitatively high in terms of reaching the most at risk population. Our findings are likely to be highly relevant to addressing future vaccination strategies in Flanders.

Broad range detection of viral and bacterial pathogens in bronchoalveolar lavage fluid of children to identify the cause of lower respiratory tract infections

BACKGROUND

Knowledge on the etiology of LRTIs is essential for improvement of the clinical diagnosis and accurate treatment. Molecular detection methods were applied to identify a broad range of bacterial and viral pathogens in a large set of bronchial alveolar lavage (BAL) fluid samples. The patterns of detected pathogens were correlated to the clinical symptoms.

METHODS

BAL fluid samples and clinical data were collected from 573 hospitalized children between 1 month and 14 years of age with LRTIs, enrolled from January to December 2018. Pathogens were detected using standardized clinical diagnostics, with a sensitive, high-throughput GeXP-based multiplex PCR and with multiplex qPCR. Data were analyzed to describe the correlation between the severity of respiratory tract disease and the pathogens identified.

RESULTS

The pathogen detection rate with GeXP-based PCR and multiplex qPCR was significantly higher than by clinical routine diagnostics (76.09% VS 36.13%,χ2 = 8.191, P = 0.004). The most frequently detected pathogens in the BAL fluid were human adenovirus (HADV)(21.82%), Mycoplasma pneumoniae (20.24%), human rhinovirus (13.96%), Streptococcus pneumoniae (8.90%) and Haemophilus influenzae (8.90%). In 16.4% of the cases co-detection with two or three different pathogens was found. Viral detection rates declined with age, while atypical pathogen detection rates increased with age. Oxygen supply in the HADV and Influenza H1N1 infected patients was more frequent (49.43%) than in patients infected with other pathogens.

CONCLUSION

Broad range detection of viral and bacterial pathogens using molecular methods is a promising and implementable approach to improve clinical diagnosis and accurate treatment of LRTI in children.

Evaluation of semi-quantitative compared to quantitative cultures of tracheal aspirates for the yield of culturable respiratory pathogens - a cross-sectional study

Background

Diagnosis of lower respiratory tract infections (LRTI) depends on the presence of clinical, radiological and microbiological findings. Endotracheal suction aspirate (ETSA) is the commonest respiratory sample sent for culture from intubated patients. Very few studies have compared quantitative and semi-quantitative processing of ETSA cultures for LRTI diagnosis. We determined the diagnostic accuracy of quantitative and semi-quantitative ETSA culture for LRTI diagnosis, agreement between the quantitative and semi quantitative culture techniques and the yield of respiratory pathogens with both methods.

Methods

This was a cross-sectional study conducted at the Aga Khan University clinical laboratory, Karachi, Pakistan. One hundred and seventy-eight ETSA samples sent for routine bacteriological cultures were processed quantitatively as part of regular specimen processing method and semi-quantitatively. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and diagnostic accuracy was calculated for both methods using clinical diagnosis of pneumonia as reference standard. Agreement between the quantitative and semi quantitative methods was assessed via the kappa statistic test. Pathogen yield between the two methods was compared using Pearson’s chi-square test.

Results

The quantitative and semi-quantitative methods yielded pathogens in 81 (45.5%) and 85 (47.8%) cases respectively. There was complete concordance of both techniques in 155 (87.1%) ETSA samples. No growth was observed in 45 (25.3%) ETSA specimens with quantitative culture and 37 (20.8%) cases by semi-quantitative culture. The diagnostic accuracy of both techniques were comparable; 64.6% for quantitative and 64.0% for semi-quantitative culture. The kappa agreement was found to be 0.84 (95% CI, 0.77–0.91) representing almost perfect agreement between the two methods. Although semi-quantitative cultures yielded more pathogens (47.8%) as compared to quantitative ETSA cultures (45.5%), the difference was only 2.3%. However, this difference achieved statistical (chi-square p-value < 0.001) favoring semi-quantitative culture methods over quantitative culture techniques for processing ETSA.

Conclusion

In conclusion, there is a strong agreement between the performances of both methods of processing ETSA cultures in terms of accuracy of LRTI diagnosis. Semi-quantitative cultures of ETSA yielded more pathogens as compared to quantitative cultures. Although both techniques were comparable, we recommend processing of ETSA using semi-quantitative technique due to its ease and reduced processing time.

Secondary infections in patients hospitalized with COVID-19: incidence and predictive factors

Objectives

The aim of our study was to describe the incidence and predictive factors of secondary infections in patients with coronavirus disease 2019 (COVID-19).

Methods

This was a cohort study of patients hospitalized with COVID-19 at IRCCS San Raffaele Hospital between 25th February and 6th April 2020 (NCT04318366). We considered secondary bloodstream infections (BSIs) or possible lower respiratory tract infections (pLRTIs) occurring 48 hours after hospital admission until death or discharge. We calculated multivariable Fine–Gray models to assess factors associated with risk of secondary infections.

