Acute bronchitis is an inflammation of the large airways that is characterized by cough and/or sputum that usually lasts one to three weeks. It is one of the most common illnesses among outpatients, and many patients receive antibiotic therapy [1–3].

Traditionally, viruses have been considered the main causative agent of acute bronchitis, possibly explaining the limited benefits of antibiotics [3–5]. However, data regarding the causative microorganisms are still limited. In previous studies, viruses were isolated in 8–23% of community-based cases, not frequently enough to conclude that viruses are the main causal agents for acute bronchitis. Macfarlane et al. identified viruses in only 19% of patients, while typical and atypical bacteria were identified in 25.9% and 23.7% of patients, respectively. In other studies, bacteria were detected in sputum samples in 45% of acute bronchitis patients [8, 9]. In addition, several authors suggested that some patients with acute bronchitis had mixed infections involving both viruses and bacteria. However, the exact prevalence and clinical characteristics of mixed infections have not been well studied. Moreover, it is not clear which subgroup of patients with acute bronchitis could benefit from antibiotic treatments. Recent big data from the UK show that antibiotics substantially reduce the risk of pneumonia after acute bronchitis, particularly in elderly people in whom the risk is highest.

Therefore, in the present study, we aimed to investigate the frequencies and characteristics of viral, bacterial, and mixed infections in acute bronchitis in the community. We also hypothesized that the frequencies of these etiologies would vary with underlying lung co-morbidities and age.

Respiratory viruses represent an important role in the etiology of community-acquired pneumonia in adults. Respiratory viruses are also the leading cause of acute exacerbations of chronic obstructive pulmonary disease (COPD)/asthma patients, resulting in frequent consultations with a general practitioner and hospitalisations. In some cases, invasive ventilation is required. The number of studies that document the presence of viruses in respiratory samples of critically ill patients is currently growing in the literature. What is really needed, however, are more data on the clinical significance of these findings, particularly as regards morbidity and mortality.

In a previous work we investigated the incidence of nosocomial viral ventilator-associated pneumonia. The aims of the present study were to determine the epidemiology of and risk factors for virus-positive respiratory samples taken at the time of intubation in acutely ill patients, and to compare clinical outcome (survival and time to ventilated acquired pneumonia) with and without respiratory viruses, according to the presence (group 1) or the absence (group 2) of respiratory disorder at admission.

Metapneumovirus was first recognized in 2001 in the Netherlands from nasopharyngeal aspirates collected during a 20-year period in 28 hospitalized children and infants with acute respiratory tract infection (RTI) having signs and symptoms similar to that of RSV infection. The virus genomic sequence was identified by using a randomly primed PCR protocol and revealed to be closely related to the avian pneumovirus, a member of the Metapneumovirus genus, in the Paramixoviridae family, Initial studies following the first hMPV identification indicate that it causes upper and lower RTIs in patients of all ages, but mostly in children aged below 5 years. A large epidemiological retrospective study examined nasal washes collected over a 20-year period during acute respiratory illnesses in an outpatient cohort of children. Over the entire study period, hMPV was detected in 1%-5% of pediatric upper RTIs (UTRIs), with variation from year to year. Several reports indicate that hMPV is a commonly identified cause of pediatric lower RTIs, and is second only to RSV as cause of bronchiolitis in early childhood. While bronchiolitis, is the most common presentation of hMPV illness, other reported syndromes have included asthma exacerbation, otitis media, flulike illness, and community-acquired pneumonia. Several studies have found hMPV –RSV co-infection rates of approximately 5-14%. Nevertheless, in a study conducted in the Netherlands in children admitted to hospital for lower RTIs (LRTIs), no virus co-infection between RSV and hMPV was detected. Different controversial reports suggest an association between RSV-hMPV coinfection and an increase in the disease severity or the absence of an association between dual infection and disease severity. Greensill and colleagues reported a 70% rate of co-infection with hMPV in a cohort of infants with critical RSV bronchiolitis who required intensive care in the United Kingdom, suggesting that dual infection with RSV and hMPV may predispose for a more severe disease. In another study from the United Kingdom, hMPV and RSV co-infection was associated with increased disease severity and higher risk of admission to the pediatric intensive care unit. Similar findings are supported by other studies suggesting that in young children, coinfections with RSV and hMPV are more severe than infections with either RSV or hMPV alone, requiring a longer hospitalization and supplemental oxygenation. However, such synergistic association has not been found in other population-based and case–control studies of hospitalized children. In particular, two studies evaluated the epidemiology of hMPV coinfection in children with LRTI caused by RSV and demonstrated no hMPV and RSV co-infection in mechanically ventilated children suggesting that co-infection with hMPV is not associated with a more severe course of RSV-LRTI. In addition, in a prospective 2-year study in hospitalized infants with acute respiratory diseases, the role of RSV as a major respiratory pathogen was not influenced by the co-circulation of other emerging viral agents with similar seasonal distribution. In particular, RSV-hMPVs co-infections were significantly observed in less severe respiratory disease when compared to unique RSV infections. The possible synergistic interaction between hMPV and the severe acute respiratory syndrome (SARS) coronavirus was also suggested during the 2003 SARS outbreak in Hong Kong and Canada. In one case report, in an infant with SARS CoV infection, fatal encephalitis was correlated with hMPV infection as hMPV RNA was detected post-mortem in brain and lung tissue. Nevertheless, in experimental studies performed in macaques, a synergy between hMPV and SARS was not confirmed. In addition, infections of hMPV with respiratory viruses different from RSV, have also been occasionally reported but no sufficient data are available to discuss epidemiology or association with clinical disease presentation (Table 1).

