Episodes of bacterial superinfections have been well identified for several respiratory viruses, notably influenza. In this retrospective study, we compared the frequency of superinfections in COVID-19 patients to those found in influenza-positive patients, and to controls without viral infection. We included 42 468 patients who had been diagnosed with COVID-19 and 266 261 subjects who had tested COVID-19 negative between 26 February 2020 and 1 May 2021. In addition, 4059 patients were included who had tested positive for the influenza virus between 1 January 2017 and 31 December 2019. Bacterial infections in COVID-19 patients were more frequently healthcare-associated, and acquired in ICUs, were associated with longer ICU stays, and occurred in older and male patients when compared to controls and to influenza patients (P < 0.0001 for all). The most common pathogens proved to be less frequent in COVID-19 patients, including fewer cases of bacteraemia involving E. coli (P < 0.0001) and Klebsiella pneumoniae (P = 0.027) when compared to controls. In respiratory specimens Haemophilus influenzae (P < 0.0001) was more frequent in controls, while Streptococcus pneumoniae (P < 0.0001) was more frequent in influenza patients. Likewise, species associated with nosocomial transmission, such as Pseudomonas aeruginosa and Staphylococcus epidermidis, were more frequent among COVID-19 patients. Finally, we observed a high frequency of Enterococcus faecalis bacteraemia among COVID-19 patients, which were mainly ICU-acquired and associated with a longer timescale to acquisition.

There is limited information on the volume of antibiotic prescribing that is influenza-associated, resulting from influenza infections and their complications (such as streptococcal pharyngitis). We estimated that for the Kaiser Permanente Northern California population during 2010–2018, 3.4% (2.8%–4%) of all macrolide prescriptions (fills), 2.7% (2.3%–3.2%) of all aminopenicillin prescriptions, 3.1% (2.4%–3.9%) of all 3rd generation cephalosporins prescriptions, 2.2% (1.8%–2.6%) of all protected aminopenicillin prescriptions and 1.3% (1%–1.6%) of all quinolone prescriptions were influenza-associated. The corresponding proportions were higher for select age groups, e.g. 4.3% of macrolide prescribing in ages over 50 years, 5.1% (3.3%–6.8%) of aminopenicillin prescribing in ages 5–17 years and 3.3% (1.9%–4.6%) in ages <5 years was influenza-associated. The relative contribution of influenza to antibiotic prescribing for respiratory diagnoses without a bacterial indication in ages over 5 years was higher than the corresponding relative contribution to prescribing for all diagnoses. Our results suggest a modest benefit of increasing influenza vaccination coverage for reducing prescribing for the five studied antibiotic classes, particularly for macrolides in ages over 50 years and aminopenicillins in ages <18 years, and the potential benefit of other measures to reduce unnecessary antibiotic prescribing for respiratory diagnoses with no bacterial indication, both of which may contribute to the mitigation of antimicrobial resistance.

From 24 January 2020 to 18 May 2020, Chaoshan took measures to limit the spread of coronavirus disease 2019 (COVID-19), such as restricting public gatherings, wearing masks and suspending classes. We explored the effects of these measures on the pathogen spectrum of paediatric respiratory tract infections in Chaoshan. Pharyngeal swab samples were collected from 4075 children hospitalised for respiratory tract infection before (May–December 2019) and after (January–August 2020) the COVID-19 outbreak. We used liquid chip technology to analyse 14 respiratory pathogens. The data were used to explore between-group differences, age-related differences and seasonal variations in respiratory pathogens. The number of cases in the outbreak group (1222) was 42.8% of that in the pre-outbreak group (2853). Virus-detection rates were similar in the outbreak (48.3%, 590/1222) and pre-outbreak groups (51.5%, 1468/2853; χ2 = 3.446, P = 0.065), while the bacteria-detection rate was significantly lower in the outbreak group (26.2%, 320/1222) than in the pre-outbreak group (44.1%, 1258/2853; χ2 = 115.621, P < 0.05). With increasing age, the proportions of respiratory syncytial virus (RSV) and cytomegalovirus (CMV) infections decreased, while those of Mycoplasma pneumoniae and adenovirus infections increased. Streptococcus pneumoniae, CMV and rhinovirus infections peaked in autumn and winter, while RSV infections peaked in summer and winter. We found that the proportion of virus-only detection decreased with age, while the proportion of bacteria-only detection increased with age (Table 2). Anti-COVID-19 measures significantly reduced the number of paediatric hospitalisations for respiratory tract infections, significantly altered the pathogen spectrum of such infections and decreased the overall detection rates of 14 common respiratory pathogens. The proportion of bacterial, but not viral, infections decreased.

