Comparison of combined nose-throat swabs with nasopharyngeal aspirates for detection of pandemic influenza A/H1N1 2009 virus by real-time reverse transcriptase PCR

Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods

Early and accurate diagnosis of respiratory pathogens and associated outbreaks can allow for the control of spread, epidemiological modeling, targeted treatment, and decision making-as is evident with the current COVID-19 pandemic. Many respiratory infections share common symptoms, making them difficult to diagnose using only syndromic presentation. Yet, with delays in getting reference laboratory tests and limited availability and poor sensitivity of point-of-care tests, syndromic diagnosis is the most-relied upon method in clinical practice today. Here, we examine the variability in diagnostic identification of respiratory infections during the annual infection cycle in northern New Mexico, by comparing syndromic diagnostics with polymerase chain reaction (PCR) and sequencing-based methods, with the goal of assessing gaps in our current ability to identify respiratory pathogens. Of 97 individuals that presented with symptoms of respiratory infection, only 23 were positive for at least one RNA virus, as confirmed by sequencing. Whereas influenza virus (n = 7) was expected during this infection cycle, we also observed coronavirus (n = 7), respiratory syncytial virus (n = 8), parainfluenza virus (n = 4), and human metapneumovirus (n = 1) in individuals with respiratory infection symptoms. Four patients were coinfected with two viruses. In 21 individuals that tested positive using PCR, RNA sequencing completely matched in only 12 (57%) of these individuals. Few individuals (37.1%) were diagnosed to have an upper respiratory tract infection or viral syndrome by syndromic diagnostics, and the type of virus could only be distinguished in one patient. Thus, current syndromic diagnostic approaches fail to accurately identify respiratory pathogens associated with infection and are not suited to capture emerging threats in an accurate fashion. We conclude there is a critical and urgent need for layered agnostic diagnostics to track known and unknown pathogens at the point of care to control future outbreaks.

Assessment of SARS-CoV-2 viral loads in combined nasal-and-throat swabs collected from COVID-19 individuals under the Universal Community Testing Programme in Hong Kong

BACKGROUND

Combined nasal-and-throat swabs (CNTS) is less invasive and easy to execute. CNTS also induces lower risk to healthcare workers upon collection. However, there is a lack of data on viral load assessment for population-wide testing.

OBJECTIVE

This study assessed if CNTS is suitable as an alternative specimen type for the detection of SARS-CoV-2.

METHODS

We assessed the viral load of SARS-CoV-2 in CNTS collected from COVID-19 individuals through the 2-week period of the Universal Community Testing Programme (UCTP) conducted in Hong Kong. In addition, we compared viral loads of SARS-CoV-2 for the paired CNTS and non-CNTS specimens among these individuals.

RESULTS

This UCTP identified 48 COVID-19 individuals from nearly 2 million specimens collected. The viral loads of SARS-CoV-2 varied widely, cycle threshold values Ct 16.28-36.94, among symptoms and asymptomatic individuals. The viral loads for the paired CNTS and non-CNTS specimens were comparable.

CONCLUSIONS

This study demonstrated that CNTS could be a specimen of choice for diagnosis of SARS-CoV-2.

Effect of Throat Washings on Detection of 2019 Novel Coronavirus

The 2019 novel coronavirus was detected in the self-collected throat washings. Positive testing rate of throat washing was much higher than that of Nasopharyngeal swabs. Throat washing is a promising candidate for 2019-nCoV screening and monitoring due to its noninvasive and reliability.

Comparison of detection rate of 16 sampling methods for respiratory viruses: a Bayesian network meta-analysis of clinical data and systematic review

BACKGROUND

Respiratory viruses (RVs) is a common cause of illness in people of all ages, at present, different types of sampling methods are available for respiratory viral diagnosis. However, the diversity of available sampling methods and the limited direct comparisons in randomised controlled trials (RCTs) make decision-making difficult. We did a network meta-analysis, which accounted for both direct and indirect comparisons, to determine the detection rate of different sampling methods for RVs.

METHODS

Relevant articles were retrieved comprehensively by searching the online databases of PubMed, Embase and Cochrane published before 25 March 2020. With the help of R V.3.6.3 software and 'GeMTC V.0.8.2' package, network meta-analysis was performed within a Bayesian framework. Node-splitting method and I ² test combined leverage graphs and Gelman-Rubin-Brooks plots were conducted to evaluate the model's accuracy. The rank probabilities in direct and cumulative rank plots were also incorporated to rank the corresponding sampling methods for overall and specific virus.

RESULTS

16 sampling methods with 54 438 samples from 57 literatures were ultimately involved in this study. The model indicated good consistency and convergence but high heterogeneity, hence, random-effect analysis was applied. The top three sampling methods for RVs were nasopharyngeal wash (NPW), mid-turbinate swab (MTS) and nasopharyngeal swab (NPS). Despite certain differences, the results of virus-specific subanalysis were basically consistent with RVs: MTS, NPW and NPS for influenza; MTS, NPS and NPW for influenza-a and b; saliva, NPW and NPS for rhinovirus and parainfluenza; NPW, MTS and nasopharyngeal aspirate for respiratory syncytial virus; saliva, NPW and MTS for adenovirus and sputum; MTS and NPS for coronavirus.

CONCLUSION

This network meta-analysis provides supporting evidences that NPW, MTS and NPS have higher diagnostic value regarding RVs infection, moreover, particular preferred methods should be considered in terms of specific virus pandemic. Of course, subsequent RCTs with larger samples are required to validate our findings.

