Epidemiology Of Respiratory Infections Research Articles

Post-pandemic consumption of outpatient antibiotics in Switzerland up to pre-pandemic levels, 2018–2023: An interrupted time series analysis

BackgroundThe COVID-19 pandemic has been a challenge for health-care systems and antibiotic stewards as uncertainty regarding treatment and bacterial coinfections raised concern. MethodsThis retrospective observational study examined the association of the pandemic on outpatient antibiotic sales and prescriptions in Switzerland using interrupted time series (ITS) analyses. Data from IQVIA™ and the Sentinella Network were used to analyze antibiotic consumption and prescription patterns over a 72-month period from January 2018 to December 2023, divided into pre-pandemic, pandemic, and post-pandemic periods. ResultsAntibiotic consumption decreased during the pandemic and returned to pre-pandemic levels in the post-pandemic period. A decrease in level was most pronounced in the French-speaking region (−2.82 defined daily doses per 1,000 inhabitants per day (DID) per month, 95 %CI [−4.34, −1.30], p < 0.001) and the Italian-speaking region (−2.80 DID per month, 95 %CI [−4.78, −0.82], p < 0.01), followed by the German-speaking region (−1.72 DID per month, 95 %CI [−2.71, −0.74], p < 0.01). Similarly, in the ITS, the relative change of model estimates in antibiotic prescriptions by GPs and pediatricians for upper respiratory tract infections, was of −36.0 % and −50.3 % resp. in the pandemic period and +10.1 % and −2.6 % in the post-pandemic period compared with the pre-pandemic period. ConclusionsA decrease of antibiotic prescriptions was observed in GPs and pediatricians during the COVID-19 pandemic, followed by a return to pre-pandemic levels. The patterns in antibiotic prescriptions aligned with the epidemiology of respiratory infections and demonstrated a pronounced association with the implementation and subsequent removal of non-pharmaceutical interventions.

Effect of Elexacaftor/Tezacaftor/Ivacaftor on Pseudomonas aeruginosa Acquisition and Chronic Infection at a Single Pediatric Cystic Fibrosis Care Center

OBJECTIVES As cystic fibrosis (CF) lung disease progresses, the airways become infected with opportunistic pathogens, such as Pseudomonas aeruginosa (PA). In October 2019, the US Food and Drug Administration approved elexacaftor/tezacaftor/ivacaftor (ETI), a highly effective modulator therapy (HEMT), for individuals 12 years and older with 1 copy of the F508del cystic fibrosis transmembrane conductance regulator (CFTR) mutation. ETI increases the amount of and function of CFTR in the respiratory epithelium, improving mucociliary clearance and reducing static airway mucus, a major trigger for chronic infection and inflammation. METHODS A retrospective analysis of inhaled tobramycin (iTOB) prescriptions between January 1, 2016, and December 31, 2021, was performed. This captured data before and after ETI approval at Children’s Mercy Kansas City (CMKC). The number of individuals with new PA acquisition and individuals considered ­chronically infected was analyzed. RESULTS The number of eradication prescriptions declined in 2020 and 2021, with 15 (7%) and 12 (5%) ­individuals prescribed therapy for those years, respectively. A similar pattern was observed for ­prescriptions for chronic infection. A reduction was seen in 2020 and 2021, with 28 (13%) and 20 (9%) individuals ­prescribed therapy for the respective years. CONCLUSIONS The CMKC experienced a decrease in the number of courses of iTOB prescribed during the last 6 years. The reasons for this are likely multifactorial and may include the implementation of standardized PA surveillance and eradication protocols, the effect of HEMT on mucociliary clearance and airway microbiology, and the poorly understood effects of the SARS-CoV-2 pandemic on the epidemiology of respiratory infections.

Effects of COVID-19 pandemic on epidemiological features of viral respiratory tract infections in children: a single-centre study.

