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

Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23

OBJECTIVES

We evaluated Nanopore sequencing for influenza surveillance.

METHODS

Influenza A and B PCR-positive samples from hospital patients in Oxfordshire, UK, and a UK-wide population survey from winter 2022-23 underwent Nanopore sequencing following targeted rt-PCR amplification.

RESULTS

From 941 infections, successful sequencing was achieved in 292/388 (75 %) available Oxfordshire samples: 231 (79 %) A/H3N2, 53 (18 %) A/H1N1, and 8 (3 %) B/Victoria and in 53/113 (47 %) UK-wide samples. Sequencing was more successful at lower Ct values. Most same-sample replicate sequences had identical haemagglutinin segments (124/141, 88 %); 36/39 (92 %) Illumina vs. Nanopore comparisons were identical, and 3 (8 %) differed by 1 variant. Comparison of Oxfordshire and UK-wide sequences showed frequent inter-regional transmission. Infections were closely-related to 2022-23 vaccine strains. Only one sample had a neuraminidase inhibitor resistance mutation. 849/941 (90 %) Oxfordshire infections were community-acquired. 63/88 (72 %) potentially healthcare-associated cases shared a hospital ward with ≥ 1 known infectious case. 33 epidemiologically-plausible transmission links had sequencing data for both source and recipient: 8 were within ≤ 5 SNPs, of these, 5 (63 %) involved potential sources that were also hospital-acquired.

CONCLUSIONS

Nanopore influenza sequencing was reproducible and antiviral resistance rare. Inter-regional transmission was common; most infections were genomically similar. Hospital-acquired infections are likely an important source of nosocomial transmission and should be prioritised for infection prevention and control.

Nosocomial influenza in a pediatric general ward: Effects of isolation and cohort placement of children with influenza

OBJECTIVE

Many studies have described nosocomial outbreaks of influenza in specialized wards. We evaluated nosocomial transmission of influenza in a pediatric general ward.

DESIGN

Retrospective observational study.

SETTING

Single secondary hospital.

PATIENTS

The study included 814 hospitalized children with influenza between September 2015 and August 2020.

METHODS

The medical records of the included children were retrospectively reviewed, and clinical characteristics of children with community-acquired (CA) influenza and hospital-acquired (HA) influenza were determined. The room of each included child during hospitalization was traced to identify the children exposed to them.

RESULTS

CA influenza and HA influenza were diagnosed in 789 (96.9%) and 25 (3.1%) children, respectively. Among children with CA influenza, 691 (87.6%) were isolated or place in a cohort on admission. In total, 98 children (12.4%) admitted to multibed rooms exposed 307 children with noninfluenza diseases to influenza during 772 patient days; 3 exposed children (1.0%) were diagnosed with HA influenza. Including these 3 children, 25 children (19 without definite in-hospital exposure to influenza and 3 exposed to other children with HA influenza) were diagnosed with HA influenza, and 11 (44.0%) exposed 31 children with noninfluenza diseases to influenza for 85 patient days. Also, 3 exposed children (9.7%) were diagnosed with HA influenza, a significantly higher rate than that for CA influenza (P = .005). The clinical characteristics were comparable between children with HA influenza and those with CA influenza.

CONCLUSIONS

Cohort placement of children with influenza in a pediatric general ward can be effective in controlling nosocomial transmission of influenza. However, control measures for children with HA influenza should be emphasized.

Vaccine mandates for healthcare workers beyond COVID-19

We provide ethical criteria to establish when vaccine mandates for healthcare workers are ethically justifiable. The relevant criteria are the utility of the vaccine for healthcare workers, the utility for patients (both in terms of prevention of transmission of infection and reduction in staff shortage), and the existence of less restrictive alternatives that can achieve comparable benefits. Healthcare workers have professional obligations to promote the interests of patients that entail exposure to greater risks or infringement of autonomy than ordinary members of the public. Thus, we argue that when vaccine mandates are justified on the basis of these criteria, they are not unfairly discriminatory and the level of coercion they involve is ethically acceptable-and indeed comparable to that already accepted in healthcare employment contracts. Such mandates might be justified even when general population mandates are not. Our conclusion is that, given current evidence, those ethical criteria justify mandates for influenza vaccination, but not COVID-19 vaccination, for healthcare workers. We extend our arguments to other vaccines.

