Influence of time to diagnosis of severe influenza on antibiotic use, length of stay, isolation precautions, and mortality: a retrospective study

Childhood Pneumonia Diagnostics in Sub-Saharan Africa: A Systematic Review

BACKGROUND

The prompt and accurate aetiological diagnosis of childhood pneumonia remains a challenge, especially in sub-Saharan Africa (SSA) because of limited resources for disease management.

OBJECTIVE

To review existing diagnostics for childhood pneumonia and potential modalities available to differentiate between bacterial and viral aetiologies in SSA.

METHODS

Online databases were searched for relevant articles published between January 2010 and December 2020 regarding childhood pneumonia diagnosis, conducted in SSA in children less than 18 years of age. The 2020 PRISMA checklist was utilized in appraising the selected studies and the QUADAS-2 tool was employed to assess the risk of bias in each of the studies selected.

RESULTS

A total of 1542 study titles and abstracts were screened following which 45 studies (39 on childhood pneumonia diagnostics and 6 on discriminating between bacterial and viral childhood pneumonia) were selected for review. Microbiological investigations (79.7%) constituted the most utilized index tests with blood-related specimen (32.8%) being the most utilized specimen. The most performed index diagnostic modality was polymerase chain reaction (PCR) (53.1%). The commonest reference gold standard technique was based on clinical diagnosis of the disease (46.2%). Only six studies in SSA attempted at using serum biomarkers, either singly or in combination to distinguish between aetiologies with use of combined biomarkers showing promise.

CONCLUSION

Microbiological investigations are the most employed diagnostic methods for childhood pneumonia in SSA. More studies are required to evaluate the potential use of serum biomarkers; either singly or in combination with the goal of discriminating bacterial and viral childhood pneumonia.

Clinical characteristics and outcomes in hospitalized adult influenza patients: an observational study from Norway 2014-2018

BACKGROUND

Seasonal influenza causes substantial numbers of hospitalizations annually. We have characterized the clinical picture and treatment practice in hospitalized adult influenza patients and assessed whether clinical risk scores on admission or influenza type were associated with severe outcomes.

METHODS

Clinical characteristics and risk scores on admission (CRB65, CRB, SIRS and quick Sequential Organ Failure Assessment [qSOFA]), treatment and severe outcomes (defined as: stay in intensive care unit (ICU), receiving oxygen supplementation or staying ≥5 days in hospital), were recorded in patients hospitalized with influenza at Oslo University Hospital, Norway, between 2014 and 2018.

RESULTS

Among the 156 included patients, 52.6% had influenza A(H3N2), 32.6% influenza B and 12.8% influenza A(H1N1). Median age was 70 years and 59.6% of patients were ≥65 years. Nine (5.8%) of the patients were treated in ICU, 43.0% received oxygen and 47.4% stayed ≥5 days in hospital. Overall, 34.6% of the patients had a high CRB score on admission which was associated with stay in ICU and oxygen supplementation. Multivariate analyses identified age, and pneumonia (46.8%), but not influenza type, to be associated with severe outcomes. Antiviral treatment was given to 37.2% of the patients, while 77.6% received antibiotics. Only 25.5% of patients with influenza B received antiviral therapy.

CONCLUSIONS

The influenza patients were mostly elderly, and few patients were treated in ICU. A high CRB score was associated with severe outcomes with possible implications for patient monitoring. Less than 40% of the patients received antiviral therapy, whereas the majority were treated with antibiotics, indicating potential for optimising treatment strategies.

Risk Factors Associated with Invasive Pulmonary Mycosis Among Severe Influenza Patients in Beijing City, China

Objective

Influenza co-infection with fungal infection increases the risk of death. Our study was to estimate risk factors associated with invasive pulmonary mycosis (IPM) among severe influenza patients at a single center in Beijing, China.

Methods

A retrospective chart review was carried out of all patients with severe influenza admitted to respiratory the department including the respiratory intensive care unit (RICU) during the 2014 to 2019 influenza seasons in Beijing Chao-yang hospital, China. We compared the differences of characteristics and examination outcomes between IPM patients and non-IPM patients, and explored the predictors of IPM by a multivariate logistic regression.