Adult patients with acute bronchitis were prospectively recruited at 31 Korean hospital outpatient departments and primary clinics between July 2011 and June 2012 (6 university-affiliated teaching hospitals, 5 non-teaching community hospitals, and 20 primary clinics). Sputum samples for Gram stains, conventional cultures, and polymerase chain reaction (PCR) were collected from each patient before any medications (including antibiotics) were prescribed. Medications were chosen at the physicians’ discretion. The study protocol was approved by the Institutional Review Board of Hallym University Sacred Heart Hospital (the principal institute, 2011-I049) and each participating hospital. All participants provided informed written consent.

Patients were eligible if they were ≥18 years old and visited the outpatient clinic because of cough (duration < 1 month) with sputum production. Acute bronchitis is a clinical diagnosis, and therefore, a wrong diagnosis is possible. Coughing symptom may have almost all respiratory illnesses as a differential diagnosis. However, symptoms such as sputum production, after carefully discriminating from postnasal drip, could also lead to a diagnosis of lower respiratory inflammation. Patients with typical upper respiratory infection (URI) and symptoms of influenza or influenza-like illness (ILI) during the epidemic period were excluded by participating physicians. We tried to rule out URI by conducting detailed medical interviews, throat examination, and by auscultation. Typically, URI was defined as an infection affecting patients presenting with key symptoms such as sore throat, and nasal symptoms (nasal obstruction, runny nose) with cough. ILI was defined as an abrupt onset of fever with non-productive cough or sore throat. The period of the influenza epidemic was determined by means of a national respiratory virus surveillance system which was broadcast weekly. In some cases, chest radiographs were done at the investigating physician’s discretion, in order to rule out pneumonia. Other exclusion criteria were: 1) history of antibiotic treatment < 7 days before the visit, 2) exacerbation of chronic lung disease within 6 months, 3) active lesion on the chest or paranasal sinus radiographs (when available), 4) immunocompromised status, and 5) confirmed alternative cause for the cough (e.g., drugs [newly started on angiotensin-converting enzyme inhibitors], pneumonia, allergic rhinitis, sinusitis, or gastro-esophageal reflux). Stable chronic lung disease patients were not excluded.

Patient characteristics recorded at the time of intubation included age, sex, main reason for ICU admission, scoring of disease severity within the first day in the ICU – assessed by the admission Simplified Acute Physiology Score type II, the Acute Physiology and Chronic Health Evaluation II score and the admission logistic organ dysfunction system – and concomitant diseases such as immunocompromised status defined as HIV infection, neoplasia, innate immunity deficit, cystic fibrosis, chronic use of steroids or immunosuppressive drugs. Other comorbidities such as diabetes, COPD/asthma or cardiovascular diseases were also recorded at admission.

The main reasons for ICU admission (defined on enrolment without the knowledge of viral assessment) included cardiac arrest, septic shock, cardiac shock, mixed shock, hemorrhagic shock, respiratory distress alone (without other associated organ failure), acute renal failure, coma, intoxication, surgery and other. In addition, clinical outcomes assessed by the occurrence of ventilator-associated pneumonia and death were recorded.

According to French legislation at the time of the study and given the observational nature of our study, no ethical committee approval was requested and thus no informed consent was obtained from the patients.

Following the discovery of SARS-CoV, other human coronaviruses, HCoV-NL63 and HCoV-HKU1, were identified and recognized to be common causes of community-acquired respiratory infections.

HCoV-NL63, a member of the group I coronaviruses, was first detected in 2004 in the Netherlands from a child with bronchiolitis by using a new method for virus discovery based on the cDNA-amplified restriction fragment−length polymorphism technique (cDNA-AFLP).

HCoV-HKU1, a group II coronavirus, was first detected in Hong Kong in 2005 from an adult patient with chronic pulmonary disease. All attempts to grow a virus from his respiratory secretions failed until recently, but coronavirus RNA was initially detected by RT-PCR using pol gene consensus primers.

Like other coronaviruses, NL63 and HKU1 can also be detected in individuals of all ages, including elderly patients with fatal outcome and those with underlying diseases of the respiratory tract. However most frequently, the newly discovered coronaviruses are reported in 7 to 12-month old children with both upper and lower RTIs. In studies conducted in children hospitalized with RTIs in China, from 2.6% to 3.8% of patients were positive for HCoV-NL63 and, in addition to causing upper respiratory disease, HCoV-NL63 was found in croup, asthma exacerbation, febrile seizures, wheezing and high fever cases. The occurrence of co-infection with NL63 and other respiratory viruses, including other human coronaviruses, RSV, PIV, influenza A and B viruses and hMPV has been reported. In a large study from Germany evaluating children under 3 years of age with LRTIs, most co-infections were with RSV-A, probably because of the high percentage of RSV-A infections and an overlap in seasonality. In addition, double infection of NL63 with RSV-B, and with PIV3 occurred in a minority of cases. HCoV-NL63 co-infection with RSV-A occurred predominantly in the hospitalised patients in contrast to HCoV-NL63 co-infections with PIV3 that were exclusively present in the outpatient group.

Following the first identification, HKU1 was found in respiratory samples from elderly patients and children mainly with underlying diseases. The most common symptoms are rhinorrhea, fever, and abdominal breath sounds, but pneumonia, bronchopneumonia, bronchiolitis, and acute asthma exacerbations were also described in children in China.

