The impact of viral infections in children with community-acquired pneumonia

Detecting Respiratory Pathogens for Diagnosing Lower Respiratory Tract Infections at the Point of Care: Challenges and Opportunities

Lower respiratory tract infections (LRTIs) are a leading cause of mortality worldwide, claiming millions of lives each year and imposing significant healthcare costs. Accurate detection of respiratory pathogens is essential for the effective management of LRTIs. However, this process often relies on sputum analysis, which requires extensive pretreatment steps. The viscous nature and complex composition of sputum present additional challenges, especially in settings where a rapid diagnosis at the point of care is essential. In this review, we describe the main types of LRTI, highlighting different patient care pathway and points of care. We review current methods for liquefying sputum samples and provide an overview of current commercially available diagnostic tools used in hospitals for LRTI detection. Furthermore, we critically review recent advancements in the literature focused on detecting respiratory pathogens and mechanisms of antimicrobial resistance in sputum, including nucleic acid amplification tests, immunoassays and other innovative approaches. Throughout the paper, we highlight challenges and opportunities associated with developing new biosensor technologies tailored for detecting respiratory pathogens in lower respiratory specimens. By shedding light on these pressing issues, we aim to inspire scientific community to create innovative diagnostic tools to address the urgent healthcare burden of lung diseases.

Detection of human adenoviruses in influenza-negative patients with respiratory tract infections in Nanning, China

BACKGROUND

Human adenoviruses (HAdV) have been known to cause a range of diseases, including respiratory tract infections (RTIs). However, there is limited information available regarding the genotype diversity and epidemiology of HAdV associated with RTIs in Nanning.

METHODS

Between June 2019 and December 2021, throat swab, nasal swab, or nasopharyngeal swab samples were obtained from individuals hospitalized with respiratory tract infections (RTIs). Statistical software was used to analyze the epidemiological data. The highly conserved 132-bp gene region of the HAdV hexon was targeted for the detection of HAdV using a qPCR assay. An 875-bp hexon gene fragment was subjected to phylogenetic analysis.

RESULTS

Significant variations were observed in the age and gender distribution of HAdV-positive patients (P = 0.004 and P = 0.025, respectively). The age distribution of HAdV-positive patients showed that 67.89% of those who tested positive were the age group of 0-6 years. Furthermore, the prevalence of HAdV detection was highest during spring and autumn, with a peak in February. Additionally, genotyping of the 36 HAdV-positive samples with 875-bp fragments identified the presence of circulating HAdV species B, C, and E in Nanning between 2019 and 2021.

CONCLUSIONS

This study identified an association between HAdV prevalence and age as well as season. Among hospitalized patients with RTIs in Nanning, HAdV-B, HAdV-C, and HAdV-E were found to be co-circulating. The most commonly detected genotypes were HAdV-C1, HAdV-C6, and HAdV-E4.

Human Species D Adenoviruses Isolated from Diarrheal Feces Show Low Infection Rates in Primary Nasal Epithelial Cells

The importance of adenovirus (Ad) research is significantly increasing with respect to virotherapy for vaccine development, tumor, and gene therapy. Due to the different species and subtypes of this virus, the characterization of the biological significance of especially rare Ad is necessary. Previously, rare Ad types 70, 73, and 74 were originally isolated from fecal samples of immunocompromised patients and they represent recombinants of other Ad types. Here we investigated transduction experiments of these reporter gene tagged Ad types in primary cells exemplified by subject-derived primary nasal epithelial cells (NAEPCs). To analyze the transduction rates, we performed flow cytometry, quantitative polymerase chain reaction (PCR), and cytokine analyses 25 h post-infection. We found that, in contrast to Ad type 5 (as a positive control), the transduction rates of NAEPCs with Ad types 70, 73, and 74 were interestingly low. The major Ad receptor (coxsackievirus-adenovirus receptor and CD46) expression levels showed no significant change after infection with Ad types 70, 73 and 74. Moreover, Interleukin 6 (IL-6) was not released after in vitro Ad transduction. Due to the high risk of developing life-threatening complications in immunocompromised patients by these human species D Ads, even more attention needs to be investigated into the development of diagnostic and therapeutic concepts to prevent and treat those opportunistic infections in susceptible patients.

Viral etiology, seasonality and severity of hospitalized patients with severe acute respiratory infections in the Eastern Mediterranean Region, 2007-2014

Introduction

Little is known about the role of viral respiratory pathogens in the etiology, seasonality or severity of severe acute respiratory infections (SARI) in the Eastern Mediterranean Region.

Methods

Sentinel surveillance for SARI was conducted from December 2007 through February 2014 at 20 hospitals in Egypt, Jordan, Oman, Qatar and Yemen. Nasopharyngeal and oropharyngeal swabs were collected from hospitalized patients meeting SARI case definitions and were analyzed for infection with influenza, respiratory syncytial virus (RSV), adenovirus (AdV), human metapneumovirus (hMPV) and human parainfluenza virus types 1–3 (hPIV1-3). We analyzed surveillance data to calculate positivity rates for viral respiratory pathogens, describe the seasonality of those pathogens and determine which pathogens were responsible for more severe outcomes requiring ventilation and/or intensive care and/or resulting in death.