Results

Among 731 patients, a secondary infection was diagnosed in 68 patients (9.3%); 58/731 patients (7.9%) had at least one BSI and 22/731 patients (3.0%) at least one pLRTI. The overall 28-day cumulative incidence was 16.4% (95%CI 12.4–21.0%). Most of the BSIs were due to Gram-positive pathogens (76/106 isolates, 71.7%), specifically coagulase-negative staphylococci (53/76, 69.7%), while among Gram-negatives (23/106, 21.7%) Acinetobacter baumanii (7/23, 30.4%) and Escherichia coli (5/23, 21.7%) predominated. pLRTIs were caused mainly by Gram-negative pathogens (14/26, 53.8%). Eleven patients were diagnosed with putative invasive aspergillosis. At multivariable analysis, factors associated with secondary infections were low baseline lymphocyte count (≤0.7 versus >0.7 per 10⁹/L, subdistribution hazard ratios (sdHRs) 1.93, 95%CI 1.11–3.35), baseline PaO₂/FiO₂ (per 100 points lower: sdHRs 1.56, 95%CI 1.21–2.04), and intensive-care unit (ICU) admission in the first 48 hours (sdHR 2.51, 95%CI 1.04–6.05).

Conclusions

Patients hospitalized with COVID-19 had a high incidence of secondary infections. At multivariable analysis, early need for ICU, respiratory failure, and severe lymphopenia were identified as risk factors for secondary infections.

Laboratory evaluation of the BioFire FilmArray Pneumonia plus panel compared to conventional methods for the identification of bacteria in lower respiratory tract specimens: a prospective cross-sectional study from South Africa

Lower respiratory tract infections are important causes of morbidity and mortality. The global increase in antimicrobial resistance necessitates rapid diagnostic assays. The BioFire FilmArray Pneumonia plus (FAPP) panel is a Food and Drug Administration-approved multiplex polymerase chain reaction assay that detects the most important etiological agents of pneumonia and associated antibiotic resistance genes, in approximately 1 hour. This study assessed the diagnostic performance of this assay by comparing it to conventional culture methods in the analysis of 59 lower respiratory tract specimens. The sensitivity and specificity of the FAPP panel for bacterial detection were 92.0% (95% confidence interval [CI], 80.8% to 97.8%) and 93.8% (95% CI, 91.1% to 95.3%) respectively. For detecting antibiotic resistance, the positive- and negative percent agreement were 100% (95% CI, 81.5% to 100.0%) and 98.5% (95% CI, 216 96.7% to 99.4%) respectively. The FAPP panel was found to be highly accurate in evaluating tracheal aspirate specimens from hospitalized patients.

[Smoking and Breastfeeding - CNGOF-SFT Expert Report and Guidelines on the management for Smoking Management During Pregnancy]

INTRODUCTION

The consequences of smoking have been studied more during pregnancy than during breastfeeding. There is a passage of nicotine and other substances in breast milk and some modifications of milk composition. The objectives of this chapter are to study the benefits of breastfeeding in women who smoke, and the adaptation of smoking, medication and behavioral habits in case of incomplete withdrawal to better guide women.

METHODS

The Medline database, the Cochrane Library and foreign guidelines from 1999 to 2019 have been consulted.

RESULTS

The conservation of the benefit of breastfeeding in smokers with regard to the prevention of respiratory infections, infantile colic, cognitive deficits, obesity, sudden infant death, is not known to date. It is therefore not recommended to include smoking status in the choice of feeding mode for the newborn (professional agreement). However, since breastfeeding is a factor associated with a reduction in smoking and/or withdrawal (NP2), it is recommended to promote breastfeeding in non-weaned women in order to limit smoking (grade B). The use of nicotine replacement therapy is possible during breastfeeding (professional agreement). In the absence of data, bupropion (Zyban®) and varenicline (Champix®) are not recommended for women who are breastfeeding (professional agreement). A free interval between smoking and breastfeeding reduces the concentration of nicotine in milk (NP4). For non-weaned women who are breastfeeding, it is therefore recommended not to smoke just before breastfeeding (professional agreement).

CONCLUSION

The results indicate that breastfeeding is possible in smokers, although less often initiated by them. If the conservation of its benefits for the child is not demonstrated to date, breastfeeding allows the mother to limit smoking.

Evaluation of the Biofire Filmarray Pneumonia panel plus for lower respiratory tract infections

Background: Standard diagnostic methods for lower respiratory tract infections are currently too slow and insensitive to guide early clinical decisions concerning treatment and isolation. Syndrome-specific, diagnostic panels have potential to provide information about aetiology quickly. Available panels have been of limited use in lower respiratory tract infections due to slow turn-around-time, lack of quantification of important pathogens and lack of detection of resistance genes.Materials/methods: We evaluated the newly developed Biofire^® Filmarray^® Pneumonia Panel plus (Biomérieux). Eighty-eight consecutive lower respiratory tract samples were analyzed by both standard microbiological methods, as requested by the referring clinician, and by the panel. The agreement with standard methods, empirical treatment coverage and possible impact on isolation practices were assessed by comparing the results from standard diagnostic methods with the panel results in relation to clinical data and information of antimicrobial therapy.Results: Both qualitative and semi-quantitative results from the panel generally displayed good agreement with standard methods and by combining methods, a possible aetiology was detected in 73% of patients. Due to the panel approach, the panel detected viruses more frequently. In 25% of the 60 patients assessed for empirical treatment coverage, a pathogen not covered by current therapy was detected and in 30% of in-house patients the panel results were found to potentially influence clinical decisions related to isolation care.Conclusions: The new diagnostic panel shows promise in improving aetiological diagnostics of lower respiratory tract infections. Correctly applied it has potential to offer support in clinical decision-making within hours of sampling.