Comparison of participant-collected nasal and staff-collected oropharyngeal specimens for human ribonuclease P detection with RT-PCR during a community-based study

We analyzed 4,352 participant- and staff-collected respiratory specimens from 2,796 subjects in the Oregon Child Absenteeism due to Respiratory Disease Study. Trained staff collected oropharyngeal specimens from school-aged children with acute respiratory illness while household participants of all ages collected their own midturbinate nasal specimens in year one and anterior nasal specimens in year two. Human ribonuclease P levels were measured using RT-PCR for all staff- and participant-collected specimens to determine adequacy, defined as Cycle threshold less than 38. Overall, staff- and participant-collected specimens were 99.9% and 96.4% adequate, respectively. Participant-collected midturbinate specimens were 95.2% adequate in year one, increasing to 97.2% in year two with anterior nasal collection. The mean human ribonuclease P Cycle threshold for participant-collected specimens was 31.18 in year one and 28.48 in year two. The results from this study suggest that community-based participant collection of respiratory specimens is comparable to staff-collected oropharyngeal specimens, is feasible, and may be optimal with anterior nasal collection.

Adenovirus load correlates with respiratory disease severity among hospitalized pediatric patients

OBJECTIVES

Human adenoviruses (HAdVs) are common pathogens that can cause respiratory, gastrointestinal and other infections. We investigated the correlation between adenovirus viral load in clinical respiratory samples and the respiratory disease severity in pediatric patients.

METHODS

Medical records of patients hospitalized in the Sheba Medical Center (SMC) with confirmed adenovirus infection were retrospectively analyzed. The possible correlation between disease severity score and Real time PCR 'cycle threshold' (Ct), a proxy of viral load, was assessed in patients aged 9 years and under. In addition, Ct values of hospitalized versus community-care patient samples, positive for various respiratory viruses including adenovirus, were compared.

RESULTS

Adenovirus load in respiratory samples, as measured by Ct values, was found to be negatively correlated with respiratory disease severity in hospitalized pediatric patients aged under 9 years. Moreover, hospitalized patients presented with significantly higher Ct levels for various respiratory viruses as compared to community-care patients.

CONCLUSION

In this study we found a correlation between Ct values obtained from adenovirus q-PCR analysis of respiratory clinical samples and disease severity in patients aged 9 years and under. Such finding may serve as a predictor of respiratory disease course in pediatric patients and will be beneficial for the differential diagnosis and treatment of pediatric patients.

Suspension microarray-based comparison of oropharyngeal swab and bronchoalveolar lavage fluid for pathogen identification in young children hospitalized with respiratory tract infection

BACKGROUND

Respiratory tract infection (RTI) in young children is a leading cause of morbidity and hospitalization worldwide. There are few studies assessing the performance for bronchoalveolar lavage fluid (BALF) versus oropharyngeal swab (OPS) specimens in microbiological findings for children with RTI. The primary purpose of this study was to compare the detection rates of OPS and paired BALF in detecting key respiratory pathogens using suspension microarray.

METHODS

We collected paired OPS and BALF specimens from 76 hospitalized children with respiratory illness. The samples were tested simultaneously for 8 respiratory viruses and 5 bacteria by suspension microarray.

RESULTS

Of 76 paired specimens, 62 patients (81.6%) had at least one pathogen. BALF and OPS identified respiratory pathogen infections in 57 (75%) and 49 (64.5%) patients, respectively (P > 0.05). The etiology analysis revealed that viruses were responsible for 53.7% of the patients, whereas bacteria accounted for 32.9% and Mycoplasma pneumoniae for 13.4%. The leading 5 pathogens identified were respiratory syncytial virus, Streptococcus pneumoniaee, Haemophilus influenzae, Mycoplasma pneumoniae and adenovirus, and they accounted for 74.2% of etiological fraction. For detection of any pathogen, the overall detection rate of BALF (81%) was marginally higher than that (69%) of OPS (p = 0.046). The differences in the frequency distribution and sensitivity for most pathogens detected by two sampling methods were not statistically significant.

CONCLUSIONS

In this study, BALF and OPS had similar microbiological yields. Our results indicated the clinical value of OPS testing in pediatric patients with respiratory illness.

N95 Respirators vs Medical Masks for Preventing Influenza Among Health Care Personnel: A Randomized Clinical Trial

Importance

Clinical studies have been inconclusive about the effectiveness of N95 respirators and medical masks in preventing health care personnel (HCP) from acquiring workplace viral respiratory infections.

Objective

To compare the effect of N95 respirators vs medical masks for prevention of influenza and other viral respiratory infections among HCP.

Design, Setting, and Participants

A cluster randomized pragmatic effectiveness study conducted at 137 outpatient study sites at 7 US medical centers between September 2011 and May 2015, with final follow-up in June 2016. Each year for 4 years, during the 12-week period of peak viral respiratory illness, pairs of outpatient sites (clusters) within each center were matched and randomly assigned to the N95 respirator or medical mask groups.

Interventions

Overall, 1993 participants in 189 clusters were randomly assigned to wear N95 respirators (2512 HCP-seasons of observation) and 2058 in 191 clusters were randomly assigned to wear medical masks (2668 HCP-seasons) when near patients with respiratory illness.

Main Outcomes and Measures

The primary outcome was the incidence of laboratory-confirmed influenza. Secondary outcomes included incidence of acute respiratory illness, laboratory-detected respiratory infections, laboratory-confirmed respiratory illness, and influenzalike illness. Adherence to interventions was assessed.