Results

Influenza associated IPM was found in 65 of 131 (49.62%) patients. The average age of IPM patients was 57.28±14.56 years and 70.77% were male. The mortality rate was much higher in the IPM group than the non-IPM group (34.85% versus 18.46%, P=0.026). Older age, hypoimmunity, liver disease, hypertension, positive serum GM test, steroids using, gasping, gastrointestinal symptoms, high APECHEII, low oxygenation index, other viruses co-infection, bacterial co-infection, low lymphocyte counts, low CD4+ T-cell counts, low CD8+ T-cell counts, low RBC, low hemoglobin, low platelets, high N%, low total protein, high CRP, low albumin, low fibrinogen, high BUN, positive serum GM test, more mechanical ventilation requirement, and more renal replacement requirement were risk factors of influenza IPM co-infection.

Conclusion

IPM is a severe complication of influenza hospitalizations. It is associated with increasing mortality, longer hospital stays, and higher hospital charges compared with non-IPM patients. Clinicians caring for patients with severe influenza should consider IPM.

Lower antibiotic prescription rates in hospitalized COVID-19 patients than influenza patients, a prospective study

BACKGROUND

COVID-19 patients are extensively treated with antibiotics despite few bacterial complications. We aimed to study antibiotic use in hospitalized COVID-19 patients compared to influenza patients in two consecutive years. Furthermore, we investigated changes in antibiotic use from the first to second pandemic wave.

METHODS

This prospective study included both patients from two referral hospitals in Bergen, Norway, admitted with influenza (n = 215) during the 2018/2019 epidemic and with COVID-19 (n = 82) during spring/summer 2020, and national data on registered Norwegian COVID-19 hospital admissions from March 2020 to January 2021 (n = 2300). Patient characteristics were compared, and logistic regression analysis was used to identify risk factors for antibiotic use.

RESULTS

National and local COVID-19 patients received significantly less antibiotics (53% and 49%) than influenza patients (69%, p < .001). Early antibiotics contributed to >90% of antibiotic prescriptions in the two local hospitals, and >70% of prescriptions nationally. When adjusted for age, comorbidities, symptom duration, chest X-ray infiltrates and oxygen treatment, local COVID-19 patients still had significantly lower odds of antibiotic prescription than influenza patients (aOR 0.21, 95%CI 0.09-0.50). At the national level, we observed a significant reduction in antibiotic prescription rates in the second pandemic wave compared to the first (aOR 0.35, 95% CI 0.29-0.43).

CONCLUSION

Fewer COVID-19 patients received antibiotics compared to influenza patients admitted to the two local hospitals one year earlier. The antibiotic prescription rate was lower during the second pandemic wave, possibly due to increased clinical experience and published evidence refuting the efficacy of antibiotics in treating COVID-19 pneumonia.

Design and Evaluation of Multiplex One-Step Reverse Transcription PCR-Dipstick Chromatography Method for the Analysis of Seven Respiratory Pathogens

Influenza A, influenza B, severe acute respiratory syndrome coronavirus 2, adenovirus, respiratory syncytial virus, Mycoplasma pneumoniae, and Chlamydophila pneumoniae are common pathogens that can cause severe pneumonia and other symptoms, resulting in acute lower respiratory tract infections. The objective of this study was to design and evaluate a sensitive and specific multiplex one-step reverse transcription PCR (RT-PCR)–dipstick chromatography method for simultaneous rapid detection of these seven pathogens. Streptavidin-coated blue latex particles were used to read out a positive signal. Based on the DNA–DNA hybridization of oligonucleotide sequences (Tag) for forward primer with the complementary oligonucleotide sequence (cTag) on the dipstick and biotin–streptavidin interactions, PCR products were able to be illuminated visually on the dipstick. The specificity and the limit of detection (LOD) were also evaluated. Moreover, the clinical performance of this method was compared with Sanger sequencing for 896 samples. No cross reaction with other pathogens was found, confirming the high specificity of this method. The LOD was 10 copies/µL for each of the tested pathogens, and the whole procedure took less than 40 min. Using 896 samples, the sensitivity and specificity were shown to be no lower than 94.5%. The positive predictive value was higher than 82.1%, and the negative predictive value was higher than 99.5%. The kappa value between the PCR–dipstick chromatography method and Sanger sequencing ranged from 0.869 to 0.940. In summary, our one-step RT-PCR–dipstick chromatography method is a sensitive and specific tool for rapidly detecting multiplex respiratory pathogens.