In a study aimed to evaluate the overall prevalence of 10 respiratory viruses in children with acute LRTIs in China from 2006 to 2009, 73.47% of the HCoV-HKU1 and HCoV-NL63-positive samples tested positive for at least one other virus, most commonly HRV and RSV. Similar data describing a high rate of coinfection of coronaviruses with RSV has also been previously reported. In a report from the UK both dual and single infections associated with respiratory outcomes were observed for HKU1 as well as for NL63 and OC43 coronaviruses. In this study a high number of coinfections was observed for HKU1, NL63 as well as for OC43, mostly with RSV. Similar rates of lower and upper infections were observed in single HKU1 or OC43 infection compared with coinfection, whereas both URTI and LRTI were observed more frequently in single compared to mixed infection with NL63. No differences in clinical outcome were observed between single and dual infections with RSV and Coronaviruses NL63, HKU1 or OC43 indicating that RSV may presumably facilitate coronavirus infection without increasing disease severity. However, in the same study considering viral load data, a role of these coronaviruses in coinfections in respiratory disease was suggested. In fact no differences were observed when coronavirus load was evaluated in single infection and in RSV coinfection, indicating both that infection with another respiratory virus does not affect the ability of NL63, HKU1 or OC43 to establish infection and replicate, and that detection of coronaviruses in mixed infection should not be considered a secondary infection without contribution to disease pathogenesis. This quantitative evaluation is in contrast with previous results obtained by van der Hoek and colleagues describing a significantly lower HCoV-NL63 viral load in patients coinfected with RSV or PIV3 than in patients infected with HCoV-NL63 alone. However, the prolonged persistence of HCoV-NL63 at low levels, the different time of sampling relative to the time of disease onset, or the use of different diagnostic technologies could have affected these evaluations (Table 1).

EV-D68 preferentially causes severe respiratory symptoms in children and adults that have a prior history of asthma. Thus, in addition to naïve mice, HDM-sensitized and -challenged mice also been studied. In mice with allergic airways disease, EV-D68 enhances allergen-induced type 2 inflammation with increased expression of lung IL-5, IL-13 and Muc5ac and augmentation of bronchoalveolar lavage fluid eosinophils and airway responsiveness.

Acute lower respiratory tract infections (LRTIs) are responsible for significant morbidity and mortality in infants and young children worldwide. Childhood pneumonia accounts for 16% of all deaths of children under 5 years of age and 7–13% of all community cases are life-threatening and require hospitalization. The most common causes of acute LRTIs with divergent presentation are viruses. Respiratory syncytial virus (RSV) is the most common viral cause of pneumonia in young children [1, 2].

Human bocavirus 1 (HBoV1), the second human pathogenic virus in the family Parvoviridae, was discovered in 2005 in nasopharyngeal aspirates (NPAs) of children with acute respiratory tract infection (ARTI). Since then, HBoV1-associated ARTIs have been reported worldwide.

On the one hand, there are studies showing evidence of HBoV1 as a pathogen in association with LRTIs, mainly in children up to 3 years of age [5–10]. On the other hand, HBoV1 has also been found in asymptomatic children [11–14]. These states of affairs at first may seem contradictory; however, HBoV1 has been shown to remain in the nasopharynx for several weeks and even months, thereby causing clinically false polymerase chain reaction (PCR) diagnoses. Moreover, life-threatening and even fatal HBoV1 infections have been reported [15–19]. The definition and diagnosis of acute HBoV1 respiratory tract infection is challenging. Detection of HBoV1 deoxyribonucleic acid (DNA) in blood, messenger ribonucleic acid (mRNA), and viral load assessment in respiratory samples and serology have been recommended as the markers to diagnose active HBoV1 infection [6, 7, 20, 21]. According to the best of our knowledge, there are no studies up to now showing detection of HBoV1 mRNA in the peripheral blood mononuclear cells (PBMCs) as a diagnostic marker for acute HBoV1 infection.

In this study, we report an acute HBoV1 infection in an otherwise healthy child with life-threatening acute bilateral bronchiolitis and right-side pneumonia with detected HBoV1-specific immunoglobulin (Ig) M and DNA in cell-free blood plasma as well as HBoV1 mRNA in PBMC.

To evaluate the presence of noninfluenza respiratory viruses circulating in Mexican population in the different seasons of the year, we analized every pharyngeal exudate sample received by the Laboratorio Central de Epidemiología (LCE) (Central Epidemiology Laboratory) between the epidemiological week 40 of 2014 and the week 39 of 2015, according to the following criteria.

All samples had a previous negative result for influenza by RT-qPCR and met one of the following operational case definitions:

Influenza-like illness (ILI): A person of any age who presents a fever greater than or equal to 38°C, a cough, and cephalalgia accompanied by one or more of the following symptoms: rhinorrhoea, coryza, arthralgias, myalgias, prostration, odynophagia, thoracic pain, abdominal pain, or nasal congestion. In patients under five years of age, irritability is considered a cardinal sign in place of cephalalgia. In patients older than 65 years, fever is not required as a cardinal symptom.

Severe acute respiratory infection (SARI): A person of any age who presents difficulty breathing accompanied by a fever greater than or equal to 38°C and a cough with one or more of the following symptoms: poor general condition, thoracic pain, polypnoea or acute respiratory distress syndrome (ARDS) or any death associated with ILI or SARI.

A total of 872 samples were selected. (S1 Table)

The study population comprised all children between the first month of life and 14 years of age with a respiratory tract disease admitted to the secondary public hospital Severo Ochoa (Leganés, Madrid), between September 2005 and June 2014 which corresponded to nine consecutive seasons. All patients were evaluated by an attending physician. Clinical characteristics of patients were analyzed. During the hospital stay, and as part of the study, a physician filled out a study questionnaire with the clinical data.