Results

Among 2862 randomized participants (mean [SD] age, 43 [11.5] years; 2369 [82.8%]) women), 2371 completed the study and accounted for 5180 HCP-seasons. There were 207 laboratory-confirmed influenza infection events (8.2% of HCP-seasons) in the N95 respirator group and 193 (7.2% of HCP-seasons) in the medical mask group (difference, 1.0%, [95% CI, -0.5% to 2.5%]; P = .18) (adjusted odds ratio [OR], 1.18 [95% CI, 0.95-1.45]). There were 1556 acute respiratory illness events in the respirator group vs 1711 in the mask group (difference, -21.9 per 1000 HCP-seasons [95% CI, -48.2 to 4.4]; P = .10); 679 laboratory-detected respiratory infections in the respirator group vs 745 in the mask group (difference, -8.9 per 1000 HCP-seasons, [95% CI, -33.3 to 15.4]; P = .47); 371 laboratory-confirmed respiratory illness events in the respirator group vs 417 in the mask group (difference, -8.6 per 1000 HCP-seasons [95% CI, -28.2 to 10.9]; P = .39); and 128 influenzalike illness events in the respirator group vs 166 in the mask group (difference, -11.3 per 1000 HCP-seasons [95% CI, -23.8 to 1.3]; P = .08). In the respirator group, 89.4% of participants reported "always" or "sometimes" wearing their assigned devices vs 90.2% in the mask group.

Conclusions and Relevance

Among outpatient health care personnel, N95 respirators vs medical masks as worn by participants in this trial resulted in no significant difference in the incidence of laboratory-confirmed influenza.

Trial Registration

ClinicalTrials.gov Identifier: NCT01249625.

Comparison of Respiratory Specimen Collection Methods for Detection of Influenza Virus Infection by Reverse Transcription-PCR: a Literature Review

The detection of influenza virus in respiratory specimens from ill individuals is the most commonly used method to identify influenza virus infection. A number of respiratory specimen types may be used, including swabs, brush, aspirate, and wash, and specimens may be collected from numerous sites, including the anterior and posterior nasopharynx, oropharynx, and nares. Traditionally, respiratory specimens from the nasopharynx have been considered to have the highest sensitivity for viral detection. However, as molecular assays such as reverse transcription-PCR (RT-PCR) have increased the sensitivity of viral detection from respiratory specimens, the use of less-invasive and easier-to-obtain specimens has increased for the detection of influenza virus. This review presents and evaluates the sensitivities of respiratory specimen methods used in epidemiologic studies that used RT-PCR to detect influenza virus in respiratory specimens from ill patients. This literature review suggested that a combination of two less-invasive swabbing methods, such as nasal and oropharyngeal swabs, had about the same sensitivity as did nasopharyngeal specimens for influenza virus detection by RT-PCR. By combining two less-invasive collection methods, it may be possible to reduce barriers to enrollment without compromising influenza virus detection sensitivity.

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.

Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections

Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.

Respiratory RNA Viruses

Acute upper and lower respiratory infections are a major public health problem and a leading cause of morbidity and mortality worldwide. At greatest risk are young children, the elderly, the chronically ill, and those with suppressed or compromised immune systems. Viruses are the predominant cause of respiratory tract illnesses and include RNA viruses such as respiratory syncytial virus, influenza virus, parainfluenza virus, metapneumovirus, rhinovirus, and coronavirus. Laboratory testing is required for a reliable diagnosis of viral respiratory infections, as a clinical diagnosis can be difficult since signs and symptoms are often overlapping and not specific for any one virus. Recent advances in technology have resulted in the development of newer diagnostic assays that offer great promise for rapid and accurate detection of respiratory viral infections. This chapter emphasizes the fundamental characteristics and clinical importance of the various RNA viruses that cause upper and lower respiratory tract diseases in the immunocompromised host. It highlights the laboratory methods that can be used to make a rapid and definitive diagnosis for the greatest impact on the care and management of ill patients, and the prevention and control of hospital-acquired infections and community outbreaks.

Comparison of gargle samples and throat swab samples for the detection of respiratory pathogens

Respiratory illness causes significant morbidity especially in children, the elderly and the immunocompromised. The sample type taken and the quality of that sample are of great significance in providing an accurate diagnosis. Gargle samples are easy to take and sample the same area as a throat swab (THS). In this study, we assessed the utility of gargle samples for the molecular detection of common respiratory infections. Paired gargle and THS samples collected on the same day from the same patient were compared. We also included in our analysis paired THS and gargle samples that were collected within three days of each other as these samples are likely to have been taken during the same illness. Overall the data suggests that gargle samples are a more sensitive sample type than THS samples as overall the diagnostic yield was higher in the gargle samples and the Ct value of the gargle samples was stronger for the majority of samples in comparison to THS samples. Similar data was seen in the paired samples collected within one to three days of each other, as although the diagnostic yield between the sample types was similar (similar discrepant results), the majority of gargles had stronger Ct values than THS samples. This paper highlights the usefulness of gargle samples as non-invasive sensitive respiratory sample in comparison to THS samples. We recommend that other testing sites should consider using gargle samples for respiratory diagnosis as it will bring benefits in terms of sensitivity and sampling ease of use.