Hong Kong is an intermediate tuberculosis (TB) burden city in Asia Pacific with slow decline of case notification in the last decade. By 24-loci mycobacterial interspersed repetitive units – variable number of tandem repeats genotyping, we examined 534 Mycobacterium tuberculosis isolates collected from culture-positive hospitalised TB patients in a 1.7 million population geographic region in the city. Overall, 286 (75%) were classified as Beijing genotype, of which 216 (76%) and 59 (21%) belonged to modern and ancient sub-lineage, respectively. Only two cases were genetically clustered while spatial clustering was absent. Male gender, permanent residency in Hong Kong and born in Hong Kong or Mainland China were associated with Beijing genotype. The high prevalence of Beijing modern lineage was similar to that in East Asia, which reflected the pattern resulting from population migration. The paucity of clustering suggested that reactivation accounted for most of the TB disease cases, which was and echoed by observation that half were 60 years old or above, and the presence of co-morbid medical conditions. The predominance of reactivation TB cases in intermediate burden localities implies that the detection and control of latent TB infection would be the major challenge in achieving TB elimination.

We report key learning from the public health management of the first two confirmed cases of COVID-19 identified in the UK. The first case imported, and the second associated with probable person-to-person transmission within the UK. Contact tracing was complex and fast-moving. Potential exposures for both cases were reviewed, and 52 contacts were identified. No further confirmed COVID-19 cases have been linked epidemiologically to these two cases. As steps are made to enhance contact tracing across the UK, the lessons learned from earlier contact tracing during the country's containment phase are particularly important and timely.

The prevalence of many diseases in pigs displays seasonal distributions. Despite growing concerns about the impacts of climate change, we do not yet have a good understanding of the role that weather factors play in explaining such seasonal patterns. In this study, national and county-level aggregated abattoir inspection data were assessed for England and Wales during 2010–2015. Seasonally-adjusted relationships were characterised between weekly ambient maximum temperature and the prevalence of both respiratory conditions and tail biting detected at slaughter. The prevalence of respiratory conditions showed cyclical annual patterns with peaks in the summer months and troughs in the winter months each year. However, there were no obvious associations with either high or low temperatures. The prevalence of tail biting generally increased as temperatures decreased, but associations were not supported by statistical evidence: across all counties there was a relative risk of 1.028 (95% CI 0.776–1.363) for every 1 °C fall in temperature. Whilst the seasonal patterns observed in this study are similar to those reported in previous studies, the lack of statistical evidence for an explicit association with ambient temperature may possibly be explained by the lack of information on date of disease onset. There is also the possibility that other time-varying factors not investigated here may be driving some of the seasonal patterns.

Adenovirus (AdV) can cause severe respiratory infections in children and immunocompromised patients, but less is known about severe AdV pneumonia in immunocompetent adults. In this retrospective study, we compared respiratory tract infections and pneumonia caused by AdV in immunocompromised and immunocompetent adult patients regarding clinical presentation and severity of infection. The results show that AdV can cause severe infections in both immunocompetent and immunocompromised patients, and the clinical presentation and need for hospitalisation, mechanical ventilation and antiviral treatment were equal in both groups. No underlying risk factors for severe AdV infection in healthy individuals were identified.

