Transmission and effect of multiple clusters of seasonal influenza in a Swiss geriatric hospital

Comparison of 28-Day Mortality Between Hospital- and Community-Acquired Influenza Patients

Objective

This study aimed to compare 28-day mortality between patients have hospital-acquired influenza (HAI) and those have community-acquired influenza (CAI) during the 2017-2019 influenza seasons in a tertiary care center in İstanbul, Türkiye.

Materials and Methods

This retrospective cohort included all hospitalized patients who had confirmed influenza infection and were over 17 years old. HAI was defined as a case of influenza that tested negative in a PCR test or had no signs of influenza on admission but with a positive test result at any point after 72 hours of admission. CAI was defined as a case of influenza diagnosed within 72 hours of admission or before admission. The primary outcome was 28-day mortality after diagnosis. Biological sex, admission to the intensive care unit (ICU), presence of chronic obstructive pulmonary disease, cardiovascular and immunosuppressive comorbidities, influenza subtype, and other variables identified with univariate analyses (p<0.25) were entered into logistic regression analysis.

Results

During the study period, 92 (46%) of 201 hospitalized patients who tested positive for influenza were identified as HAI, and the rest (109) were identified as CAI. Univariate analysis showed no differences between survivors and non-survivors in patient characteristics, except non-survivors were more likely to have an ICU admission. The multivariable logistic regression analysis results showed that HAI was associated with 5.6-fold increased odds of mortality (95% confidence interval [CI]=1.6-19.3; p=0.006), after adjustment for age, gender, comorbidity, and ICU admission.

Conclusion

The results of this study revealed that patients who had HAI were more likely to die within 28 days compared to those who had CAI after controlling for key confounders. The high rate of HAI underscores the critical importance of robust infection control measures for hospital-acquired viral infections. Additional research and targeted interventions are necessary to improve the HAI prognosis.

A Cold Case of Equine Influenza Disentangled with Nanopore Sequencing

Massive sequencing techniques have allowed us to develop straightforward approaches for the whole genome sequencing of viruses, including influenza viruses, generating information that is useful for improving the levels and dimensions of data analysis, even for archival samples. Using the Nanopore platform, we determined the whole genome sequence of an H3N8 equine influenza virus, identified from a 2005 outbreak in Apulia, Italy, whose origin had remained epidemiologically unexplained. The virus was tightly related (>99% at the nucleotide level) in all the genome segments to viruses identified in Poland in 2005–2008 and it was seemingly introduced locally with horse trading for the meat industry. In the phylogenetic analysis based on the eight genome segments, strain ITA/2005/horse/Bari was found to cluster with sub-lineage Florida 2 in the HA and M genes, whilst in the other genes it clustered with strains of the Eurasian lineage, revealing a multi-reassortant nature.

An anti-influenza combined therapy assessed by single cell RNA-sequencing

Influenza makes millions of people ill every year, placing a large burden on the healthcare system and the economy. To develop a treatment against influenza, we combined virucidal sialylated cyclodextrins with interferon lambda and demonstrated, in human airway epithelia, that the two compounds inhibit the replication of a clinical H1N1 strain more efficiently when administered together rather than alone. We investigated the mechanism of action of the combined treatment by single cell RNA-sequencing analysis and found that both the single and combined treatments impair viral replication to different extents across distinct epithelial cell types. We showed that each cell type comprises multiple sub-types, whose proportions are altered by H1N1 infection, and assessed the ability of the treatments to restore them. To the best of our knowledge this is the first study investigating the effectiveness of an antiviral therapy against influenza virus by single cell transcriptomic studies.

When combined with interferon lambda, virucidal sialylated cyclodextrins inhibit the replication of a clinical H1N1 influenza strain in ex vivo human airway epithelia more efficiently than when delivered alone.

Transmission visualizations of healthcare infection clusters: A scoping review

OBJECTIVE

To evaluate infectious pathogen transmission data visualizations in outbreak publications.

DESIGN

Scoping review.

METHODS

Medline was searched for outbreak investigations of infectious diseases within healthcare facilities that included ≥1 data visualization of transmission using data observable by an infection preventionist showing temporal and/or spatial relationships. Abstracted data included the nature of the cluster(s) (pathogen, scope of transmission, and individuals involved) and data visualization characteristics including visualization type, transmission elements, and software.

RESULTS

From 1,957 articles retrieved, we analyzed 30 articles including 37 data visualizations. The median cluster size was 20.5 individuals (range, 7-1,963) and lasted a median of 214 days (range, 12-5,204). Among the data visualization types, 10 (27%) were floor-plan transmission maps, 6 (16%) were timelines, 11 (30%) were transmission networks, 3 (8%) were Gantt charts, 4 (11%) were cluster map, and 4 (11%) were other types. In addition, 26 data visualizations (70%) contained spatial elements, 26 (70%) included person type, and 19 (51%) contained time elements. None of the data visualizations contained contagious periods and only 2 (5%) contained symptom-onset date.

CONCLUSIONS

The data visualizations of healthcare-associated infectious disease outbreaks in the systematic review were diverse in type and visualization elements, though no data visualization contained all elements important to deriving hypotheses about transmission pathways. These findings aid in understanding the visualizing transmission pathways by describing essential elements of the data visualization and will inform the creation of a standardized mapping tool to aid in earlier initiation of interventions to prevent transmission.

Strategies to prevent ventilator-associated pneumonia, ventilator-associated events, and nonventilator hospital-acquired pneumonia in acute-care hospitals: 2022 Update

The purpose of this document is to highlight practical recommendations to assist acute care hospitals to prioritize and implement strategies to prevent ventilator-associated pneumonia (VAP), ventilator-associated events (VAE), and non-ventilator hospital-acquired pneumonia (NV-HAP) in adults, children, and neonates. This document updates the Strategies to Prevent Ventilator-Associated Pneumonia in Acute Care Hospitals published in 2014. This expert guidance document is sponsored by the Society for Healthcare Epidemiology (SHEA), and is the product of a collaborative effort led by SHEA, the Infectious Diseases Society of America, the American Hospital Association, the Association for Professionals in Infection Control and Epidemiology, and The Joint Commission, with major contributions from representatives of a number of organizations and societies with content expertise.

