Respiratory Pathogens in Infants Diagnosed with Acute Lower Respiratory Tract Infection in a Tertiary Care Hospital of Western India Using Multiplex Real Time PCR

Viral etiology of severe lower respiratory tract infections in SARS-CoV-2 negative hospitalized patients during the COVID-19 pandemic in Kuwait

Background

The prevalence of respiratory infections is largely underexplored in Kuwait. The aim of our study is to determine the etiology of infections from patients who are SARS-CoV-2 negative hospitalized with severe lower respiratory tract infections (LRTIs) in Kuwait during the coronavirus disease 2019 (COVID-19) pandemic.

Methods

We conducted an observational cross-sectional study among severe LRTI patients between September 2021 and March 2022. Respiratory samples from 545 non-COVID-19 severe LRTIs patients were prospectively evaluated with FTD Respiratory 21 Plus® real-time PCR, targeting 20 different viruses and 1 atypical bacterial pathogen.

Results

Among all 545 hospitalized cases, 411 (75.4 %) tested positive for at least one respiratory pathogen. The most common were rhinovirus (HRV) (32.7 %), respiratory syncytial virus (RSV) (20.9 %), metapneumovirus (HMPV) (14.1 %), bocavirus (13.2 %), and influenza A (12.7 %). The proportion of pathogens detected was highest in the under-5 age group, while HKU1 (44.4 %) predominated in the elderly (>50 years).

Conclusion

Our study reveals a high prevalence of respiratory viruses in severe acute lower respiratory tract infections among non-COVID-19 hospitalized patients in Kuwait. HRV remains the main etiology affecting the country, particularly in infants. These results underscore the necessity of employing multiplex PCR for accurate diagnosis and describing the epidemiology of infections among severe lower respiratory tract infections. This will facilitate the use of specific antiviral therapy and help avoid excessive or inappropriate antibiotic therapy.

Patterns of antibiotic use for acute respiratory infections in under-three-year-old children in India: A cross-sectional study

Background

Despite its mostly viral etiology, antibiotics are frequently used to treat acute respiratory infections (ARIs) in children. India is one of the largest global consumers of antibiotics and has one of the highest rates of resistance to antimicrobial treatments. However, the epidemiology of antibiotic treatment among young children in India is poorly understood.

Methods

Using nationally representative household survey data from the Indian National Family Health Surveys (NFHS) conducted between 2015 and 2016 and 2019 and 2021, we estimated the prevalence of antibiotic use among 17 472 children under the age of three who reported ARI symptoms within two weeks before their mothers were interviewed. To assess the factors associated with antibiotic use for the treatment of ARI symptoms, we used multivariable logistic regression models that included sociodemographic, child-related, household, and health care related characteristics, with results reported on the prevalence difference (PD) scale.

Results

We estimated that 18.7% (95% CI = 17.8-19.6) of under-three-year-old (U3) children who exhibited ARI symptoms in the two weeks prior to the survey were given antibiotics as a treatment. The highest prevalence was observed in the southern and northern geographic zones of India. Furthermore, multivariable regression models indicated that children with greater access to health services were more likely to receive antibiotics for ARI treatment, regardless of the type of health care facility (public, private or pharmacy/unregulated). Additionally, the prevalence of antibiotic consumption was higher among children from families with religious affiliations other than Muslim and Hindu backgrounds (i.e. Christian, Sikh, Buddhist/neo-Buddhist, Jain, Jewish, Parsi, no religion and other) (PD = 11.7 (95% CI = 6.3-16.7)) compared to Hindu families and among mothers with a secondary or higher education (PD = 5.8 (95% CI = 1.7-9.9)) compared to mothers lacking formal education.

Conclusions

Our findings provide an important baseline for monitoring the use of antibiotics for the treatment of acute respiratory infections, and for designing interventions to mitigate potential misuse among young children in India.

Utility of multiplex real-time PCR for diagnosing paediatric acute respiratory tract infection in a tertiary care hospital

Background

Acute respiratory infections (ARIs) are responsible for considerable morbidity and mortality among children all over the world. Many of the etiologic agents of the infections especially viral go undiagnosed for lack of requisite facility and the cost factors. We have used a commercially available platform for diagnosis of ARIs in children receiving inpatient and outpatient services in a tertiary care centre.