The epidemiology of respiratory infections may vary depending on factors such as climate changes, geographical features, and urbanization. Pandemics also change the epidemiological characteristics of not only the relevant infectious agent itself but also other infectious agents. This study aims to assess the impact of the COVID-19 pandemic on the epidemiology of viral respiratory infections in children. We retrospectively reviewed the medical records of children aged ≤18years with laboratory-confirmed viral respiratory infections other than COVID-19 from January 2018 to March 2023. Data on demographic characteristics, month and year of admission, and microbiological results were collected. During the study period, 1,829 respiratory samples were sent for polymerase chain reaction testing. Rhinovirus was identified in 24% of the patients, mixed infections in 21%, influenza virus in 20%, and respiratory syncytial virus in 12.5%. A 38.6% decrease in viral respiratory infections was observed in 2020, followed by a 188% increase in 2021. The respiratory syncytial virus was significantly more common in the post-pandemic period (13.8%) compared to the pre-pandemic period (8.1%), but no seasonal shift in respiratory syncytial virus infection was observed. There was also a yearly increase in influenza infections in the post-pandemic period compared to the pre-pandemic period. After the COVID-19 pandemic, the frequency of parainfluenza virus infections increased during the summer months, and this finding provides a new contribution to the existing literature.

Epidemiology of Respiratory Infections during the COVID-19 Pandemic.

To face the COVID-19 outbreak, a wide range of non-pharmaceutical interventions (NPIs) aimed at limiting the spread of the virus in communities, such as mask-wearing, hand hygiene, social distancing, travel restrictions, and school closures, were introduced in most countries. Thereafter, a significant reduction of new asymptomatic and symptomatic COVID-19 cases occurred, although there were differences between countries according to the type and duration of the NPIs. In addition, the COVID-19 pandemic has been accompanied by significant variations in the global incidence of diseases due to the most common non-SARS-CoV-2 respiratory viruses and some bacteria. In this narrative review, the epidemiology of the most common non-SARS-CoV-2 respiratory infections during the COVID-19 pandemic is detailed. Moreover, factors that could have had a role in modifying the traditional circulation of respiratory pathogens are discussed. A literature analysis shows that NPIs were the most important cause of the general reduction in the incidence of influenza and respiratory syncytial virus infection in the first year of the pandemic, although the different sensitivity of each virus to NPIs, the type and duration of measures used, as well as the interference among viruses may have played a role in modulating viral circulation. Reasons for the increase in the incidences of Streptococcus pneumoniae and group A Streptococcus infections seem strictly linked to immunity debt and the role played by NPIs in reducing viral infections and limiting bacterial superimposed infections. These results highlight the importance of NPIs during pandemics, the need to monitor the circulation of infectious agents that cause diseases similar to those caused by pandemic agents, and the need to make efforts to improve coverage with available vaccines.

Characterization of viral pathogens associated with symptomatic upper respiratory tract infection in adults during a low COVID-19 transmission period.

The epidemiology of respiratory tract infections (RTI) has dramatically changed over the course of the COVID-19 pandemic. A major effort in the clinical management of RTI has been directed toward diagnosing COVID-19, while the causes of other, common community RTI often remain enigmatic. To shed light on the etiological causes of RTI during a low COVID-19 transmission period in 2021, we did a pilot study using molecular testing for virologic causes of upper RTI among adults with respiratory symptoms from Almaty, Kazakhstan. Adults presenting at two public hospitals with respiratory symptoms were screened using SARS-CoV-2 PCR on nasopharyngeal swabs. A subset of RTI+, COVID-19-negative adults (n = 50) was then tested for the presence of common RTI viruses and influenza A virus (IAV). Next generation virome sequencing was used to further characterize the PCR-detected RTI pathogens. Of 1,812 symptomatic adults, 21 (1.2%) tested SARS-CoV-2-positive. Within the COVID-19 negative outpatient subset, 33/50 subjects (66%) had a positive PCR result for a common community RTI virus, consisting of human parainfluenza virus 3-4 (hPIV 3-4) in 25/50 (50%), rhinovirus (hRV) in 2 (4%), hPIV4-hRV co-infection in four (8%) and adenovirus or the OCR43/HKU-1 coronavirus in two (4%) cases; no IAV was detected. Virome sequencing allowed to reconstruct sequences of most PCR-identified rhinoviruses and hPIV-3/human respirovirus-3. COVID-19 was cause to a low proportion of symptomatic RTI among adults. Among COVID-negative participants, symptomatic RTI was predominantly associated with hPIV and hRV. Therefore, respiratory viruses other than SARS-CoV-2 should be considered in the clinical management and prevention of adult RTI in the post-pandemic era.

