Epidemiology of Respiratory Pathogens in Children with Severe Acute Respiratory Infection and Impact of the Multiplex PCR Film Array Respiratory Panel: A 2-Year Study

Dynamic analysis of the epidemiology and pathogen distribution of bronchoalveolar lavage fluid in children with severe pulmonary infection: a retrospective study

BACKGROUND

Severe pulmonary infection is the primary cause of death in children aged < 5 years. The early identification of pathogenic bacteria and targeted anti-infective therapies can significantly improve the prognosis of children with severe infections. This study aims to provide a reference for the rational use of antibiotics at an early stage in children with severe pulmonary infections.

METHODS

A retrospective, single-center longitudinal study included children with severe pulmonary infections between January 2017 and December 2022 by obtaining their bacterial culture results of bronchoalveolar lavage fluid.

RESULTS

This study included 4080 samples. The age of onset for severe pulmonary infection increased annually. The proportion of severe pulmonary infections across the different age groups and years was statistically significant (p < 0.001). Among children with severe pulmonary infections, bacilli were the most prevalent, followed by cocci and fungi. The predominant bacilli were Acinetobacter baumannii and Klebsiella pneumoniae. The predominant cocci identified in this study were Streptococcus pneumoniae and Staphylococcus aureus. The primary fungi included Candida albicans and Aspergillus fumigatus, which showed significant differences (p < 0.05). The incidence of drug-resistant bacteria has gradually declined, with infection rates of multidrug-resistant bacteria and extended-spectrum beta-lactamases consistently decreasing annually. For carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa, the infection rates peaked in 2018, with statistical significance (p < 0.001).

CONCLUSIONS

Severe pulmonary infections in children are significantly associated with age and types of infectious pathogens. Gram-negative bacteria are the primary cause of severe pulmonary infections in children. Clinicians should rationally use antibiotics according to the local distribution and drug resistance of pathogens, thereby enhancing therapeutic outcomes.

Burden of pertussis in infants in the Eastern Mediterranean Region and the impact of maternal vaccination: a systematic review

BACKGROUND

Despite vaccine availability, Pertussis remains a global public health challenge, especially among infants. The Eastern Mediterranean Region (EMR) presents a diverse epidemiological landscape with varying vaccination coverages and healthcare infrastructures. This systematic review aimed to assess the burden of pertussis in infants < 1 year of age in the EMR and evaluate the use and impact of pertussis vaccination during pregnancy.

METHODS

Following PRISMA guidelines, we conducted a systematic search of Scopus, Embase, CINAHL Ultimate, and PubMed from inception until April 30, 2024. Studies included reported on pertussis burden in infants or maternal vaccination. Data extraction and quality assessment were performed in duplicate, focusing on incidence, age distribution, disease severity, and vaccination uptake and impact when data were available.

RESULTS

Thirty-six studies were included, the majority from Iran (N = 11), Morocco (N = 5), Tunisia (N = 5), and Oman (N = 3), with underrepresentation of other EMR countries. The incidence of PCR-confirmed pertussis among children with suspected pertussis varied significantly, from 6.7% to 8.9% (Morocco 2018-2019) to 50.4% and 51.6% (Palestine 2004-2008) among children < 12 and < 6 months, respectively, and between 16.3% (Tunisia 2007-2016) to 73.0% (Morocco 2013-2015) in children < 2 months. Age distribution data indicated the highest burden was in infants < 2 months regardless of the population studied. High hospitalization rates and severe complications, including seizures and the need for ventilatory support, were frequently reported in infants < 6 months of age. Only one study from Saudi Arabia addressed maternal pertussis vaccination, reflecting low vaccine uptake and awareness among pregnant women.

CONCLUSIONS

This review underscores the substantial burden of pertussis among infants in the EMR and the lack of data on maternal immunization. The findings emphasize the need for enhanced surveillance and targeted public health interventions to reduce disease incidence. Future research should prioritize underrepresented countries to ensure comprehensive data for informed public health strategies.

