Comparison between nasopharyngeal swab and nasal wash, using culture and PCR, in the detection of potential respiratory pathogens

3D printed fluidic swab for COVID-19 testing with improved diagnostic yield and user comfort

The current standard method of diagnosing coronavirus disease 2019 (COVID-19) involves uncomfortable and invasive nasopharyngeal (NP) sampling using cotton swabs (CS), which can be unsuitable for self-testing. Although mid-turbinate sampling is an alternative, it has a lower diagnostic yield than NP sampling. Nasal wash (NW) has a similar diagnostic yield to NP sampling, but is cumbersome to perform. In this study, we introduce a 3D printed fluidic swab (3DPFS) that enables easy NW sampling for COVID-19 testing with improved diagnostic yield. The 3DPFS comprises a swab head, microchannel, and socket that can be connected to a syringe containing 250 µL of NW solution. The 3DPFS efficiently collects nasal fluid from the surface of the nasal cavity, resulting in higher sensitivity than CS for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This was confirmed by both reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and lateral flow assays (LFA) in virus-spiked nasal samples and clinical samples. Additionally, users reported greater comfort when using the 3DPFS compared to CS. These findings suggest that the 3DPFS can improve the performance of COVID-19 testing by facilitating efficient and less painful nasal sample collection.

Paroxysmal Atrial Fibrillation with Rapid Ventricular Response Following COVID-19 Nasopharyngeal Swab: A Case Report

Nasopharyngeal (NP) swab sampling is a simple procedure that has become extremely popular in the coronavirus disease 2019 (COVID-19) era, with hundreds of million specimens collected every day. However, rare but serious complications have been reported following NP swab acquisition. Here we present a case of paroxysmal atrial fibrillation associated with NP specimen collection in a healthy healthcare provider undergoing COVID-19 testing during departmental screening. This response may have been caused by an exaggerated vagal tone triggered by the trigeminocardiac reflex. Less invasive collection methods, such as saliva testing, may be warranted in predisposed individuals.

Nasopharyngeal Swabs vs. Nasal Aspirates for Respiratory Virus Detection: A Systematic Review

Nasal pathogen detection sensitivities can be as low as 70% despite advances in molecular diagnostics. This may be linked to the choice of sampling method. A diagnostic test accuracy review for sensitivity was undertaken to compare sensitivity of swabbing to the nasopharynx and extracting nasal aspirates, using the PRISMA protocol, Cochrane rapid review methodology, and QUADAS-2 risk of bias tools, with meta-analysis of included studies. Sensitivities were calculated by a consensus standard of positivity by either method as the ‘gold standard.’ Insufficient sampling methodology, cross sectional study designs, and studies pooling samples across anatomical sites were excluded. Of 13 subsequently eligible studies, 8 had ‘high’ risk of bias, and 5 had ‘high’ applicability concerns. There were no statistical differences in overall sensitivities between collection methods for eight different viruses, and this did not differ with use of PCR, immunofluorescence, or culture. In one study alone, Influenza H1N1(2009) favored nasopharyngeal swabs, with aspirates having 93.3% of the sensitivity of swabs (p > 0.001). Similarly equivocal sensitivities were noted in reports detecting bacteria. The chain of sampling, from anatomical site to laboratory results, features different potential foci along which sensitivity may be lost. A fair body of evidence exists that use of a different sampling method will not yield more respiratory pathogens.

A feasibility study of controlled human infection with Streptococcus pneumoniae in Malawi

Background

Persistent carriage of pneumococcal vaccine serotypes has occurred after introduction of PCV13 vaccination in Africa but the mechanisms are unclear. We tested the feasibility of using a human pneumococcal challenge model in Malawi to understand immune correlates of protection against carriage and to trial alternative vaccine candidates. We aimed to identify a dose of Streptococcus pneumoniae serotype 6B sufficient to establish nasopharyngeal carriage in 40% of those nasally inoculated and evaluate nasal mucosal immunity before and after experimental inoculation.

Methods

Healthy student volunteers were recruited and inoculated with saline, 20,000 CFU/naris or 80,000 CFU/naris of Streptococcus pneumoniae serotype 6B Post inoculation carriage was determined by nasal sampling for bacterial culture and lytA PCR. Immunological responses were measured in serum and nasal mucosal biopsies before and after bacterial inoculation.

Findings

Twenty-four subjects completed the feasibility protocol with minimal side effects. pneumococcal carriage was established in 0/6, 3/9 and 4/9 subjects in the saline, 20,000 CFU/naris and 80,000 CFU/naris groups, respectively. Incidental (natural) serotype carriage was common (7/24 participants carried non-6B strains, 29.2%. Experimentally induced type 6B pneumococcal carriage was associated with pro-inflammatory nasal mucosal responses prior to inoculation and altered mucosal recruitment of immune cells post bacterial challenge. There was no association with serum anti-capsular antibody.

Interpretation

The serotype 6B experimental human pneumococcal carriage model is feasible in Malawi and can now be used to determine the immunological correlates of protection against carriage and vaccine efficacy in this population.