Methods

The framework of the study was prospective and observational. In this study, clinical samples of children suffering from ARIs were subjected to real-time multiplex PCR targeting both viral and bacterial pathogens.

Results

Of 94 samples received at our centre (49 male and 45 female), the positivity for respiratory pathogens was detected in 50 (53.19%) samples. Clinical symptoms of patients and age distribution have been elaborated in text. A single pathogen (n = 29/50), two pathogens (15/50) and three pathogens (n = 6/50) were detected by multiplex RT-PCR. Of 77 isolates detected, maximum numbers were of human rhinovirus (HRV) (n = 14) (18.18%) Streptococcus pneumoniae (n = 14) (18.18%) followed by Staphylococcus aureus (n = 10) (12.98%).

Conclusion

The epidemiology of ARIs considering viral etiologies is poorly understood due to less number of studies especially in Indian subcontinent. The advent of latest advanced molecular methods has made it possible to identify common respiratory pathogens and has contributed to cover the gap in existing knowledge.

Respiratory viruses among ethnic Nicobarese during COVID-19 pandemic

Background

Acute respiratory infections (ARIs) and severe acute respiratory illness (SARI) are public health burdens globally. The percentage of non-SARS CoV-2 respiratory viruses among patients having ARI and SARI who visit Car Nicobar's hospital settings is undocumented. Changes in the epidemiology of other respiratory viruses during COVID19 pandemic is being reported worldwide.

Methods

Inpatient and outpatient settings at BJR hospital, Car Nicobar Island, India, were used to conduct prospective monitoring for ARI and SARI among Nicobarese tribal members. The patients with ARI and SARI were enlisted in BJR hospital from June 2019 to May 2021. At the ICMR-NIV in Pune, duplex RT-PCR assays were used to test the presence of respiratory viruses. The prevalence of non- SARS CoV-2 respiratory viruses was measured by comparing here between pandemic and pre-pandemic periods.

Results

During the COVID19 pandemic, Influenza A (H3N2) and rhinovirus were predominantly reported non-SARS CoV-2 respiratory viruses while Human metapneumovirusand influenza A (H1N1)pdm09were most commonly reported in the prepandemic period. This result indicates the altered circulation of non-SARS CoV-2 during pandemic.

Conclusions

A considerable proportion of respiratory infection was correlated with respiratory viruses. Prevalence of non-SARS CoV-2 respiratory viruses was high at the time of infection when compared with pre-pandemic period, at Car Nicobar Island. This study enlightened the change in circulation of other respiratory viruses among the indigenous Nicobarese tribes. Clinicians and allied medical staff should be more prudent of these respiratory infections.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07435-x.

Epidemiological studies on lower respiratory tract infection in children in the District Bannu, Khyber Pakhtunkhwa, Pakistan

Background

Lower respiratory tract infections are the leading cause of death in children globally and are transmitted by inhaling airborne droplets. The study demonstrated the prevalence of lower respiratory tract infections in children admitted to the Women and Children Hospital Bannu from February through November 2019. The cross-sectional study was conducted by obtaining indoor data from the official record maintained in the children’s wards.

Results

Males accounted for 649 (61.6%) and females 405 (38.4%) cases out of 1054 cases of the disease. Age group of ≤ 6 months showed 36.2% prevalence, followed by > 6 m ≤ 1 y (25.6%), > 1 y ≤ 2 y (17.1%), > 2 y ≤ 5 y (14.3%), > 5 ≤ 10 y (6.0%), and > 10 y ≤ 15 y (0.8%). Pediatric patients of age ≤ 2 y and ≤ 5 y contributed 78.9% and 93.3% to overall disease, respectively. The disease was at its peak in February (17.9%) while lowest in May (5.5%). The age group (≤ 6 m) was the dominant group in all months except August when replaced by the age group (> 6 m ≤ 1 y). The disease revealed higher prevalence during February-April and October-November.

Conclusions

Different age groups showed variation in the prevalence of the disease with an age group of ≤ 5 y contributing the largest share and seasonal peaks in the disease occurred. The present findings help in adopting strategies for effective control of the disease in different age groups of the children for their peak season.

