Introduction: Polymerase chain reaction (PCR) method has improved the diagnosis rates for patients with community-acquired pneumonia (CAP). We aimed to evaluate the bacterial and viral etiology of hospitalized CAP cases and compare clinical and laboratory findings of patients with pure bacterial and bacterial and viral (mixed) infections. Methodology: A total of 55 patients hospitalized with CAP were enrolled into the prospective study between February 2010 and December 2010. Clinical and laboratory follow-up were performed on days 0, 7 and 14. Deep tracheal aspiration samples were examined for bacterial and viral pathogens by multiplex PCR, and standard bacteriological culture method. Results: The etiological identification rate in 50 patients for bacteria, viruses and mixed virus-bacteria combination by PCR were 62%, 4%, 32%, respectively and 60% in 55 patients by bacterial culture method. Streptococcus pneumoniae concomitant with Haemophilus influenzae (36%) and rhinovirus (16%) was very common, whereas atypical pathogens (only Mycoplasma pneumoniae) were rare (6%). Rhinovirus was the most common viral agent (20%). Recently identified viruses, human coronavirus HKU1 and human bocavirus were not detected except for human metapneumovirus (one case). There was no significant difference in terms of mean age, immune status, leukocyte count, Creactive protein (CRP) values, hospitalization duration and CURB-65 score between bacterial and mixed viral-bacterial detections. Advanced age (p < 0.01) and higher CURB-65 score (p = 0.01) were found to be associated with increased mortality. Conclusion: Concomitance of bacterial and viral agents is frequent and resemble with bacterial infections alone. Further studies are needed for the clinical significance of mixed detections.

Background: Influenza virus is one of the most common respiratory pathogens for all age groups and may cause seasonal outbreaks. Our aim was to identify risk groups and factors associated with severe clinical course including mortality in children with influenza-related lower respiratory tract infection (LRTI). Methods: We conducted a retrospective study in children hospitalized with influenza virus LRTI from 2008 to 2018. Data on demographic features, influenza type, viral coinfection, primary and secondary bacterial infections (SBIs), time of onset of antiviral treatment, comorbidities, hospitalization length, pediatric intensive care unit admission/invasive mechanical ventilation (IMV) need and mortality were collected from medical records. Results: There were 280 patients hospitalized with LRTI and median hospitalization length was 9 days. Congenital heart disease, neuromuscular disease, SBIs and late-onset antiviral treatment were independent risk factors for prolonged hospital stay (P < 0.05). Pediatric intensive care unit admission was present in 20.4% (57) of the patients and 17.1% (48) of all patients required IMV. SBIs, lymphopenia, neutrophilia, immunosuppression and human bocavirus coinfection were independent risk factors for IMV support (P < 0.05). Eighteen patients died and immunosuppression, lymphopenia and SBIs were independent risk factors for mortality (P < 0.05). Conclusions: Presence of comorbidity, SBIs, neutrophilia and lymphopenia at admission identified as risk factors for severe influenza infections including need for IMV and death. Although several studies showed that antiviral treatment reduce hospitalization, complications and mortality, there is a lack of prospective trials and patients for antiviral therapy should be carefully chosen by the clinician.

The aim of this study was to investigate the prevalence and seasonal distribution of respiratory viruses in pediatric and adult outpatients and inpatients who were admitted to hospital with the symptoms of upper and lower respiratory tract infections, during a 12-year period. A total of 5102 clinical samples (4372 nasopharyngeal swabs, 316 bronchoalveolar lavages, 219 transtracheal aspirates, 163 nasopharyngeal aspirates, 20 sputum, 10 nasal swabs) examined in our laboratory between January 1st 2002 and July 17th 2014, were evaluated retrospectively. Of the specimens, 1107 (21.7%) were obtained from outpatients and 3995 (78.3%) from hospitalized patients. Of the patients, 2851 (55.9%) were male and 2251 (44.1%) were female, while 1233 (24.2%) were adults and 3869 (75.8%) were children (age range: 1 day - 93 years; median: 3 years). Respiratory samples were investigated for the presence of respiratory syncytial virus (RSV), influenza virus type A and B (INF-A, INF-B), adenovirus (AdV), parainfluenza viruses (PIV types 1-4), human rhinoviruses (HRV), human coronaviruses (HCoV), human metapneumovirus (HMPV) and human bocavirus (HBoV). All specimens were tested by both direct immunofluorescence antibody (DFA) and shell vial cell culture (SVCC) methods. In DFA assay the samples were initially screened by fluorescent-labeled polyclonal antibodies, and the positive ones were typed by using monoclonal antibodies (Light Diagnostics, Merck Millipore, USA). In SVCC, HEp-2, MDCK, A-549 and Vero cell lines were used for the isolation of viruses. In addition to these methods, real-time multiplex PCR methods (RealAccurate®, Respiratory RT PCR, PathoFinder, Netherlands and Seeplex® RV15 ACE Detection, Seegene, South Korea) were used for the detection of respiratory viruses in samples (n= 2104) obtained from 2007 to 2014. Respiratory viruses were detected in a total of 1705 (33.4%) patients, of them 967 (19%) were male and 738 (14.4%) were female. Three hundred and eighteen (18.6%) of the 1705 patients were infected with multiple respiratory viruses. The most frequently observed co-infections were RSV+INF-A (40/318; 12.6%), and RSV+PIV (33/318; 10.4%). The rate of positivity for the respiratory viruses in pediatric and adult groups were 35.4% (1369/3869) and 27.3% (336/1233), respectively (p< 0.000). The most frequently detected virus in pediatric group was RSV (336/1369; 24.5%), followed by influenza viruses (314/1369; 22.9%), PIV (197/1369; 14.4%), HRV (118/1369; 8.6%), AdV (75/1369; 5.5%) and the others (49/1369; 3.6%). On the other hand the most frequently detected virus in adult group was influenza viruses (181/336; 53.8%) followed by AdV (37/336; 11%), RSV (24/336; 7.1%), PIV (24/336; 7.1%), HRV (23/336; 6.8%) and the others (9/336; 2.7%). The rate of multiple virus infections in pediatric and adult groups were 7.2% (280/3869) and 3% (38/1233), respectively. Most of the coinfections (280/318; 88%) were detected in children. Respiratory viruses were detected positive in 40.2% (445/1107) of outpatients, and in 31.5% (1260/399...

The purpose of this study was to evaluate the viral frequency, seasonality, and clinical and demographic features of patients hospitalized with acute bronchiolitis. A cross-sectional, descriptive study was performed in 316 infants younger than 2 years of age who were hospitalized for acute viral bronchiolitis. Respiratory tract infection agents were investigated with polymerase chain reaction (PCR). A total of 316 infants were included in this study. Of the 316 infants, at least one respiratory tract pathogen was detected in 75% (237/316). Respiratory syncytial virus (RSV) was the most common virus identified in 127 infants (40.1%) followed by rhinovirus (n = 78, 24.6%). In this study, where viral agents were determined via PCR in patients who were followed-up due to the diagnosis of acute bronchiolitis, RSV was detected as the most common agent, as in other studies. In almost half of the RSV-positive patients, RSV was accompanied by a second or third agent.

Although only supportive therapies are administered generally in viral infections, viral investigations are important in terms of determining the measures to be taken by determining the causes as well as in terms of establishing a general database. Another benefit of this study would be strengthening clinical approach to patients and decreasing unnecessary antibiotic use.