Upper respiratory tract infection (URTI) was diagnosed in patients with rhinorrhea and/or cough and no signs of wheezing, dyspnea, crackles or bronchodilator use, with or without fever. Acute expiratory wheezing was considered to be bronchiolitis when it occurred for the first time in children aged less than 2 years following the McConnockie classical criteria. All other episodes of acute expiratory wheezing were considered to be recurrent wheezing. Asthma was diagnosed by the National Asthma Education and Prevention Program guidelines. Laryngotracheobronchitis was associated with inspiratory dyspnea and wheezing. Laryngitis was related to inspiratory dyspnea without wheezing. Cases with both focal infiltrates and consolidation in chest X-rays were, in the absence of wheezing, classified as pneumonia.

Acute respiratory infections (ARIs) represent the leading cause of morbidity and mortality worldwide [1–2], are the most common cause of outpatient care in adult patients, and are responsible for 70% of hospitalisations due to respiratory diseases in child populations aged 1–4 years and up to 90% in infants under 1 year of age.

ARIs are a group of diseases with normally less than 15 days of evolution that are caused by different microorganisms. A viral aetiological agent is estimated to be present in up to 80% of cases [5–7]. These infections can occur in the upper and lower respiratory tract. Upper ARIs may include one or more of the following conditions: rhinopharyngitis, pharyngoamygdalitis, sinusitis, and acute otitis media [8–9]. Lower ARIS include epiglottitis, laryngitis, laryngotracheobronchitis (croup), bronchitis, bronchiolitis, and pneumonia.

These infections are easily transmitted via coughing or sneezing. Contagion occurs through the inhalation of aerosols and microdroplets that contain the causative agent. Another important form of contagion is through direct contact of hands with objects contaminated with respiratory secretions from infected individuals, which can be self-inoculated into the nasal and buccal mucosae and/or into the ocular cavity.

A large amount of information is available concerning the timing and distribution of influenza viruses in the population following the reappearance of avian influenza A subtype H5N1 in 2003 and 2004 and the influenza A subtype H1N1 pandemic in 2009. Influenza viruses are one of the main causative agents of ARIs worldwide; however, many other respiratory viruses for which insufficient epidemiological information is available can also cause ARIs.

Studies performed at the international level have frequently identified human respiratory syncytial virus (HRSV), human parainfluenza virus (HPIV), influenza virus (flu), human mastadenovirus (HMdV), rhinovirus (RV), and enterovirus (EV) and less frequently identified human metapneumovirus (HMPV), primate bocaparvovirus (PBpV), and human coronavirus (HCoV). These viruses can serve as the causative agents for ARIs that occur outside of influenza season, when the rate of positivity can drop below 10%.

Although a large percentage of ARIs are caused by viral infections, the causative viruses have not been specifically identified in the majority of cases due to difficulties such as the high number of possible aetiological agents, similar symptoms among ARIs caused by different aetiological agents, the emergence of new viruses or new variants of previously described viruses, and the high cost of the detection tests. Thus, little information is available concerning the prevalence and seasonality of these viruses, mainly in undeveloped countries, where the possibilities of carrying out this type of study on a regular basis is unusual.

The investigation of the causative agents of acute respiratory infections is important in order to lead the development of vaccines to target the most prevalent viruses and to reduce the unnecessary prescription of antibiotics and of antiviral oseltamivir phosphate. In addition, analysis like this can help to identify the age groups more susceptible to infection by each virus, in order to take the necessary actions for prevention and treatment.

Therefore, our aim was to determine the viral aetiology of ARIs in samples from patients who presented respiratory symptomatology but were negative for influenza by RT-qPCR testing.

Human respiratory syncytial virus (RSV) is the major cause of serious respiratory disease in infants and young children, usually manifested as a bronchiolitis with wheezing. RSV also produces significant morbidity and mortality in elderly and immune compromised adults. Most infants are infected by 2 years of age, with the incidence of severe disease peaking between 6 weeks and 6 months. RSV regularly re-infects older children and adults, causing colds and, in patients with chronic lung disease, exacerbations of asthma or COPD. As noted above, infants experiencing community RSV infection suffer from asthma-type symptoms like cough and wheeze which resolve by 13 years of age. However, infants with severe RSV bronchiolitis requiring hospitalization may have an increased frequency of asthma in later childhood.

Human RSV is a member of the Pneumoviridae family, Orthopneumovirus genus, along with closely related Orthopneumoviruses, including bovine RSV, ovine RSV and pneumonia virus of mice (PVM). Orthopneumoviruses are enveloped viruses with the genome organized with a negative-sense, non-segmented RNA, which is about 15,000 nucleotides in length and encodes for 11 viral proteins. A two-step process is used for RSV entry, a viral glycoprotein-mediated attachment step and a fusion step through binding of the viral fusion protein (F protein) to the receptor nucleolin. In the lower airway, the airway epithelium is the primary infection site and macrophages in the lung may be infected as well.

The study was approved by The Medical Ethics Committee of the Instituto de Salud Carlos III. Informed written consent was obtained from parents or legal guardians.

acute renal failure in a previously vaccinated cystic fibrosis

patient

Respiratory tract infections are one of the most common causes of disease and in humans and for absenteeism in healthcare workers.1,2 In Canada, influenza-like illness consultation rates ranged from 15 to 20 per 1000 patients in the 2005–2006 and 2006–2007 influenza seasons, with 7–15% of illness caused by influenza.3,4 The primary tool for preventing influenza is annual vaccination. Osterholm et al.5 report that the efficacy of the trivalent inactivated influenza vaccines in eight randomized controlled trials of adults 18–65 years of age was 59%. Neuraminidase inhibitors may also be effective in preventing influenza, with estimated efficacy of 31–83% in placebo-controlled trials.6–8 Healthcare workers providing direct patient care may be at increased risk of developing influenza compared to other healthy adults9,10 and may transmit the disease to vulnerable patients making them a priority group for influenza vaccines and, in the event of a pandemic, for antiviral medication.11,12

During the 2008–2009 influenza season, this pilot study determined the adherence to antiviral medication for an influenza season, the relative efficacy of antiviral prophylaxis with zanamivir and seasonal influenza vaccine against laboratory-confirmed influenza infection, and determined risk factors for acute respiratory illnesses (ARI) among healthy adults.