TRIAL REGISTRATION

PROSPERO (CRD42024573471).

Epidemiology of Pertussis After the COVID-19 Pandemic: Analysis of the Factors Involved in the Resurgence of the Disease in High-, Middle-, and Low-Income Countries

Pertussis is a highly contagious bacterial disease of the respiratory tract that can be prevented by vaccination. Before the COVID-19 pandemic, the vaccine coverage rate for the third dose of a DPT-containing vaccine was 86%, with large disparities among countries. Since 2022, many high-income countries have reported a resurgence of pertussis, especially in the European region, but the disease has also caused outbreaks in middle- and low-income countries, despite their less extensive disease surveillance capacities. This paper aims to review the incidence rates (IRs) of pertussis in high-, middle-, and low-income countries following the COVID-19 pandemic and to discuss the most relevant factors associated with the resurgence of the disease. The epidemiology of pertussis is highly variable and is influenced not only by the type of vaccine used but also by the specific characteristics of the disease, vaccine coverage rates, vaccination schedules, and the quality of surveillance. Since the cessation of COVID-19 measures, there have been significant pertussis outbreaks that could have been partially mitigated with higher coverage rates and more comprehensive pertussis vaccination throughout life.

Hospital-based cross-sectional study on the clinical characteristics of children with severe acute respiratory infections in Hungary

BACKGROUND

Severe acute respiratory infection (SARI) is a major cause for hospital admission and associated with high mortality among children worldwide. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza viruses and respiratory syncytial virus (RSV) are the most frequently identified pathogens in children with SARI. The duration of care can be affected by the type of infection and patient characteristics. Therefore, the objective of this study was to identify factors affecting the length of hospitalization in children infected with SARS-CoV-2, influenza A and RSV.

METHODS

We collected data on 713 children with SARI from the medical databases of a university hospital in Hungary. To examine whether there is a difference in the length of hospitalization in children with the SARI Kruskal-Wallis test was performed. To determine the factors that may have an impact on the duration of care a multiple logistic regression analysis was executed.

RESULTS

Our results showed that among RSV infected patients the proportions of children requiring intensive care (8.94%), mechanical ventilation (8.94%) and oxygen therapy (13.01%) and suffering from pneumonia (29.27%) were larger than among cases with SARS-CoV-2 and influenza A infection. Considering the age distribution and the duration of care in children with SARI, cases with RSV were significantly younger (p < 0.001) and stayed longer in the hospital (median: 5 days, IQR: 4-7 days, p < 0.001) than those with SARS-CoV-2 and influenza A virus. Multiple logistic regression analysis showed that RSV infection (adjusted odds ratio (aOR): 3.25, 95% confidence interval (CI): 1.43-7.38; p = 0.005), pneumonia (aOR: 3.65, 95% CI: 2.14-6.24; p < 0.001), mechanical ventilation or oxygen therapy (aOR: 3.23, 95% CI: 1.29-8.11; p = 0.012) and underlying illnesses (aOR: 2.39, 95% CI: 1.35-4.23; p = 0.003) significantly increased the odds of hospitalization for more than 4 days.

CONCLUSIONS

Our research showed that of the viruses causing SARI, RSV had the greatest clinical relevance, contributing to hospital stays of more than 4 days in a large share of paediatric patients below 1 year of age. Our results supply new information on children with SARI, and provide evidence for health policy makers to allocate additional resources to hospitals during SARI epidemics.