We aimed to provide comprehensive estimates of laboratory-confirmed respiratory syncytial virus (RSV)-associated hospitalisations. Between 2012 and 2015, active surveillance of acute respiratory infection (ARI) hospitalisations during winter seasons was used to estimate the seasonal incidence of laboratory-confirmed RSV hospitalisations in children aged <5 years in Auckland, New Zealand (NZ). Incidence rates were estimated by fine age group, ethnicity and socio-economic status (SES) strata. Additionally, RSV disease estimates determined through active surveillance were compared to rates estimated from hospital discharge codes. There were 5309 ARI hospitalisations among children during the study period, of which 3923 (73.9%) were tested for RSV and 1597 (40.7%) were RSV-positive. The seasonal incidence of RSV-associated ARI hospitalisations, once corrected for non-testing, was 6.1 (95% confidence intervals 5.8–6.4) per 1000 children <5 years old. The highest incidence was among children aged <3 months. Being of indigenous Māori or Pacific ethnicity or living in a neighbourhood with low SES independently increased the risk of an RSV-associated hospitalisation. RSV hospital discharge codes had a sensitivity of 71% for identifying laboratory-confirmed RSV cases. RSV infection is a leading cause of hospitalisation among children in NZ, with significant disparities by ethnicity and SES. Our findings highlight the need for effective RSV vaccines and therapies.

Several studies have reported evidence of interference between respiratory viruses: respiratory viruses rarely reach their epidemic peak concurrently and there appears to be a negative association between infection with one respiratory virus and co-infection with another. We used results spanning 16 years (2002–2017) of a routine diagnostic multiplex panel that tests for nine respiratory viruses to further investigate these interactions in Victoria, Australia. Time series analyses were used to plot the proportion positive for each virus. The seasonality of all viruses included was compared with respiratory syncytial virus (RSV) and influenza A virus using cross-correlations. Logistic regression was used to explore the likelihood of co-infection with one virus given infection with another. Seasonal peaks were observed each year for influenza A and RSV and less frequently for influenza B, coronavirus and parainfluenza virus. RSV circulated an average of 6 weeks before influenza A. Co-infection with another respiratory virus was less common with picornavirus, RSV or influenza A infection. Our findings provide further evidence of a temporal relationship in the circulation of respiratory viruses. A greater understanding of the interaction between respiratory viruses may enable better prediction of the timing and magnitude of respiratory virus epidemics.

Social patterning of infectious diseases is increasingly recognised. Previous studies of social determinants of acute respiratory illness (ARI) have found that highly educated and lower income families experience more illnesses. Subjective social status (SSS) has also been linked to symptomatic ARI, but the association may be confounded by household composition. We examined SSS and ARI in the Household Influenza Vaccine Evaluation (HIVE) Study in 2014–2015. We used SSS as a marker of social disadvantage and created a workplace disadvantage score for working adults. We examined the association between these measures and ARI incidence using mixed-effects Poisson regression models with random intercepts to account for household clustering. In univariate analyses, mean ARI was higher among children <5 years old (P < 0.001), and females (P = 0.004) at the individual level. At the household level, mean ARI was higher for households with at least one child <5 years than for those without (P = 0.002). In adjusted models, individuals in the lowest tertile of SSS had borderline significantly higher rates of ARI than those in the highest tertile (incidence rate ratio (IRR) 1.34, 95% confidence interval (CI) 0.98–1.92). Households in the lowest tertile of SSS had significantly higher ARI incidence in household-level models (IRR 1.46, 95% CI 1.05–2.03). We observed no association between workplace disadvantage and ARI. We detected an increase in the incidence of ARI for households with low SSS compared with those with high SSS, suggesting that socio-economic position has a meaningful impact on ARI incidence.