A 17-month-old Latvian boy was admitted to the Children’s Clinical University Hospital of Riga, Latvia, on the seventh day of illness in January 2015. He presented with a history of rhinorrhea and cough for 6 days and fever (axillar temperature 39.0 °C) for the last 2 days prior to admission. Due to severe respiratory distress, he was immediately transferred from the regional hospital to our intensive care unit.

On admission, his respiratory rate was 44 breaths/minute (reference 20–30), heart rate 146 beats/minute (reference 80–130), oxygen saturation 99% (with an oxygen flow of 5 liters/minute via face mask), and axillary temperature 38.7 °C. Auscultation of his lungs revealed bilateral wheezing and crepitation with severe intercostal and subcostal recessions. The other organ systems were without pathology. Due to the severe respiratory distress, tracheal intubation was performed.

The child had been born full term as the seventh in the family. He had no known underlying illness, history of previous hospitalizations, or severe acute illnesses. He had been fully immunized according to the national immunization scheme.

On admission, his white blood cell (WBC) count was 30.6 × 103/μL with 66.9% of granulocytes (in absolute numbers 20.6 × 103/μL), hemoglobin 12.4 g/dL, and platelet count 321 × 103/μL. His C-reactive protein (CRP) was 5.09 mg/L. A chest radiograph showed infiltration of the upper lobe of his right lung (Fig. 1).

At the time of admission, a nasopharyngeal swab (NPS) tested negative by direct immunofluorescence (IMAGEN™ OXOID, UK) for antigens of RSV, influenza virus A and B, parainfluenza virus types 1–3, and adenovirus. Bacterial blood cultures were negative. NPA, blood, and stool samples were collected for HBoV1 molecular diagnostics and serology.

NPA tested by qualitative multiplex PCR (Seegene Respiratory Panel, South Korea) was negative for: influenza virus A and B; RSV A and B; flu A types H1, H1pdm09, and H3; adenovirus; enterovirus; parainfluenza virus types 1–4; metapneumovirus; rhinovirus; and coronavirus types NL63, 229E, and OC43. However, the NPA tested by qualitative multiplex PCR was positive for HBoV1. NPA, whole blood with corresponding cell-free blood plasma, and stool samples underwent qualitative PCR for HBoV1 NS1 DNA, as described. An HBoV1-containing plasmid was used as a positive control in PCR. All these samples were HBoV1 DNA positive. Upon re-examination by quantitative PCR (qPCR) (Human bocavirus genomes, Standard kit, Genesig, Primerdesign Ltd., UK), the copy numbers in NPA and stool were high, 5.7 × 105 per μg DNA in NPA and 1.4 × 108 per μg DNA in stool. The viral load in blood was 21 copies/μg DNA, but in cell-free blood plasma the viral load was under detection level.

To prove that the HBoV1 infection was actively ongoing, HBoV1 transcription in PBMCs was applied. Total ribonucleic acid (RNA) was extracted from PBMCs using TRI Reagent® solution according to the manufacturer’s instructions (Thermo Fisher Scientific, USA). The extracted RNA was quantified spectrophotometrically and analyzed by electrophoresis in a 1% agarose gel. RNA was treated with DNase (TURBO DNA-free™ Kit, Thermo Fisher Scientific, USA) before the synthesis of complementary DNA (cDNA) by the reverse transcriptase (RT) using RevertAid™ First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, USA). The β-actin gene sequence was detected by PCR to assess the quality of synthesized cDNA (Fig. 2).

HBoV1-specific cDNA was detected by PCR targeting the HBoV1 NS1 gene as described by Sloots et al., in 2006, followed by electrophoretic visualization of the amplification products in a 1.7% agarose gel (Fig. 3). The same DNase-treated RNA sample but without the RT step, served as a negative control in both the β-globin and HBoV1 PCRs to make sure that there was no contamination with DNA.

Biotinylated virus-like particles (VLPs) of the recombinant major capsid protein VP3 were used as antigen in enzyme immunoassays (EIAs) for detection of HBoV1-specific immunoglobulin M (IgM) and immunoglobulin G (IgG) in our patient’s plasma sample [23, 24]. For removal of possible cross-reacting heterologous human bocavirus 2 (HBoV2) and human bocavirus 3 (HBoV3) IgG, non-biotinylated VLPs in competition assays were used as described. Our patient’s plasma sample was positive for both HBoV1-specific IgM and IgG antibodies.

Because of the right lung upper lobe infiltration and increased WBC initially, the child was treated with intravenously administered ceftriaxone 350 mg twice a day for 7 days and per-oral oseltamivir 30 mg twice a day (due to influenza season). Oseltamivir was discontinued after 3 days due to the negative influenza virus A and B antigen findings. Extubated on day 3, our patient was brought to the Department of Paediatrics, where intravenously administered ceftriaxone was continued, inhalations via nebulizer with salbutamol and budesonide were begun and pulmonary rehabilitation started. During the next 10 days, the child’s general condition improved, his body temperature was normal, lung sounds were without the pathology, and no additional oxygen was needed. During the hospitalization, poor weight gain was observed for our patient; therefore, additional diagnostic tests were done and his hospitalization length increased. On day 17 of hospitalization, he developed a new episode of fever for 2 days. The second NPS tested negative for RSV, and influenza virus A and B; however, self-limiting viral upper respiratory tract infection was suspected and he was treated with intravenously administered rehydration and ibuprofen 70 mg for these 2 days. Due to the very low socioeconomic status of the family, he was kept in the hospital mainly for observation, although his general condition was good. On day 30 he developed a new episode of fever, cough, and wheezing lasting 6 days. In this episode, LRTI was diagnosed based on the clinical symptoms and he was treated with nebulized salbutamol and budesonide.