The Impact of a Standardized Pre-visit Laboratory Testing Panel in the Internal Medicine Outpatient Clinic: a Controlled "On-Off" Trial

BACKGROUND

In several settings, a shorter time to diagnosis has been shown to lead to improved clinical outcomes. The implementation of a rapid laboratory testing allows for a pre-visit testing in the outpatient clinic, meaning that test results are available during the first outpatient visit.

OBJECTIVE

To determine whether the pre-visit laboratory testing leads to a shorter time to diagnosis in the general internal medicine outpatient clinic.

DESIGN

An "on-off" trial, allocating subjects to one of two treatment arms in consecutive alternating blocks.

PARTICIPANTS

All new referrals to the internal medicine outpatient clinic of a university hospital were included, excluding second opinions. A total of 595 patients were eligible; one person declined to participate, leaving data from 594 patients for analysis.

INTERVENTION

In the intervention group, patients had a standardized pre-visit laboratory testing before the first visit.

MAIN MEASURES

The primary outcome was the time to diagnosis. Secondary outcomes were the correctness of the preliminary diagnosis on the first day, health care utilization, and patient and physician satisfaction.

KEY RESULTS

There was no difference in time to diagnosis between the two groups (median 35 days vs 35 days; hazard ratio 1.03 [0.87-1.22]; p = .71). The pre-visit testing group had higher proportions of both correct preliminary diagnoses on day 1 (24% vs 14%; p = .003) and diagnostic workups being completed on day 1 (10% vs 3%; p < .001). The intervention group had more laboratory tests done (50.0 [interquartile range (IQR) 39.0-69.0] vs 43.0 [IQR 31.0-68.5]; p < .001). Otherwise, there were no differences between the groups.

CONCLUSIONS

Pre-visit testing did not lead to a shorter overall time to diagnosis. However, a greater proportion of patients had a correct diagnosis on the first day. Further studies should focus on customizing pre-visit laboratory panels, to improve their efficacy.

TRIAL REGISTRATION

NL5009.

Surveillance of respiratory syncytial virus infections in adults, Austria, 2017 to 2019

Respiratory syncytial virus (RSV) testing is generally available in most care centres, but it is rarely performed because clinicians' seldom suspect RSV to be the underlying pathogen in adults with respiratory disease. Here, we evaluate the impact of broad combined influenza/RSV testing on the clinical practice. Overall, 103 patients were tested positively for RSV. Our study indicates that positively tested patients were mostly of advanced age and suffered from chronic diseases. Mortality was significant in our cohort and higher in patients with advanced age. Further, we report a significant increase in detected RSV cases but also in detection rate. Together, these findings suggest that implementation of a combined influenza/RSV testing led to a significant increase in detection rate, supported clinicians establishing the correct diagnosis and allowed a safe and controlled handling of RSV patients.

Clinical performance of the GenMark Dx ePlex respiratory pathogen panels for upper and lower respiratory tract infections

The GenMark Dx ePlex Respiratory Pathogen Panel (RP) is a multiplexed nucleic acid test for the qualitative detection of common viral and a few bacterial causes of respiratory tract infections. The ePlex RP has received FDA clearance for nasopharyngeal swab (NPS) specimens collected in viral transport media. In this study, we evaluated the performance of the ePlex RP panel in comparison to the NxTAG Respiratory Pathogen Panel (NxTAG-RPP) from Luminex in use in our laboratory, not only for NPS but also for bronchoalveolar lavage specimens (BAL). We also evaluated the impact of implementing the ePlex RP on the test turn-around time (TAT). The newest panel from GenMark Dx, the ePlex Respiratory Pathogen Panel 2 (RP2), which added the SARS-CoV-2 target to the RP was also evaluated for NPS. Verification of the performance of the ePlex RP for both NPS and BAL showed 93.3 % and 84.9 % total agreement with the NxTAG-RPP respectively. An overall comparison of the TAT after implementing the ePlex RP as compared to the NxTAG-RPP assay showed an average decrease of almost seven-fold.