Seasonal influenza vaccination of healthcare workers: a narrative review

Influenza is an acute respiratory disease caused by the influenza virus which often occurs in outbreaks and epidemics worldwide. The World Health Organization recommends annual vaccination of healthcare workers (HCWs) against influenza, because most of them are involved in the direct care of patients with a high risk of influenza-related complications. Given the significance of the disease burden, a targeted literature review was conducted to assess issues related to influenza vaccination among HCWs. The primary aim of this review was to assess the incidence of influenza among medical personnel and healthcare-associated influenza, and to outline the benefits of influenza vaccination for patients and HCWs themselves. Vaccination of HCWs seems to be an important strategy for reducing the transmission of influenza from healthcare personnel to their patients and, therefore, for reducing patient morbidity and mortality, increasing patient safety, and reducing work absenteeism among HCWs. The benefits of influenza vaccination for their patients and for HCWs themselves are addressed in literature, but the evidence is mixed and often of low-quality. Int J Occup Med Environ Health. 2022;35(2):127-39.

Severe acute respiratory coronavirus virus 2 (SARS-CoV-2) seroconversion and occupational exposure of employees at a Swiss university hospital: A large longitudinal cohort study

BACKGROUND

The dynamics of coronavirus disease 2019 (COVID-19) seroconversion of hospital employees are understudied. We measured the proportion of seroconverted employees and evaluated risk factors for seroconversion during the first pandemic wave.

METHODS

In this prospective cohort study, we recruited Geneva University Hospitals employees and sampled them 3 times, every 3 weeks from March 30 to June 12, 2020. We measured the proportion of seroconverted employees and determined prevalence ratios of risk factors for seroconversion using multivariate mixed-effects Poisson regression models.

RESULTS

Overall, 3,421 participants (29% of all employees) were included, with 92% follow-up. The proportion of seroconverted employees increased from 4.4% (95% confidence interval [CI], 3.7%-5.1%) at baseline to 8.5% [(95% CI, 7.6%-9.5%) at the last visit. The proportions of seroconverted employees working in COVID-19 geriatrics and rehabilitation (G&R) wards (32.3%) and non-COVID-19 G&R wards (12.3%) were higher compared to office workers (4.9%) at the last visit. Only nursing assistants had a significantly higher risk of seroconversion compared to office workers (11.7% vs 4.9%; P = .006). Significant risk factors for seroconversion included the use of public transportation (adjusted prevalence ratio, 1.59; 95% CI, 1.25-2.03), known community exposure to severe acute respiratory coronavirus virus 2 (2.80; 95% CI, 2.22-3.54), working in a ward with a nosocomial COVID outbreak (2.93; 95% CI, 2.27-3.79), and working in a COVID-19 G&R ward (3.47; 95% CI, 2.45-4.91) or a non-COVID-19 G&R ward (1.96; 95% CI, 1.46-2.63). We observed an association between reported use of respirators and lower risk of seroconversion (0.73; 95% CI, 0.55-0.96).

CONCLUSION

Additional preventive measures should be implemented to protect employees in G&R wards. Randomized trials on the protective effect of respirators are urgently needed.

Secondary attack rates from asymptomatic and symptomatic influenza virus shedders in hospitals: Results from the TransFLUas influenza transmission study

Objective:

Nosocomial transmission of influenza is a major concern for infection control. We aimed to dissect transmission dynamics of influenza, including asymptomatic transmission events, in acute care.

Design:

Prospective surveillance study during 2 influenza seasons.

Setting:

Tertiary-care hospital.

Participants:

Volunteer sample of inpatients on medical wards and healthcare workers (HCWs).

Methods:

Participants provided daily illness diaries and nasal swabs for influenza A and B detection and whole-genome sequencing for phylogenetic analyses. Contacts between study participants were tracked. Secondary influenza attack rates were calculated based on spatial and temporal proximity and phylogenetic evidence for transmission.

Results:

In total, 152 HCWs and 542 inpatients were included; 16 HCWs (10.5%) and 19 inpatients (3.5%) tested positive for influenza on 109 study days. Study participants had symptoms of disease on most of the days they tested positive for influenza (83.1% and 91.9% for HCWs and inpatients, respectively). Also, 11(15.5%) of 71 influenza-positive swabs among HCWs and 3 (7.9%) of 38 influenza-positive swabs among inpatients were collected on days without symptoms; 2 (12.5%) of 16 HCWs and 2 (10.5%) of 19 inpatients remained fully asymptomatic. The secondary attack rate was low: we recorded 1 transmission event over 159 contact days (0.6%) that originated from a symptomatic case. No transmission event occurred in 61 monitored days of contacts with asymptomatic influenza-positive individuals.

Conclusions:

Influenza in acute care is common, and individuals regularly shed influenza virus without harboring symptoms. Nevertheless, both symptomatic and asymptomatic transmission events proved rare. We suggest that healthcare-associated influenza prevention strategies that are based on preseason vaccination and barrier precautions for symptomatic individuals seem to be effective.

Pneumonia prevention in the elderly patients: the other sides

Pneumonia is one of the leading causes of morbidity and mortality from infection in elderly patients. The increased frequency of pneumonia among elderly subjects can be explained by the physiological changes linked to the progressive aging of the respiratory tree and the diminished immunological response. A spiral of event leads to frailty, infection and possible death; preventing pneumonia consists of controlling the risk factors. Dysphagia, which is associated with malnutrition and dehydration, is recognized as one of the major pathophysiological mechanism leading to pneumonia and its screening is crucial for the pneumonia risk assessment. The impairment in the oropharyngeal reflexes results in stagnation of foreign material in the lateral cavities of the pharynx which may then get aspirated repeatedly in the lungs and cause pneumonia. Pneumonia prevention starts with lifestyle modifications such as alcohol and tobacco cessation. A careful review of the risk-benefit of the prescribed medication is critical and adaptation may be required in elders with multiple morbidities. Respiratory physiotherapy and mobilization improve the functional status and hence may help reduce the risk of pneumonia. Maintaining teeth and masticatory efficiency is important if malnutrition and its consequences are to be avoided. Daily oral hygiene and regular professional removal of oral biofilm can prevent the onset of periodontitis and can avoid an oral environment favoring the colonization of respiratory pathogens than can then be aspirated into the lungs.