Enhanced detection of respiratory pathogens with nanotrap particles

The Influenza virus is a leading cause of respiratory disease in the United States each year. While the virus normally causes mild to moderate disease, hospitalization and death can occur in many cases. There are several methodologies that are used for detection; however problems such as decreased sensitivity and high rates of false-negative results may arise. There is a crucial need for an effective sample preparation technology that concentrates viruses at low abundance while excluding resident analytes that may interfere with detection. Nanotrap particles are hydrogel particles that are coupled to chemical dye affinity baits that bind a broad range of proteins and virions. Within minutes (<30 minutes), Nanotrap particles concentrate low abundant proteins and viruses from clinically complex matrices. Nanotrap particles with reactive red baits concentrated numerous respiratory viruses including various strains and subtypes of Influenza virus, Coronavirus, and Respiratory Syncytial Virus from saliva, nasal fluid swab specimens, and nasal aspirates. Detection was enhanced more than 10-fold when coupled to plaque assays and qRT-PCR. Importantly, Nanotrap particle can efficiently capture and concentrate multiple viral pathogens during a coinfection scenario. These results collectively demonstrate that Nanotrap particles are an important tool that can easily be integrated into various detection methodologies.

The Respiratory Protection Effectiveness Clinical Trial (ResPECT): a cluster-randomized comparison of respirator and medical mask effectiveness against respiratory infections in healthcare personnel

Background

Although N95 filtering facepiece respirators and medical masks are commonly used for protection against respiratory infections in healthcare settings, more clinical evidence is needed to understand the optimal settings and exposure circumstances for healthcare personnel to use these devices. A lack of clinically germane research has led to equivocal, and occasionally conflicting, healthcare respiratory protection recommendations from public health organizations, professional societies, and experts.

Methods

The Respiratory Protection Effectiveness Clinical Trial (ResPECT) is a prospective comparison of respiratory protective equipment to be conducted at multiple U.S. study sites. Healthcare personnel who work in outpatient settings will be cluster-randomized to wear N95 respirators or medical masks for protection against infections during respiratory virus season. Outcome measures will include laboratory-confirmed viral respiratory infections, acute respiratory illness, and influenza-like illness. Participant exposures to patients, coworkers, and others with symptoms and signs of respiratory infection, both within and beyond the workplace, will be recorded in daily diaries. Adherence to study protocols will be monitored by the study team.

Discussion

ResPECT is designed to better understand the extent to which N95s and MMs reduce clinical illness among healthcare personnel. A fully successful study would produce clinically relevant results that help clinician-leaders make reasoned decisions about protection of healthcare personnel against occupationally acquired respiratory infections and prevention of spread within healthcare systems.

Trial registration

The trial is registered at clinicaltrials.gov, number NCT01249625 (11/29/2010).

Respiratory Infections

The majority of respiratory tract infections (RTIs) are community acquired and are the single most common cause of physician office visits and among the most common causes of hospitalizations. The morbidity and mortality associated with RTIs are significant and the financial and social burden high due to lost time at work and school. The scope of clinical symptoms can significantly overlap among the respiratory pathogens, and the severity of disease can vary depending on patient age, underlying disease, and immune status, thereby leading to inaccurate presumptions about disease etiology. The rapid and accurate diagnosis of the causative agent of RTIs improves patient care, reduces morbidity and mortality, promotes effective hospital bed utilization and antibiotic stewardship, and reduces length of stay. This chapter focuses on the clinical utility, advantages, and disadvantages of viral and bacterial tests cleared by the Food and Drug Administration (FDA), and new promising technologies for the detection of bacterial agents of pneumonia currently in development or in US FDA clinical trials are briefly reviewed.

Throat and nasal swabs for molecular detection of respiratory viruses in acute pharyngitis

BACKGROUND

Detection of specific respiratory viruses is important for surveillance programs, where nasopharyngeal or nasal swabs have traditionally been used. Our objective was to determine whether sampling with a throat swab provides incremental benefit-when used in conjunction with a nasal swab-to detect respiratory viruses among patients with acute pharyngitis in the outpatient setting.

FINDINGS

Among 83 university students with acute pharyngitis, we detected respiratory viruses with molecular assays on two samples collected per student: with a flocked nasal mid-turbinate swab and a rayon throat swab. Forty-eight (58 %) patients had virus-positive samples, with 49 virus positives detected by either swab (one patient had a dual viral co-infection). The most common viruses were rhinovirus, coronavirus, and influenza A virus. Specifically, 29 virus positives were detected by both swabs, 14 exclusively by the nasal swab, and six exclusively by the throat swab. The additional six virus positives detected by the throat swab corresponded to an absolute increase in viral detection of 7.1 % (95 % CI: 1.2-12.9 %); the specific viruses detected were four rhinoviruses and two coronaviruses.

CONCLUSIONS

The flocked nasal swab samples respiratory viruses well, even among patients whose primary complaint is a sore throat. The rayon throat swab has modest incremental value over and above using the flocked nasal mid-turbinate swab alone, which suggests that while throat swabs alone would not be adequate for respiratory viral surveillance, they may have value as a supplementary test.

Characterisation of acute respiratory infections at a United Kingdom paediatric teaching hospital: observational study assessing the impact of influenza A (2009 pdmH1N1) on predominant viral pathogens

Background

According to the World Health Organisation, influenza A (2009 pdmH1N1) has moved into the post-pandemic phase, but there were still high numbers of infections occurring in the United Kingdom in 2010-11. It is therefore important to examine the burden of acute respiratory infections at a large children’s hospital to determine pathogen prevalence, occurrence of co-infection, prevalence of co-morbidities and diagnostic yield of sampling methods.