Investigating Epidemiologic and Molecular Links Between Patients With Community- and Hospital-Acquired Influenza A: 2017-2018 and 2019-2020, Michigan

Background

Hospital-acquired influenza virus infection (HAII) can cause severe morbidity and mortality. Identifying potential transmission routes can inform prevention strategies.

Methods

We identified all hospitalized patients testing positive for influenza A virus at a large, tertiary care hospital during the 2017-2018 and 2019-2020 influenza seasons. Hospital admission dates, locations of inpatient service, and clinical influenza testing information were retrieved from the electronic medical record. Time-location groups of epidemiologically linked influenza patients were defined and contained ≥1 presumed HAII case (first positive ≥48 hours after admission). Genetic relatedness within time-location groups was assessed by whole genome sequencing.

Results

During the 2017-2018 season, 230 patients tested positive for influenza A(H3N2) or unsubtyped influenza A including 26 HAIIs. There were 159 influenza A(H1N1)pdm09 or unsubtyped influenza A-positive patients identified during the 2019-2020 season including 33 HAIIs. Consensus sequences were obtained for 177 (77%) and 57 (36%) of influenza A cases in 2017-2018 and 2019-2020, respectively. Among all influenza A cases, there were 10 time-location groups identified in 2017-2018 and 13 in 2019-2020; 19 of 23 groups included ≤4 patients. In 2017-2018, 6 of 10 groups had ≥2 patients with sequence data, including ≥1 HAII case. Two of 13 groups met this criteria in 2019-2020. Two time-location groups from 2017-2018 each contained 3 genetically linked cases.

Conclusions

Our results suggest that HAIIs arise from outbreak transmission from nosocomial sources as well as single infections from unique community introductions.

Genomic Epidemiology and Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Congregate Healthcare Facilities in Santa Clara County, California

BACKGROUND

Outbreaks of SARS-CoV-2 in long-term care facilities (LTCFs) cause significant morbidity and mortality. Mapping viral transmission within and between facilities by combining genomic sequencing with epidemiologic investigations enables targeting infection-control interventions.

METHODS

We conducted weekly surveillance of residents and staff in LTCFs in Santa Clara County, California, with ≥1 confirmed COVID-19 case between March and July 2020. Positive samples were referred for whole-genome sequencing. Epidemiological investigations and phylogenetic analyses of the largest outbreaks (>30 cases) were carried out in 6 LTCFs (Facilities A through F).

RESULTS

Among the 61 LTCFs in the county, 41 had ≥1 confirmed case during the study period, triggering weekly SARS-CoV-2 testing. The 6 largest outbreaks accounted for 60% of cases and 90% of deaths in LTCFs, although the bed capacity of these facilities represents only 11% of the LTCF beds in the county. Phylogenetic analysis of 196 whole-genome sequences recovered from those facilities showed that each outbreak was monophyletic, with staff and residents sharing a common viral lineage. Outbreak investigations revealed that infected staff members often worked at multiple facilities, and in 1 instance, a staff member infected while working in 1 facility was the likely index case in another.

CONCLUSIONS

We detected a pattern of rapid and sustained transmission after a single introduction of SARS-CoV-2 in 6 large LTCF outbreaks, with staff playing a key role in transmission within and between facilities. Infection control, testing, and occupational policies to reduce exposure and transmission risk for staff are essential components to keeping facility residents safe.

Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review

In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, selecting a method can be difficult. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We identified 22 methods from the 41 selected articles. We defined three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family, and a simultaneous phylogenetic family. We discussed methods according to the data needed as well as the underlying sequence mutation, within-host evolution, transmission, and case observation. In the non-phylogenetic family consisting of eight methods, pairwise genetic distances were estimated. In the phylogenetic families, transmission trees were inferred from phylogenetic trees either simultaneously (nine methods) or sequentially (five methods). While a majority of methods (17/22) modeled the transmission process, few (8/22) took into account imperfect case detection. Within-host evolution was generally (7/8) modeled as a coalescent process. These practical and theoretical considerations were highlighted in order to help select the appropriate method for an outbreak.

New Insights into the Prevention of Hospital-Acquired Pneumonia/Ventilator-Associated Pneumonia Caused by Viruses

A fifth or more of hospital-acquired pneumonias may be attributable to respiratory viruses. The SARS-CoV-2 pandemic has clearly demonstrated the potential morbidity and mortality of respiratory viruses and the constant threat of nosocomial transmission and hospital-based clusters. Data from before the pandemic suggest the same can be true of influenza, respiratory syncytial virus, and other respiratory viruses. The pandemic has also helped clarify the primary mechanisms and risk factors for viral transmission. Respiratory viruses are primarily transmitted by respiratory aerosols that are routinely emitted when people exhale, talk, and cough. Labored breathing and coughing increase aerosol generation to a much greater extent than intubation, extubation, positive pressure ventilation, and other so-called aerosol-generating procedures. Transmission risk is proportional to the amount of viral exposure. Most transmissions take place over short distances because respiratory emissions are densest immediately adjacent to the source but then rapidly dilute and diffuse with distance leading to less viral exposure. The primary risk factors for transmission then are high viral loads, proximity, sustained exposure, and poor ventilation as these all increase net viral exposure. Poor ventilation increases the risk of long-distance transmission by allowing aerosol-borne viruses to accumulate over time leading to higher levels of exposure throughout an enclosed space. Surgical and procedural masks reduce viral exposure but do not eradicate it and thus lower but do not eliminate transmission risk. Most hospital-based clusters have been attributed to delayed diagnoses, transmission between roommates, and staff-to-patient infections. Strategies to prevent nosocomial respiratory viral infections include testing all patients upon admission, preventing healthcare providers from working while sick, assuring adequate ventilation, universal masking, and vaccinating both patients and healthcare workers.

New insights and antimicrobial stewardship opportunities in viral pneumonia: five lung ultrasound cases

Background

Antimicrobial stewardship is crucial to avoid antimicrobial resistance in microbes and adverse drug effects in patients. In respiratory infections, however, viral pneumonia is difficult to distinguish from bacterial pneumonia, which explains the overuse of antibiotic therapy in this indication.

Cases

Five cases of lung consolidation are presented. Lung ultrasound, in conjunction with procalcitonin levels, were used to exclude or corroborate bacterial pneumonia.

Conclusion

Lung ultrasound is easy to learn and perform and is helpful in guiding diagnosis in unclear cases of pneumonia and may also offer new insights into the spectrum of certain virus diseases. The use of lung ultrasound can raise awareness in clinicians of the need for antimicrobial stewardship and may help to avoid the unnecessary use of antibiotics.

Supplementary Information

The online version of this article (10.1007/s00508-021-01946-4) contains supplementary material, which is available to authorized users.

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.

Real-Time Investigation of a Large Nosocomial Influenza A Outbreak Informed by Genomic Epidemiology

BACKGROUND

Nosocomial respiratory virus outbreaks represent serious public health challenges. Rapid and precise identification of cases and tracing of transmission chains is critical to end outbreaks and to inform prevention measures.

METHODS

We combined conventional surveillance with influenza A virus (IAV) genome sequencing to identify and contain a large IAV outbreak in a metropolitan healthcare system. A total of 381 individuals, including 91 inpatients and 290 health care workers (HCWs), were included in the investigation.