The nose is the best niche for detection of experimental pneumococcal colonisation in adults of all ages, using nasal wash

Previous studies have suggested that the pneumococcal niche changes from the nasopharynx to the oral cavity with age. We use an Experimental Human Pneumococcal Challenge model to investigate pneumococcal colonisation in different anatomical niches with age. Healthy adults (n = 112) were intranasally inoculated with Streptococcus pneumoniae serotype 6B (Spn6B) and were categorised as young 18-55 years (n = 57) or older > 55 years (n = 55). Colonisation status (frequency and density) was determined by multiplex qPCR targeting the lytA and cpsA-6A/B genes in both raw and culture-enriched nasal wash and oropharyngeal swab samples collected at 2-, 7- and 14-days post-exposure. For older adults, raw and culture-enriched saliva samples were also assessed. 64% of NW samples and 54% of OPS samples were positive for Spn6B in young adults, compared to 35% of NW samples, 24% of OPS samples and 6% of saliva samples in older adults. Many colonisation events were only detected in culture-enriched samples. Experimental colonisation was detected in 72% of young adults by NW and 63% by OPS. In older adults, this was 51% by NW, 36% by OPS and 9% by saliva. The nose, as assessed by nasal wash, is the best niche for detection of experimental pneumococcal colonisation in both young and older adults.

Performing nasopharyngeal swabs-Guidelines based on an anatomical study

Nasopharyngeal swabs are performed to collect material for diagnosing diseases affecting the respiratory system, such as Covid‐19. Yet, no systematic anatomical study defines concrete prerequisites for successfully targeting the nasopharyngeal mucosa. We therefore aim at simulating nasopharyngeal swabs in human body donors to characterize parameters allowing and supporting to enter the nasopharynx with a swab, while avoiding endangering the cribriform plate. With the aid of metal probes and commercial swabs a total of 314 nasopharyngeal swabs in anatomical head/neck specimens stemming from 157 body donors were simulated. Important anatomical parameters were photo‐documented and measured. We provide information on angles and distances between prominent anatomical landmarks and particularly important positions the probe occupies during its advancement through the nares to the upper and lower parts of the nasopharynx and cribriform plate. Based on these data we suggest a simple and safe three‐step procedure for conducting nasopharyngeal swabs. In addition, we define easily recognizable signals for its correct performance. Evaluations prove that this procedure in all specimens without deformations of the nasal cavity allows the swab to enter the nasopharynx, whereas a widespread used alternative only succeeds in less than 50%. Our data will be the key for the successful collection of nasopharyngeal material for detecting and characterizing pathogens, such as SARS‐CoV‐2, which have a high affinity to pharyngeal mucosa. They demonstrate that the danger for damaging the cribriform plate or olfactory mucosa with swabs is unlikely, but potentially higher when performing nasal swabs.

Asystole During Nasopharyngeal Swab: Is COVID-19 to Blame?

The use of nasopharyngeal (NP) swab sampling for the detection of various respiratory pathogens has been a standard procedure in medicine for many years. While this is a fairly common procedure, there has been a significant increase in utilization recently due to the SARS-CoV-2 pandemic. We describe a case of a 40-year-old SARS-CoV-2 positive patient with no prior cardiac history who developed asystole while an NP swab was being used to obtain a sample for a SARS-CoV-2 assay. Return of normal sinus rhythm was achieved with chest compressions alone. The incident was deemed to have been an exaggerated vagal response to intranasal stimulation; better known as the trigeminocardiac reflex. This is the first reported case describing asystole during use of an NP swab. This case occurred in a patient with no known cardiac disease and highlights the potential importance of the arrhythmogenic nature of COVID-19 that could potentiate the vagal response in susceptible individuals undergoing NP sampling.

The microbiome of the nasopharynx

The nasopharyngeal microbiome is a dynamic microbial interface of the aerodigestive tract, and a diagnostic window in the fight against respiratory infections and antimicrobial resistance. As its constituent bacteria, viruses and mycobacteria become better understood and sampling accuracy improves, diagnostics of the nasopharynx could guide more personalized care of infections of surrounding areas including the lungs, ears and sinuses. This review will summarize the current literature from a clinical perspective and highlight its growing importance in diagnostics and infectious disease management.