Methods

This was a retrospective study of respiratory virus aetiology in acute admissions to a paediatric teaching hospital in the North West of England between 1st April 2010 and 31st March 2011. Respiratory samples were analysed either with a rapid RSV test if the patient had symptoms suggestive of bronchiolitis, followed by multiplex PCR testing for ten respiratory viruses, or with multiplex PCR testing alone if the patient had suspected other ARI. Patient demographics and data regarding severity of illness, presence of co-morbidities and respiratory virus sampling method were retrieved from case notes.

Results

645 patients were admitted during the study period. 82/645 (12.7%) patients were positive for 2009 pdmH1N1, of whom 24 (29.2%) required PICU admission, with 7.3% mortality rate. Viral co-infection occurred in 48/645 (7.4%) patients and was not associated with more severe disease. Co-morbidities were present more frequently in older children, but there was no significant difference in prevalence of co-morbidity between 2009 pdmH1N1 patients and those with other ARI. NPA samples had the highest diagnostic yield with 192/210 (91.4%) samples yielding an organism.

Conclusions

Influenza A (2009 pdmH1N1) is an ongoing cause of occasionally severe disease affecting both healthy children and those with co-morbidities. Surveillance of viral pathogens provides valuable information on patterns of disease.

School-located influenza vaccination decreases laboratory-confirmed influenza and improves school attendance

BACKGROUND

School-located influenza vaccination (SLV) programs can efficiently immunize large numbers of school-aged children. We evaluated the impact of SLV on laboratory-confirmed influenza and absenteeism.

METHODS

Active surveillance for influenza-like illness (ILI) was conducted on 4455 children in 4 SLV intervention and 4 control elementary schools (grades K-6) matched for sociodemographic characteristics during the 2010-2011 influenza season in Los Angeles County, California. Combined nose/throat swabs were collected from febrile children with ILI at presentation to the school nurse or during absenteeism.

RESULTS

In SLV schools, 26.9%-46.6% of enrolled students received at least 1 dose of either inactivated or live attenuated influenza vaccine compared with 0.8%-4.3% in control schools. Polymerase chain reaction for respiratory viruses (PCR) was performed on 1021 specimens obtained from 898 children. Specimens were positive for influenza in 217 (21.3%), including 2009 H1N1 (30.9%), H3 (9.2%), and B (59.9%). Children attending SLV schools, regardless of vaccination status, were 30.8% (95% confidence interval, 10.1%-46.8%) less likely to acquire influenza compared with children at control schools. Unvaccinated children were indirectly protected in the school with nearly 50% vaccination coverage compared with control schools (influenza rate, 27.1 vs 60.0 per 1000 children; P = .023). Unvaccinated children missed more school days than vaccinated children (4.3 vs 2.8 days per 100 school days; P < .001).

CONCLUSIONS

Vaccination of at least a quarter of the school population resulted in decreased influenza rates and improved school attendance. Herd immunity for unvaccinated children may occur in schools with vaccination coverage approaching 50%.

Lower respiratory tract virus findings in mechanically ventilated patients with severe community-acquired pneumonia

BACKGROUND

The role of viral infections in the etiology of severe community-acquired pneumonia (SCAP) was prospectively evaluated from 2008 to 2012 at a university-level intensive care unit.

METHODS

Clinical data and microbiological tests were assessed: blood cultures, urine pneumococcal and legionella antigens, Mycoplasma pneumoniae and Chlamydia pneumoniae antibodies from paired serums, and respiratory virus detection by multiplex, real-time polymerase chain reaction (PCR) from nasopharyngeal swabs and lower tracheal specimens via intubation tube.

RESULTS

Of 49 mechanically ventilated SCAP patients (21 men and 28 women; median age, 54 years), the etiology was identified in 45 cases (92%). There were 21 pure bacterial infections (43%), 5 probably pure viral infections (10%), and 19 mixed bacterial-viral infections (39%), resulting in viral etiology in 24 patients (49%). Of 26 viruses, 21 (81%) were detected from bronchial specimens and 5 (19%) from nasopharyngeal swabs. Rhinovirus (15 cases, 58%) and adenovirus (4 cases, 15%) were the most common viral findings. The bacterial-viral etiology group had the highest peak C-reactive protein levels (median, 356 [25th-75th percentiles, 294-416], P = .05), whereas patients with probably viral etiology had the lowest peak procalcitonin levels (1.7 [25th-75th percentiles, 1.6-1.7]). The clinical characteristics of pure bacterial and mixed bacterial-viral etiologies were comparable. Hospital stay was longest among the bacterial group (17 vs 14 days; P = .02).

CONCLUSIONS

Viral findings were demonstrated in almost half of the SCAP patients. Clinical characteristics were similar between the pure bacterial and mixed bacterial-viral infections groups. The frequency of viral detection depends on the availability of PCR techniques and lower respiratory specimens.

Evaluation of yield of currently available diagnostics by sample type to optimize detection of respiratory pathogens in patients with a community-acquired pneumonia

BACKGROUND

For the detection of respiratory pathogens, the sampling strategy may influence the diagnostic yield. Ideally, samples from the lower respiratory tract are collected, but they are difficult to obtain.

OBJECTIVES

In this study, we compared the diagnostic yield in sputum and oropharyngeal samples (OPS) for the detection of respiratory pathogens in patients with community-acquired pneumonia (CAP), with the objective to optimize our diagnostic testing algorithm.