Increased social contact within school settings is thought to be an important factor in seasonal outbreaks of acute respiratory infection (ARI). To better understand the degree of impact, we analysed electronic health records and compared risks of respiratory infections within communities while schools were in session and out-of-session. A time series analysis of weekly respiratory infection diagnoses from 28 family medicine clinics in Wisconsin showed that people under the age of 65 experienced an increased risk of ARI when schools were in session. For children aged 5–17 years, the risk ratio for the first week of a school session was 1.12 (95% confidence interval (CI) 0.93–1.34), the second week of a session was 1.39 (95% CI 1.15–1.68) and more than 2 weeks into a session was 1.43 (95% CI 1.20–1.71). Less significant increased risk ratios were also observed in young children (0–4 years) and adults (18–64 years). These results were obtained after modelling for baseline seasonal variations in disease prevalence and controlling for short-term changes in ambient temperature and relative humidity. Understanding the mechanisms of seasonality make it easier to predict outbreaks and launch timely public health interventions.

Our objective was to identify predictors of severe acute respiratory infection in hospitalised patients and understand the impact of vaccination and neuraminidase inhibitor administration on severe influenza. We analysed data from a study evaluating influenza vaccine effectiveness in two Michigan hospitals during the 2014–2015 and 2015–2016 influenza seasons. Adults admitted to the hospital with an acute respiratory infection were eligible. Through patient interview and medical record review, we evaluated potential risk factors for severe disease, defined as ICU admission, 30-day readmission, and hospital length of stay (LOS). Two hundred sixteen of 1119 participants had PCR-confirmed influenza. Frailty score, Charlson score and tertile of prior-year healthcare visits were associated with LOS. Charlson score >2 (OR 1.5 (1.0–2.3)) was associated with ICU admission. Highest tertile of prior-year visits (OR 0.3 (0.2–0.7)) was associated with decreased ICU admission. Increasing tertile of visits (OR 1.5 (1.2–1.8)) was associated with 30-day readmission. Frailty and prior-year healthcare visits were associated with 30-day readmission among influenza-positive participants. Neuraminidase inhibitors were associated with decreased LOS among vaccinated participants with influenza A (HR 1.6 (1.0–2.4)). Overall, frailty and lack of prior-year healthcare visits were predictors of disease severity. Neuraminidase inhibitors were associated with reduced severity among vaccine recipients.

The definition of severe acute respiratory infection (SARI) – a respiratory illness with fever and cough, occurring within the past 10 days and requiring hospital admission – has not been evaluated for critically ill patients. Using integrated electronic health records data, we developed an automated search algorithm to identify SARI cases in a large cohort of critical care patients and evaluate patient outcomes. We conducted a retrospective cohort study of all admissions to a medical intensive care unit from August 2009 through March 2016. Subsets were randomly selected for deriving and validating a search algorithm, which was compared with temporal trends in laboratory-confirmed influenza to ensure that SARI was correlated with influenza. The algorithm was applied to the cohort to identify clinical differences for patients with and without SARI. For identifying SARI, the algorithm (sensitivity, 86.9%; specificity, 95.6%) outperformed billing-based searching (sensitivity, 73.8%; specificity, 78.8%). Automated searching correlated with peaks in laboratory-confirmed influenza. Adjusted for severity of illness, SARI was associated with more hospital, intensive care unit and ventilator days but not with death or dismissal to home. The search algorithm accurately identified SARI for epidemiologic study and surveillance.

Transmission of acute respiratory infections (ARI) and acute gastroenteritis (AGE) often occurs in households. The aim of this study was to assess which proportion of ARI and AGE is introduced and transmitted by children in German households with children attending child care. We recruited families with children aged 0–6 years in Braunschweig (Germany), for a 4 months prospective cohort study in the winter period 2014/2015. Every household member was included in a health diary and used nasal swabs for pathogen identification in case of ARI. We defined a transmission if two persons had overlapping periods with symptoms and used additional definitions for sensitivity analyses. In total, 77 households participated with 282 persons. We observed 277 transmission events for ARI and 23 for AGE. In most cases, the first infected person in a household was a child (ARI: 63%, AGE: 53%), and the risk of within-household transmission was two times higher when the index case was a child. In 26 ARI-transmission events, pathogens were detected for both cases; hereof in 35% (95% confidence interval (17–56%)) the pathogens were different. Thus, symptomatic infections in household members, apparently linked in time, were in 2/3 associated with the same pathogens.