Activity of ceftolozane-tazobactam against Gram-negative pathogens isolated from lower respiratory tract infections in the Asia-Pacific region: SMART 2015-2016

The aim of this study was to investigate the susceptibility of respiratory Gram-negative bacteria to ceftolozane/tazobactam and other antibiotics in the Asia-Pacific region during 2015-2016. MICs were determined using the CLSI standard broth microdilution method and interpreted accordingly. Pseudomonas aeruginosa (1574 isolates), Klebsiella pneumoniae (1226), Acinetobacter baumannii (627) and Escherichia coli (476) accounted for 73.1% of 5342 Gram-negative respiratory pathogens. Susceptibility to ceftolozane/tazobactam of individual Enterobacteriaceae was >80%, except for Enterobacter cloacae (76.6%). Ceftolozane/tazobactam inhibited 81.9% of K. pneumoniae and 91.9% of E. coli, with respective MIC₅₀/MIC₉₀ values of 0.5/>32 and 0.25/2 mg/L. For carbapenem-susceptible, ESBL-producing K. pneumoniae and E. coli, susceptibility was 65.5% and 93.3%, respectively, and respective MIC₅₀/MIC₉₀ values were 2/>32 and 0.5/2 mg/L. Bla_{CTX-M-1 group} was most prevalent in selected ESBL-producing K. pneumoniae (40 of 54 isolates) and E. coli (15 of 22 isolates), with ceftolozane/tazobactam susceptibility rates of 50% and 80%, respectively. Bla_SHV-ESBL was the second most prevalent, and ceftolozane/tazobactam inhibited 20% of 20 K. pneumoniae isolates with bla_SHV-ESBL. The only effective antibiotics for carbapenem-non-susceptible K. pneumoniae (111 isolates) and E. coli (24 isolates) were amikacin and colistin. Ceftolozane/tazobactam was effective against almost all tested P. aeruginosa and carbapenem-non-susceptible strains, with susceptibility of 92.3% and 72.8%, respectively; the respective MIC₅₀/MIC₉₀ values were 1/4 and 2/>32 mg/L. The high susceptibility of ceftolozane/tazobactam remained in different age groups, patient locations, recovery times and countries, except Vietnam. In conclusion, ceftolozane/tazobactam was effective against most respiratory Gram-negative pathogens in the Asia-Pacific region; however, the emergence of carbapenem resistance mandates ongoing surveillance.

Effect of Vitamin D Supplementation in the Prevention of Recurrent Pneumonia in Under-Five Children

OBJECTIVE

To assess the effect of vitamin D supplementation in the prevention of recurrent pneumonia in under-five children.

METHODS

The present one year 8 months longitudinal, community-based randomized controlled study included a total of 100 under-five children with pneumonia. Children were divided into two groups: intervention group (Group I: standard treatment with vitamin D 300,000 IU; n = 50) and control group (Group C: standard treatment only; n = 50). As nine samples were hemolyzed, groups I and C comprised of 46 and 45 children, respectively. The children were followed up for 1 y and signs of upper respiratory tract infections (URTI), lower respiratory tract infections (LRTI), vitamin D deficiency, and vitamin D toxicity were recorded.

RESULTS

The male to female ratio in group C and I was 1.27:1 and 1.5:1, respectively (P = 0.420). Age, gender, birth, anthropometric and clinical characteristics, and feeding habits were not statistically significant (P > 0.05) between both the cohorts (Group C and I). Children with reduced vitamin D levels were high in group C (25) when compared to the group I (15). During all the follow-ups, the URTI and LRTI episodes, severity of pneumonia, number of hospital admissions, complications, mean episodes of LRTI, and mean duration of LRTI were comparable between group I and group C (P > 0.05).

CONCLUSIONS

Overall, the present study highlights that oral vitamin D (300,000 IU bolus dose quarterly) has some beneficial effect in the prevention of recurrent pneumonia in under-five children, although, not to a significant degree. Hence, it is recommended that further studies are required to demonstrate a significant effect of vitamin D in the prevention of pneumonia.

Diagnostic value of serum neutrophil gelatinase-associated lipocalin, interleukin-6 and anti-citrullinated alpha-enolase peptide 1 for lower respiratory tract infections

OBJECTIVES

The aim of this study was to explore the auxiliary diagnostic value of neutrophil gelatinase-associated lipocalin (NGAL) and anti-citrullinated alpha-enolase peptide 1 (CEP-1) in lower respiratory tract infections (LRTIs).

METHODS

Blood samples were collected from 99 in-patients with LRTIs [62 community-acquired pneumonia (CAP), 14 acute exacerbated chronic obstructive pulmonary diseases (AECOPD), 23 other diseases] and 50 healthy subjects. NGAL, CEP-1 and IL-6 were measured and compared. IL-6 was tested by electrochemiluminescence assay kit on Roche E601 immunology analyzer, CEP-1 was assessed with enzyme-linked immunosorbent assay kit, and NGAL was detected by latex immunoturbidimetric assay kit on Beckman Coulter AU2700.