METHODS

Matched sputum samples, OPS, blood cultures, serum, and urine samples were taken from patients (>18 years) with CAP and tested for the presence of possible respiratory pathogens using bacterial cultures, PCR for 17 viruses and five bacteria and urinary antigen testing.

RESULTS

When using only conventional methods, that is, blood cultures, sputum culture, urinary antigen tests, a pathogen was detected in 49·6% of patients (n = 57). Adding molecular detection assays increased the yield to 80%. A pathogen was detected in 77 of the 115 patients in OPS or sputum samples by PCR. The sensitivity of the OPS was lower than that of the sputum samples (57% versus 74%). In particular, bacterial pathogens were more often detected in sputum samples. The sensitivity of OPS for the detection of most viruses was higher than in sputum samples (72% versus 66%), except for human rhinovirus and respiratory syncytial virus.

CONCLUSION

Addition of PCR on both OPS and sputum samples significantly increased the diagnostic yield. For molecular detection of bacterial pathogens, a sputum sample is imperative, but for detection of most viral pathogens, an OPS is sufficient.

Detection of Pneumocystis in the nasal swabs of immune-suppressed rats by use of PCR and microscopy

BACKGROUND

Detection of Pneumocystis jiroveci colonization in lungs or oral samples due to high sensitivity of PCR methods results in undue treatment of patients without any symptoms of Pneumocystis pneumonia. The aim of the present study is to demonstrate Pneumocystis carinii in rats, immune suppressed by oral and subcutaneous administration of dexamethasone.

MATERIAL/METHODS

Blood, oral, nasal and eye swabs were collected prior to immune suppression and 2, 6, 12 weeks after administration of dexamethasone. Also, samples were collected from lung, heart, liver, kidney, diaphragm, brain, spleen, tongue, muscle, eye, intestine, and feces. Cysts and trophozoites were investigated in stained slides and MSG gene was detected by PCR.

RESULTS

The results showed that weight loss is significantly higher in rats administered oral dexamethasone (P<0.05). Microscopy was positive only in lungs of rats orally administered dexamethasone. PCR was positive in lungs and oral swabs of rats prior to the administration of dexamethasone. After the administration of dexamethasone, the MSG gene was detected in oral swabs, lungs, spleen, kidney and (for the first time) in nasal swabs. PCR was positive in nasal swabs during the second and sixth weeks of oral and subcutaneous administration of dexamethasone, respectively.

CONCLUSIONS

Presence of P. jiroveci in nasopharyngeal aspirate, oropharyngeal wash, oral swab, induced sputum or BAL, and absence in nasal swab in a patient without symptoms of PCP may support clinician's decision regarding colonization. Overall, detection of P. carinii in nasal swabs of rats by PCR demonstrated that nasal sampling can be used for the diagnosis of Pneumocystis pneumonia.

Comparison of nasal and nasopharyngeal swabs for influenza detection in adults

OBJECTIVE

Examine differences in the detection of influenza by specimen and test type using paired nasal and nasopharyngeal swabs.

DESIGN

Prospective study

SETTING

Enrollment took place between January and March 2007 in a central Wisconsin population.

PARTICIPANTS

Adult patients were screened and enrolled by trained research coordinators following medical encounters for acute respiratory illnesses of <10 days duration.

METHODS

Paired nasal and nasopharyngeal swabs were collected from consenting patients and tested by both real-time reverse transcriptase polymerase chain reaction (rRT-PCR) and viral culture. A composite measure of positivity was used as the gold standard; cases included any positive result by rRT-PCR or viral culture from either specimen type.

RESULTS

Paired samples were collected from 240 adults; 33 (14%) individuals tested positive for influenza by rRT-PCR. Using rRT-PCR, the sensitivity of the nasal swab was 89% (95% CI, 78%-99%) and the sensitivity of the nasopharyngeal swab was 94% (95% CI, 87%-100%), compared to a composite gold standard.

CONCLUSION

Test sensitivity did not vary significantly by swab type when using a highly sensitive molecular diagnostic test, but power was limited to detect modest differences.

Limiting severe outcomes and impact on intensive care units of moderate-intermediate 2009 pandemic influenza: role of infectious diseases units

PURPOSE

The rate of severe outcomes of patients with 2009 pandemic (A/H1N1) influenza (2009pI) hospitalized in non-intensive care units (ICUs) has not been defined thus far. This study aims to assess the efficacy of the management of patients with influenza-like illness (ILI) of moderate intermediate severity in an infectious diseases unit (IDU) during the first wave of 2009pI and its influence on the burden of ICUs.

METHODS

All patients hospitalized from October 27, 2009, to February 5, 2010, with ILI were included in this prospective observational study. The IDU was organized and the staff was trained to provide intermediate care; patients were transferred to the ICU only if they required invasive ventilation, extracorporeal membrane oxygenation, or advanced cardiovascular support. Demographic data, clinical presentation, coexisting medical conditions, and laboratory and radiological findings were recorded and analyzed, as well as treatment and outcome data.

RESULTS

Overall, 108 patients (median age 36 years [IQR 27-54], 57.4% males) including 66.7% with ≥ 1 risk factor for severe influenza, 47.2% with confirmed 2009pI by RT-PCR and 63.9% with pneumonia, were enrolled in the study. All subjects received intravenous fluids and 83.3% were administered oseltamivir, 96.3% antibacterials, 19.4% oxygen therapy without ventilatory support, and 10.2% non-invasive ventilation. A total of 106 (98.1%) subjects were discharged after a 6-day median hospital stay [IQR 4-9]. Two patients (1.9%) were transferred to the ICU. There were no deaths.