The Burden of Respiratory Viruses and Their Prevalence in Different Geographical Regions of India: 1970-2020

As per the 2019 report of the National Health Portal of India, 41,996,260 cases and 3,740 deaths from respiratory infections were recorded across India in 2018. India contributes to 18% of the global population, with severe acute respiratory infection (SARI) as one of the prominent causes of mortality in children >5 years of age. Measures in terms of the diagnosis and surveillance of respiratory infections are taken up globally to discover their circulating types, detect outbreaks, and estimate the disease burden. Similarly, the purpose of this review was to determine the prevalence of respiratory infections in various regions of India through published reports. Understanding the pattern and prevalence of various viral entities responsible for infections and outbreaks can help in designing better strategies to combat the problem. The associated pathogens comprise respiratory syncytial virus (RSV), rhinovirus, influenza virus, parainfluenza virus, adenovirus, etc. Identification of these respiratory viruses was not given high priority until now, but the pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has sensitized our system to be alert about the burden of existing infections and to have proper checks for emerging ones. Most of the studies reported to date have worked on the influenza virus as a priority. However, the data describing the prevalence of other respiratory viruses with their seasonal pattern have significant epidemiological value. A comprehensive literature search was done to gather data from all geographical regions of India comprising all states of India from 1970 to 2020. The same has been compared with the global scenario and is being presented here.

Respiratory microbes detected in hospitalized adults with acute respiratory infections: associations between influenza A(H1N1)pdm09 virus and intensive care unit admission or fatal outcome in Vietnam (2015-2017)

Background

Acute respiratory tract infection (ARI) is a leading cause of hospitalization, morbidity, and mortality worldwide. Respiratory microbes that were simultaneously detected in the respiratory tracts of hospitalized adult ARI patients were investigated. Associations between influenza A(H1N1)pdm09 virus (H1N1pdm) detection and intensive care unit (ICU) admission or fatal outcome were determined.

Methods

This prospective observational study was conducted between September 2015 and June 2017 at Bach Mai Hospital, Hanoi, Vietnam. Inclusion criteria were hospitalized patients aged ≥15 years; one or more of symptoms including shortness of breath, sore throat, runny nose, headache, and muscle pain/arthralgia in addition to cough and fever > 37.5 °C; and ≤ 10 days from the onset of symptoms. Twenty-two viruses, 11 bacteria, and one fungus in airway specimens were examined using a commercial multiplex real-time PCR assay. Associations between H1N1pdm detection and ICU admission or fatal outcome were investigated by univariate and multivariate logistic regression analyses.

Results

The total of 269 patients (57.6% male; median age, 51 years) included 69 ICU patients. One or more microbes were detected in the airways of 214 patients (79.6%). Single and multiple microbes were detected in 41.3 and 38.3% of patients, respectively. Influenza A(H3N2) virus was the most frequently detected (35 cases; 13.0%), followed by H1N1pdm (29 cases; 10.8%). Hematological disease was associated with ICU admission (p < 0.001) and fatal outcomes (p < 0.001) using the corrected significance level (p = 0.0033). Sex, age, duration from onset to sampling, or number of detected microbes were not significantly associated with ICU admission or fatal outcomes. H1N1pdm detection was associated with ICU admission (odds ratio [OR] 3.911; 95% confidence interval [CI] 1.671–9.154) and fatal outcome (OR 5.496; 95% CI 1.814–16.653) after adjusting for the confounding factors of comorbidities, bacteria/Pneumocystis jirovecii co-detection, and age.

Conclusions

H1N1pdm was associated with severe morbidity and death in adult patients hospitalized with respiratory symptoms. The diagnosis of subtype of influenza virus may be epidemiologically important.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-05988-x.