Characteristics and Effectiveness of the Coronavirus Disease 2019 (COVID-19) Prevention and Control in a Representative City in China

BACKGROUND SARS-CoV-2 has caused a pandemic. Control measures differ among countries. It is necessary to assess the effectiveness of these control measures. MATERIAL AND METHODS We collected the data of COVID-19 patients and control measures between January 18, 2020 and September 18, 2020 from the Changshou District and analyzed the clinical characteristics, epidemiological data, and the adjustment of policies to assess the effectiveness of control measures. The control of COVID-19 was divided into 2 stages, with the lifting of lockdown in Hubei province (March 25, 2020) as a dividing line. RESULTS We identified 32 patients through different means in the first stage. All the imported patients entered this area before the lockdown. In 93.1% of patients, the last exposure occurred before the implementation of the stay-at-home order and centralized isolation. Tracing of high-risk people and RT-PCR screening identified 56.3% of cases. In the second stage, all the high-risk people were under centralized isolation. Nine asymptomatic patients were identified. City lockdown and stay-at-home orders were not issued again, and no second-generation patients were found. CONCLUSIONS We have provided a successful model to control the transmission of COVID-19 in a short period.

Point-of-care influenza testing impacts clinical decision, patient flow and length of stay in hospitalized adults

Background

Influenza is difficult to distinguish clinically from other acute respiratory infections. Rapid laboratory diagnosis can help initiate early effective antiviral treatment and isolation. Implementing a novel point-of-care test (POCT) for influenza in the emergency department (ED) could improve treatment and isolation strategies and reduce the length of stay (LOS).

Methods

In a prospective, controlled observational cohort study, we enrolled patients admitted due to acute respiratory illness to 2 public hospitals in Bergen, Norway, one using a rapid POCT for influenza (n = 400), the other (n = 167) using conventional rapid laboratory-based assay.

Results

Prevalence of influenza was similar in the 2 hospitals (154/400, 38% vs 38%, 63/167; P = .863). Most patients in both hospitals received antiviral (83% vs 81%; P = .703) and antibiotic treatment (72% vs 62%; P = .149). Isolation was more often initiated in ED in the hospital using POCT (91% vs 80%; P = .025). Diagnosis by POCT was associated with shorter hospital stay; old age, diabetes, cancer, and use of antibiotics, particularly broad-spectrum antibiotics, were associated with prolonged stay.

Conclusions

POCT implementation in ED resulted in improved targeted isolation and shorter LOS. Regardless of POCT use, most influenza patients received antivirals (>80%) and antibiotics (>69%).

Outbreak detection of influenza-like illness in Prey Veng Province, Cambodia: a community-based surveillance

On June 4, 2016, the Prey Veng Provincial Health Department reported a total of 107 patients with influenza-like illness (ILI) from Chakhlanh village to the Cambodian Ministry of Health. To confirm the outbreak and evaluate its clinical and epidemiological characteristics, the investigation team visited the village and reviewed the case-based surveillance (CBS) data on severe respiratory infection (SRI) and patients' records in health facilities. The team interviewed all households in the village from May 1 to June 5, 2016 and obtained the following data: age, medical history, date of onset, treatment, symptoms, and history of contact with patients or dead poultry. Nasal swab samples were collected from suspected ILI cases to test for influenza virus by RT-PCR. The investigation detected 498 suspected ILI cases, including 288 females. Although the incidence of suspected ILI cases who visited health centers was 63.0 per 1,000 persons per month, the attack rate was 27.1 per 100 population. The major age group was 5-14 years followed by 0-4 years. Major symptoms were cough, fever, runny nose, and headache. Six of seven nasal swab samples were positive for influenza A/H1N1 pdm09 virus. Most children with flu symptoms had contact with previous cases. This study showed that the ILI outbreak might be caused by seasonal influenza A/H1N1 pdm09 spread from person to person. Poor living conditions and poor hygiene and sanitation practices were environmental factors that caused the outbreak. As the CBS system was unable to identify this epidemic, it needs to be improved.