Experimental Human Pneumococcal Colonization in Older Adults Is Feasible and Safe, Not Immunogenic

Rationale: Pneumococcal colonization is key to the pathogenesis of invasive disease but is also immunogenic in young adults, protecting against recolonization. Colonization is rarely detected in older adults, despite high rates of pneumococcal disease.Objectives: To establish experimental human pneumococcal colonization in healthy adults aged 50-84 years, to measure the immune response to pneumococcal challenge, and to assess the protective effect of prior colonization against autologous strain rechallenge.Methods: Sixty-four participants were inoculated with Streptococcus pneumoniae (serotype 6B; 80,000 cfu in each nostril). Colonization was determined by bacterial culture of nasal wash, and humoral immune responses were assessed by anticapsular and antiprotein IgG concentrations.Measurements and Main Results: Experimental colonization was established in 39% of participants (25/64) with no adverse events. Colonization occurred in 47% (9/19) of participants aged 50-59 compared with 21% (3/14) in those aged ≥70 years. Previous pneumococcal polysaccharide vaccination did not protect against colonization. Colonization did not confer serotype-specific immune boosting, with a geometric mean titer (95% confidence interval) of 2.7 μg/ml (1.9-3.8) before the challenge versus 3.0 (1.9-4.7) 4 weeks after colonization (P = 0.53). Furthermore, pneumococcal challenge without colonization led to a drop in specific antibody concentrations from 2.8 μg/ml (2.0-3.9) to 2.2 μg/ml (1.6-3.0) after the challenge (P = 0.006). Antiprotein antibody concentrations increased after successful colonization. Rechallenge with the same strain after a median of 8.5 months (interquartile range, 6.7-10.1) led to recolonization in 5/16 (31%).Conclusions: In older adults, experimental pneumococcal colonization is feasible and safe but demonstrates different immunological outcomes compared with younger adults in previous studies.

Improved Influenza Diagnostics through Thermal Contrast Amplification

Influenza poses a serious health threat and creates an economic burden for people around the world. The accurate diagnosis of influenza is critical to the timely clinical treatment of patients and the control of outbreaks to protect public health. Commercially available rapid influenza diagnostic tests (RIDTs) that are operated by visual readout are widely used in clinics to screen influenza infections, but RIDTs suffer from imperfect analytical sensitivity, especially when the virus concentration in the sample is low. Fortunately, the sensitivity can be simply improved through an add-on signal amplification step, i.e., thermal contrast amplification (TCA). To demonstrate the advantage of TCA for influenza diagnosis, we conducted a prospective cohort study on 345 clinical specimens collected for influenza A and B testing during the 2017-2018 influenza season. All samples were tested using the Quidel QuickVue Influenza A + B test, followed by a TCA readout, and then confirmatory polymerase chain reaction testing. Through the TCA detecting sub-visual weak positives, TCA reading improved the overall influenza sensitivity by 53% for influenza A and 33% for influenza B over the visual RIDTs readings. Even though the specificity was compromised slightly by the TCA protocol (relative decrease of 0.09% for influenza A and 0.01% for influenza B), the overall performance was still better than that achieved by visual readout based on comparison of their plots in receiver operating characteristic space and F1 scores (relative increase of 14.5% for influenza A and 12.5% for influenza B). Performing a TCA readout on wet RIDTs also improved the overall TCA performance (relative increase in F1 score of 48%). Overall, the TCA method is a simple and promising way to improve the diagnostic performance of commercial RIDTs for infectious diseases, especially in the case of specimens with low target analytes.

Ultra-short antibiotic prophylaxis guided by preoperative microbiological nasal swabs in endoscopic endonasal skull base surgery

PURPOSE

Endoscopic endonasal skull base surgery (EESBS) is a clean-contaminated procedure. Guidelines regarding the antibiotic prophylaxis in EESBS have not been developed yet, and today, there are no universally accepted protocols. In this article, we investigated the efficacy of our new ultra-short antibiotic prophylaxis protocol for EESBS guided by the cultural results of preoperative microbiological nasal swabs.

METHODS

We defined as "nasal swab-related antibiotic protocol" the administration of a first-generation cephalosporin (cefazolin 2 g) in patients whose nasal swabs revealed the presence of normal nasal flora or methicillin-sensitive Staphylococcus aureus (MSSA), and the administration of vancomycin 1 g intravenously in patients whose nasal swabs revealed the presence of methicillin-resistant Staphylococcus aureus (MRSA) or with reported cephalosporin/penicillin allergy. This case-control study included 120 patients who underwent EESBS. The case group included 60 cases who received the "nasal swab-related antibiotic protocol," while the control group included 60 cases who received the "standard hospital antibiotic protocol" used in neurosurgery (cefazolin 2 g plus metronidazole 500 mg at induction, and 2 g of cefazolin repeated after 180 min).

RESULTS

The preoperative microbiological nasal swabs showed normal nasal flora in 42 patients (70%), MSSA in 17 patients (28.3%), and MRSA in 1 patient (1.6%). During the study period, no cases of meningitis or sinusitis occurred in the case group ("nasal swab-related antibiotic protocol"), while two infections (3.3%, 1 sinusitis and 1 meningitis) were reported in the control group ("standard hospital antibiotic protocol"). Mean length of hospitalization was 6.5 days for the case group and 8.5 days in the control group. "Standard hospital antibiotic protocol" is less expensive (range, 2.88-5.42 euros) compared with our new "nasal swab-related antibiotic protocol" (range, 10.02-32.56 euros), but in line with other antibiotic prophylaxis protocols reported in literature.