After 46 days of hospitalization he recovered completely from HBoV1-associated acute bilateral bronchiolitis with right-side pneumonia and a subsequent hospital-acquired upper and LRTI and was discharged.

Human bocavirus (HBoV) (genus Bocavirus, family Parvoviridae) has been recently identified in children with respiratory tract infection (RTI), first in Sweden, and subsequently in different parts of the world [2–10]. However, most studies so far have only retrospectively studied virus prevalence and only a few have addressed whether HBoV infection is associated with respiratory disease symptoms.

The aim of the present study was to define the epidemiological profile and the clinical characteristics associated with HBoV in hospitalized children with respiratory tract infection (RTI) in Greece.

HBoV DNA was detected in samples of 12 children (3.3%), 6 of them males. Sequencing and phylogenetic analysis revealed that HBoV sequences of 11 cases were identical to each other and to the Swedish strain st2 (NC007455), differing by 1 nucleotide from the 12th case (GR186), which was identical to strain CHSD4 (DQ471814) from USA.

All cases had clinical evidence of lower RTI (fever, tachypnoea, hypoxia, retractions, and abnormal auscultation findings). Four of the 12 cases were co-infections, 3 of them with influenza A virus and 1 with coronavirus OC43.

Concerning the 8 patients in whom only HBoV was detected, they were 3 males and 5 girls, aged 2–33 months (mean age ± SD: 17 ±9 months), hospitalized with the clinical diagnosis of 2 each: laryngotracheobronchitis, bronchiolitis, pneumonia, and asthma exacerbation.

Common symptoms of viral respiratory tract infection such as fever, cough, rhinorrhoea and pharyngitis were found in the majority of our patients (87.5–100%). Six patients (75%) presented with various degrees of respiratory distress. Those patients had tachypnoea (a respiratory rate of 45–90 breaths/min) and low haemoglobin oxygen saturation levels (SaO2) in the range 90–94%. These children received oxygen supplementation until 1 day before discharge. Wheezing was the most common clinical finding (5 patients) while another 1 child presented with stridor. Hoarseness was noticed in 2 children. Difficulty in feeding was also a common complaint, reported by 5 patients. Other clinical findings included diarrhoea (2 patients, 25%), a symptom previously described in HBoV infections [11, 12], and otitis media (1 patient, 12.5%). The major clinical and laboratory findings in the 8 patients in whom HBoV was the sole pathogen detected are presented in Table I.

Chest X-rays were available for all 8 children. The most common finding, present in 6 patients, was bilateral interstitial infiltrates. Consolidation was detected in the other 2 children.

Clinical expression was not different in children with HBoV co-infection. The child with coronavirus OC43 co-infection also presented with conjunctivitis, while respiratory distress was the main concern in a child with influenza-A virus co-infection.

All children recovered uneventfully. The median hospitalization time was 5 days (range 4-9 days). For 1 patient a second throat swab sample, taken 20 days after the first one, was found negative for HBoV DNA.

Dampness and mold in buildings have been associated in many studies with adverse respiratory health effects. A number of qualitative summaries of this literature are available. In their review, the Institute of Medicine (IOM) of the National Academy of Sciences found sufficient evidence to document an association between qualitatively assessed indoor dampness or mold and upper respiratory tract symptoms, cough, wheeze, and asthma symptoms in sensitized persons. A later review by the World Health Organization (WHO), including additional studies, expanded the documented associations to include asthma development, current asthma, dyspnea, and respiratory infections. While both reviews concluded that excessive indoor dampness was an important public health problem meriting prevention and remediation, neither review produced quantitative summaries of association between dampness or mold and specific health outcomes.

Two prior quantitative meta-analyses have been published on indoor dampness and mold and selected health effects. In 2007, Fisk et al. quantitatively summarized the associations of home dampness and mold with a set of respiratory and asthma-related health effects, based on available studies published in peer-reviewed journals in English. Health outcomes included were upper respiratory tract symptoms, cough, wheeze, asthma diagnosis ever, current asthma, and asthma development. The meta-analyses produced central estimates of ORs ranging from 1.34 to 1.75 for these health outcomes, with 95% confidence intervals (CIs) excluding the null in nine of ten instances. Antova et al. analyzed pooled data from 12 European cross-sectional studies of visible mold in residences and respiratory or allergic health outcomes of children. Outcomes included bronchitis, wheeze, asthma, nocturnal dry cough, morning cough, sensitivity to inhaled allergens, hay fever, and "woken by wheeze." Central estimates of ORs ranged from 1.30 to 1.50, with all 95% CIs excluding the null.

Thus while prior non-quantitative reviews have reported consistent associations between dampness or mold and respiratory infections, no quantitative meta-analysis of this relationship has been reported. A substantial number of epidemiologic studies on dampness or mold and respiratory infections are available for this purpose.

Respiratory (tract) infections are generally considered to include infections of the lower and upper respiratory tract, and otitis media. Lower respiratory tract infections include pneumonia, acute bronchitis, and acute exacerbation of chronic bronchitis. While acute bronchitis is generally caused by an infection, chronic bronchitis is generally non-infectious in origin. Upper respiratory tract infections are acute infections of the nose, sinuses, and throat. Otitis media, an infection or inflammation of the middle ear often resulting from a prior upper respiratory tract infection, can be bacterial or viral in origin.