RESULTS

Compared with healthy controls, NGAL and IL-6 levels were significantly increased in the patients with LRTIs, the area under the curves (AUC) was 0.97 and 0.88 respectively (P < 0.01). The sensitivity and specificity of NGAL at a cut-off of 86 ng/ml were 93.0% and 96.0%, respectively, in which the sensitivity was consistent with IL-6 (P = 0.21) and the specificity was better than IL-6 (P < 0.01). CEP-1 slightly increases in the patient group, however the difference was not significant (P = 0.41). The levels of NGAL and IL-6 was no differences in different diseases, the P-value was 0.50 and 0.29, respectively. LRTIs with and without underlying diseases have similar NGAL and IL-6 values.

CONCLUSIONS

NGAL, rather than CEP-1, may be appealing adjuncts for diagnosis of LRTIs. NGAL proved to be a better biomarker than IL-6.

The Diagnostic Accuracy of the Pitch Glide to Identify Aspiration in Patients with Respiratory Diseases: A Pilot Study

INTRODUCTION

Initial research has been conducted to determine the diagnostic accuracy of the pitch glide during the clinical swallow evaluation to identify aspiration in adults after stroke. Findings suggest that reduced pitch glide can predict aspiration in patients with dysphagia after stroke. This study aimed to identify the diagnostic accuracy of the pitch glide in detecting aspiration, pharyngeal residue and hyo-laryngeal excursion during swallowing in adults with respiratory diseases.

MATERIAL AND METHODS

17 adults (9 males and 8 females) with dysphagia who had a background of respiratory diseases (chronic obstructive pulmonary disease = 11; lower respiratory tract infection = 6) were consecutively recruited in an acute hospital setting. Participants completed two pitch glide tasks (/a/ and /i/) immediately before a videofluoroscopic swallowing study (VFSS). Pitch glide recordings were analysed by blinded researchers both acoustically (Praat software) to obtain maximum F0, pitch range and auditory-perceptually using a binary scale ("normal" or "abnormal"). Clinicians blinded to pitch glide ratings rated 5 mL, 10 mL and a sip of liquid swallows during VFSS using the Penetration-Aspiration Scale, Bolus Residue Scale and hyolaryngeal component of the MBS Measurement Tool for Swallow Impairment. Receiver operating characteristic curve, Pearson correlations and independent sample t tests were used to address the research questions.

RESULTS

Maximum F0 of sound /a/ had high sensitivity and specificity in identifying aspiration on 10 mL of liquids during VFSS. Both pitch glides (/a/ and /i/) had moderate sensitivity and specificity in predicting aspiration on a sip of liquids. However, auditory-perceptual measures of pitch glide had weak accuracy in identifying people who were aspirating during VFSS. Finally, all pitch glide measures (acoustic and auditory-perceptual) had low accuracy in predicting pharyngeal residue and hyolaryngeal excursion.

CONCLUSION

Based on this initial pilot study, acoustic pitch glide of sound /a/ is an accurate way to predict aspiration on 10 mL of liquids in patients with respiratory diseases. Based on findings from this study, both auditory-perceptual and acoustic analyses of pitch glide could not identify residue and hyolaryngeal excursion.

Dental caries is associated with lower respiratory tract infections: A population-based cohort study

INTRODUCTION

Dental caries and respiratory tract infections are among the most common infectious diseases worldwide and they both are appearing in the respiratory system. However, their relations are still unclear. This study investigated the association of dental caries on the risk of lower respiratory tract infections (LRTI) in young adulthood.

METHODS

The study population consisted of 1,592 Finnish young adults participating in the 20-year follow-up of The Espoo Cohort Study. The information on the occurrence of LRTIs (pneumonia or acute bronchitis) during the preceding 12 months was based on the follow-up questionnaire and the National Hospital Discharge Register. Lifelong caries on permanent teeth was defined as a self-reported number of filled teeth (FT). The risk ratios (RR) of LRTIs with 95% confidence intervals (CI) were estimated using Poisson regression models.

RESULTS

High FT number was associated with an increased occurrence of LRTIs with an adjusted RR of 1.24 per interquartile range (IQR) of FT (95% CI 1.06-1.44). The risk of LRTIs increased according to the increasing number of FTs, being highest among those subjects with 10 or more filled teeth (adjusted RR 2.30; 1.27-4.17). Family's socioeconomic status or smoking did not modify the effect.

CONCLUSIONS

Our results suggest that dental caries increases the risk of LRTIs. We did not find any significant effect modification by shared determinants of caries and LRTIs. However, it is possible, that common risk factors might explain at least partly the observed relation between FT and LRTIs or that the causality is bidirectional.

Procalcitonin and lung ultrasonography point-of-care testing to decide on antibiotic prescription in patients with lower respiratory tract infection in primary care: protocol of a pragmatic cluster randomized trial

Background

A minority of patients presenting with lower respiratory tract infection (LRTI) to their general practitioner (GP) have community-acquired pneumonia (CAP) and require antibiotic therapy. Identifying them is challenging, because of overlapping symptomatology and low diagnostic performance of chest X-ray.

Procalcitonin (PCT) can be safely used to decide on antibiotic prescription in patients with LRTI. Lung ultrasound (LUS) is effective in detecting lung consolidation in pneumonia and might compensate for the lack of specificity of PCT.

We hypothesize that combining PCT and LUS, available as point-of care tests (POCT), might reduce antibiotic prescription in LRTIs without impacting patient safety in the primary care setting.