DISCUSSION

The low complication rates of our case series (0%) is comparable to complication rates reported in literature (1.6% for meningitis and 8% for sinusitis). Compared with other perioperative antibiotic regimens reported in literature, the "nasal swab-related antibiotic protocol" is cheap and at least equally effective. We discuss the rationale on which we based the choice of chemoprophylaxis, the timing, and the length of our regimen.

CONCLUSIONS

Our study confirmed the safety and efficacy of our easily applicable and low-cost antibiotic prophylaxis protocol.

Rapid Fabrication of Sterile Medical Nasopharyngeal Swabs by Stereolithography for Widespread Testing in a Pandemic

The 3D printing of nasopharyngeal swabs during the COVID-19 pandemic presents a central case of how to efficiently address a break in the global supply chain of medical equipment. Herein a comprehensive study of swab design considerations for mass production by stereolithography is presented. The retention and comfort performance of a range of novel designs of 3D-printed swabs are compared with the standard flocked-head swab used in clinical environments. Sample retention of the 3D swab is governed by the volume, porosity density, and void fraction of the head as well as by the pore geometry. 3D-printed swabs outperform conventional flock-head swabs in terms of sample retention. It is argued that mechanically functional designs of the swab head, such as corkscrew-shaped heads and negative Poisson ratio heads, maximize sample retention and improve patient comfort. In addition, available designs of swab shafts for an optimized sample collection procedure are characterized. The study is conducted in vitro, using artificial mucus, covering the full range of human mucus viscosities in a 3D-printed model of a nasal cavity. The work sets the path for the resilient supply of widespread sterile testing equipment as a rapid response to the current and future pandemics.

Bronchoalveolar lavage-based COVID-19 testing in patients with cancer

Objective/Background

A few case reports in the setting of coronavirus disease 2019 (COVID-19) and multiplex polymerase chain reaction (PCR)-based assays for common respiratory pathogens have shown a higher yield of bronchoalveolar lavage (BAL) samples than upper airway specimens in immunocompromised patients.

Methods

A retrospective study was conducted reviewing patients diagnosed with COVID-19 at the Medical College of Wisconsin (Milwaukee, WI, USA) between March 13, 2020 and June 11, 2020. All patients tested positive for SARS-CoV-2 via real-time reverse transcriptase PCR (RT-PCR), through a nasopharyngeal or a bronchoscopy specimen.

Results

During the study period, 53 bronchoscopy procedures were performed at the institution, of which five patients tested positive for COVID-19. Of the five patients, three underwent BAL testing based on high clinical suspicion for COVID-19 after the nasopharyngeal (NP) swab(s) was negative. All three patients had underlying cancers and had lymphopenia for a considerable duration prior to being diagnosed with COVID-19. Two patients had better outcomes that could be attributed to earlier BAL specimen testing resulting in timely medical intervention.

Conclusion

This study underscores the need for early lower respiratory tract sampling, whenever possible, in patients with cancer and prolonged lymphopenia. High clinical suspicion ought to supersede false-negative NP reverse transcriptase–PCR as early bronchoscopic evaluation in cancer patients, who are either receiving active treatment or are immunosuppressed, can allow timely institution of efficacious treatment, enrollment into clinical trials, as well as effective infection control. In the apt clinical setting in patients with cancer, presumptive treatment may also be considered to minimize exposure to healthcare providers and proceduralists.

Jal Neti Sample for COVID Detection: A Novel Hypothesis

The current standard method of diagnosing COVID status has low sensitivity which led the authors to ponder on alternative ways of taking the sample. Various studies have explored the role of nasal wash, a sample taken by injecting and aspirating saline with the help of a syringe but to the best of our knowledge, the use of Jal Neti kriya sample to detect coronavirus has not been reported in the literature so far. Jal Neti kriya is an integral part of shatkarmas-six actions of purification of the human body, written in the Yogic system of healthcare. It involves pouring water in one nostril and flushing out through the other nostril with the help of special equipment called "Neti pot", to keep the nasal passage clean. The authors find it worthwhile to share their hypothesis, which can pave a way to future research in COVID-19 detection.

Toma de muestras nasofaríngeas para diagnóstico de COVID-19

RESUMEN Introducción y objetivo: La prueba de diagnóstico directo del COVID-19 de mayor sensibilidad es la toma de muestras de nasofaringe mediante un hisopo para estudio posterior mediante RT-PCR. El objetivo de nuestro trabajo es exponer pormenoriza-damente la forma más adecuada de realizar dicha técnica. Método: Descripción de los diferentes pasos necesarios para la toma de muestras nasofaríngeas en pacientes con COVID-19. Resultados: Los pasos a tener en cuenta son: 1. Previamente se des-carta que no existan contraindicaciones para la toma de muestra. 2.Etiquetado de la muestra y preparación del volante de petición. 3. Colocación de EPI según los están-dares de la institución en la que se trabaja. 4. Explicación al paciente del proceso a realizar. 5. Técnica para la toma de muestra nasofaríngea 6. Retirada del EPI. 7. Mani-pulación y transporte de la muestra al laboratorio. Discusión/Conclusiones: Dado que la sensibilidad de las muestras nasofaríngeas para diagnóstico de COVID-19 depen-de en gran parte de una adecuada técnica, es muy importante la formación adecuada del personal implicado en la recogida de esta. La persona formada a tal efecto debe conocer el objetivo claro de la misma, como se debe poner y quitar el EPI, conocer cómo se realiza la técnica y como se manipula la muestra.