Results

At least one viral respiratory pathogen was detected in 8,753/28,508 (30.7%) samples tested for at least one pathogen and 3,497/9,315 (37.5%) of samples tested for all pathogens–influenza in 3,345/28,438 (11.8%), RSV in 3,942/24,503 (16.1%), AdV in 923/9,402 (9.8%), hMPV in 617/9,384 (6.6%), hPIV1 in 159/9,402 (1.7%), hPIV2 in 85/9,402 (0.9%) and hPIV3 in 365/9,402 (3.9%). Multiple pathogens were identified in 501/9,316 (5.4%) participants tested for all pathogens. Monthly variation, indicating seasonal differences in levels of infection, was observed for all pathogens. Participants with hMPV infections and participants less than five years of age were significantly less likely than participants not infected with hMPV and those older than five years of age, respectively, to experience a severe outcome, while participants with a pre-existing chronic disease were at increased risk of a severe outcome, compared to those with no reported pre-existing chronic disease.

Conclusions

Viral respiratory pathogens are common among SARI patients in the Eastern Mediterranean Region. Ongoing surveillance is important to monitor changes in the etiology, seasonality and severity of pathogens of interest.

Frequent Detection and Genetic Diversity of Human Bocavirus in Urban Sewage Samples

The prevalence and genetic diversity of human bocaviruses (HBoVs) in sewage water samples are largely unknown. In this study, 134 raw sewage samples from 25 wastewater treatment plants (WTPs) in Italy were analyzed by nested PCR and sequencing using species-specific primer pairs and broad-range primer pairs targeting the capsid proteins VP1/VP2. A large number of samples (106, 79.1 %) were positive for HBoV. Out of these, 49 were classified as HBoV species 2, and 27 as species 3. For the remaining 30 samples, sequencing results showed mixed electropherograms. By cloning PCR amplicons and sequencing, we confirmed the copresence of species 2 and 3 in 29 samples and species 2 and 4 in only one sample. A real-time PCR assay was also performed, using a newly designed TaqMan assay, for quantification of HBoVs in sewage water samples. Viral load quantification ranged from 5.51E+03 to 1.84E+05 GC/L (mean value 4.70E+04 GC/L) for bocavirus 2 and from 1.89E+03 to 1.02E+05 GC/L (mean value 2.27E+04 GC/L) for bocavirus 3. The wide distribution of HBoV in sewages suggests that this virus is common in the population, and the most prevalent are the species 2 and 3. HBoV-4 was also found, representing the first detection of this species in Italy. Although there is no indication of waterborne transmission for HBoV, the significant presence in sewage waters suggests that HBoV may spread to other water environments, and therefore, a potential role of water in the HBoV transmission should not be neglected.

Comparison of the frequency of bacterial and viral infections among children with community-acquired pneumonia hospitalized across distinct severity categories: a prospective cross-sectional study

Background

The comparison of the frequencies of bacterial and viral infections among children with community-acquired pneumonia (CAP) admitted in distinct severity categories, in an original study, is lacking in literature to-date. We aimed to achieve this goal.

Methods

Children aged 2-59-months-old hospitalized with CAP were included in this prospective study in Salvador, Brazil. Clinical data and biological samples were collected to investigate 11 viruses and 8 bacteria. Severity was assessed by using the World Health Organization criteria.

Results

One hundred eighty-one patients were classified as “non-severe” (n = 53; 29.3 %), “severe” (n = 111; 61.3 %), or “very severe” (n = 17; 9.4 %) CAP. Overall, aetiology was detected among 156 (86.2 %) cases; viral (n = 84; 46.4 %), bacterial (n = 26; 14.4 %) and viral-bacterial (n = 46; 25.4 %) infections were identified. Viral infection frequency was similar in severe/very severe and non-severe cases (46.1 % vs. 47.2 %; p = 0.9). Pneumococcal infection increased across “non-severe” (13.2 %), “severe” (23.4 %), and “very severe” (35.3 %) cases (qui-squared test for trend p = 0.04). Among patients with detected aetiology, after excluding cases with co-infection, the frequency of sole bacterial infection was different (p = 0.04) among the categories; non-severe (12.5 %), severe (29.3 %) or very severe (55.6 %). Among these patients, sole bacterial infection was independently associated with severity (OR = 4.4 [95 % CI:1.1–17.6]; p = 0.04) in a model controlled for age (OR = 0.7 [95 % CI:0.5–1.1]; p = 0.1).

Conclusions

A substantial proportion of cases in distinct severity subgroups had respiratory viral infections, which did not differ between severity categories. Bacterial infection, particularly pneumococcal infection, was more likely among severe/very severe cases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12887-016-0645-3) contains supplementary material, which is available to authorized users.