The epidemiological and clinical characteristics of the hospital-acquired influenza infections: A systematic review and meta-analysis

BACKGROUND

The hospital-acquired influenza (HAI) were usually contributed to severe outcomes among the inpatients. Here, we performed a meta-analysis to summarize and quantify the epidemiological and clinical characteristics of HAI.

METHODS

We performed a literature search thorough PubMed, Web of Science, Cochrane Library, Embase, Scopus and China National Knowledge Infrastructure (CNKI), and Wanfang databases for observational studies. Random/fix-effects models were used to obtain pooled proportion, odds ratio (OR), and weighted mean difference (WMD).

RESULTS

A total of 14 studies involving 1483 HAI and 71849 non-hospital-acquired influenza infections (NHAI) cases were included.The proportion of the HAI among the influenza cases was 11.38% (95% confidence interval [CI]: 5.19%-19.55%) and it was increased after 2012 (6.15% vs 12.72%). The HAI cases were significantly older (WMD = 9.51, 95% CI: 0.04-18.98) and the patients with chronic medical diseases were at increased risk of HAI (OR = 1.85, 95% CI: 1.57-2.19). Among them, metabolic disorders (OR = 8.10, 95% CI: 2.46-26.64) ranked the highest danger, followed by malignancy (OR = 3.18, 95% CI: 2.12-4.76), any chronic diseases (OR = 2.81, 95% CI: 1.08-9.31), immunosuppression (OR = 2.13, 95% CI: 1.25-3.64), renal diseases (OR = 1.72, 95% CI:1.40-2.10), heart diseases (OR = 1.52, 95% CI: 1.03-1.44), and diabetes (OR = 1.22, 95% CI: 1.03-1.44). The HAI cases were more likely to experience longer hospital stay (WMD = 10.23, 95% CI: 4.60-15.85) and longer intensive care unit (ICU) stay (WMD = 2.99, 95% CI: 1.50-4.48). In the outcomes within 30 days, those population was still more likely to receive hospitalization (OR = 6.55, 95% CI: 5.19-8.27), death in hospital (OR = 1.99, 95% CI: 1.65-2.40) but less likely to discharged (OR = 0.20, 95% CI: 0.16-0.24).

CONCLUSION

The proportion of the HAI among the influenza cases was relatively high. Reinforcement of the surveillance systems and vaccination of the high-risk patients and their contacts are necessary for the HAI control.

Nosocomial influenza in south-western Swiss hospitals during two seasonal epidemics: an observational study

BACKGROUND

In Switzerland each year, influenza leads to between 112,000 and 275,000 medical consultations. Data on nosocomial influenza infection are limited.

AIM

To describe nosocomial cases of seasonal influenza in south-western Switzerland.

METHODS

This study was conducted during two seasonal influenza epidemics from 2016 to 2018 in 27 acute care public hospitals in south-western Switzerland. During these two time-periods, every patient hospitalized for >72 h who was positively screened by reverse transcription-polymerase chain reaction or antigen detection for influenza was included in the survey. Characteristics of patients included age, sex, and comorbidities. Included patients were followed up until discharge or death. Complications and administration of antineuraminidases and/or antibiotics were registered.

FINDINGS

The median influenza vaccine coverage of healthcare workers was 40%. In all, 836 patients were included (98% with type A influenza virus in 2016-2017; 77% with type B virus in 2017-2018). Most patients (81%) had an unknown vaccine status. Overall, the incidence of nosocomial influenza was 0.5 per 100 admissions (0.35 per 1000 patient-days). The most frequent comorbidities were diabetes (20%), chronic respiratory diseases (19%), and malnutrition (17%). Fever (77%) and cough (66%) were the most frequent symptoms. Seventy-one percent of patients received antineuraminidases, 28% received antibiotics. Infectious complications such as pneumonia were reported in 9%. Overall, the all-cause mortality was 6%.

CONCLUSION

The occurrence of nosocomial influenza underlines the importance of vaccinating patients and healthcare workers, rapidly recognizing community- or hospital-acquired cases, and applying adequate additional measures to prevent dissemination, including the timely administration of antineuraminidases to avoid antibiotic use (and misuse).

Absenteeism and presenteeism in healthcare workers due to respiratory illness

OBJECTIVE

To assess influenza symptoms, adherence to mask use recommendations, absenteesm and presenteeism in acute care healthcare workers (HCWs) during influenza epidemics.

METHODS

The TransFLUas influenza transmission study in acute healthcare prospectively followed HCWs prospectively over 2 consecutive influenza seasons. Symptom diaries asking for respiratory symptoms and adherence with mask use recommendations were recorded on a daily basis, and study participants provided midturbinate nasal swabs for influenza testing.

RESULTS

In total, 152 HCWs (65.8% nurses and 13.2% physicians) were included: 89.1% of study participants reported at least 1 influenza symptom during their study season and 77.8% suffered from respiratory symptoms. Also, 28.3% of HCW missed at least 1 working day during the study period: 82.6% of these days were missed because of symptoms of influenza illness. Of all participating HCWs, 67.9% worked with symptoms of influenza infection on 8.8% of study days. On 0.3% of study days, symptomatic HCWs were shedding influenza virus while at work. Among HCWs with respiratory symptoms, 74.1% adhered to the policy to wear a mask at work on 59.1% of days with respiratory symptoms.

CONCLUSIONS

Respiratory disease is frequent among HCWs and imposes a significant economic burden on hospitals due to the number of working days lost. Presenteesm with respiratory illness, including influenza, is also frequent and poses a risk for patients and staff.

TRIAL REGISTRATION

NCT02478905 (clinicaltrials.gov).