Upper respiratory tract colonization with Streptococcus pneumoniae in adults

INTRODUCTION

Most of the current evidence regarding pneumococcal upper respiratory colonization in adults suggests that despite high disease burden, carriage prevalence is low. Contemporary studies on adult pneumococcal colonization have largely followed the pediatric approach by which samples are obtained mostly from the nasopharynx and bacterial detection is evaluated by routine culture alone. Recent evidence suggests that the 'pediatric approach' may be insufficient in adults and pneumococcal detection in this population may be improved by longitudinal studies that include samples from additional respiratory sites combined with more extensive laboratory testing.

AREAS COVERED

In this article, relevant literature published in peer review journals on adult pneumococcal colonization, epidemiology, detection methods, and recommendations were reviewed.

EXPERT OPINION

Respiratory carriage of Streptococcus pneumoniae has been underestimated in adults. Contemporary pneumococcal carriage studies in adults that collect samples from alternative respiratory sites such as the oropharynx, saliva, or nasal wash; are culture-enriched for pneumococcus; and use molecular diagnostic methods designed to target two pneumococcal DNA sequences should enhance pneumococcal detection in the adult respiratory tract. This finding may have implications for the interpretation of dynamics of pneumococcal transmission and vaccination.

Minimally Invasive Nasal Sampling in Children Offers Accurate Pneumococcal Colonization Detection

Nasopharyngeal colonization of potential respiratory pathogens such as Streptococcus pneumoniae is the major source of transmission and precursor of invasive disease. Swabbing deeply the nasopharynx, which is currently recommended by World Health Organization, provides accurate pneumococcal detection but is unpleasant. We showed that nasal lining fluid filter strips offer equal detection sensitivity.

Comparison of Bacterial Culture Results Obtained from Nasopharyngeal and Midturbinate Swabs in Children With Upper Respiratory Tract Infection Symptoms

Paired nasopharynx and midturbinate swabs were obtained from 96 children (mean age: 2.45 years) with upper respiratory tract symptoms. Of these, 38.5% were colonized with Streptococcus pneumoniae only, 16.7% with Haemophilus influenzae only and 9.4% with both bacteria. Bacterial cultures from paired nasopharynx and midturbinate swabs demonstrated agreement for S. pneumoniae (κ = 0.75), H. influenzae (κ = 0.59) and for both pathogens (κ = 0.62). This report compares the results of bacterial cultures obtained from the nasopharynx and midturbinate specimens in children with upper respiratory tract infections.

Density Distribution of Pharyngeal Carriage of Meningococcus in Healthy Young Adults: New Approaches to Studying the Epidemiology of Colonization and Vaccine Indirect Effects

BACKGROUND

Improved understanding of Neisseria meningitidis (Nm) carriage biology and better methods for detection and quantification would facilitate studies of potential impact of new vaccines on colonization and transmission in adolescents.

METHODS

We performed plate cultures on 107 oropharyngeal swabs stored frozen in skim milk tryptone glucose glycerol (STGG) broth and previously positive for Nm. We compared quantitative polymerase chain reaction (qPCR) detection of Nm in 601 STGG-swabs with culture. Using qPCR (n = 87), a log-phase broth culture standard curve and semiquantitative plate cultures (n = 68), we measured density of carriage. We compared qPCR genogrouping of DNA extracts from STGG-swabs and from plate culture lawns (n = 110) with purified isolates (n = 80).

RESULTS

Swab storage resulted in only 10% loss of culture sensitivity. Direct sodC qPCR Nm detection yielded more positives (87/601, 14.5%) than culture (80/601, 13.3%). Most samples (57/110) positive by culture were also positive by qPCR and vice versa, but discrepancies (single positives) were frequent among low-density samples. sodC qPCR was positive in 79/80 isolates but in only 65 by ctrA qPCR. Density both by culture and qPCR varied across 4 orders of magnitude with the majority being low (<50 bacteria-gene copies/mL) and a minority being high (>1000). Genogrouping qPCRs yielded more positive results when performed on DNA extracts from lawn cultures.

CONCLUSIONS

We provide the first description of the distribution of Nm carriage density. This could be important for understanding transmission dynamics and population-level effectiveness of adolescent vaccine programs. Storage of swabs frozen in STGG for batched laboratory analysis facilitates carriage studies and direct sodC qPCR for Nm combined with qPCR genogrouping of lawn culture extracts provides accurate, detailed description of colonization.