Adenovirus infections in immunocompetent and immunocompromised patients

Human adenoviruses (HAdVs) are an important cause of infections in both immunocompetent and immunocompromised individuals, and they continue to provide clinical challenges pertaining to diagnostics and treatment. The growing number of HAdV types identified by genomic analysis, as well as the improved understanding of the sites of viral persistence and reactivation, requires continuous adaptions of diagnostic approaches to facilitate timely detection and monitoring of HAdV infections. In view of the clinical relevance of life-threatening HAdV diseases in the immunocompromised setting, there is an urgent need for highly effective treatment modalities lacking major side effects. The present review summarizes the recent progress in the understanding and management of HAdV infections.

Potential Utility of Multiplex Amplification Respiratory Viral Panel Testing in the Management of Acute Respiratory Infection in Children: A Retrospective Analysis

BACKGROUND

Multiplex real-time polymerase chain reaction respiratory viral panel (RVP) testing offers enhanced test performance characteristics compared with older testing methods. However, the impact of RVP testing on physician antimicrobial prescription practices remains unclear. Our objective was to assess the potential relationship of RVP testing to physician treatment practices for children hospitalized with acute respiratory illness (ARI).

METHODS

We performed a retrospective chart review of children hospitalized for ARI during peak prevalence of respiratory viral infections in 2009-2011. Demographics, diagnostic testing, antimicrobial use, and clinical outcomes were abstracted from the electronic medical record. Antimicrobial use was compared with RVP testing data.

RESULTS

A total of 1727 patients met inclusion criteria. Of these patients, 254 (14.7%) children who were hospitalized for ARI received oseltamivir and 856 (49.6%) children received antibiotics. More children who received oseltamivir were positive for influenza by RVP (76.9% vs 18.0%; P < .0001). Children who underwent RVP testing received antibiotics more often than those who were not tested (53.7% vs 46.0%; P = .001), but children with a positive RVP test result received antibiotics less often (51.6% vs 67.0%; P = .003). A total of 5.8% of children who were positive for a viral pathogen by RVP had antibiotics discontinued. Antibiotics were started in fewer children when RVP results were positive (10.9% vs 100.0%; P < .0001).

CONCLUSIONS

Respiratory viral panel testing was associated with more appropriate oseltamivir use in children hospitalized with ARI. Physicians started antibiotics more often in children with a negative RVP test result and occasionally discontinued antibiotics in children diagnosed with a viral pathogen. These results suggest that RVP testing may enhance physician decision-making when prescribing antimicrobials in children hospitalized with ARI.

Human Respiratory Coronaviruses Detected In Patients with Influenza-Like Illness in Arkansas, USA

Acute respiratory viruses often result in significant morbidity and mortality. The potential impact of human respiratory coronavirus (CoV) infections was underestimated until the severe acute respiratory syndrome (SARS-CoV) outbreak in 2003, which showed that new, highly pathogenic coronaviruses could be introduced to humans, highlighting the importance of monitoring the circulating coronaviruses. The use of sensitive molecular methods has contributed to the differential diagnosis of viruses circulating in humans. Our study aim was to investigate the molecular epidemiology of human CoV strains circulating in Arkansas, their genetic variability and their association with reported influenza-like symptoms. We analyzed 200 nasal swab samples, collected by the Arkansas Department of Health in 2010, for influenza diagnosis. All samples were from patients showing acute respiratory symptoms while testing negative for influenza. Samples were pre-screened, using a quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) multiprobe for coronavirus, and subjected to confirmatory pancoronavirus and/or strain-specific reverse transcriptase (RT)-PCR followed by sequence analysis. Seventy-nine samples (39.5%) were positive by qRT-PCR and 35 samples (17.5%) were confirmed by conventional RT-PCR. Twenty-three of the confirmed samples (59%) were sequenced. The most frequent strain detected was HCoV-OC43-like followed by NL63-like; only one sample was positive for HCoV-229E and one for HCoV-HKU1. Feline-like CoV strains were detected in three samples, representing possible evidence of interspecies transmission or a new human strain. Seventeen percent of the coronavirus positive samples were also positive for other respiratory viruses, such as Respiratory Syncytial Virus (RSV), Parainfluenza 2 and 3, and Rhinovirus. Thus, HCoV-OC43, NL63, HKU1 and new feline-like strains were circulating in Arkansas in 2010. HCoV was the sole respiratory virus detected in 16% of the patients who showed acute respiratory symptoms with negative diagnoses for influenza virus.

Treating paediatric community-acquired pneumonia in the era of antimicrobial resistance

Increasing levels of paediatric community-acquired pneumonia (CAP), caused by drug-resistant bacteria and antimicrobial resistance, vary with age and countries and, in some cases, serotypes. When empirical first-line treatment administration fails, paediatricians should consider second-line treatments based on the prevalence of local resistance. A more judicious use of antimicrobial agents is also required.

CONCLUSION

Knowledge of local epidemiology and an appropriate use of antimicrobial drugs are necessary to treat CAP in this era of antimicrobial resistance.