Whole genome molecular analysis of respiratory syncytial virus pre and during the COVID-19 pandemic in Free State province, South Africa

Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The Coronavirus disease 2019 (COVID-19) pandemic and resulting nonpharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South Africa. A seasonality shift and RSV resurgence was observed in 2020 and 2021, with several infected children observed. Conventional RSV-positive nasopharyngeal swabs were collected from various hospitals in the Free State province, Bloemfontein, South Africa, from children suffering from respiratory distress and severe acute respiratory infection between 2020 to 2021. Overlapping genome fragments were amplified and complete genomes were sequenced using the Illumina MiSeq platform. Maximum likelihood phylogenetic and evolutionary analysis were performed on both RSV-A/-B G-genes with published reference sequences from GISAID and GenBank. Our study strains belonged to the RSV-A GA2.3.2 and RSV-B GB5.0.5a clades. The upsurge of RSV was due to pre-existing strains that predominated in South Africa and circulating globally also driving these off-season RSV outbreaks during the COVID-19 pandemic. The variants responsible for the resurgence were phylogenetically related to pre-pandemic strains and could have contributed to the immune debt resulting from pandemic imposed restrictions. The deviation of the RSV season from the usual pattern affected by the COVID-19 pandemic highlights the need for ongoing genomic surveillance and the identification of genetic variants to prevent unforeseen outbreaks in the future.

Acute Respiratory Tract Infections (ARTIs) in Children after COVID-19-Related Social Distancing: An Epidemiological Study in a Single Center of Southern Italy

In Sicily (Italy), respiratory syncytial virus (RSV), rhinovirus (HRV), and influenza virus triggered epidemics among children, resulting in an increase in acute respiratory tract infections (ARTIs). Our objective was to capture the epidemiology of respiratory infections in children, determining which pathogens were associated with respiratory infections following the lockdown and whether there were changes in the epidemiological landscape during the post-SARS-CoV-2 pandemic era.

MATERIALS AND METHODS

We analyzed multiplex respiratory viral PCR data (BioFire® FilmArray® Respiratory Panel 2.1 Plus) from 204 children presenting with respiratory symptoms and/or fever to our Unit of Pediatrics and Pediatric Emergency.

RESULTS

Viruses were predominantly responsible for ARTIs (99%), with RSV emerging as the most common agent involved in respiratory infections, followed by human rhinovirus/enterovirus and influenza A. RSV and rhinovirus were also the primary agents in coinfections. RSV predominated during winter months, while HRV/EV exhibited greater prevalence than RSV during the fall. Some viruses spread exclusively in coinfections (human coronavirus NL63, adenovirus, metapneumovirus, and parainfluenza viruses 1-3), while others primarily caused mono-infections (influenza A and B). SARS-CoV-2 was detected equally in both mono-infections (41%) and coinfections (59%).

CONCLUSIONS

Our analysis underlines the predominance of RSV and the importance of implementing preventive strategies for RSV.

Epidemiological Characterization of Respiratory Pathogens Using the Multiplex PCR FilmArray™ Respiratory Panel

Various pathogens can cause upper respiratory tract infections, presenting challenges in accurate diagnosis due to similar symptomatology. Therefore, rapid and precise diagnostic tests are crucial for effective treatment planning. Traditional culture-based methods for diagnosis are limited by their reliance on skilled personnel and lengthy processing times. In contrast, multiplex polymerase chain reaction (PCR) techniques offer enhanced accuracy and speed in identifying respiratory pathogens. In this study, we aimed to assess the efficacy of the FilmArray™ Respiratory Panel (RP), a multiplex PCR test capable of simultaneously screening 20 pathogens. This retrospective analysis was conducted at Dankook University Hospital, South Korea, between January 2018 and December 2022. Samples from patients with upper respiratory tract infections were analyzed. Results revealed adenovirus as the most prevalent pathogen (18.9%), followed by influenza virus A (16.5%), among others. Notably, a 22.5% co-infection rate was observed. The FilmArray™ RP method successfully identified 20 pathogens within 2 h, facilitating prompt treatment decisions and mitigating unnecessary antibiotic prescriptions. This study underscores the utility of multiplex PCR in respiratory pathogen identification, offering valuable insights for epidemiological surveillance and diagnosis.