Complicating Infections Associated with Common Endemic Human Respiratory Coronaviruses

Coronaviruses OC43, 229E, NL63, and HKU1 are endemic human respiratory coronaviruses that typically cause mild to moderate upper respiratory infections, similar to the common cold. They also may cause simple and complicated lower respiratory infections, otitis media, asthma exacerbations, gastroenteritis, and a few systemic complications. These viruses are usually seasonal (with winter dominance) and affect nearly all age groups. The seasonal and annual variation in virus prevalence has implications for understanding the concept of acquired immunity and its persistence or diminution. Coronaviruses generally have outbreak potential in susceptible populations of any age, particularly in patients with comorbidities, who tend to have increased clinical disease. These 4 coronaviruses are often found in the context of what appears to be coinfection with other pathogens, but especially other viruses. If coronaviruses are not specifically tested for, the sole detection of a viral copathogen would suggest the pathogen is the causative agent, when a coronavirus may be culpable, or both. The detection of these viruses in circumstances where respiratory viruses are generally sought in clinical samples is, therefore, justified. These pathogens can be chronically shed from the respiratory tract, which is more likely to occur among immunocompromised and complicated patients. These viruses share the potential for genetic drift. The genome is among the largest of RNA viruses, and the capability of these viruses to further change is likely underestimated. Given the potential disease among humans, it is justified to search for effective antiviral chemotherapy for these viruses and to consider uses in niche situations should effective therapy be defined. Whereas SARS-CoV-2 may follow the epidemiological pattern of SARS-CoV and extinguish slowly over time, there is yet concern that SARS-CoV-2 may establish itself as an endemic human respiratory coronavirus similar to OC43, 2299E, NL63, and HKU1. Until sufficient data are acquired to better understand the potential of SARS-CoV-2, continued work on antiviral therapy and vaccination is imperative.

Severity of influenza virus and respiratory syncytial virus coinfections in hospitalized adult patients

BACKGROUND

With the introduction of molecular diagnostic techniques over the past decades, different kinds of viral pathogens in the same sample are detected simultaneously more frequently. Nevertheless, influenza virus (Flu) and respiratory syncytial virus (RSV) coinfection in adults was reported only occasionally. Moreover, the clinical implications of Flu/RSV coinfection in the respiratory tract of adults remain unclear.

METHODS

This retrospective study analyzed adult patients with acute respiratory infection from January 2017 to June 2019 in China-Japan Friendship Hospital.

RESULTS

A total of 574, 235 and 113 patients were positive for influenza A-only (FA-only), influenza B-only (FB-only) and RSV-only in influenza seasons (from Nov 2017 to Mar 2018 and from Nov 2018 to Mar 2019), respectively. Of these, 19 cases were coinfected by Flu and RSV and admitted to this hospital. Compared with 809 Flu-only infected patients and 113 RSV-only infected patients, both the rates of intensive care unit(ICU) admission and use of invasive mechanical ventilation in Flu/RSV coinfected patients were higher (ICU admission: 47.4% vs. 20.1%, P=0.004; 47.4% vs. 22.1%, P=0.020; invasive mechanical ventilation: 47.4% vs.13.2%, P<0.001; 47.4% vs. 17.7%, P=0.004). Furthermore, 60-day all-cause mortality attributed to Flu/RSV coinfections was significantly greater than that for Flu and RSV mono-infected patients (36.8% vs. 8.0%,P<0.001; 36.8% vs. 11.5%, P=0.004.

CONCLUSION

The findings of this study suggest that coinfection of Flu/RSV in adults is associated with a high adverse outcome. Thus, Flu/RSV coinfections should be increasingly appreciated and given appropriate management.

Peripheral blood T cells response in human parainfluenza virus-associated lower respiratory tract infection in children

Human Parainfluenza virus (HPIV) causes lower respiratory tract infections (LRTI) mostly in young children. Respiratory viral infections may decline T cells in circulation and display enhanced pathogenicity. This study is aimed to analyze T cells alterations due to HPIV in children with LRTIs. Children (N = 152) with bronchitis or pneumonia, admitted in tertiary care hospitals were included in the study. Respiratory samples (throat or nasopharyngeal swabs) were taken and HPIV genotypes (1-4) were analyzed through RT-PCR. Peripheral blood T cells, CD3+, CD4+, CD8+, and CD19+, were analyzed in confirmed HPIV positive and healthy control group children through flow cytometry. The positivity rate of HPIV was 24.34% and the most prevalent genotype was HPIV-3 (20.40%). HPIV-1 and HPIV-2 were detected in 0.66% and 02% children respectively. The T lymphocyte counts were observed significantly reduced in children infected with HPIV-3. CD4+ cell (1580 ± 97.87) counts did not change significantly but the lowest CD8+ T cell counts (518.5 ± 74.00) were recorded. Similarly, CD3+ and CD19 cell ratios were also reduced. The CD4/CD8 ratio was significantly higher (3.12 ± 0.59) in the study population as compared to the control group (2.18 ± 0.654). Changes in the count of CD8+ T cells were more pronounced in patients with bronchiolitis and pneumonia. It is concluded that CD8+ T cells show a reduced response to HPIV-3 in children with severe LRTIs suggesting a strong association of these cells with disease severity.

DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment

Pandemics require a fast and immediate response to contain potential infectious carriers. In the recent 2020 Covid-19 worldwide pandemic, authorities all around the world have failed to identify potential carriers and contain it on time. Hence, a rapid and very sensitive testing method is required. Current diagnostic tools, reverse transcription PCR (RT-PCR) and real-time PCR (qPCR), have its pitfalls for quick pandemic containment such as the requirement for specialized professionals and instrumentation. Versatile electrochemical DNA/RNA sensors are a promising technological alternative for PCR based diagnosis. In an electrochemical DNA sensor, a nucleic acid hybridization event is converted into a quantifiable electrochemical signal. A critical challenge of electrochemical DNA sensors is sensitive detection of a low copy number of DNA/RNA in samples such as is the case for early onset of a disease. Signal amplification approaches are an important tool to overcome this sensitivity issue. In this review, the authors discuss the most recent signal amplification strategies employed in the electrochemical DNA/RNA diagnosis of pathogens.

The Epidemiology of Admission-Requiring Pediatric Respiratory Infections in a Japanese Community Hospital Using Multiplex PCR

Respiratory tract infections (RTIs) are the most common diseases globally among children. This study aimed to assess the epidemiology of admission-requiring pediatric RTI cases and evaluate the effect of the pathogen type on the length of hospital stay (LOS) using the FilmArray^® respiratory panel, a multiplex PCR test. The age-specific distribution and seasonality of viruses were investigated between March 26, 2018 and April 12, 2019. Multivariable linear regression analyses were performed to evaluate the effect of pathogen type and coinfection on LOS. Among 153 hospitalized RTI patients, respiratory syncytial virus was the leading cause of hospitalization in infants < 12 months of age (27.7%). Human metapneumovirus and parainfluenza virus were also major causes of hospitalization in patients aged 2-3 years (22.6% and 22.6%, respectively). In the multivariable linear regression model excluding rhinovirus/enterovirus, there was a significant association between viral coinfection and longer LOS (p = 0.012), while single viral infection of any type was not positively correlated with LOS. This study revealed the epidemiology of admission-requiring pediatric RTIs.

The Rise and Impact of COVID-19 in India

The coronavirus disease (COVID-19) pandemic, which originated in the city of Wuhan, China, has quickly spread to various countries, with many cases having been reported worldwide. As of May 8th, 2020, in India, 56,342 positive cases have been reported. India, with a population of more than 1.34 billion-the second largest population in the world-will have difficulty in controlling the transmission of severe acute respiratory syndrome coronavirus 2 among its population. Multiple strategies would be highly necessary to handle the current outbreak; these include computational modeling, statistical tools, and quantitative analyses to control the spread as well as the rapid development of a new treatment. The Ministry of Health and Family Welfare of India has raised awareness about the recent outbreak and has taken necessary actions to control the spread of COVID-19. The central and state governments are taking several measures and formulating several wartime protocols to achieve this goal. Moreover, the Indian government implemented a 55-days lockdown throughout the country that started on March 25th, 2020, to reduce the transmission of the virus. This outbreak is inextricably linked to the economy of the nation, as it has dramatically impeded industrial sectors because people worldwide are currently cautious about engaging in business in the affected regions.

Molecular Diagnosis of Pneumonia Using Multiplex Real-Time PCR Assay RespiFinder® SMART 22 FAST in a Group of Moroccan Infants

Background

In Morocco, pediatric pneumonia remains a serious public health problem, as it constitutes the first cause of mortality due to infectious diseases. The etiological diagnosis of acute respiratory tract infections is difficult. Therefore, it is necessary to use Multiplex real-time polymerase chain reaction assay tests in a routine setting for exact and fast identification.