Development and application of multiplex PCR assays for detection of virus-induced respiratory disease complex in dogs

Canine infectious respiratory disease complex (CIRDC) viruses have been detected in dogs with respiratory illness. Canine influenza virus (CIV), canine parainfluenza virus (CPIV), canine distemper virus (CDV), canine respiratory coronavirus (CRCoV), canine adenovirus type 2 (CAdV-2) and canine herpesvirus 1 (CaHV-1), are all associated with the CIRDC. To allow diagnosis, two conventional multiplex polymerase chain reactions (PCR) were developed to simultaneously identify four RNA and two DNA viruses associated with CIRDC. The two multiplex PCR assays were then validated on 102 respiratory samples collected from 51 dogs with respiratory illness by sensitivity and specificity determination in comparison to conventional simplex PCR and a rapid three-antigen test kit. All six viruses were detected in either individual or multiple infections. The developed multiplex PCR assays had a >87% sensitivity and 100% specificity compared to their simplex counterpart. Compared to the three-antigen test kit, the multiplex PCR assays yielded 100% sensitivity and more than 83% specificity for detection of CAdV-2 and CDV, but not for CIV. Therefore, the developed multiplex PCR modalities were able to simultaneously diagnose a panel of CIRDC viruses and facilitated specimen collection through being suitable for use of nasal or oral samples.

The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study

BACKGROUND

Respiratory tract infections and subsequent airway inflammation occur early in the life of infants with cystic fibrosis. However, detailed information about the microbial composition of the respiratory tract in infants with this disorder is scarce. We aimed to undertake longitudinal in-depth characterisation of the upper respiratory tract microbiota in infants with cystic fibrosis during the first year of life.

METHODS

We did this prospective cohort study at seven cystic fibrosis centres in Switzerland. Between Feb 1, 2011, and May 31, 2014, we enrolled 30 infants with a diagnosis of cystic fibrosis. Microbiota characterisation was done with 16S rRNA gene pyrosequencing and oligotyping of nasal swabs collected every 2 weeks from the infants with cystic fibrosis. We compared these data with data for an age-matched cohort of 47 healthy infants. We additionally investigated the effect of antibiotic treatment on the microbiota of infants with cystic fibrosis. Statistical methods included regression analyses with a multivariable multilevel linear model with random effects to correct for clustering on the individual level.

FINDINGS

We analysed 461 nasal swabs taken from the infants with cystic fibrosis; the cohort of healthy infants comprised 872 samples. The microbiota of infants with cystic fibrosis differed compositionally from that of healthy infants (p=0·001). This difference was also found in exclusively antibiotic-naive samples (p=0·001). The disordering was mainly, but not solely, due to an overall increase in the mean relative abundance of Staphylococcaceae in infants with cystic fibrosis compared with healthy infants (multivariable linear regression model stratified by age and adjusted for season; second month: coefficient 16·2 [95% CI 0·6-31·9]; p=0·04; third month: 17·9 [3·3-32·5]; p=0·02; fourth month: 21·1 [7·8-34·3]; p=0·002). Oligotyping analysis enabled differentiation between Staphylococcus aureus and coagulase-negative Staphylococci. Whereas the analysis showed a decrease in S aureus at and after antibiotic treatment, coagulase-negative Staphylococci increased.

INTERPRETATION

Our study describes compositional differences in the microbiota of infants with cystic fibrosis compared with healthy controls, and disordering of the microbiota on antibiotic administration. Besides S aureus, coagulase-negative Staphylococci also contributed to the disordering identified in these infants. These findings are clinically important in view of the crucial role that bacterial pathogens have in the disease progression of cystic fibrosis in early life. Our findings could be used to inform future studies of the effect of antibiotic treatment on the microbiota in infants with cystic fibrosis, and could assist in the prevention of early disease progression in infants with this disorder.

FUNDING

Swiss National Science Foundation, Fondation Botnar, the Swiss Society for Cystic Fibrosis, and the Swiss Lung Association Bern.

An inception cohort study assessing the role of pneumococcal and other bacterial pathogens in children with influenza and ILI and a clinical decision model for stringent antibiotic use

BACKGROUND

Influenza-like illness (ILI) is a common reason for paediatric consultations. Viral causes predominate, but antibiotics are used frequently. With regard to influenza, pneumococcal coinfections are considered major contributors to morbidity/mortality.

METHODS

In the context of a perennial quality management (QM) programme at the Charité Departments of Paediatrics and Microbiology in collaboration with the Robert Koch Institute, children aged 0-18 years presenting with signs and symptoms of ILI were followed from the time of initial presentation until hospital discharge (Charité Influenza-Like Disease = ChILD Cohort). An independent QM team performed highly standardized clinical assessments using a disease severity score based on World Health Organization criteria for uncomplicated and complicated/progressive disease. Nasopharyngeal and pharyngeal samples were collected for viral reverse transcription polymerase chain reaction and bacterial culture/sensitivity and MaldiTOF analyses. The term 'detection' was used to denote any evidence of viral or bacterial pathogens in the (naso)pharyngeal cavity. With the ChILD Cohort data collected, a standard operating procedure (SOP) was created as a model system to reduce the inappropriate use of antibiotics in children with ILI. Monte Carlo simulations were performed to assess cost-effectiveness.