Epidemiology of respiratory tract infections using multiplex PCR in a Japanese acute care hospital during the COVID19 pandemic

IntroductionWe aimed to investigate the epidemiology of respiratory infections by season and age during the COVID-19 pandemic in a Japanese acute care hospital using multiplex PCR testing. MethodsWe detected 21 pathogens in specimens from outpatients with respiratory symptoms at the Nara Prefecture General Medical Center using the multiplex PCR-based FilmArray Respiratory Panel 2.1 (bioMérieux). ResultsOf the 3177 cases, 1215 (38.2%) were infected with at least one causative virus, and 1641 viruses were detected. The most common viruses detected were human rhinovirus/enterovirus (n = 655) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (n = 264). Additionally, 321 (10.1%) of these cases were infected with two or more overlapping viruses. There were 23 cases of co-infection with SARS-CoV-2 and other viruses. In the winter months from December 2020 to March 2021, the number of detected viruses was relatively low, followed by the surge of human rhinovirus/enterovirus, respiratory syncytial virus (RSV), and parainfluenza type 3 in the spring and summer of 2021. While the number of human rhinovirus/entero-virus remained relatively high after the 2021 summer, the number of other viruses detected since September 2021 was low. After December 2021, the number of SARS-CoV-2 increased rapidly. ConclusionsContinuous monitoring of the epidemiology of respiratory infection is important to understand the prolonged impact of the COVID-19 pandemic.

Rhinovirus as the main co-circulating virus during the COVID-19 pandemic in children

ObjectiveChanges in the epidemiology of respiratory infections during the restrictions imposed as a response to the coronavirus disease 2019 (COVID-19) pandemic have been reported elsewhere. The present study's aim was to describe the prevalence of a large array of respiratory pathogens in symptomatic children and adolescents during the pandemic in Southern Brazil. MethodsHospitalized and outpatients aged 2 months to 18 years with signs and symptoms of acute COVID-19 were prospectively enrolled in the study from May to November 2020 in two hospitals in a large metropolitan area in a Brazilian city. All participants performed a real-time PCR panel assessing 20 respiratory pathogens (three bacteria and 17 viruses). Results436 participants were included, with 45 of these hospitalized. Rhinovirus was the most prevalent pathogen (216/436) followed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, 97/436), with a coinfection of these two viruses occurring in 31/436 participants. The remaining pathogens were found in 24 symptomatic participants (adenovirus, n = 6; Chlamydophila pneumoniae, n = 1; coronavirus NL63, n = 2; human enterovirus, n = 7; human metapneumovirus, n = 2; Mycoplasma pneumoniae, n = 6). Hospitalization was more common among infants (p = 0.004) and those with pathogens other than SARS-CoV-2 (p = 0.001). ConclusionDuring the period of social distancing in response to COVID-19, the prevalence of most respiratory pathogens was unusually low. Rhinovirus remained as the main virus co-circulating with SARS-CoV-2. COVID-19 in symptomatic children was less associated with hospitalization than with other respiratory infections in children and adolescents.

Epidemiology of Respiratory Tract Infections Using Multiplex PCR in a Japanese Acute Care Hospital During the COVID19 Pandemic

Epidemiology of Respiratory Tract Infections Using Multiplex PCR in a Japanese Acute Care Hospital During the COVID19 Pandemic

Etiology of Community-Acquired Pneumonia during the Epidemic Spread of COVID-19 and Healthcare-Associated Pneumonia Risk Assessment