Clinical impact of rapid diagnostics using Xpert Flu/RSV™ PCR on antimicrobial stewardship initiatives during influenza season

BACKGROUND

Despite the availability of several rapid Influenza tests (RIT), the literature on its impact on antimicrobial stewardship programs (AMS) is minimal. Studies utilising rapid point of care tests (POCT) have shown benefit in terms of shortening antimicrobial therapy and prescriptions of antivirals. We designed this study to assess whether RIT had an impact on antibiotic cessation.

METHODS

Xpert Flu/RSV (Cepheid, CA) was performed on all patients who presented with influenza-like illness (ILI) in 2017. Clinical data was collected from electronic medical records (eMR). Patients with RSV were not included. Turnaround time (TAT) for the test was time from specimen collection until when the result was either notified or appeared on eMR. Standard univariate analysis and multivariable regression analysis (MVRA) were done.

RESULTS

A total of 665 patients tested positive-Influenza A (63%) and B (37%). After positive results, antimicrobials were ceased in 34% (226/665) or not given in 10% (71/665) cases. Median TAT was 7 h, with 50% of tests completed in less than 6 h 56% (368/665) of patients had their antibiotics continued. On MVRA, results of RIT within 6-12 h resulted in most antibiotic cessation (73%, OR 1.55, p = 0.01). It was found that antibiotics are continued in immunosuppressed patients (OR 2.88, p < 0.01), patients with pneumonia (OR 18.8, p < 0.01) and with underlying COPD (OR 2.43, p = 0.03).

CONCLUSION

Influenza patients are more likely to have their antibiotics continued with underlying COPD, pneumonia, or immunosuppression. Results of RIT within 6-12 h can help clinicians in deciding on cessation of antibiotics in patients.

Factors affecting the discharge of patients from hospital with seasonal influenza-the role of the Rapid Influenza testing in hospital discharges

Influenza is a major cause of presentations to the emergency departments. Introduction of the Rapid Influenza tests has assisted with diagnosis and facilitated patient discharges. We designed this study to identify factors affecting hospital discharge and to understand the role of Rapid Influenza testing. A retrospective observational study of patients was done during influenza season in 2017. Clinical data was obtained from electronic medical records. Rapid Influenza testing was performed using Xpert Flu/RSV (Cepheid, USA). Univariate and multivariate analysis was done using SPSS Version 26 (IBM, NY). A total of 665 patients presented with laboratory-confirmed influenza. Patients discharged from the hospital were younger (median age 62 vs 68, p = 0.031). Patients with immunosuppression, chronic obstructive pulmonary disease (COPD) and pneumonia were more likely to be admitted to hospital. Rapid testing done with a turnaround (TAT) of 2 h (27.8% vs 17.8%, p = 0.002) and with a TAT of 6 h (55% vs 46.3%, p = 0.026) of the patient presentation was associated with a higher rate of hospital discharge. Median TAT of the RIT was 6 h (IQR 1-40 h). On multivariable analysis, RIT TAT of ≤ 2 h (OR 1.62, p = 0.013) was associated with higher likelihood of patients being discharged, whereas immunosuppressed patients (OR 2.25, p = 0.011), COPD (OR 2.42, p = 0.001) and pneumonia on presentation (OR 8.10, p < 0.001) were more likely to get admitted. Patients with COPD, pneumonia on presentation and those with immunosuppression are more likely to be admitted. Rapid Influenza tests can facilitate the discharge of patients from hospital.

The TransFLUas influenza transmission study in acute healthcare - recruitment rates and protocol adherence in healthcare workers and inpatients

Background

Detailed knowledge about viral respiratory disease transmission dynamics within healthcare institutions is essential for effective infection control policy and practice. In the quest to study viral transmission pathways, we aimed to investigate recruitment rates and adherence of healthcare workers (HCWs) and hospital inpatients with a study protocol that involves prospective surveillance based on daily mid-turbinate nasal swabs and illness diaries.

Methods

Single center prospective surveillance of patients and HCWs in three different hospital departments of a tertiary care center during an entire influenza season in Switzerland. Inpatients and acute care HCWs were asked to provide mid-turbinate nasal swabs and illness diaries on a daily basis. Study protocol adherence and recruitment rates were the primary outcomes of interest.