RESULTS

Among 2,569 ChILD Cohort patients enrolled from 12/2010 to 04/2013 (55% male, mean age 3.2 years, range 0-18, 19% >5 years), 411 patients showed laboratory-confirmed influenza, with bacterial co-detection in 35%. Influenza and pneumococcus were detected simultaneously in 12/2,569 patients, with disease severity clearly below average. Pneumococcal vaccination rates were close to 90%. Nonetheless, every fifth patient was already on antibiotics upon presentation; new antibiotic prescriptions were issued in an additional 20%. Simulation of the model SOP in the same dataset revealed that the proposed decision model could have reduced the inappropriate use of antibiotics significantly (P<0.01) with an incremental cost-effectiveness ratio of -99.55€.

CONCLUSIONS

Physicians should be made aware that in times of pneumococcal vaccination the prevalence and severity of influenza infections complicated by pneumococci may decline. Microbiological testing in combination with standardized disease severity assessments and review of vaccination records could be cost-effective, as well as promoting stringent use of antibiotics and a personalized approach to managing children with ILI.

Pneumococcal Colonization Rates in Patients Admitted to a United Kingdom Hospital with Lower Respiratory Tract Infection: a Prospective Case-Control Study

Current diagnostic tests are ineffective for identifying the etiological pathogen in hospitalized adults with lower respiratory tract infections (LRTIs). The association of pneumococcal colonization with disease has been suggested as a means to increase the diagnostic precision. We compared the pneumococcal colonization rates and the densities of nasal pneumococcal colonization by (i) classical culture and (ii) quantitative real-time PCR (qPCR) targetinglytAin patients with LRTIs admitted to a hospital in the United Kingdom and control patients. A total of 826 patients were screened for inclusion in this prospective case-control study. Of these, 38 patients were recruited, 19 with confirmed LRTIs and 19 controls with other diagnoses. Nasal wash (NW) samples were collected at the time of recruitment. Pneumococcal colonization was detected in 1 patient with LRTI and 3 controls (P= 0.6) by classical culture. By qPCR, pneumococcal colonization was detected in 10 LRTI patients and 8 controls (P= 0.5). Antibiotic usage prior to sampling was significantly higher in the LRTI group than in the control group (19 versus 3;P< 0.001). With a clinically relevant cutoff of >8,000 copies/ml on qPCR, pneumococcal colonization was found in 3 LRTI patients and 4 controls (P> 0.05). We conclude that neither the prevalence nor the density of nasal pneumococcal colonization (by culture and qPCR) can be used as a method of microbiological diagnosis in hospitalized adults with LRTI in the United Kingdom. A community-based study recruiting patients prior to antibiotic therapy may be a useful future step.

Density and duration of experimental human pneumococcal carriage

The density and duration of pneumococcal carriage are considered to affect the likelihood of transmission and invasive disease. Because of its importance in both spreading and causing disease, carriage has been suggested as an endpoint in future vaccine studies. Culture is the current gold standard for detection, but may not be sensitive enough to detect changes at low density. Healthy adult volunteers received an intranasal inoculation of Streptococcus pneumoniae serotype 6B. Pneumococcal density in nasal washes collected at six time-points post-inoculation was determined by culture and quantitative PCR (qPCR). Natural pneumococcal carriers detected at initial screening were followed in parallel. In 331 nasal washes from 79 volunteers, the sensitivity and specificity of pneumococcal detection by qPCR, as compared with culture, were 92.3% and 75.9%. The estimation of pneumococcal density by culture and qPCR was highly correlated (r_s = 0.73, p <0.0001), although qPCR had a lower detection limit. Pneumococcal density fluctuated within a carriage episode, and occasionally fell below the detection limit of both methods. The duration of carriage episodes was underestimated when only one method was used. Similar fluctuations in density were observed in natural carriers. Pneumococcal carriage is a dynamic event. Culture and qPCR are complementary for surveying the density and duration of pneumococcal carriage episodes.

Standard method for detecting upper respiratory carriage of Streptococcus pneumoniae: updated recommendations from the World Health Organization Pneumococcal Carriage Working Group

In 2003 the World Health Organization (WHO) convened a working group and published a set of standard methods for studies measuring nasopharyngeal carriage of Streptococcus pneumoniae (the pneumococcus). The working group recently reconvened under the auspices of the WHO and updated the consensus standard methods. These methods describe the collection, transport and storage of nasopharyngeal samples, as well as provide recommendations for the identification and serotyping of pneumococci using culture and non-culture based approaches. We outline the consensus position of the working group, the evidence supporting this position, areas worthy of future research, and the epidemiological role of carriage studies. Adherence to these methods will reduce variability in the conduct of pneumococcal carriage studies undertaken in the context of pneumococcal vaccine trials, implementation studies, and epidemiology studies more generally so variability in methodology does not confound the interpretation of study findings.