Clinical Presentation and Co-Detection of Respiratory Pathogens in Children Under 5 Years with Non-COVID-19 Bacterial and Viral Respiratory Tract Infections: A Prospective Study in Białystok, Poland (2021-2022)

BACKGROUND Respiratory tract infections (RTIs) in children often involve a complex interplay between viruses and bacteria. This study aimed to evaluate clinical presentation in children under 5 years old diagnosed with non-COVID-19 bacterial and viral respiratory tract co-infections between October 2021 and May 2022 in Białystok, Poland. MATERIAL AND METHODS We recruited 100 children under 5 years with RTIs who tested negative for SARS-CoV-2. Nasopharyngeal swabs were screened for 19 viruses and 7 bacterial strains using molecular assays. RESULTS Viral pathogens were detected in 71% of patients and bacterial pathogens were detected in 59%. The most common pathogens were Haemophilus influenzae (n=48), rhinoviruses (n=32), and Streptococcus pneumoniae (n=30). Single pathogens were detected in 36%, dual in 37%, triple in 15%, and quadruple in 2%. Bacterial pathogens were co-detected with viruses in 40 cases, mostly with rhinoviruses (n=15). Two different viruses were found in 14 children and the most common co-detection was adenovirus with rhinovirus (n=5); dyspnea (63% vs 11%) and wheezing (75% vs 22%) were more common in children with human bocavirus. Fever was a common symptom in children with human adenovirus (88% vs 58%). Detection of bacteria and multiple detections were more common in day-care attendees, but were not associated with clinical picture of RTI. CONCLUSIONS Consistent with previous studies, we found a high prevalence of rhinoviruses, despite ongoing implementation of non-pharmaceutical interventions to contain the COVID-19 pandemic. Co-detection of 2 different respiratory pathogens was frequent, but we found no evidence that this was associated with the severity of infections.

Contribution of the FilmArray BioFire® Technology in the Diagnosis of Viral Respiratory Infections during the COVID-19 Pandemic at Ibn Sina University Hospital Center in Rabat: Epidemiological Study about 503 Cases

Respiratory viruses are the most involved pathogens in acute respiratory infections. During the COVID-19 pandemic, new elements have been brought to this topic, especially at the diagnostic and therapeutic level. The objective of this work is to describe the epidemiology of respiratory viruses in patients admitted to the Ibn Sina University Hospital of Rabat during a period characterized by the emergence and spread of SARS-CoV-2. We conducted a retrospective study from January 1 to December 31. We included all patients treated for acute respiratory infection and for whom a multiplex respiratory panel PCR was requested. Virus detection was performed using a FilmArray RP 2.1 plus BioFire multiplex respiratory panel. The study population was relatively adults with a mean age of 39 years. The sex ratio M/F was 1.20. The survey revealed a high prevalence of 42.3% of patients hospitalized in the adult intensive care unit whose respiratory distress was the most common reason for hospitalization (58%). The positivity rate was 48.1%. This rate was higher in the pediatric population 83.13% compared to adults 29.7%. Monoinfection was found in 36.4% of cases, and codetection in 11.7% of cases. This survey revealed that a total of 322 viruses were detected, HRV being the most incriminated virus (48.7%), followed by RSV in 13.8% of patients. Considering the five most detected viruses in our study (HRV, RSV, PIV3, ADV, and hMPV), we found that the incidence was significantly higher in the pediatric population. SARS-CoV-2 was detected only in adult's population. In our study, we found that influenza A and B viruses, PIV2, MERS, and all bacteria were not detected by this kit during the study period. Regarding the seasonal distribution, RSV and hMPV showed a significantly high incidence during autumn and summer and SARS-CoV-2 and CoV OC43 showed a high peak during winter. In this study, we found a lack of detection of influenza virus and a shift in the usual winter peak of RSV to the summer, while the detection of ADV and HRV was less affected. This difference in detection could be due on the one hand to the difference in stability between enveloped and nonenveloped viruses and on the other hand to the escape of certain viruses to the different sanitary measures introduced after the declaration of the COVID-19 pandemic. These same measures were effective against enveloped viruses such as RSV and influenza viruses. The emergence of SARS-CoV-2 has modified the epidemiology of other respiratory viruses, either directly by viral interference or indirectly by the preventive measures taken.