Influenza Vaccination Hesitancy among Healthcare Workers in South Al Batinah Governorate in Oman: A Cross-Sectional Study

Background: Seasonal influenza infections are a major cause of morbidity and mortality worldwide. Healthcare workers (HCWs) are an important target group for vaccination against influenza due to their increased risk of infection and their potential to transmit the infection to their patients, families and communities. The aim of this study was to assess the potential hesitancy and its associated factors towards influenza vaccination amongst HCWs in the South Al Batinah governorate in Oman. Methods: A cross-sectional survey of 390 HCWs with direct or indirect patient contact was conducted in May and June 2019 using a self-administered questionnaire. Associations between HCW characteristics and vaccination status were examined using bivariate and multivariate analyses to identify the likelihood of vaccination against seasonal influenza among HCWs. Results: Overall, 60% of HCWs were vaccinated in the 2018/2019 season; vaccine uptake among nurses was 52% and uptake was higher among women. Self-protection and protection of the community were the most cited reasons for vaccine acceptance, with side effects being the main reason for hesitancy. Vaccinated respondents had a higher mean knowledge score (7.18; standard deviation SD: 2.14) than unvaccinated respondents (6.30; SD: 2.2). Odds of vaccination were highest among respondents who believed influenza vaccine should be mandatory for HCWs (Odds ratio (OR): 2.04 [1.30–3.18]), those working in the general medicine, emergency medicine, or intensive care units (OR: 1.92 [1.20–3.10]), nurses and doctors (OR: 1.75 [1.09–2.79]) and those who believe that HCWs should receive an influenza vaccine (OR: 1.35 [1.07–2.77]). Conclusions: The study provides valuable insights into the enablers and barriers of influenza vaccination practices among HCWs and may inform interventions to increase acceptance of vaccination.

Absences from work among healthcare workers: are they related to influenza shot adherence?

Background

The coverage for influenza vaccination among healthcare workers (HCWs) is inadequate in many countries despite strong recommendations; is there evidence that influenza vaccination is effective in preventing absenteeism? Aim of the study is to evaluate the influenza vaccination coverage and its effects on absences from work among HCWs of an Italian academic healthcare trust during the 2017–2018 influenza season.

Methods

We performed a retrospective study to identify predictive characteristics for vaccination, and a retrospective cohort study to establish the effect of vaccination on absences among the vaccinated and non-vaccinated cohorts between December 2017 and May 2018. Overall absence rates over the whole observation period and sub-rates over 14-days intervals were calculated; then comparison between the two groups were conducted applying Chi-square test.

Results

Influenza vaccination coverage among 4419 HCWs was 14.5%. Age, university degree, medical care area and physician profile were positively associated with vaccine uptake. Globally during influenza season non-vaccinated HCWs lost 2.47/100 person-days of work compared to 1.92/100 person-days of work among vaccinated HCWs (p < 0.001); significant differences in absences rates resulted when focusing on the influenza epidemic peak.

Conclusions

Factors predicting influenza uptake among HCWs were male sex, working within medical care area and being a physician. Absenteeism among HCWs resulted to be negatively correlated with vaccination against influenza. These findings add evidence to the urgent need to implement better influenza vaccination strategies towards HCWs to tackle vaccine hesitancy among professionals.

Incidence and characteristics of nosocomial influenza in a country with low vaccine coverage

BACKGROUND

Influenza vaccination coverage is low in France, in at-risk patients and in healthcare workers.

AIM

We aimed to estimate the incidence of nosocomial influenza, its characteristics and outcome.

METHODS

During one influenza season, we retrospectively evaluated all cases of documented influenza. Inpatients with symptoms onset ≥48 h after admission were enrolled. Data were collected on a standardized questionnaire.

RESULTS

From November 2017 to April 2018, 860 patients tested positive for influenza by polymerase chain reaction analysis on a respiratory sample. Among them, 204 (23.7%) were diagnosed ≥48 h after admission, of whom 57 (6.6% of all influenza cases) fulfilled inclusion criteria for nosocomial influenza: 26 women and 31 men, median age 82 years (interquartile range, 72.2-86.9). Twenty patients (38.6%) had recently (<6 months) received the seasonal influenza vaccine. Median time between admission and symptoms onset, and between symptoms onset and diagnosis were, respectively, 11 days (7-19.5) and 29 h (15.5-48). Influenza was mostly acquired in a double-bedded room (N = 39, 68.4%), with documented exposure in 14 cases. Influenza B virus was more common in nosocomial (46/57, 80.7%), than in community-acquired cases (359/803, 44.6%), P<0.001. Mortality rate at three months was 15.8% (N = 9). Incidence of nosocomial influenza was estimated at 0.22 per 1000 hospital-days during the study period.

CONCLUSION

Nosocomial influenza is not rare in elderly inpatients, and may have severe consequences. Influenza B virus was over-represented, which suggests higher transmissibility and/or transmission clusters.

Are healthcare workers more likely than the general population to consult in primary care for an influenza-like illness? Results from a case-control study

Background

Healthcare workers are at increased risk of contracting influenza. However, existing studies do not differentiate professional categories or domains of the healthcare system that are most at risk.

Methods

This case‐control study compared proportions of patients with professional activity in the healthcare system between cases consulting their primary care physician for an influenza‐like illness (ILI) and controls from the general patient population of the same practices of the Swiss sentinel network. Influenza was confirmed by rRT‐PCR in a subset of practices. Analysis used a mixed logistic regression model, including age and sex as potential confounders.

Results

During the 2018/2019 influenza surveillance season, out of 4287 ILI cases and 28 561 controls reported in 168 practices, 235 (5.5%), respectively 872 (3.1%), were active in the healthcare system. After adjustment, being active in health care increased the odds of consulting for an ILI (OR 1.66, 95% CI 1.40‐1.97). The association was strongest for physicians and nursing aides. In terms of work setting, odds of consulting for ILI were increased for professionals of almost all healthcare settings except home‐based care.

Conclusion

Individuals active in the healthcare system were more likely to consult their primary care physician for an influenza‐like illness than for another reason, compared with individuals not active in the healthcare system. These results warrant further efforts to understand influenza transmission in the healthcare system at large.

Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014)

BACKGROUND

The extent of transmission of influenza in hospital settings is poorly understood. Next generation sequencing may improve this by providing information on the genetic relatedness of viral strains.