Methods

This is a three-arm pragmatic cluster randomized controlled clinical trial. GPs are randomized either to PCT and LUS-guided antibiotic therapy or to PCT only-guided therapy or to usual care. Consecutive adult patients with an acute cough due to a respiratory infection will be screened and included if they present a clinical pneumonia as defined by European guidelines. Exclusion criteria are previous antibiotics for the current episode, working diagnosis of sinusitis, severe underlying lung disease, severe immunosuppression, hospital admission, pregnancy, inability to provide informed consent and unavailability of the GP. Patients will fill in a 28 day-symptom diary and will be contacted by phone on days 7 and 28. The primary outcome is the proportion of patients prescribed any antibiotic up to day 28. Secondary outcomes include clinical failure by day 7 (death, admission to hospital, absence of amelioration or worsening of relevant symptoms) and by day 28, duration of restricted daily activities, episode duration as defined by symptom score, number of medical visits, number of days with side effects due to antibiotics and a composite outcome combining death, admission to hospital and complications due to LRTI by day 28. An evaluation of the cost-effectiveness and of processes in the clinic using a mixed qualitative and quantitative approach will also be conducted.

Discussion

Our intervention targets only patients with clinically suspected CAP who have a higher pretest probability of definite pneumonia. The intervention will not substitute clinical assessment but completes it by introducing new easy-to-perform tests.

Trial registration

The study was registered on the 19th of June 2017 on the clinicaltrials.gov registry using reference number; NCT03191071.

Electronic supplementary material

The online version of this article (10.1186/s12890-019-0898-3) contains supplementary material, which is available to authorized users.

Serological and molecular detection of Mycoplasma pneumoniae in children with community-acquired lower respiratory tract infections

This study was designed to evaluate the incidence of Mycoplasma pneumoniae infection in children with community-acquired lower respiratory tract infections (LRTIs). A total of 245 patients 6 months to 12 years of age were investigated for M. pneumoniae employing serological tests, polymerase chain reaction (PCR), nested PCR, and reverse transcription PCR (RT-PCR) on throat swab samples. Forty five (59.2%) children <5 years and 31 (40.7%) children ≥5 years age group were positive for M. pneumoniae infection, and this difference was statistically significant (P ≤ 0.01).Clinical and radiological findings across M.pneumoniae-positive and -negative cases were comparable. Serology, PCR, nested PCR, and RT-PCR together detected M. pneumoniae infection in 76 (31%) patients. Sensitivity, specificity, and positive and negative predictive values of PCR were 16.18%, 95.48%, 57.89%, and 74.78%, respectively, and those of serology were 57.89%, 74.78%, 16.18%, and 95.48%, respectively. Serological and molecular detection in combination is useful for rapid and reliable diagnosis of M. pneumoniae infections in children with LRTIs.

Sociodemographic, climatic variability and lower respiratory tract infections: a systematic literature review

Pneumonia is the leading cause of mortality and morbidity in developing countries, particularly for children and elderly. The main objective of this review paper is to review the epidemiological evidence about the effects of sociodemographic and climatic variability on pneumonia and other lower respiratory tract infections. A detailed literature search was conducted in PubMed and Scopus following PRISMA guidelines. The articles, which considered the effect of only climatic or both climatic and sociodemographic factors on pneumonia and other lower respiratory tract infections, included in this review. A total thirty-four relevant articles were reviewed. Of 34 studies, only 14 articles (41%) examined the joint effects of sociodemographic and climate factors on pneumonia and other lower respiratory infections while most of them (59%) assessed climate factors separately. Among these fourteen, only three articles (8.8%) considered detailed sociodemographic factors. All of the reviewed articles suggested different degrees of positive or negative relationship of temperature with pneumonia or other lower respiratory tract infections. Fifteen (44%) articles suggested an association with relative humidity and 13 (38%) with rainfall. Only 3 articles (8.8%) found a relationship with wind speed. Three articles (8.8%) considered other risk factors such as particulate matter 2.5 (PM_2.5) and particulate matter 10 (PM₁₀). One study among the reviewed articles used spatial analysis methods but this study did not examine the joint effects. Among the reviewed articles, 18 (53%) articles used different time series models, one article (3%) used spatiotemporal time series model, 8 (23%) studies used other models and rest 7 (21%) studies used simple descriptive analysis. A total of 18 studies (53%) were conducted in Asia, most of them in China. There were 6 studies (17%) in Europe and 8 studies (23%) in America (South, North and Central). In Africa and Oceania, only one study was found for each region. The joint effect of climate and sociodemographic factors on pneumonia and other lower respiratory tract infections remain to be determined and further research is highly recommended for future prevention of this important and common disease.

C-reactive protein and procalcitonin profile in ventilator-associated lower respiratory infections

PURPOSE

Ventilator-associated tracheobronchitis (VAT) has been suggested as an intermediate process between tracheobronchial colonization and ventilator-associated pneumonia (VAP) in patients receiving mechanical ventilation. The aim of this study was to evaluate the ability of C-reactive protein (CRP) and procalcitonin (PCT) to differentiate between VAT and VAP.

METHODS

Pre-planned analysis of the prospective multinational TAVeM database, performed on 2960 patients receiving mechanical ventilation for >48 h, including 689 patients with VA-LRTI. Patients with the diagnosis of VAT or VAP microbiologically documented and with one measurement of CRP and/or PCT on the day of diagnosis were included.