In 2020, the COVID-19 pandemic contributed to the epidemiology of respiratory tract infections. The importance of timely differential diagnosis of COVID-19 and seasonal acute respiratory diseases is hard to overestimate. Patients with the novel coronavirus disease are at risk of developing hospital-acquired pneumonia. The analysis of specific features of circulation of various strains of pathogens of nosocomial infections resistant to antibacterial chemotherapeutic agents is relevant. Our objective was to study the etiological structure of community-acquired pneumonia during the epidemic spread of COVID-19 and to assess risks of developing healthcare-associated pneumonia. Materials and methods. Biological specimens from 446 inpatients and outpatients diagnosed with community-acquired pneumonia in the city of Rostov-on-Don were tested. Verification of respiratory viruses, including RNA of SARS-CoV-2, M. pneumoniae, C. pneumoniae, and L. pneumophila, was performed by polymerase chain reaction in nasopharyngeal swab specimens. Bacteriological analysis of sputum was carried out using differential diagnostic media, and isolated pathogens were then identified by time-of-flight mass spectrometry on an Autoflex instrument (Bruker Daltonics GmbH, Germany) using the MALDI BioTyper R 3.0 software. Results and discussion. In December 2020, the proportion of SARS-CoV-2 positive test results among patients diagnosed with community-acquired pneumonia was 35.6 %. The frequency of mixed viral infections in patients with a confirmed diagnosis of COVID-19 was not significantly different from that in patients tested negative (25.9 % and 26.2 %, respectively). The microbiota in pneumonia unrelated to SARS-CoV-2 was dominated by Candida fungi and plasma-coagulating staphylococci while cultures of non-fermenting gram-negative bacteria were significantly more often isolated from COVID-19 cases. Secondary infection presumably induced by environmental contamination or disease transmission from healthcare personnel was registered in 51.6 % of inpatients. Transmission of nosocomial infections between patients was not observed.

Viral etiology and epidemiology of pediatric patients hospitalized for acute respiratory tract infections in Macao: a retrospective study from 2014 to 2017

BackgroundAcute respiratory infections (ARIs) are among the leading causes of hospitalization in children. Understanding the local dominant viral etiologies is important to inform infection control practices and clinical management. This study aimed to investigate the viral etiology and epidemiology of respiratory infections among pediatric inpatients in Macao.MethodsA retrospective study using electronic health records between 2014 and 2017 at Kiang Wu Hospital was performed. Nasopharyngeal swab specimens were obtained from hospitalized children aged 13 years or younger with respiratory tract diseases. xMAP multiplex assays were employed to detect respiratory agents including 10 respiratory viruses. Data were analyzed to describe the frequency and seasonality.ResultsOf the 4880 children enrolled in the study, 3767 (77.1%) were positive for at least one of the 13 viral pathogens tested, of which 2707 (55.5%) being male and 2635 (70.0%) under 2 years old. Among the positive results, there were 3091 (82.0%) single infections and 676 (18.0%) multiple infections. The predominant viruses included human rhinovirus/enterovirus (HRV/EV 27.4%), adenovirus (ADV, 15.8%), respiratory syncytial virus B (RSVB, 7.8%) and respiratory syncytial virus A (RSVA, 7.8%). The detection of viral infection was the most prevalent in autumn (960/1176, 81.6%), followed by spring (1095/1406, 77.9%), winter (768/992, 77.4%), and summer (944/1306, 72.3%), with HRV/EV and ADV being most commonly detected throughout the 4 years of study period. The detection rate of viral infection was highest among ARI patients presented with croup (123/141, 87.2%), followed by lower respiratory tract infection (1924/2356, 81.7%) and upper respiratory tract infection (1720/2383, 72.2%). FluA, FluB and ADV were positive factors for upper respiratory tract infections. On the other hand, infection with RSVA, RSVB, PIV3, PIV4, HMPV, and EV/RHV were positively associated with lower respiratory tract infections; and PIV1, PIV2, and PIV3 were positively associated with croup.ConclusionsThis is the first study in Macao to determine the viral etiology and epidemiology of pediatric patients hospitalized for ARIs. The study findings can contribute to the awareness of pathogen, appropriate preventative measure, accurate diagnosis, and proper clinical management of respiratory viral infections among children in Macao.