RESULTS

During a 12-day period in early 2019, infection preventionists identified 89 HCWs and 18 inpatients as cases of influenza-like illness (ILI), using an amended definition without the requirement for fever. Sequencing of IAV genomes from available nasopharyngeal (NP) specimens identified 66 individuals infected with a nearly identical strain of influenza A H1N1pdm09 (43 HCWs, 17 inpatients, and 6 with unspecified affiliation). All HCWs infected with the outbreak strain had received the seasonal influenza virus vaccination. Characterization of five representative outbreak viral isolates did not show antigenic drift. In conjunction with IAV genome sequencing, mining of electronic records pinpointed the origin of the outbreak as a single patient and a few interactions in the emergency department that occurred one day prior to the index ILI cluster.

CONCLUSIONS

We used precision surveillance to delineate a large nosocomial IAV outbreak, mapping the source of the outbreak to a single patient rather than HCWs as initially assumed based on conventional epidemiology. These findings have important ramifications for more effective prevention strategies to curb nosocomial respiratory virus outbreaks.

Point of care testing of Influenza A/B and RSV in an adult respiratory assessment unit is associated with improvement in isolation practices and reduction in hospital length of stay

Introduction. Every winter seasonal influenza and other viral respiratory infections increase pressure on the health services and are associated with nosocomial infection and morbidity.Aim. To compare provision of point-of-care (POC) testing with laboratory-based testing for influenza and RSV detection on an adult respiratory assessment unit to assess the impact on isolation practices and length of stay (LOS).Methodology. Prospective interrupted 'on-off' study in adults admitted to the respiratory unit between December 2018 and April 2019 with a suspected respiratory tract infection. Nasopharyngeal samples were tested using either the GeneXpert rapid POC test for influenza and RSV (on-period), or were sent to the laboratory for multiplex PCR testing against a panel of 12 respiratory viruses (off-period). Outcome measures were time to patient isolation for infection control, LOS and turnaround time from admission to test results.Results. Of 1145 patients evaluated, 755 were tested with POC and 390 with laboratory multiplex; a respiratory virus was identified in 164 (21.7 %) and 138 (35.4 %) patients respectively. A positive POC test was associated with a shorter time to isolation (mean difference 16.9 h, P<0.001), shorter LOS (mean difference 15.5 h, P=0.05,) and shorter turnaround time (mean difference 28.3 h, P<0.001), compared to laboratory testing.Conclusion. Use of GeneXpert POC testing for Flu/RSV is associated with rapid reporting of results with significant improvements in isolation practices and reductions in LOS.

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.

Recommended hospital preparations for future cases and outbreaks of novel influenza viruses

Introduction: Seasonal influenza epidemics and periodic pandemics are important causes of morbidity and mortality. Influenza transmits predominantly by respiratory droplets and fomites but opportunistic airborne transmission may occur in the hospital setting due to overcrowding, poor compliance with infection control measures, and performance of aerosol-generating procedures.Areas covered: This article reviews the risk factors of nosocomial influenza outbreaks and discusses clinical, diagnostic, and treatment aspects of seasonal and avian influenza to facilitate hospital preparations for future influenza outbreaks. Literature search was conducted through PubMed of relevant peer-reviewed full papers in English journals with inclusion of relevant publications by the WHO and US CDC.Expert opinion: Accurate and rapid identification of an influenza outbreak is important to facilitate patient care and prevent nosocomial transmission. Timely treatment with a neuraminidase inhibitor (NAI) for adults hospitalized with severe influenza is associated with lower mortality and better clinical outcomes. Baloxavir, a polymerase endonuclease inhibitor, offers a new treatment alternative and its role in combination with NAI for treatment of severe influenza is being investigated. High-dose systemic corticosteroids are associated with worse outcomes in patients with severe influenza. It is important to develop more effective antiviral and immuno-modulating therapies for the treatment of influenza infections.