RESULTS

Four hundred and four patients (mean age 63 years, 298 men, ICU mortality 40%) were studied, 207 with VAT and 197 with VAP. On the day of infection diagnosis, the median CRP was elevated in both groups but significantly higher in VAP (18 mg/dL vs. 14 mg/dL, p = .001). Median PCT was also significantly higher in VAP (2.1 ng/dL vs. 0.64 ng/d L, p < .001). Both biomarkers could not help distinguish between VAT and VAP.

CONCLUSION

Although PCT and CRP presented lower values in VAT as compared to VAP, there was a marked overlap of both biomarkers values in both VA-LRTI not allowing adequate discrimination.

Observational multi-centre, prospective study to characterize novel pathogen-and host-related factors in hospitalized patients with lower respiratory tract infections and/or sepsis - the "TAILORED-Treatment" study

Background

The emergence and spread of antibiotic resistant micro-organisms is a global concern, which is largely attributable to inaccurate prescribing of antibiotics to patients presenting with non-bacterial infections. The use of ‘omics’ technologies for discovery of novel infection related biomarkers combined with novel treatment algorithms offers possibilities for rapidly distinguishing between bacterial and viral infections. This distinction can be particularly important for patients suffering from lower respiratory tract infections (LRTI) and/or sepsis as they represent a significant burden to healthcare systems. Here we present the study details of the TAILORED-Treatment study, an observational, prospective, multi-centre study aiming to generate a multi-parametric model, combining host and pathogen data, for distinguishing between bacterial and viral aetiologies in children and adults with LRTI and/or sepsis.

Methods

A total number of 1200 paediatric and adult patients aged 1 month and older with LRTI and/or sepsis or a non-infectious disease are recruited from Emergency Departments and hospital wards of seven Dutch and Israeli medical centres. A panel of three experienced physicians adjudicate a reference standard diagnosis for all patients (i.e., bacterial or viral infection) using all available clinical and laboratory information, including a 28-day follow-up assessment. Nasal swabs and blood samples are collected for multi-omics investigations including host RNA and protein biomarkers, nasal microbiota profiling, host genomic profiling and bacterial proteomics. Simplified data is entered into a custom-built database in order to develop a multi-parametric model and diagnostic tools for differentiating between bacterial and viral infections. The predictions from the model will be compared with the consensus diagnosis in order to determine its accuracy.

Discussion

The TAILORED-Treatment study will provide new insights into the interplay between the host and micro-organisms. New host- or pathogen-related biomarkers will be used to generate a multi-parametric model for distinguishing between bacterial and viral infections. This model will be helpful to better guide antimicrobial therapy for patients with LRTI and sepsis. This study has the potential to improve patient care, reduce unnecessary antibiotic prescribing and will contribute positively to institutional, national and international healthcare economics.

Trial Registration

NCT02025699. Registration Date: January, 1, 2014.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3300-9) contains supplementary material, which is available to authorized users.

Simultaneous Detection of 13 Key Bacterial Respiratory Pathogens by Combination of Multiplex PCR and Capillary Electrophoresis

OBJECTIVE

Lower respiratory tract infections continue to pose a significant threat to human health. It is important to accurately and rapidly detect respiratory bacteria. To compensate for the limits of current respiratory bacteria detection methods, we developed a combination of multiplex polymerase chain reaction (PCR) and capillary electrophoresis (MPCE) assay to detect thirteen bacterial pathogens responsible for lower respiratory tract infections, including Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Mycoplasma pneumoniae, Legionella spp., Bordetella pertussis, Mycobacterium tuberculosis complex, Corynebacterium diphtheriae, and Streptococcus pyogenes.

METHODS

Three multiplex PCR reactions were built, and the products were analyzed by capillary electrophoresis using the high-throughput DNA analyzer. The specificity of the MPCE assay was examined and the detection limit was evaluated using DNA samples from each bacterial strain and the simulative samples of each strain. This assay was further evaluated using 152 clinical specimens and compared with real-time PCR reactions. For this assay, three nested-multiplex-PCRs were used to detect these clinical specimens.

RESULTS

The detection limits of the MPCE assay for the 13 pathogens were very low and ranged from 10-7 to 10-2 ng/μL. Furthermore, analysis of the 152 clinical specimens yielded a specificity ranging from 96.5%-100.0%, and a sensitivity of 100.0% for the 13 pathogens.

CONCLUSION

This study revealed that the MPCE assay is a rapid, reliable, and high-throughput method with high specificity and sensitivity. This assay has great potential in the molecular epidemiological survey of respiratory pathogens.

Drug utilization review of cephalosporins in a secondary care hospital in United Arab Emirates

Background Cephalosporins are one of the most commonly used antibiotics in United Arab Emirates (UAE). Few studies have been carried out to evaluate the antibiotic utilization pattern in UAE in spite of the obvious increase in cephalosporins resistance during the past decade. Objective To assess the prescriptions pattern of cephalosporins among physicians at a secondary care hospital in Ras Al Khaimah, UAE. Method This observational prospective study was carried out during October 2013 to April 2014. The data of in patients were documented in the predesigned patient profile form and was analyzed for patient's, drug's and drug's therapy related parameters. Results The 3rd generation cephalosporins constituted 83.6 % of the prescriptions, with ceftriaxone being the most commonly used one (81.1 %). They were mainly prescribed for the treatment of the lower respiratory tract infections (60.2 %). Seven (3.5 %) different ADRs linked to cephalosporin use were observed ranging from oral thrush to clostridium difficile infection. A total of 1039 antimicrobial and nonantimicrobial medications were prescribed concomitantly with cephalosporins. Conclusion The 3rd generation cephalosporins were commonly prescribed by parenteral route. Thus, there is a strong need for rationalizing their use to preserve their efficacy and prevent the development of resistance in the region.