Study of respiratory viruses and the co-infection with bacterial and fungal pathogens in acute exacerbation of chronic obstructive pulmonary diseases

Background: The study on infectious etiology of AECOPD is largely restricted to only viral or only bacterial etiology. This prospective study was conducted over 2 years to estimate the overall incidence rate and profile of viral infections in AECOPD patients, co-infection of the viral agents with other bacterial and fungal agents, association of the type and pattern of infective agent with the clinical severity. Methods and materials: From all patients, nasopharyngeal (NP) swab, sputum, and blood were collected. qRT-Multiplex PCR was performed from the nasopharyngeal swab using FTD respiratory pathogens 21 plus kit. ZN stain, modified MZN, KOH mount were performed for mycobacteria, nocardia and fungal elements. Bacterial cultures, fungal cultures were done as per standard techniques. Serum samples were tested for Mycoplasma and Chlamydia pneumonia Ig M ELISA and semiquantitative CRP. Results: 74 AECOPD cases were included in the study. The AECOPD events which had only viral infection, only bacterial infection, bacterial–viral co-infection, fungal infection and no infection were 23 (31%), 12 (16%), 20 (27%), 3 (4%) and 16 (22%) respectively. Most common virus identified was Influenza A (22/43; 51%). The number of cases having monoviral (MV) and polyviral (PV) infections were 26 and 17 respectively. In PV infection most common pattern being IAV + IBV, followed by HRV + PIV3. Most common bacteria isolated were Pseudomonas aeruginosa (9/32, 28%). Sputum sample of 3 patients (3/74; 4%) were positive for Aspergillus flavus. 49 samples (66%) had elevated CRP. Elevated CRP level was significantly associated with presence of any infective agents, bacterial infection and with co-infection (p < 0.001), (p < 0.001), (p = 0.002), respectively. Conclusion: This information on the epidemiology of respiratory infections in AECOPD will improve the management of AECOPD using timely institution of antivirals and reduce the overuse of antibiotics and the implementation of routine influenza vaccination.

Thank you to our reviewers in 2019

At Health Science Reports, we aim to publish scientifically sound research from across the medical sciences. For this, the feedback from experts in the field is essential, who, through detailed, fair, and unbiased evaluation of the work under consideration, have contributed tremendously not only to the strengthening of the submitted articles, but also, to the success of the journal as a unified and comprehensive resource of health science research. As such, we are extremely grateful to all reviewers who generously give their time and expertise to evaluate the research submitted to Health Science Reports, and ultimately, help advance scientific communication and open access medical research. The names of all reviewers who contributed during 2019 are listed below (the list includes those who reviewed manuscripts submitted between January 1 and December 31, 2019). Starting this year, we will honor two outstanding reviewers with our Reviewer of the year Award. Nominations for the Award were put forward and discussed by the Chief Editors during a recent meeting. The key criteria for nomination included high quality of the submitted reviews (both critical and constructive, highlighting both the positive aspects of the study as well as those that may require improvement, and providing authors with specific comments on how the article may be revised), timely responses, and supporting the journal, by being generally available for reviews when invited. After careful consideration, we are pleased to recognize Dr. Flor Muñoz and Dr. Hidenori Toyoda as the recipients of this year's Award. Flor Muñoz, MD, is an associate professor of Pediatrics and Infectious Diseases at Baylor College of Medicine, and Director of Transplant Infectious Diseases at Texas Children's Hospital in Houston, TX. She is a clinician-investigator with various projects supported by the US NIH, Centers for Disease Control and Prevention (CDC), Bill & Melinda Gates Foundation, and industry, focusing on vaccines, the epidemiology of respiratory infections in healthy and immunocompromised hosts, and the evaluation of safety and immunogenicity of vaccines in pregnant women, children, and transplant recipients. She has published extensively on topics related to influenza, RSV, vaccines, and maternal immunization. Dr Muñoz is a member of the American Academy of Pediatrics (AAP) Committee on Infectious Diseases (COID), the CDC's Advisory Committee on Immunization Practices (ACIP) influenza and pertussis working groups, and the American College of Obstetrics and Gynecology (ACOG) Immunization Expert Work Group. Dr Muñoz serves as chair of the Institutional Review Board (IRB) at Baylor College of Medicine, and is a member of various academic societies, including the Infectious Diseases Society of America (IDSA), the Pediatric Infectious Diseases Society (PIDS) and the PIDS Transplant Committee, the Society for Pediatric Research (SPR), and the Research Committee of the European Society of Pediatric Infectious Diseases (Figure 1). Hidenori Toyoda, MD, PhD, FACP is Director of Gastroenterology and Hepatology at Ogaki Municipal Hospital, Japan. He currently works as an hepatologist and clinical investigator, and his research is focused on liver disease. Dr Toyoda has published over 350 scientific articles, mostly on topics related to viral hepatitis and hepatocellular carcinoma. Dr Toyoda is a member of the American College of Physicians (ACP), American Association of the Study of Liver Diseases (AASLD), and American College of Gastroenterology (ACG) (Figure 2). Alexopoulou, Alexandra Bailey, Cathy Brito, Juan P. Butsashvili, Maia Chaturvedi, Shruti Chiesi, Francesca Cortez-Pinto, Helena Damen, Johanna A. A. G. de Hertogh, Willem de Velasco, Guillermo Emmerechts, Jan Fix, Gemmae Fortune, Brett Ganger, Daniel Gist, Katja Greeley, Christopher S. Griffin, Benjamin R. Haddy, Nadia Hain, Timothy Hort, Krishna Im, Gene Ingiliz, Patrick Innos, Kaire Iyer, Hari Jackson, Rod Kennecke, Hagen Kestens, Luc Kingstone, Tom Lall, Dorothy Leslie, Hannah H. Lin, Lifeng Liu, Dandan Mahmud, Nadim Mammen, Jennifer Martinello, Marianne Mayo-Gamble, Tilicia Mehata, Suresh Muñoz, Flor Paranhos-Baccalà, Gláucia Penk, Jamie S. Progovac, Ana M. Razvi, Salman Sammour, Tarik Sayani, Farzana Shepperd, James Stanhope, Victoria Street, Richard L. Sung, Shih-Hsien Takahashi, Masayuki Toyoda, Hidenori van Leeuwen, Flora E. van Smeden, Maarten Wang, Ji-Guang Wu, Han-Ping Wyss, Richard Zimbudzi, Edward Zini, Gina