The burden of morbidity and mortality and the financial costs of respiratory tract infections are enormous. Little effective prevention is currently possible outside of two strategies: attempting to avoid contact with or spreading of infectious agents in aerosols, droplets, or surfaces, such as by hand washing, avoiding infected individuals, avoiding face-touching, and covering sneezes; and vaccination for influenza and pneumococcal pneumonia. It is important to determine whether avoidance of dampness and mold can provide another means of reducing respiratory tract infection. As a step toward that goal, we performed a quantitative meta-analysis to summarize findings in the peer-reviewed medical literature on associations between dampness or mold in residences and respiratory tract infections or bronchitis.

A lack of improvement or worsening of symptoms even after 3–5 days of antibiotic therapy for acute rhinosinusitis is considered a treatment failure. The exact cause should be identified when the patient is nonresponsive even to the second-line antibiotic regimen as well as in cases of recurrent rhinosinusitis, defined as more than four episodes of acute rhinosinusitis per year with symptom-free intervals.

Potential causes include chronic rhinosinusitis, allergic rhinitis, abnormal anatomical structure within the nasal cavity, reduced immunity, fungal infection, granuloma, and tumor. For accurate differentiation of the cause and administration of appropriate treatment, the patient must be referred to a specialist who can perform nasal endoscopy and, when necessary, imaging tests such as CT and MRI.

Paranasal sinuses are in close proximity to the orbits laterally and to the base of the skull superiorly. Therefore, an infection in the sinuses may spread to the orbits and cranium, causing fatal diseases such as cellulitis, cerebromeningitis, and abscess. A lack of proper antibiotic therapy and surgical drainage may lead to blindness, brain injury, and in severe cases, to death.

Severe ocular pain, periocular edema, oculomotor disability, exophthalmos, purulent conjunctivitis, and reduced visual acuity in patients with acute rhinosinusitis are suggestive of ocular complications whereas high fever, severe headache, meningeal irritation sign, and insanity are suggestive of intracranial complications. Patients with such conditions must be referred to a specialist immediately.

Table 8 shows a comparison of the recommendations pertaining to acute sinusitis of the present guideline, IDSA (2012), American Academy of Otolaryngology-Head and Neck Surgery (2015), American Academy of Pediatrics (2013), and Korean Guideline for Antibiotics Usage in Children with Acute Upper Respiratory Infections (2016).

Overuse and inappropriate use of antibiotics drive the emergence and spread of antimicrobial resistance [1, 2]. In the Republic of Korea, the number of antibiotic prescriptions is relatively higher (31.7 defined daily dose [DDD] per 1000 inhabitants per day) than in other member countries of the Organization for Economic Co-operation and Development (mean, 23.7 DDD per 1000 inhabitants per day). In Korea, the majority of antibiotics (ca. 90%) are prescribed in primary care and mainly for acute respiratory tract infections (ARTIs; ca. 57%). ARTIs are mainly viral in origin, are generally self-limiting, and do not require antibiotics [5, 6]. Secondary bacterial pneumonia is the most important clinical complication of respiratory viral infections. However, previous studies have shown that antibiotics do not improve outcomes for patients with ARTIs [7–10].

To prevent overuse and inappropriate use of antibiotics, it is essential to identify and understand antibiotic prescribing patterns and determining factors, however, little is known about antibiotic prescribing patterns in the Republic of Korea. The purpose of this study was to describe antibiotic prescription patterns in primary care clinics over a 6-year period and to identify its temporal relationship with respiratory viruses and ARTIs.

Most cases of acute pharyngotonsillitis are viral. Currently known respiratory viruses include rhinovirus, adenovirus, influenza virus, parainfluenza virus, coxsackievirus, coronavirus, echovirus, respiratory syncytial virus, and metapneumovirus. These conditions should be differentiated from infectious mononucleosis, which is caused by Epstein–Barr virus (EBV) generally among young adults, acute human immunodeficiency virus (HIV) infection, cytomegalovirus infection, and herpes simplex virus infection. Universal use of antibiotics for patients with sore throat is beneficial in terms of shortening the length of acute pharyngotonsillitis symptoms and reducing the frequency of bacterial complications; however, such use may heighten the prevalence of side effects and facilitate the spread of antimicrobial-resistant bacteria, thereby increasing medical costs. Therefore, antibiotic prescription should be avoided for acute viral pharyngotonsillitis and appropriate antimicrobial therapy should be administered for acute bacterial pharyngotonsillitis based on aggressive differentiation of the causative pathogen in the clinical setting.

The most common cause of acute bacterial pharyngotonsillitis is S. pyogenes, which accounts for 5–15% of all cases of acute bacterial pharyngotonsillitis in adults. S. pyogenes-induced acute pharyngotonsillitis may lead to acute suppurative complications, such as otitis media and peritonsillar abscess, as well as non-suppurative complications, such as rheumatic fever and acute glomerulonephritis; therefore, prompt diagnosis and appropriate antimicrobial therapy are necessary. Although acute rheumatic fever is considerably less prevalent today, its clinical significance is substantial. Group C or G beta-hemolytic streptococci, C. pneumoniae, M. pneumoniae, Arcanobacterium haemolyticum, Corynebacterium diphtheriae, Fusobacterium necrophorum, Neisseria gonorrheae, Treponema pallidum, and Francisella tularensis are also rare pathogens of acute pharyngotonsillitis.