Spatial patterns and spatially-varying factors associated with childhood acute respiratory infection: data from Ethiopian demographic and health surveys (2005, 2011, and 2016)

BACKGROUND

In Ethiopia, acute respiratory infections (ARIs) are a leading cause of morbidity and mortality among children under five years. Geographically linked data analysis using nationally representative data is crucial to map spatial patterns of ARIs and identify spatially-varying factors of ARI. Therefore, this study aimed to investigate spatial patterns and spatially-varying factors of ARI in Ethiopia.

METHODS

Secondary data from the Ethiopian Demographic Health Survey (EDHS) of 2005, 2011, and 2016 were used. Kuldorff's spatial scan statistic using the Bernoulli model was used to identify spatial clusters with high or low ARI. Hot spot analysis was conducted using Getis-OrdGi statistics. Eigenvector spatial filtering regression model was carried out to identify spatial predictors of ARI.

RESULTS

Acute respiratory infection spatially clustered in 2011 and 2016 surveys year (Moran's I:-0.011621-0.334486). The magnitude of ARI decreased from 12.6% (95%, CI: 0.113-0.138) in 2005 to 6.6% (95% CI: 0.055-0.077) in 2016. Across the three surveys, clusters with a high prevalence of ARI were observed in the North part of Ethiopia. The spatial regression analysis revealed that the spatial patterns of ARI was significantly associated with using biomass fuel for cooking and children not initiating breastfeeding within 1-hour of birth. This correlation is strong in the Northern and some areas in the Western part of the country.

CONCLUSION

Overall there has been a considerable decrease in ARI, but this decline in ARI varied in some regions and districts between surveys. Biomass fuel and early initiation of breastfeeding were independent predictors of ARI. There is a need to prioritize children living in regions and districts with high ARI.

Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa

Prompt detection of viral respiratory pathogens is crucial in managing respiratory infection including severe acute respiratory infection (SARI). Metagenomics next-generation sequencing (mNGS) and bioinformatics analyses remain reliable strategies for diagnostic and surveillance purposes. This study evaluated the diagnostic utility of mNGS using multiple analysis tools compared with multiplex real-time PCR for the detection of viral respiratory pathogens in children under 5 years with SARI. Nasopharyngeal swabs collected in viral transport media from 84 children admitted with SARI as per the World Health Organization definition between December 2020 and August 2021 in the Free State Province, South Africa, were used in this study. The obtained specimens were subjected to mNGS using the Illumina MiSeq system, and bioinformatics analysis was performed using three web-based analysis tools; Genome Detective, One Codex and Twist Respiratory Viral Research Panel. With average reads of 211323, mNGS detected viral pathogens in 82 (97.6%) of the 84 patients. Viral aetiologies were established in nine previously undetected/missed cases with an additional bacterial aetiology (Neisseria meningitidis) detected in one patient. Furthermore, mNGS enabled the much needed viral genotypic and subtype differentiation and provided significant information on bacterial co-infection despite enrichment for RNA viruses. Sequences of nonhuman viruses, bacteriophages, and endogenous retrovirus K113 (constituting the respiratory virome) were also uncovered. Notably, mNGS had lower detectability rate for severe acute respiratory syndrome coronavirus 2 (missing 18/32 cases). This study suggests that mNGS, combined with multiple/improved bioinformatics tools, is practically feasible for increased viral and bacterial pathogen detection in SARI, especially in cases where no aetiological agent could be identified by available traditional methods.

Molecular epidemiology of respiratory syncytial virus in children with acute respiratory illnesses in Africa: A systematic review and meta-analysis

Background

Globally, the respiratory syncytial virus (RSV) is the most common etiologic agent of acute respiratory illnesses in children. However, its burden has not been well addressed in developing countries. We aimed to estimate the molecular epidemiology of RSV in children less than 18 years of age with acute respiratory infections in Africa by conducting a systematic review and meta-analysis.