Idiopathic pulmonary haemosiderosis in paediatric patients: how to make an early diagnosis

BACKGROUND

Idiopathic pulmonary haemosiderosis (IPH) is a rare but potentially lethal condition in paediatric patients. This condition is considered an immune-mediated disorder, but its pathogenesis is still unknown. Idiopathic pulmonary haemosiderosis is characterized by the classical triad of haemoptysis, iron-deficiency anaemia, and diffuse parenchymal consolidation on chest radiology. Unfortunately, this triad of signs is not frequent in children at the onset of this disease, resulting in a delay in diagnosis and a negative outcome.

CASE PRESENTATION

This case report describes a 4-year-old girl who was admitted for an acute episode of lower respiratory tract infection associated with severe dyspnoea, polypnoea, and severe anaemia (haemoglobin levels, 5.9 g/dL). She had a history of previous similar episodes, with anaemia treated unsuccessfully with iron supplementation and managed through repeated blood transfusions in the acute phase. She did not experience haemoptysis. A computed tomography (CT) scan of the thorax showed ground-glass opacity suggestive of pulmonary haemorrhage. After other causes of intra-alveolar haemorrhage were excluded, IPH was confirmed by the presence of siderophages in bronchoalveolar lavage. Immunosuppressive corticosteroid treatment was immediately started with a good clinical response.

CONCLUSION

This case highlights the fact that IPH should be suspected in children with recurrent lower respiratory tract infections who have a history of iron-deficiency anaemia who shows no signs of improvement with iron supplementation and may require repeated blood transfusions. The absence of haemoptysis does not exclude the diagnosis of IPH in children. An early and prompt diagnosis is recommended in order to start adequate immunosuppressive treatment.

The Use of Guidelines for Lower Respiratory Tract Infections in Tanzania: A Lesson from Kilimanjaro Clinicians

Background:

Evaluations of the guidelines for the management of Lower Respiratory Tract Infections (LRTI) Sub-Saharan Africa, particularly in Tanzania is scant.

Aim:

The aim of the study was to assess the usefulness of the current Tanzanian treatment guideline for the management lower respiratory tract infection.

Subjects and Methods:

A descriptive cross sectional study in 11 hospitals of different levels in the Kilimanjaro region Data were collected from May 2012 to July 2012 by semi-structured interview for clinicians using 2 dummy cases for practical assessment. Data were analyzed by STATA v11 (StataCorp, TX, USA). Qualitative narratives from the interviews were translated, transcribed then coded by colors into meaningful themes.

Results:

A variety of principles for diagnosing and managing LRTI were demonstrated by 53 clinicians of Kilimanjaro. For the awareness, 67.9% (36/53) clinicians knew their responsibility to use Standard Treatment Guideline for managing LRTI. The content derived from Standard Treatment Guideline could be cited by 11.3% of clinicians (6/53) however they all showed concern of gaps in the guideline. Previous training in the management of patients with LRTI was reported by 25.9% (14/53), majority were pulmonary TB related. Correct microorganisms causing different forms of LRTI were mentioned by 11.3% (6/53). Exact cause of Atypical pneumonia and Q fever as an example was stated by 13.0% (7/53) from whom the need of developing the guideline for LRTI was explicitly elaborated.

Conclusion:

The current guidelines have not been used effectively for the management of LRTI in Tanzania. There is a need to review its content for the current practical use.

Optimal dosing regimen of biapenem in Chinese patients with lower respiratory tract infections based on population pharmacokinetic/pharmacodynamic modelling and Monte Carlo simulation

In this study, a population pharmacokinetic (PPK) model of biapenem in Chinese patients with lower respiratory tract infections (LRTIs) was developed and optimal dosage regimens based on Monte Carlo simulation were proposed. A total of 297 plasma samples from 124 Chinese patients were assayed chromatographically in a prospective, single-centre, open-label study, and pharmacokinetic parameters were analysed using NONMEN. Creatinine clearance (CLCr) was found to be the most significant covariate affecting drug clearance. The final PPK model was: CL (L/h)=9.89+(CLCr-66.56)×0.049; Vc (L)=13; Q (L/h)=8.74; and Vp (L)=4.09. Monte Carlo simulation indicated that for a target of ≥40% T>MIC (duration that the plasma level exceeds the causative pathogen's MIC), the biapenem pharmacokinetic/pharmacodynamic (PK/PD) breakpoint was 4μg/mL for doses of 0.3g every 6h (3-h infusion) and 1.2g (24-h continuous infusion). For a target of ≥80% T>MIC, the PK/PD breakpoint was 4μg/mL for a dose of 1.2g (24-h continuous infusion). The probability of target attainment (PTA) could not achieve ≥90% at the usual biapenem dosage regimen (0.3g every 12h, 0.5-h infusion) when the MIC of the pathogenic bacteria was 4μg/mL, which most likely resulted in unsatisfactory clinical outcomes in Chinese patients with LRTIs. Higher doses and longer infusion time would be appropriate for empirical therapy. When the patient's symptoms indicated a strong suspicion of Pseudomonas aeruginosa or Acinetobacter baumannii infection, it may be more appropriate for combination therapy with other antibacterial agents.