OBJECTIVES

We aimed to apply next generation sequencing to describe transmission in hospital and compare with methods based on routinely-collected data.

METHODS

All influenza samples taken through routine care from patients at University College London Hospitals NHS Foundation Trust (September 2012 to March 2014) were included. We conducted Illumina sequencing and identified genetic clusters. We compared nosocomial transmission estimates defined using classical methods (based on time from admission to sample) and genetic clustering. We identified pairs of cases with space-time links and assessed genetic relatedness.

RESULTS

We sequenced influenza sampled from 214 patients. There were 180 unique genetic strains, 16 (8.8%) of which seeded a new transmission chain. Nosocomial transmission was indicated for 32 (15.0%) cases using the classical definition and 34 (15.8%) based on genetic clustering. Of the 50 patients in a genetic cluster, 11 (22.0%) had known space-time links with other cases in the same cluster. Genetic distances between pairs of cases with space-time links were lower than for pairs without spatial links (P < .001).

CONCLUSIONS

Genetic data confirmed that nosocomial transmission contributes significantly to the hospital burden of influenza and elucidated transmission chains. Prospective next generation sequencing could support outbreak investigations and monitor the impact of infection and control measures.

Identification of influenza urban transmission patterns by geographical, epidemiological and whole genome sequencing data: protocol for an observational study

INTRODUCTION

Urban transmission patterns of influenza viruses are complex and poorly understood, and multiple factors may play a critical role in modifying transmission. Whole genome sequencing (WGS) allows the description of patient-to-patient transmissions at highest resolution. The aim of this study is to explore urban transmission patterns of influenza viruses in high detail by combining geographical, epidemiological and immunological data with WGS data.

METHODS AND ANALYSIS

The study is performed at the University Hospital Basel, University Children's Hospital Basel and a network of paediatricians and family doctors in the Canton of Basel-City, Switzerland. The retrospective study part includes an analysis of PCR-confirmed influenza cases from 2013 to 2018. The prospective study parts include (1) a household survey regarding influenza-like illness (ILI) and vaccination against influenza during the 2015/2016 season; (2) an analysis of influenza viruses collected during the 2016/2017 season using WGS-viral genomic sequences are compared with determine genetic relatedness and transmissions; and (3) measurement of influenza-specific antibody titres against all vaccinated and circulated strains during the 2016/2017 season from healthy individuals, allowing to monitor herd immunity across urban quarters. Survey data and PCR-confirmed cases are linked to data from the Statistics Office of the Canton Basel-City and visualised using geo-information system mapping. WGS data will be analysed in the context of patient epidemiological data using phylodynamic analyses, and the obtained herd immunity for each quarter. Profound knowledge on the key geographical, epidemiological and immunological factors influencing urban influenza transmission will help to develop effective counter measurements.

ETHICS AND DISSEMINATION

The study is registered and approved by the regional ethics committee as an observational study (EKNZ project ID 2015-363 and 2016-01735). It is planned to present the results at conferences and publish the data in scientific journals.

TRIAL REGISTRATION NUMBER

NCT03010007.

A rapid evidence appraisal of influenza vaccination in health workers: An important policy in an area of imperfect evidence

INTRODUCTION

The World Health Organization recommends vaccination of health workers (HWs) against influenza, but low uptake is intransigent.We conducted a Rapid Evidence Appraisal on: the risk of influenza in HWs, transmission risk from HWs to patients, the benefit of HW vaccination, and strategies for improving uptake. We aimed to capture a 'whole-of-system' perspective to consider possible benefits for HWs, employers and patients.

METHODS

We executed a comprehensive search of the available literature published from 2006 to 2018 in the English language. We developed search terms for seven separate questions following the PICO framework (population, intervention, comparators, outcomes) and queried nine databases.

RESULTS

Of 3784 publications identified, 52 met inclusion criteria. Seven addressed HW influenza risk, of which four found increased risk; 15 addressed influenza vaccine benefit to HWs or their employers, of which 10 found benefit; 11 addressed influenza transmission from HWs to patients, of which 6 found evidence for transmission; 12 unique studies addressed whether vaccinating HWs produced patient benefit, of which 9 concluded benefits accrued. Regarding the number of HWs needed to vaccinate (NNV) to deliver patient benefit, NNV estimates ranged from 3 to 36,000 but were in significant disagreement. Fourteen studies provided insights on strategies to improve uptake; the strongest evidence was for mandatory vaccination.

CONCLUSIONS

The evidence on most questions related to influenza vaccination in HWs is mixed and often of low-quality. Substantial heterogeneity exists in terms of study designs and settings, making comparison between studies difficult. Notwithstanding these limitations, a majority of studies suggests that influenza vaccination benefit HWs and their employers; and HWs are implicated in transmission events. The effects of vaccinating HWs on patient morbidity and mortality may include reductions in all-cause mortality and influenza-like illness (ILI). Taken together, the evidence suggests that HW vaccination is an important policy for HWs themselves, their employers, and their patients.

Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenzaa

These clinical practice guidelines are an update of the guidelines published by the Infectious Diseases Society of America (IDSA) in 2009, prior to the 2009 H1N1 influenza pandemic. This document addresses new information regarding diagnostic testing, treatment and chemoprophylaxis with antiviral medications, and issues related to institutional outbreak management for seasonal influenza. It is intended for use by primary care clinicians, obstetricians, emergency medicine providers, hospitalists, laboratorians, and infectious disease specialists, as well as other clinicians managing patients with suspected or laboratory-confirmed influenza. The guidelines consider the care of children and adults, including special populations such as pregnant and postpartum women and immunocompromised patients.

Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenzaa

These clinical practice guidelines are an update of the guidelines published by the Infectious Diseases Society of America (IDSA) in 2009, prior to the 2009 H1N1 influenza pandemic. This document addresses new information regarding diagnostic testing, treatment and chemoprophylaxis with antiviral medications, and issues related to institutional outbreak management for seasonal influenza. It is intended for use by primary care clinicians, obstetricians, emergency medicine providers, hospitalists, laboratorians, and infectious disease specialists, as well as other clinicians managing patients with suspected or laboratory-confirmed influenza. The guidelines consider the care of children and adults, including special populations such as pregnant and postpartum women and immunocompromised patients.