CONCLUSIONS

These results suggest that the aggressive treatment of patients with moderate intermediate severity 2009 pandemic ILI in non-ICU wards may result in a low rate of severe outcomes and brief hospitalization. IDUs, if properly organized for intermediate care, may efficiently provide correct disease management, in addition to complying with infection control requirements, thus reducing the burden of the pandemic on ICUs. Further studies are warranted to evaluate the outcome of patients with moderate intermediate 2009pI in different non-ICU settings.

Recent advances in the diagnosis and treatment of influenza pneumonia

A potentially fatal complication of influenza infection is the development of pneumonia, caused either directly by the influenza virus, or by secondary bacterial infection. Pneumonia related to the 2009 influenza A pandemic was found to be underestimated by commonly used pneumonia severity scores in many cases, and to be rapidly progressive, leading to respiratory failure. Confirmation of etiology by laboratory testing is warranted in such cases. Rapid antigen and immunofluorescence testing are useful screening tests, but have limited sensitivity. Confirmation of pandemic H1N1 influenza A infection can only be made by real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) or viral culture. The most effective preventive measure is annual influenza vaccination in selected individuals. Decisions to administer antiviral medications for influenza treatment or chemoprophylaxis should be based upon clinical and epidemiological factors, and should not be delayed by confirmatory laboratory testing results. Neuraminidase inhibitors (NI) are the agents of choice.

[A case of severe influenza (H1N1) 2009 virus pneumonia identified by virus culture instead of PCR]

A 70-year-old man was being treated for asthma and chronic obstructive pulmonary disease, which had been well controlled. He was seen at our emergency outpatient department on October 24, 2009, for respiratory distress and mild fever. Point-of-care testing for influenza, general bacteria, and acid-fast bacilli in the sputum, were negative. With antibiotics ineffective, his respiratory status worsened, requiring him to be intubated and ventilated mechanically. Steroid pulse therapy temporarily improved his condition, as confirmed by imaging studies, but he died on hospital day 38. Polymerase chain reaction (PCR) analysis of tracheal secretion and bronchial washings collected on hospital day 14 and 21 were negative for influenza (H1N1) 2009 virus, which was identified in a subsequent culture. Negative results for reverse transcriptase-PCR analysis leave (H1N1) 2009 virus unable to be diagnosed clinically. Culture tests and repeated PCR analysis have been done in cases of strongly suspected clinical infection to confirm results. Our case, in which the virus was identified by culture, suggests that the viral load may have been too low or the time of culture inappropriate.

Influenza-related pneumonia

Influenza-related pneumonia encompasses both primary viral pneumonia and secondary bacterial pneumonia, which may be difficult to differentiate clinically. A high index of suspicion, prompt initiation of antiviral and antibiotic therapy, and appropriate escalation to secondary/critical care are key to improving outcome.

[Recommendations of the Infectious Diseases Work Group (GTEI) of the Spanish Society of Intensive and Critical Care Medicine and Coronary Units (SEMICYUC) and the Infections in Critically Ill Patients Study Group (GEIPC) of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC) for the diagnosis and treatment of influenza A/H1N1 in seriously ill adults admitted to the Intensive Care Unit]

The diagnosis of influenza A/H1N1 is mainly clinical, particularly during peak or seasonal flu outbreaks. A diagnostic test should be performed in all patients with fever and flu symptoms that require hospitalization. The respiratory sample (nasal or pharyngeal exudate or deeper sample in intubated patients) should be obtained as soon as possible, with the immediate start of empirical antiviral treatment. Molecular methods based on nucleic acid amplification techniques (RT-PCR) are the gold standard for the diagnosis of influenza A/H1N1. Immunochromatographic methods have low sensitivity; a negative result therefore does not rule out active infection. Classical culture is slow and has low sensitivity. Direct immunofluorescence offers a sensitivity of 90%, but requires a sample of high quality. Indirect methods for detecting antibodies are only of epidemiological interest. Patients with A/H1N1 flu may have relative leukopenia and elevated serum levels of LDH, CPK and CRP, but none of these variables are independently associated to the prognosis. However, plasma LDH> 1500 IU/L, and the presence of thrombocytopenia <150 x 10(9)/L, could define a patient population at risk of suffering serious complications. Antiviral administration (oseltamivir) should start early (<48 h from the onset of symptoms), with a dose of 75 mg every 12h, and with a duration of at least 7 days or until clinical improvement is observed. Early antiviral administration is associated to improved survival in critically ill patients. New antiviral drugs, especially those formulated for intravenous administration, may be the best choice in future epidemics. Patients with a high suspicion of influenza A/H1N1 infection must continue with antiviral treatment, regardless of the negative results of initial tests, unless an alternative diagnosis can be established or clinical criteria suggest a low probability of influenza. In patients with influenza A/H1N1 pneumonia, empirical antibiotic therapy should be provided due to the possibility of bacterial coinfection. A beta-lactam plus a macrolide should be administered as soon as possible. The microbiological findings and clinical or laboratory test variables may decide withdrawal or not of antibiotic treatment. Pneumococcal vaccination is recommended as a preventive measure in the population at risk of suffering severe complications. Although the use of moderate- or low-dose corticosteroids has been proposed for the treatment of influenza A/H1N1 pneumonia, the existing scientific evidence is not sufficient to recommend the use of corticosteroids in these patients. The treatment of acute respiratory distress syndrome in patients with influenza A/H1N1 must be based on the use of a protective ventilatory strategy (tidal volume <10 ml / kg and plateau pressure <35 mmHg) and positive end-expiratory pressure set to high patient lung mechanics, combined with the use of prone ventilation, muscle relaxation and recruitment maneuvers. Noninvasive mechanical ventilation cannot be considered a technique of choice in patients with acute respiratory distress syndrome, though it may be useful in experienced centers and in cases of respiratory failure associated with chronic obstructive pulmonary disease exacerbation or heart failure. Extracorporeal membrane oxygenation is a rescue technique in refractory acute respiratory distress syndrome due to influenza A/H1N1 infection. The scientific evidence is weak, however, and extracorporeal membrane oxygenation is not the technique of choice. Extracorporeal membrane oxygenation will be advisable if all other options have failed to improve oxygenation. The centralization of extracorporeal membrane oxygenation in referral hospitals is recommended. Clinical findings show 50-60% survival rates in patients treated with this technique. Cardiovascular complications of influenza A/H1N1 are common. Such problems may appear due to the deterioration of pre-existing cardiomyopathy, myocarditis, ischemic heart disease and right ventricular dysfunction. Early diagnosis and adequate monitoring allow the start of effective treatment, and in severe cases help decide the use of circulatory support systems. Influenza vaccination is recommended for all patients at risk. This indication in turn could be extended to all subjects over 6 months of age, unless contraindicated. Children should receive two doses (one per month). Immunocompromised patients and the population at risk should receive one dose and another dose annually. The frequency of adverse effects of the vaccine against A/H1N1 flu is similar to that of seasonal flu. Chemoprophylaxis must always be considered a supplement to vaccination, and is indicated in people at high risk of complications, as well in healthcare personnel who have been exposed.