Lower respiratory tract infections among HIV positive and control group in Nepal

Lower respiratory tract infections (LRTIs) are the most frequent respiratory diseases among HIV infected patients and are frequently the first clinical manifestations of the HIV infections. LRTIs are common not only among the HIV seropositive cases but also the commonest domiciliary and nosocomial infections among the general population. The present study was carried out to determine the comparative prevalence of common bacterial and fungal organism among the HIV positive and control population. This cross sectional study was conducted among 220 people attending National Public Health Laboratory, Kathmandu, Nepal. Out of them 120 were HIV sero-positive and rest were HIV sero-negative. Sputum samples were collected and processed soon after its collection. Macroscopic examination was done to determine the sample integrity. Gram stain, AFB stain and KOH preparation was performed for preliminary identification of the pathogens. Culture was carried out for bacterial and fungal pathogens. Antibiotic susceptibility test (Kirby-Bauer disc diffusion method) was performed from the isolated organisms. The 85 out of 120 HIV sero-positive patients were found to be infected with one or more microbial pathogens. The overall infection rate was found to be significantly lower in HIV seronegative people (27 %). Among HIV seropositive cases prevalence of LRTIs was strongly associated with lower CD4 counts (<200/mm(3)). The prevalence of mycobacterium tuberculosis was found to be 10 % among HIV/AIDS patients which was significantly higher than among the non-HIV cases (3 %). The bacterial pathogens was observed among 46.6 % of HIV positive and 22.0 % of HIV negative people. Among the positive cases, K. pneumoniae was the predominant bacterial pathogens, followed by E. coli and S. pneumoniae. C. albicans was found to be predominant fungal pathogen followed by Aspergillus spp. germ tube negative Candida spp. and Penicillium spp. Similar types of organisms were found to be associated with LRTIs among HIV positive and negative people. The prevalence of both fungal and bacterial infections was significantly higher among HIV seropositive people than HIV seronegative people. All in all, lower respiratory tract illness is significantly higher in HIV/AIDS cases than in HIV seronegative cases.

Prenatal exposure to p,p'-DDE and p,p'-DDT in relation to lower respiratory tract infections in boys from a highly exposed area of Mexico

BACKGROUND

Prenatal exposure to 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (p,p'-DDE), the major breakdown product of DDT, has been associated with recurrent lower respiratory tract infections (LRTIs) in infants. However, epidemiological investigations are limited.

OBJECTIVE

To assess the association of prenatal exposure to p,p'-DDE and p,p'-DDT with the occurrence of LRTI in boys from Chiapas, a highly exposed area of Mexico.

METHODS

We analyzed data from 747 singleton boys whose prenatal exposure to p,p'-DDE and p,p'-DDT was determined in maternal serum drawn at delivery (2002-2003). LRTI (i.e., pneumonia, bronchiolitis, and other illness of the bronchi) experienced by the children were reported by their mothers during in-person interviews. The median age of the children when they were last seen was 21.4 months (quartiles 19.1 and 25.3 months).

RESULTS

Median exposure to p,p'-DDE in this population was higher (2.7 µg/g lipid) than recent U.S. levels (0.20 µg/g). There were 0.19 episodes of LRTI per child-year. After adjusting for potential confounders, children in the highest category of p,p'-DDE (>9.00 µg/g) exposure compared to those in the lowest (≤ 3.00 µg/g) had an adjusted incidence rate ratio (aIRR) of LRTI of 0.77 (95% confidence interval [CI], 0.41-1.46). The corresponding aIRR for p,p'-DDT (≥ 2.00 µg/g compared to ≤ 0.25 µg/g) was 0.65 (95% CI: 0.30-1.39).

CONCLUSION

An association of prenatal exposure to p,p'-DDE and p,p'-DDT with LRTI during childhood was not supported in this population with relatively high levels of exposure.

Antibiotics in respiratory tract infections in hospital pediatric emergency departments

BACKGROUND

Respiratory tract infections are one of the most frequent problems in pediatric clinics and generate an elevated prescription of antibiotics. The aim of this study was to find out the standard of care practice about antibiotic use in these infections in a pediatric emergency department and to evaluate compliance with clinical guidelines.

METHODS

A pediatric emergency department database was reviewed from July 2005 to October 2007 under the category "respiratory infection", including variables such as age, antibiotic prescription and compliance with current clinical recommendations.

RESULTS

Out of the 23,114 reviewed reports, 32.7% (7,567) were upper respiratory tract infections (URTI) (cold, acute otitis media [AOM], sinusitis and tonsillopharyngitis) or lower respiratory tract infections (LRTI) (laryngitis, bronchitis, bronchiolitis and pneumonia). Children under the age of 2 were the most represented age group. Amongst URTI, rhinopharyngitis was the most frequent infection, while bronchitis was the most frequent among LRTI. Antibiotic therapy (mainly amoxicillin) was prescribed in 30.8% of URTI (5.7% rhinopharyngitis, 96.5% AOM, and 36.7% tonsillopharyngitis) and in 12.4% of LRTI.

CONCLUSIONS

The percentage of respiratory tract infections was similar to previous studies and the antibiotic prescriptions followed current guidelines, except for cases diagnosed with AOM. Prescription compliance and clinical course of the cases should be monitored.