Acute respiratory infections cause significant morbidity and mortality accounting for 5.8 million deaths worldwide. In Australia, influenza-like illness (ILI), defined as cough, fever and fatigue is a common presentation in general practice and results in reduced productivity and lost working days. Little is known about the epidemiology of ILI in working-age adults. Using data from the ASPREN influenza surveillance network in Australia (2010–2013) we found that working-age adults made up 45.2% of all ILI notifications with 55% of samples positive for at least one respiratory virus. Viruses most commonly detected in our study included influenza A (20.6%), rhinovirus (18.6%), influenza B (6.2%), human meta-pneumovirus (3.4%), respiratory syncytial virus (3.1%), para-influenza virus (2.6%) and adenovirus (1.3%). We also demonstrated that influenza A is the predominant virus that increases ILI (by 1.2% per month for every positive influenza A case) in working-age adults during autumn–winter months while other viruses are active throughout the year. Understanding the epidemiology of viral respiratory infections through a year will help clinicians make informed decisions about testing, antibiotic and antiviral prescribing and when the beginning of the ‘flu season’ can be more confidently predicted.

Streptococcus pneumoniae is an important cause of community-acquired pneumonia and pneumococcal conjugate vaccines (PCVs) may reduce this burden. This study's goal was to analyse trends in lower respiratory tract infections (LRTI) hospitalisations before and during a routine vaccination programme targeting all newborns with PCV was started in the province of Quebec, Canada in December 2004. The study population included hospital admissions with a main diagnosis of LRTI among 6–59 month-old Quebec residents from April 2000 to December 2014. Trends in proportions and rates were analysed using Cochran-Armitage tests and Poisson regression models. We observed a general downward trend in all LTRI hospitalisations rate: from 11·55/1000 person-years in 2000–2001 to 9·59/1000 in 2013–2014, a 17·0% reduction, which started before the introduction of PCV vaccination. Downward trends in hospitalisation rates were more pronounced for all-cause of pneumonia (minus 17·8%) than for bronchiolitis (minus 15·4%). There was also a decrease in the mean duration of hospital stay. There was little evidence that all-cause pneumonia decreased over the study period due mainly to the introduction of PCVs. Trends may be related to changes in clinical practice. This study casts doubt on the interpretation of ecological analyses of the implementation of PCV vaccination programmes.

In autumn 2014, enterovirus D68 (EV-D68) cases presenting with severe respiratory or neurological disease were described in countries worldwide. To describe the epidemiology and virological characteristics of EV-D68 in England, we collected clinical information on laboratory-confirmed EV-D68 cases detected in secondary care (hospitals), between September 2014 and January 2015. In primary care (general practitioners), respiratory swabs collected (September 2013–January 2015) from patients presenting with influenza-like illness were tested for EV-D68. In secondary care 55 EV-D68 cases were detected. Among those, 45 cases had clinical information available and 89% (40/45) presented with severe respiratory symptoms. Detection of EV-D68 among patients in primary care increased from 0.4% (4/1074; 95% CI 0.1–1.0) (September 2013–January 2014) to 0.8% (11/1359; 95% CI 0.4–1.5) (September 2014–January 2015). Characterization of EV-D68 strains circulating in England since 2012 and up to winter 2014/2015 indicated that those strains were genetically similar to those detected in 2014 in USA. We recommend reinforcing enterovirus surveillance through screening respiratory samples of suspected cases.