Current Best Practices for Respiratory Virus Testing

Diagnostic testing for respiratory viruses has been revolutionized by recent advances that have made rapid and highly accurate tests accessible to clinical laboratories, and it is important that these improved methods be utilized. Accurate detection of respiratory viruses is important in patient care, as it guides both therapy and infection control measures. On a larger scale, the CDC and its collaborating laboratories collect both data and isolates from clinical laboratories for national surveillance, and the use of high-quality tests in clinical laboratories can improve the quality of these data.

The clinical usefulness of the SD Bioline Influenza Antigen Test® for detecting the 2009 influenza A (H1N1) virus

Though the 2009 worldwide influenza A (H1N1) pandemic has been declared to have ended, the influenza virus is expected to continue to circulate from some years as a seasonal influenza. A rapid antigen test (RAT) can aid in rapid diagnosis and allow for early antiviral treatment. We evaluated the clinical usefulness of RAT using SD Bioline Influenza Antigen Test® kit to detect the influenza virus, considering various factors. From August 1, 2009 to October 10, 2009, a total of 938 patients who visited the outpatient clinic at Korea University Guro Hospital with influenza-like illnesses were enrolled in the study. Throat or nasopharyngeal swab specimens were obtained from each of the patients. Using these specimens, we evaluated the influenza detection rate by rapid antigen test based on the real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) method. In comparison with rRT-PCR, the sensitivity and specificity of the RAT were 44.0% and 99.9%, respectively. The cyclic threshold values of RAT negative specimens were higher than RAT positive specimens (30.1±3.1 vs. 28.3±3.9, p=0.031). The sensitivity of the RAT kit was higher in patients who visited clinics within two days of symptom onset (60.4% vs. 11.1%, p=0.026). The results of this study show that the RAT cannot be recommended for general use in all patients with influenza-like illness because of its low sensitivity. The RAT may be used, only in the settings with limited diagnostic resources, for patients who visit a clinic within two days of symptom onse.

Comparison of nasopharyngeal and oropharyngeal swabs for the diagnosis of eight respiratory viruses by real-time reverse transcription-PCR assays

Background

Many acute respiratory illness surveillance systems collect and test nasopharyngeal (NP) and/or oropharyngeal (OP) swab specimens, yet there are few studies assessing the relative measures of performance for NP versus OP specimens.

Methods

We collected paired NP and OP swabs separately from pediatric and adult patients with influenza-like illness or severe acute respiratory illness at two respiratory surveillance sites in Kenya. The specimens were tested for eight respiratory viruses by real-time reverse transcription-polymerase chain reaction (qRT-PCR). Positivity for a specific virus was defined as detection of viral nucleic acid in either swab.

Results

Of 2,331 paired NP/OP specimens, 1,402 (60.1%) were positive for at least one virus, and 393 (16.9%) were positive for more than one virus. Overall, OP swabs were significantly more sensitive than NP swabs for adenovirus (72.4% vs. 57.6%, p<0.01) and 2009 pandemic influenza A (H1N1) virus (91.2% vs. 70.4%, p<0.01). NP specimens were more sensitive for influenza B virus (83.3% vs. 61.5%, p = 0.02), parainfluenza virus 2 (85.7%, vs. 39.3%, p<0.01), and parainfluenza virus 3 (83.9% vs. 67.4%, p<0.01). The two methods did not differ significantly for human metapneumovirus, influenza A (H3N2) virus, parainfluenza virus 1, or respiratory syncytial virus.

Conclusions

The sensitivities were variable among the eight viruses tested; neither specimen was consistently more effective than the other. For respiratory disease surveillance programs using qRT-PCR that aim to maximize sensitivity for a large number of viruses, collecting combined NP and OP specimens would be the most effective approach.