Bacterial and Viral Identification Rate in Acute Exacerbation of Chronic Obstructive Pulmonary Disease in Korea

PurposeThe most common cause of acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is respiratory infection. Most studies of bacterial or viral cause in AECOPD have been conducted in Western countries. We investigated bacterial and viral identification rates in AECOPD in Korea.Materials and MethodsWe reviewed and analyzed medical records of 736 cases of AECOPD at the Korea University Guro Hospital. We analyzed bacterial and viral identification rates and classified infections according to epidemiological factors, such as Global Initiative for Chronic Obstructive Lung Disease stage, mortality, and seasonal variation.ResultsThe numbers of AECOPD events involving only bacterial identification, only viral identification, bacterial-viral co-identification, and no identification were 200 (27.2%), 159 (21.6%), 107 (14.5%), and 270 (36.7%), respectively. The most common infectious bacteria identified were Pseudomonas aeruginosa (13.0%), Streptococcus pneumoniae (11.4%), and Haemophilus influenzae (5.3%); the most common viruses identified were influenza virus (12.4%), rhinovirus (9.4%), parainfluenza virus (5.2%), and metapneumovirus (4.9%). The bacterial identification rate tended to be higher at more advanced stages of chronic obstructive pulmonary disease (p=0.020 overall, p=0.011 for P. aeruginosa, p=0.048 for S. pneumoniae). Staphylococcus aureus and Klebsiella pneumoniae were identified more in mortality group (p=0.003 for S. aureus, p=0.009 for K. pneumoniae). All viruses were seasonal (i.e., greater prevalence in a particular season; p<0.050). Influenza virus and rhinovirus were mainly identified in the winter, parainfluenza virus in the summer, and metapneumovirus in the spring.ConclusionThis information on the epidemiology of respiratory infections in AECOPD will improve the management of AECOPD using antibiotics and other treatments in Korea.