Evaluation of two workflows for whole genome sequencing-based typing of influenza A viruses

We compared two sample preparation protocols for whole genome sequencing of influenza A viruses. Each protocol was assessed using cDNA quantity and quality and the resulting mean genome coverage after sequencing. Both protocols produced acceptable result for samples with high viral load, whereas one protocol performed slightly better with limited virus count.

Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15

Adequacy of the current clinical definition of institutional influenza outbreaks is unclear. We performed a retrospective genome sequencing and epidemiologic analysis of institutional influenza outbreaks that occurred during the 2014-15 influenza season in Toronto, Canada. We sequenced the 2 earliest submitted samples positive for influenza A(H3N2) from each of 38 reported institutional outbreaks in long-term care facilities. Genome sequencing showed most outbreak pairs identified by using the current clinical definition were highly related. Inclusion of surveillance samples demonstrated that outbreak sources were likely introductions from broader circulating lineages. Pairwise distance analysis using majority genome and hemagglutinin-specific genes enabled identification of thresholds for discrimination of within and between outbreak pairs; the area under the curve ranged 0.93-0.95. Routine genome sequencing for defining influenza outbreaks in long-term care facilities is unlikely to add significantly to the current clinical definition. Sequencing may prove most useful for investigating sources of outbreak introductions.

Molecular characterization of a nosocomial outbreak of influenza B virus in an acute care hospital setting

Aim

To describe a hospital outbreak of influenza B virus (InfB) infection during season 2015/2016 by combining clinical and epidemiological data with molecular methods.

Methods

Twenty patients diagnosed with InfB from a hospital outbreak over a four-week-period were included. Nasopharyngeal samples (NPS) positive for InfB by multiplex real-time polymerase chain reaction were sent for lineage typing and whole genome sequencing (WGS). Medical records were reviewed retrospectively for data regarding patient characteristics, localization, exposure and outcome, and assembled into a timeline. In order to find possible connections to the hospital outbreak, all patients with a positive NPS for influenza from the region over an extended time period were also reviewed.

Findings

All 20 cases of InfB were of subtype B/Yamagata, and 17 of 20 patients could be linked to each other by either shared room or shared ward. WGS was successful or partially successful for 15 of the 17 viral isolates, and corroborated the epidemiological link supporting a close relationship. In the main affected ward, 19 of 75 inpatients were infected with InfB during the outbreak period, resulting in an attack rate of 25%. One probable case of influenza-related death was identified.

Conclusion

InfB may spread within an acute care hospital, and advanced molecular methods may facilitate assessment of the source and extent of the outbreak. A multi-faceted approach, including rapid diagnosis, early recognition of outbreak situations, simple rules for patient management and the use of regular infection control measures, may prevent nosocomial transmission of influenza virus.

Factors associated with influenza vaccination among healthcare workers in acute care hospitals in Canada

BACKGROUND

Influenza vaccine coverage rates among healthcare workers (HCWs) in acute care facilities in Canada remain below national targets.

OBJECTIVE

To determine factors associated with influenza vaccine uptake among HCWs.

METHODS

This secondary analysis of a prospective cohort study included HCWs aged 18-69 years, working ≥20 h/wk in a Canadian acute care hospital. Questionnaires were administered to participants in the fall of the season of participation (2011/12-2013/14) which captured demographic/household characteristics, medical histories, occupational, behavioural and risk factors for influenza. Generalized estimating equation logistic regression was used to determine factors associated with vaccine uptake in the season of participation.

RESULTS

The adjusted odds ratio for influenza vaccination in the current season was highest for those vaccinated in 3 of 3 previous seasons (OR 156; 95% CI 98, 248) followed by those vaccinated in 2 of 3 and 1 of 3 previous seasons when compared with those not vaccinated. Compared with nurses, physicians (OR 4.2; 95% CI 1.4, 13.2) and support services staff (OR 1.8; 95% CI 1.3, 2.4) had higher odds ratios for vaccine uptake. Conversely, HCWs identifying as Black had lower odds of uptake compared with those with European ancestry (OR 0.44, 95% CI 0.26-0.75) when adjusted for other factors in the model.

CONCLUSION

Healthcare workers differ in their annual uptake of influenza vaccine based on their past vaccination history, occupation and ethnicity. These findings indicate a need to determine whether there are other vaccine-hesitant groups within healthcare settings and learn which approaches are successful in increasing their uptake of influenza vaccines.

Nosocomial influenza: encouraging insights and future challenges

PURPOSE OF REVIEW

The prevalence and incidence of viral nosocomial influenza infections in healthcare settings are underestimated. Nosocomial influenza outbreaks are frequent, and control remains challenging in acute care and long-term healthcare settings. This review examines recent publications on the determinants of nosocomial influenza prevention and control.

RECENT FINDINGS

Nosocomial influenza outbreaks occur in various healthcare settings, especially among the frail and elderly. The correct diagnosis is commonly missed because a substantial proportion of asymptomatic cases can transmit infections. Rapid diagnosis will facilitate rapid identification of cases and the implementation of control measures but needs confirmation in some circumstances, such as the description of transmission chains. Links between patients and healthcare personnel (HCP) have been well explored by phylogenetic virus characterization and need additional refinement and study. The preventive role of HCP vaccination in influenza incidence among patients should be investigated further in various settings to take into account different strategies for vaccination (i.e. voluntary or mandatory vaccination policies). Indeed, in Europe, influenza vaccination remains modest, whereas in North America hospitals and some states and provinces are now mandating influenza vaccination among HCP. The variability of vaccine effectiveness by seasonal epidemics is also an important consideration for control strategies.

SUMMARY

When influenza cases occur in the community, the risk of transmission and nosocomial cases increase in healthcare settings requiring vigilance among staff. Surveillance and early warning systems should be encouraged. Outbreak control needs appropriate identification of cases and transmission chains, and rapid implementation of control measures. Vaccination policies in conjunction with appropriate infection control measures could reduce virus spreading in hospitals. HCP vaccination coverage must be improved.