Results

A total 251 participants (59 (23.5%) health care workers and 192 (76.5%) inpatients) were recruited from three different hospital wards. Recruitment rates differed between HCWs (62.1% of eligible HCWs) and inpatients (32.5%; P < 0.001), but not within HCWs (P = 0.185) or inpatients (P = 0.301) of the three departments. The total number of study-days was 7874; 2321 (29.5%) for inpatients and 5553 (70.5%) for HCWs. HCWs were followed for a median of 96 days (range, 71–96 days) and inpatients for 8 days (range, 3–77 days). HCWs provided swabs on 73% (range, 0–100%) of study days, and diaries on 77% (range 0–100%). Inpatients provided swabs and diaries for 83% (range, 0–100%) of days in hospital. In HCWs, increasing age, working in internal medicine and longer duration of total study participation were positively associated with the proportion of swabs and diaries collected. Adherence to the study protocol was significantly lower in physicians as compared to nurses for both swabs (P = 0.042) and diaries (P = 0.033). In inpatients, no association between demographic factors and adherence was detected.

Conclusions Prospective surveillance of respiratory viral disease was feasible in a cohort of inpatients and HCWs over an entire influenza season, both in terms of recruitment rates and adherence to a study protocol that included daily specimen collection and illness diaries.

Trial registration

clinicaltrials.govNCT02478905. Date of registration June 23, 2015.

Laboratory Diagnosis of Respiratory Tract Infections in Children - the State of the Art

In the pediatric population, respiratory infections are the most common cause of physician visits. Although many respiratory illnesses are self-limiting viral infections that resolve with time and supportive care, it can be critical to identify the causative pathogen at an early stage of the disease in order to implement effective antimicrobial therapy and infection control. Over the last few years, diagnostics for respiratory infections have evolved substantially, with the development of novel assays and the availability of updated tests for newer strains of pathogens. Newer laboratory methods are rapid, highly sensitive and specific, and are gradually replacing the conventional gold standards, although the clinical utility of these assays is still under evaluation. This article reviews the current laboratory methods available for testing for respiratory pathogens and discusses the advantages and disadvantages of each approach.

Testing for Respiratory Viruses in Adults With Severe Lower Respiratory Infection

Viral pathogens are a common cause of severe lower respiratory tract infection in adults. Our ability to rapidly and accurately identify viral infections has dramatically improved as slow culture-based techniques have been largely replaced by multiplex high-throughput systems. Given these advances, reevaluation of the role of respiratory viral testing in adults presenting with lower respiratory tract infection is important. This article reviews the potential benefits of testing, provides an overview of the most commonly used diagnostic techniques, and considers whether current evidence supports routine testing.

Influence of time to diagnosis of severe influenza on antibiotic use, length of stay, isolation precautions, and mortality: a retrospective study

Background

Timely diagnosis of influenza infection in patients might help reduce antibiotic use during influenza seasons and, consequently, antibiotic selection pressure. In this retrospective cohort study, we aimed to evaluate whether time to influenza diagnosis in patients with severe influenza is associated with the duration of antibiotic therapy.

Methods

We retrospectively included all hospitalized patients >16 years who tested positive for influenza A or B by polymerase chain reaction during influenza seasons 2013/2014 or 2014/2015 at the University Hospital Zurich. The primary aim was to assess the association between timing of laboratory‐confirmed influenza diagnosis and duration of antibiotic therapy. Secondary outcomes were length of hospital stay, duration of isolation precautions, and mortality. Early diagnosis was defined as laboratory confirmation on the day of or the day after hospital admission or symptom onset.

Results

A total of 126 patients were included (median age 57 years). Timing of influenza diagnosis was not associated with the duration of antibiotic treatment, the duration of isolation precautions, or mortality. Early influenza was associated with reduced length of hospital stay (median 7 vs 9 days [P=.014]) in patients with community‐acquired influenza.

Conclusions

Although the duration of antibiotic therapy and mortality were found unaffected by early influenza diagnosis, our data indicate that it is linked with a reduction in the length of hospitalization in patients with community‐acquired influenza. This highlights a need to also fully understand the effect of time to diagnosis of bacterial pathogens on antibiotic prescribing patterns in order to exploit the potential of early influenza diagnosis in patient care.