Global Considerations in Human Immunodeficiency Virus-Associated Respiratory Disease

Respiratory tract infection, particularly tuberculosis, is a major cause of mortality among human immunodeficiency virus (HIV)-infected individuals. Antiretroviral therapy (ART) has resulted in a dramatic increase in survival, although coverage of HIV treatment remains low in many parts of the world. There is a concurrent growing burden of chronic noninfectious respiratory disease as a result of increased survival. Many risk factors associated with the development of respiratory disease, such as cigarette smoking and intravenous drug use, are overrepresented among people living with HIV. In addition, there is emerging evidence that HIV infection may directly cause or accelerate the course of chronic lung disease. This review summarizes the clinical spectrum and epidemiology of respiratory tract infections and noninfectious pulmonary pathologies, and factors that explain the global variation in HIV-associated respiratory disease. The potential for enhancing diagnoses of noninfective chronic conditions through the use of clinical algorithms is discussed. We also consider issues in assessment and management of HIV-related respiratory disease in view of the increasing global scale up of ART.

Evaluation of viral co-infections in hospitalized and non-hospitalized children with respiratory infections using microarrays

The impact of viral co-infections and recently discovered viruses on the epidemiology of respiratory infections in children is still unclear. To simultaneously detect viruses that are involved in the aetiology of respiratory infections, we used a DNA/RNA microarray assay that identifies 17 different viruses or viral subtypes. Rhinopharyngeal washes were taken from 611 children (aged 1 month to 14 years) who presented in the emergency department with respiratory infections from June 2010 to June 2011 and were treated as outpatients (299, 48.9%) or hospitalized (312, 51.1%). Lower respiratory tract infection was diagnosed more often in hospitalized children (68% versus 36%, p 0.001). Of 397 children in which microarrays detected viral infection (70.1%), a single virus was found in 228 (57.4%) and two or more viruses in 169 (42.5%). The most prevalent viruses among children with positive samples were respiratory syncytial virus (RSV) in 225 (56.6%), parainfluenza virus (PIV) in 118 (29.7%), rhinovirus (RV) in 73 (18.4%), followed by influenza in 56 (14.1%), adenoviruses in 31 (7.8%), bocavirus in 25 (6.3%), human metapneumovirus in 15 (3.7%) and enteroviruses in 12 (3%). Most common viral co-infections were RSVA–RSVB in 46 children (27.2%), RSV–Influenza in 20 (11.8%), RSV–RV in 18 (10.6%) and PIV–RV in 13 (7.7%). Multiple logistic regression analysis revealed that viral co-infections were associated with increased probability for hospitalization (OR 1.52, 95% CI 1.01–2.29, p 0.04), and previous pneumococcal vaccination was associated with decreased probability for hospitalization (OR 0.52, 95% CI 0.33–0.81, p 0.004). We conclude that viral co-infections are involved in a significant proportion of children with an acute respiratory infection and may increase the severity of clinical presentation and the risk for hospitalization.

Seasonal variations of 15 respiratory agents illustrated by the application of a multiplex polymerase chain reaction assay

Nucleic acid amplification tests are increasingly being used to diagnose viral and bacterial respiratory tract infections. The high sensitivity of these tests affects our understanding of the epidemiology of respiratory tract infections. We have assessed the detection rate of a multiplex real-time polymerase chain reaction (PCR) test, with emphasis on epidemiology and seasonal distribution of the most common respiratory tract infections. Seven thousand eight hundred and fifty-three nasopharyngeal samples from 7220 patients (age range 0-98 y, median 22 y) obtained during 36 consecutive months (November 2006-October 2009), were analyzed with a multiplex PCR panel including influenza A (IfA) and B (IfB) virus, parainfluenza virus (PIV) 1-3, respiratory syncytial virus (RSV), human rhinovirus (HRV), human coronavirus (CoV) OC43, NL63, and 229E, human metapneumovirus (HMPV), adenovirus (AdV), enterovirus (EV), and 2 bacteria--Mycoplasma pneumoniae and Chlamydophila pneumoniae. Of the total samples, 44.5% (n = 3496) were positive for at least 1 agent, with HRV being the most common (n = 1482, 38.0%), followed by RSV (n = 526, 13.5%) and IfA (n = 403, 10.3%). The diagnostic yield was significantly higher during the winter and early spring compared to the summer (n = 2439 of 4458 samples, 54.7% and n = 1057 of 3395 samples, 31.1%, respectively; p < 0.001). The diagnostic yield was highly dependent on the month of sampling and the age of the patient. However, the overall detection rate per month was above 30%, apart for August and September. Our findings support the use of similar tests in routine clinical care all year round. HRV was the most common finding in the respiratory tract, independent of season.