Les vaccins dans la prévention des infections associées aux soins

Les infections associées aux soins (IAS) constituent un véritable problème de santé publique. Escherichia coli, Staphylococcus aureus, Clostridium difficile sont les plus souvent à l’origine des IAS. L’antibiorésistance fréquente complique encore la prise en charge et des impasses thérapeutiques existent à présent. Les mesures d’hygiène hospitalière bien qu’essentielles sont insuffisantes pour diminuer drastiquement les IAS. Ainsi, des stratégies alternatives à l’antibiothérapie s’avèrent nécessaires pour prévenir et traiter les IAS. Parmi celles-ci, la vaccination et l’immunisation passive sont probablement les plus prometteuses. Nous avons fait une mise au point sur les vaccins disponibles et en développement clinique pour lutter contre les IAS, chez les patients à risque d’IAS et les soignants. L’intérêt de la vaccination grippale et rotavirus chez les patients pour prévenir ces IAS virales a été examiné. Le développement d’un vaccin anti-S. aureus, déjà émaillé de 2 échecs est complexe. Toutefois, ces échecs ont permis d’améliorer les connaissances sur l’immunité anti-S. aureus. La mise à disposition d’un vaccin préventif anti-C. difficile semble plus proche. Pour les autres bactéries gram négatif responsables d’IAS, le développement est moins avancé. La vaccination des patients à risques d’IAS pose également des problèmes de réponse vaccinale qu’il faudra résoudre pour utiliser cette stratégie. Ainsi, la vaccination des soignants, de par l’effet de groupe permet également de prévenir les IAS. Nous faisons ici le point sur l’intérêt de la vaccination des soignants contre la rougeole, la coqueluche, la grippe, la varicelle, l’hépatite B pour réduire les IAS avec des vaccins déjà disponibles.

Assessing the reporting quality of influenza outbreaks in the community

BACKGROUND

High-quality reporting of outbreak characteristics is fundamental to understand the behaviour of various strains of influenza virus and the impact of outbreak management strategies. However, few studies have systematically evaluated the quality of outbreak reporting.

OBJECTIVES

To conduct a systematic analysis and assessment for reporting quality of influenza outbreaks based on a modified version of the STROBE statement, and to examine characteristics associated with reporting quality.

METHODS

A literature search was conducted across 3 online databases (PubMed, Web of Science, MEDLINE) for reports of influenza outbreaks (pandemic H1N1, avian, seasonal). The quality of reports meeting our eligibility criteria was assessed using the Modified STROBE criteria and assigned a score of 30. Mean differences (MD) and 95% confidence intervals (CI) were reported for comparisons of study characteristics.

RESULTS

Sixty-four outbreak reports were available for analyses. The average Modified STROBE score was 20/30. Peer-reviewed articles were associated with a better quality of reporting (MD 2.79, 95% CI 0.79-4.78). Likewise, reports from authors affiliated with public health agencies were associated with better quality than those from academic institutions (MD 1.65, 95% CI-0.27-3.56).

CONCLUSIONS

The development of explicit reporting guidelines specifically geared towards reporting of outbreak investigations proved to be useful. Providing information on patient characteristics, investigation details in introduction and results, as well as addressing limitations that could have biased the findings, were frequently missing in the published reports.

Influenza in long-term care facilities

Long-term care facility environments and the vulnerability of their residents provide a setting conducive to the rapid spread of influenza virus and other respiratory pathogens. Infections may be introduced by staff, visitors or new or transferred residents, and outbreaks of influenza in such settings can have devastating consequences for individuals, as well as placing extra strain on health services. As the population ages over the coming decades, increased provision of such facilities seems likely. The need for robust infection prevention and control practices will therefore remain of paramount importance if the impact of outbreaks is to be minimised. In this review, we discuss the nature of the problem of influenza in long-term care facilities, and approaches to preventive and control measures, including vaccination of residents and staff, and the use of antiviral drugs for treatment and prophylaxis, based on currently available evidence.

Haemagglutinin and neuraminidase sequencing delineate nosocomial influenza outbreaks with accuracy equivalent to whole genome sequencing

OBJECTIVES

We describe haemagglutinin (HA) and neuraminidase (NA) sequencing in an apparent cross-site influenza A(H1N1) outbreak in renal transplant and haemodialysis patients, confirmed with whole genome sequencing (WGS).

METHODS

Isolates were sequenced from influenza positive individuals. Phylogenetic trees were constructed using HA and NA sequencing and subsequently WGS. Sequence data was analysed to determine genetic relatedness of viruses obtained from inpatient and outpatient cohorts and compared with epidemiological outbreak information.

RESULTS

There were 6 patient cases of influenza in the inpatient renal ward cohort (associated with 3 deaths) and 9 patient cases in the outpatient haemodialysis unit cohort (no deaths). WGS confirmed clustered transmission of two genetically different influenza A(H1N1)pdm09 strains initially identified by analysis of HA and NA genes. WGS took longer, and in this case was not required to determine whether or not the two seemingly linked outbreaks were related.

CONCLUSION

Rapid sequencing of HA and NA genes may be sufficient to aid early influenza outbreak investigation making it appealing for future outbreak investigation. However, as next generation sequencing becomes cheaper and more widely available and bioinformatics software is now freely accessible next generation whole genome analysis may increasingly become a valuable tool for real-time Influenza outbreak investigation.