Objectives

In this paper, we present the clinical results of pediatric pneumonia and describe their etiology by using molecular diagnosis. Study design: Tracheal secretion was collected from infants presenting respiratory distress isolated or associated with systemic signs, attending the unit of Neonatology between December 1, 2016, and Mai 31, 2018. Samples were tested with the multiplex RespiFinder® SMART 22 FAST which potentially detects 18 viruses and 4 bacteria.

Results

Of the 86 infants considered in this study (mean age 31 ± 19 days) suspected of acute respiratory tract infections, 71 (83%) were positive for one or multiple viruses or/and bacteria. The majority of acute respiratory tract infections had a viral origin (95%): respiratory syncytial viruses (A and B) (49%), rhinovirus (21%), coronaviruses 229E (11%), humain metapneumovirus (5%), influenza A (3%), influenza H1N1 (1%), adenovirus (2%), and parainfluenza virus type 4 (2%). Among our patients, 6% had Mycoplasma pneumoniae. Coinfections were not associated with severe respiratory symptoms.

Conclusion

The clinical spectrum of respiratory infections is complex and often nonspecific. Thus, the early and fast detection of related causative agents is crucial. The use of multiplex real time polymerase chain reaction may help choose an accurate treatment, reduce the overall use of unnecessary antibiotics, preserve intestinal flora, and decrease nosocomial infection by reducing the length of hospitalization.

Immunoglobulin M profile of viral and atypical pathogens among children with community acquired lower respiratory tract infections in Luzhou, China

Background

Community-acquired lower respiratory tract infections (CA-LRTIs) are the primary cause of hospitalization among children globally. A better understanding of the role of atypical pathogen infections in native conditions is essential to improve clinical management and preventive measures. The main objective of this study was to detect the presence of 7 respiratory viruses and 2 atypical pathogens among hospitalized infants and children with community-acquired lower respiratory tract infections in Luzhou via an IgM test.

Methods

Overall, 6623 cases of local hospitalized children with 9 pathogen-IgM results from 1st July 2013 to 31st Dec 2016 were included; multidimensional analysis was performed.

Results

1) Out of 19,467 hospitalized children with lower respiratory tract infections, 6623 samples were collected, for a submission ratio of 33.96% (6623 /19467). Of the total 6623 serum samples tested, 5784 IgM stains were positive, for a ratio of 87.33% (5784 /6623). Mycoplasma pneumoniae (MP) was the dominant pathogen (2548 /6623, 38.47%), with influenza B (INFB) (1606 /6623, 24.25%), Legionella pneumophila serogroup 1 (LP1) (485 /6623, 7.32%) and parainfluenza 1, 2 and 3(PIVs) (416 /6623, 6.28%) ranking second, third and fourth, respectively.

2) The distribution of various pathogen-IgM by age group was significantly different (χ² = 455.039, P < 0.05).

3) Some pathogens were found to be associated with a certain age of children and seasons statistically.

Conclusions

The dominant positive IgM in the area was MP, followed by INFB, either of which prefers to infect children between 2 years and 5 years in autumn. The presence of atypical pathogens should not be underestimated clinically as they were common infections in the respiratory tract of children in the hospital.

Seroepidemiology of respiratory syncytial virus in western India with special reference to appropriate age for infant vaccination

Respiratory syncytial virus (RSV) causes significant infant mortality worldwide and a vaccine may be available soon. This study determined age-stratified anti-RSV antibody positivity (enzyme-linked immunosorbent assay [ELISA]) at Pune, India (cord blood-85 years). Antibody positivity declined from 100% at birth to 71.3% (3 months), and 0.7% (6 months). A significant rise was noted at 15 months (16%), 16 to 24 months (64.5%) and 4 years (95.2%) with concomitant IgM-anti-RSV positivity indicative of recent infection. Antibody decline was higher in infants born preterm than full-term. Across subsequent age groups including the elderly, antibody positivity was similar and comparable, suggestive of repeated exposure to the virus. Early protection/vaccination is essential for the infant population.