Methods

We systematically searched PubMed, Scopus, CINAHL, and Global Index Medicus databases to identify studies published from January 1, 2002, to April 27, 2022, following the PRISMA 2020 guideline. We assessed the study quality using the Joanna Brigg's Institute (JBI) critical appraisal checklists. We conducted a qualitative synthesis by describing the characteristics of included studies and performed the quantitative synthesis with random effects model using STATA-14. We checked for heterogeneity with Q statistics, quantified by I², and determined the prediction interval. We performed subgroup analyses to explain the sources of heterogeneity and assessed publication biases by funnel plots augmented with Egger's test.

Results

Eighty-eight studies with 105 139 participants were included in the review. The overall pooled prevalence of RSV in children <18 years of age was 23% (95% confidence interval (CI) = 20, 25%). Considerable heterogeneity was present across the included studies. The adjusted prediction interval was found to be 19%-27%. Heterogeneities were explained by subgroups analyses. The highest prevalence of RSV was found among inpatients, 28% (95% CI = 25, 31%) compared with inpatients/outpatients and outpatients, with statistically significant differences (P < 0.01). The RSV estimate was also highest among those with acute lower respiratory tract illnesses (ALRTIs), 28% (95% CI = 25, 31%) compared with acute upper respiratory tract illnesses (AURTIs) and both acute upper/lower respiratory manifestations, with statistically different prevalence (P < 0.01). RSV infection estimates in each sub-region of Africa were statistically different (P < 0.01). There were no statistically significant differences in RSV infections by designs, specimen types, and specimen conditions, despite them contributing to heterogeneity.

Conclusions

We found a high prevalence of RSV in pediatric populations with acute respiratory tract illnesses in Africa, highlighting that the prevention and control of RSV infections in children deserve more attention.

Registration

PROSPERO CRD42022327054.

Multiplex PCR Detection of Respiratory Tract Infections in SARS-CoV-2-Negative Patients Admitted to the Emergency Department: an International Multicenter Study during the COVID-19 Pandemic

Respiratory tract infection (RTI) is a common cause of visits to the hospital emergency department. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), nonpharmaceutical intervention has influenced the rates of circulating respiratory viruses. In this study, we sought to detect RTI etiological agents other than SARS-CoV-2 in emergency department patients from 13 countries in Europe, the Middle East, and Africa from December 2020 to March 2021. We sought to measure the impact of patient characteristics and national-level behavioral restrictions on the positivity rate for RTI agents. Using the BioFire Respiratory Panel 2.0 Plus, 1,334 nasopharyngeal swabs from patients with RTI symptoms who were negative for SARS-CoV-2 were tested. The rate of positivity for viral or bacterial targets was 36.3%. Regarding viral targets, human rhinovirus or enterovirus was the most prevalent (56.5%), followed by human coronaviruses (11.0%) and adenoviruses (9.9%). Interestingly, age stratification showed that the positivity rate was significantly higher in the children's group than in the adults' group (68.8% versus 28.2%). In particular, human rhinovirus or enterovirus, the respiratory syncytial virus, and other viruses, such as the human metapneumovirus, were more frequently detected in children than in adults. A logistic regression model was also used to determine an association between the rate of positivity for viral agents with each country's behavioral restrictions or with patients' age and sex. Despite the impact of behavioral restrictions, various RTI pathogens were actively circulating, particularly in children, across the 13 countries. IMPORTANCE As SARS-CoV-2 has dominated the diagnostic strategies for RTIs during the current COVID-19 pandemic situation, our data provide evidence that a variety of RTI pathogens may be circulating in each of the 13 countries included in the study. It is now plausible that the COVID-19 pandemic will one day move forward to endemicity. Our study illustrates the potential utility of detecting respiratory pathogens other than SARS-CoV-2 in patients who are admitted to the emergency department for RTI symptoms. Knowing if a symptomatic patient is solely infected by an RTI pathogen or coinfected with SARS-CoV-2 may drive timely and appropriate clinical decision-making, especially in the emergency department setting.