Epidemiology of Respiratory Infections Caused by Atypical Bacteria in Two Kenyan Refugee Camps

Chlamydia pneumoniae, Mycoplasma pneumoniae, and Legionella spp. are common causes of atypical pneumonia; however, data about these atypical pathogens are limited in the refugee setting. Paired nasopharyngeal and oropharyngeal specimens were collected from patients with respiratory illness presenting to healthcare centers in two refugee camps in Kenya. The specimens were tested for C. pneumoniae, M. pneumoniae, and Legionella spp. as well as eight respiratory viruses. Atypical pathogens were detected in 5.5% of the specimens of which 54% were co-infected with at least one of the eight viruses tested. Patients positive for atypical bacteria co-infected with virus were significantly more likely to have severe acute respiratory illness than patients infected with only atypical bacteria (P = 0.04). While the percentage of atypical pathogens identified was lower than expected, we found a significant relationship between atypical bacterial-viral co-infection and severity of disease in this refugee population.

Epidemiology of viral respiratory tract infections in a prospective cohort of infants and toddlers attending daycare

Background The epidemiology of respiratory tract infections (RTIs) in a daycare cohort has not been explored using molecular techniques. Objectives (1) Determine the overall incidence of RTIs in a daycare cohort using real-time reverse transcriptase polymerase chain reaction (RT-PCR). (2) Determine the relative incidence and impact of specific respiratory viruses, and characterize and compare clinical features associated with these pathogens. Study design In this prospective cohort study conducted from February 2006 to April 2008, nasal swabs were obtained from symptomatic children ages 0–30 months enrolled in fulltime daycare. RT-PCR was performed to detect respiratory syncytial virus (RSV), human metapneumovirus (MPV), influenza (Flu) viruses A and B, parainfluenza (PIV), adenovirus (AdV), human coronaviruses (CoV) and rhinovirus (RhV). Symptom diaries were completed for each illness. Results We followed 119 children (mean age 10 months; range 2–24 months) for 115 child years. The mean annual incidence of RTI per child was 4.2 the first year and 1.2 the second year of the study. At least 1 virus was identified in 67% RTIs. Co-infections were common (27% RTIs), with RhV, CoV, and AdV the most common co-pathogens. PIV was identified in 12% of RTIs with a high incidence of PIV4. The viruses with the greatest impact on our population were RSV, RhV and AdV. Conclusions Using molecular techniques, viruses were identified in approximately twice as many RTIs as previously reported in a daycare cohort. Infections with newly identified viruses, such as HMPV and CoV subtypes were less frequent and severe than infections with RSV, AdV and RhV.

The epidemiology of respiratory tract infections.

Respiratory tract infections (RTIs) are the most common, and potentially most severe, of infections treated by health care practitioners. Lower RTIs along with influenza, are the most common cause of death by infection in the United States. Risk factors for pneumonia and other respiratory tract infections include: extremes of age (very young and elderly), smoking, alcoholism, immunosuppression, and comorbid conditions. The microbial cause of RTIs vary depending on the infection (i.e., pneumonia compared with acute bacterial sinusitis), setting (i.e., community-acquired compared with nosocomial), and other factors. The causative pathogens associated with CAP have changed in prevalence over time. Although Streptococcus pneumoniae remains the most common causative pathogen, a number of newer pathogens, such as Chlamydia pneumoniae and sin nombre virus, have been recognized in recent years. The emerging antimicrobial resistance of respiratory pathogens (most notably S. pneumoniae) has also increased the challenge for appropriate management of RTI. An awareness of the epidemiology and cause of specific respiratory infections should optimize care.

The epidemiology of respiratory infections in children

The epidemiology of respiratory infections in children