History-taking and physical examination, throat swab culture, and rapid antigen tests are helpful in differentiation of the causative pathogen for acute pharyngotonsillitis. Symptoms such as nasal drainage, nasal congestion, cough, conjunctivitis, hoarseness, diarrhea, oral ulcer, or bullous oral lesions are more suggestive of viral than bacterial acute pharyngotonsillitis. On the other hand, symptoms such as swallowing difficulty (dysphagia), sore throat, fever, headache, abdominal pain, nausea, vomiting or petechial hemorrhage of the soft palate, enlarged lymph nodes in the neck, and scarlet fever rash suggest acute bacterial pharyngotonsillitis, especially caused by S. pyogenes infection. Although differentiation of the pathogen based on clinical symptoms and signs produces high concordance among physicians, the sensitivity and specificity of predicting positivity in a throat swab culture test ranges from 55–74% and 58–76%, respectively, even among highly experienced physicians.

A variety of clinical prediction tools have been proposed, although these have been associated with limited diagnostic accuracy. In practice, the most commonly used clinical instrument is the Centor criteria. It was first suggested for use in adults in 1981 to score symptoms and signs, and a modified Centor criteria (Mclsaac criteria) with the addition of age criteria was proposed in 1998 (Fig. 1). The modified Centor criteria (McIsaac criteria) is the clinical prediction model to classify the likelihood of S. pyogenes infection (Table 2). Although it varies in relation to the prevalence of S. pyogenes infection, a Centor score of 3 or higher showed a positivity predictive value of 40-60% and a negativity predictive value of 80% on the diagnosis of S. pyogenes infection using a throat swab culture, with 75% sensitivity and specificity. The 2008 National Institute of Health and Care Excellence (NICE) guideline recommends antibiotic prescription for three or more Centor criteria. Prior studies have reported that antibiotic therapy that depends on the presence of three or four Centor criteria was conducive to improving symptoms and preventing complications as well as to reducing inappropriate use of antibiotics. The present guideline recommends that clinicians use the modified Centor criteria.

According to the 2012 guideline published by the Infectious Diseases Society of America (IDSA), it is difficult to differentiate between S. pyogenes-induced pharyngotonsillitis and viral pharyngotonsillitis merely based on clinical manifestations. The guideline recommends a rapid antigen diagnostic test (RADT) or bacterial culture for cases suggestive of S. pyogenes-induced pharyngotonsillitis, except for cases in which a viral disease is highly suspected. Pharyngotonsillitis caused by S. pyogenes is diagnosed when S. pyogenes is identified using an RADT or culture test with a throat swab. A throat swab follows the steps in the Figure 2.

The RADT is a convenient test that can be performed and provides results at the point of care. Its sensitivity and specificity vary depending on the patient and test method, ranging from 65–91% and 62–97%, respectively, compared with a culture test. A throat swab culture can be performed if the RADT is negative, but performing both tests is generally not recommended in adults. If the RADT is positive, the patient can be diagnosed with pharyngotonsillitis caused by S. pyogenes without a bacterial culture. Data on the RADT in Korea generally involve children and most studies have reported that the test is useful. It is necessary that its use be more activated for proper use of antibiotics.

Antistreptolysin O (ASO) titer may be useful in the diagnosis of non-suppurative complications, such as acute rheumatic fever and acute glomerulonephritis. However, as the titer does not reach peak levels until 3–8 weeks of onset and continues to rise for several months, the ASO is not useful for the diagnosis of acute pharyngotonsillitis. In general, patients with acute pharyngotonsillitis have elevated C-reactive protein, total white blood cell count, and neutrophilic granulocyte count. The ASO test has low sensitivity (66–90%) and specificity (45–75%) for diagnosing acute bacterial pharyngotonsillitis in adults. Procalcitonin and erythrocyte sedimentation rate are also not very useful for differentiating acute bacterial pharyngotonsillitis. One report suggested that using both C-reactive protein level (35 mg/L, or 3.5 mg/dL) and the clinical score may be helpful for diagnosing acute bacterial pharyngotonsillitis; however, blood tests are not generally recommended for patients with suspected acute pharyngotonsillitis.

The 2008 NICE guideline suggests antibiotic prescription for S. pyogenes infection depending on the patient's state when the patient has three or more Centor criteria. On the other hand, IDSA recommends that clinicians prescribe antibiotics only after accurate bacteriological diagnosis. The present guideline recommends that antibiotics be prescribed for acute pharyngotonsillitis patients with complications, patients with a modified Centor score (McIsaac score) of more than 3, and patients with a positive RADT. If an RADT cannot be performed, antimicrobial therapy may be considered depending on the modified Centor score (McIsaac score) (Fig. 1).

A recent large-scale cohort study reported that delayed antibiotic therapy led to reductions of suppurative complications similar to those produced by immediate antibiotics therapy .

After 18 months of follow-up, the evolution of the presented case of cystic fibrosis

with advanced lung disease, complicated by infection by influenza A non-H1N1 with

respiratory sepsis, acute respiratory failure and acute renal failure was

favorable.

Mycoplasma pneumoniae infection can cause a number of extrapulmonary manifestations, even in the absence of pneumonia. Extrapulmonary manifestations of M. pneumoniae infection notably involve the central nervous system, gastrointestinal tract, heart, joints, skin, and blood cells. Especially, gastrointestinal manifestations account for 25% of M. pneumoniae infections, which produce nausea, vomiting, abdominal pain, diarrhea, and loss of appetite. However, acute pancreatitis is rarely associated with M. pneumoniae infection, with scarce reports and studies in literature. We report the first case in Korea of a child with acute necrotizing pancreatitis associated with M. pneumoniae infection.

The annual incidence of acute bronchitis increased significantly from 3836 (range, 1964-5665; mean, 3836) per 100,000 individuals in 2010 to 4612 (range, 2440-6034; mean, 4612) per 100,000 individuals in 2015 (p < 0.01) (Fig. 3a). The average incidences of acute bronchitis, acute tonsillitis, acute upper respiratory tract infections, and pneumonia were 4334, 1864, 1526, and 153 per 100,000 individuals, respectively (Fig. 3 (b)).