Active Surveillance for Influenza Reduces but Does Not Eliminate Hospital Exposure to Patients With Influenza

OBJECTIVE To describe the frequency, characteristics, and exposure associated with influenza in hospitalized patients in a Toronto hospital DESIGN/METHOD Prospective data collected for consenting patients with laboratory-confirmed influenza and a retrospective review of infection control charts for roommates of cases over 3 influenza seasons RESULTS Of the 661 patients with influenza (age range: 1 week-103 years), 557 were placed on additional precautions upon admission. Of 104 with symptoms detected after admission, 57 cases were community onset and 47 were nosocomial (10 nosocomial were part of outbreaks). A total of 78 cases were detected after admission exposing 143 roommates. Among roommates tested for influenza after exposure, no roommates of community-onset cases and 2 of 16 roommates of nosocomial cases were diagnosed with influenza. Of 637 influenza-infected patients, 25% and 57% met influenza-like illness definitions from the Public Health Agency of Canada (PHAC) and Centers for Disease Control and Prevention (CDC), respectively, and 70.3% met the Provincial Infectious Diseases Advisory Committee (PIDAC) febrile respiratory illness definition. Among the 56 patients with community-onset influenza detected after admission, only 13%, 23%, and 34%, met PHAC, CDC, and PIDAC classifications, respectively. CONCLUSIONS In a setting with extensive screening and testing for influenza, 1 in 6 patients with influenza was not diagnosed until patients and healthcare workers had been exposed for >24 hours. Only 30% of patients with community-onset influenza detected after admission met the Ontario definition intended to identify cases, hampering efforts to prevent patient and healthcare worker exposures and reinforcing the need for prevention through vaccination. Infect Control Hosp Epidemiol 2017;38:387-392.

Hospital surveillance of influenza strains: a concordant image of viruses identified by the Swiss Sentinel system?

BACKGROUND

The Swiss Sentinel system for influenza virus surveillance reports influenza-like illness in the community through a network of primary care practitioners, but the epidemiologic, demographic, and virological characterization may differ from that observed in hospitalized patients with influenza.

OBJECTIVE

To compare demographic and virological data from hospital influenza cases with Sentinel system data during the 2014-2015 season.

METHODS

We included 2623 in- and outpatients with a screening request for influenza A/B in a university teaching hospital in Geneva, Switzerland, and 933 participants from the Swiss Sentinel surveillance system and compared the demographic and virological data of the two populations, including the respective distribution of influenza subtypes, and conducted a phylogenetic comparison at the HA1 level of influenza viruses recovered in community and hospital cases.

RESULTS

There were similar proportions of influenza strains recovered in the hospital and in the community (H3N2, 57.1% and 56.9%; H1N1pdm09, 15.5% and 14.2%; B, 27.4% and 28.8%, respectively). HA1 sequence analysis confirmed that all three strains were genetically similar between the two populations. During this particular season, influenza cases were detected earlier in the hospital than in the Sentinel system.

CONCLUSIONS

Although an influenza surveillance system based on the community can predict the type of influenza strains that will be associated with hospitalizations, it fails to estimate the potential virulence of circulating strains. Further, the population characteristics in the community differ from those in hospitalized patients. This suggests that any national influenza surveillance system should include both community- and hospital-based surveys.

Prevention of hospital-acquired pneumonia in non-ventilated adult patients: a narrative review

Background

Pneumonia is one of the leading hospital-acquired infections worldwide and has an important impact. Although preventive measures for ventilator-associated pneumonia (VAP) are well known, less is known about appropriate measures for prevention of hospital-acquired pneumonia (HAP).

Aim

The purpose of this narrative review is to provide an overview of the current standards for preventing HAP in non-ventilated adult patients.

Methods

A search of the literature up to May 2015 was conducted using Medline for guidelines published by national professional societies or professional medical associations. In addition, a comprehensive search for the following preventive measures was performed: hand hygiene, oral care, bed position, mobilization, diagnosis and treatment of dysphagia, aspiration prevention, viral infections and stress bleeding prophylaxis.

Findings

Regarding international guidelines, several measures were recommended for VAP, whilst no specific recommendations for HAP prevention in non-ventilated patients are available. There is reasonable evidence available that oral care is associated with a reduction in HAP. Early mobilization interventions, swift diagnosis and treatment of dysphagia, and multimodal programmes for the prevention of nosocomial influenza cross-infection, have a positive impact on HAP reduction. The impact of bed position and stress bleeding prophylaxis remains uncertain. Systematic antibiotic prophylaxis for HAP prevention should be avoided.

Conclusion

Scant literature and little guidance is available for the prevention of HAP among non-ventilated adult patients. In addition, the criteria used for the diagnosis of HAP and the populations targeted in the studies selected are heterogeneous. Oral care was the most studied measure and was commonly associated with a decrease in HAP rate, although a broad range of interventions are proposed. No robust evidence is available for other measures. Further high-quality studies are required to evaluate the impact of specific measures on HAP prevention in non-ventilated adult patients.

Transmission and effect of multiple clusters of seasonal influenza in a Swiss geriatric hospital

Objectives

To investigate a nosocomial outbreak of influenza.

Design

Prospective outbreak investigation with active case finding and molecular typing.

Setting

A large academic geriatric hospital in Switzerland.

Participants

Elderly hospitalized adults.

Measurements

Based on syndromic surveillance, a nosocomial influenza outbreak was suspected in February 2012. All suspected cases were screened for respiratory viruses using real‐time reverse transcription polymerase chain reaction of nasopharyngeal swabs. Infection control procedures (droplet precautions with single room isolation whenever possible) were implemented for all suspected or confirmed cases. Specimens positive for influenza viruses were processed and sequenced whenever possible to track transmission dynamics.

Results

Respiratory samples from 155 suspected cases were analyzed during the outbreak period, of which 69 (44%) were positive for influenza virus, 26 (17%) were positive for other respiratory viruses, and 60 (39%) were negative. Three other cases fulfilled clinical criteria for influenza infection but were not sampled, and one individual was admitted with an already positive test, resulting in a total of 73 influenza cases, of which 62 (85%) were classified as nosocomial. Five distinct clusters of nosocomial transmission were identified using viral sequencing, with epidemiologically unexpected in‐hospital transmission dynamics. Seven of 23 patients who experienced influenza complications died. Sixteen healthcare workers experienced an influenza‐like illness (overall vaccination rate, 36%).

Conclusion

Nosocomial influenza transmission caused more secondary cases than repeated community importation during this polyclonal outbreak. Molecular tools revealed complex transmission dynamics. Low healthcare worker vaccination rates and gaps in recommended infection control procedures are likely to have contributed to nosocomial spread of influenza, which remains a potentially life‐threatening disease in elderly adults.