Impact of experimental human pneumococcal carriage on nasopharyngeal bacterial densities in healthy adults

Colonization of the nasopharynx by Streptococcus pneumoniae is a necessary precursor to pneumococcal diseases that result in morbidity and mortality worldwide. The nasopharynx is also host to other bacterial species, including the common pathogens Staphylococcus aureus, Haemophilus influenzae, and Moraxella catarrhalis. To better understand how these bacteria change in relation to pneumococcal colonization, we used species-specific quantitative PCR to examine bacterial densities in 52 subjects 7 days before, and 2, 7, and 14 days after controlled inoculation of healthy human adults with S. pneumoniae serotype 6B. Overall, 33 (63%) of subjects carried S. pneumoniae post-inoculation. The baseline presence and density of S. aureus, H. influenzae, and M. catarrhalis were not statistically associated with likelihood of successful pneumococcal colonization at this study’s sample size, although a lower rate of pneumococcal colonization in the presence of S. aureus (7/14) was seen compared to that in the presence of H. influenzae (12/16). Among subjects colonized with pneumococci, the number also carrying either H. influenzae or S. aureus fell during the study and at 14 days post-inoculation, the proportion carrying S. aureus was significantly lower among those who were colonized with S. pneumoniae (p = 0.008) compared to non-colonized subjects. These data on bacterial associations are the first to be reported surrounding experimental human pneumococcal colonization and show that co-colonizing effects are likely subtle rather than absolute.

The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition

BACKGROUND

Several cohort studies have indicated associations between S. pneumoniae and other microbes in the nasopharynx. To study causal relationships between the nasopharyngeal microbiome and pneumococcal carriage, we employed an experimental human pneumococcal carriage model. Healthy adult volunteers were assessed for pneumococcal carriage by culture of nasal wash samples (NWS). Those without natural pneumococcal carriage received an intranasal pneumococcal inoculation with serotype 6B or 23F. The composition of the nasopharyngeal microbiome was longitudinally studied by 16S rDNA pyrosequencing on NWS collected before and after challenge.

RESULTS

Among 40 selected volunteers, 10 were natural carriers and 30 were experimentally challenged. At baseline, five distinct nasopharyngeal microbiome profiles were identified. The phylogenetic distance between microbiomes of natural pneumococcal carriers was particularly large compared to non-carriers. A more diverse microbiome prior to inoculation was associated with the establishment of pneumococcal carriage. Perturbation of microbiome diversity upon pneumococcal challenge was strain specific. Shifts in microbiome profile occurred after pneumococcal exposure, and those volunteers who acquired carriage more often diverted from their original profile. S. pneumoniae was little prominent in the microbiome of pneumococcal carriers.

CONCLUSION

Pneumococcal acquisition in healthy adults is more likely to occur in a diverse microbiome and appears to promote microbial heterogeneity.

Serotype-independent pneumococcal vaccines

Streptococcus pneumoniae remains an important cause of disease with high mortality and morbidity, especially in children and in the elderly. The widespread use of the polysaccharide conjugate vaccines in some countries has led to a significant decrease in invasive disease caused by vaccine serotypes, but an increase in disease caused by non-vaccine serotypes has impacted on the overall efficacy of these vaccines on pneumococcal disease. The obvious solution to overcome such shortcomings would be the development of new formulations that provide serotype-independent immunity. This review focuses on the most promising approaches, including protein antigens, whole cell pneumococcal vaccines, and recombinant bacteria expressing pneumococcal antigens. The protective capacity of these vaccine candidates against the different stages of pneumococcal infection, including colonization, mucosal disease, and invasive disease in animal models is reviewed. Some of the human trials that have already been performed or that are currently ongoing are presented. Finally, the feasibility and the possible shortcomings of these candidates in relation to an ideal vaccine against pneumococcal infections are discussed.

Bacteria in the nose of young adults during wellness and rhinovirus colds: detection by culture and microarray methods in 100 nasal lavage specimens

BACKGROUND

Patients  with  viral respiratory infections/viral rhinitis/common colds are often treated with antibiotic; however, there is little information on whether or how bacterial microbiota in the nose and nasopharynx might influence the course of viral illnesses.

METHODS

To initiate investigation of possible interaction between viral respiratory illness and microbiota of the nose/nasopharynx, we used microarray technology to examine 100 nasal lavage fluid (NLF) samples for bacterial species and recorded the bacterial titer of culturable bacteria. Rhinovirus illnesses were induced by self-inoculation using the "finger to nose or eye natural transmission route" in 10 otherwise healthy young adults. NLF samples were collected during wellness and at specific time points following experimental rhinovirus inoculation.

RESULTS

The rhinovirus infection rate was 70%. There were no consistent changes in the prevalence of different bacterial species determined by microarray and bacterial titer by culture methods during rhinovirus infection. The bacterial profile in NLF samples showed high variability between volunteers but low variability in multiple NLFs obtained before and following infection from the same volunteer. Streptococcus epidermidis/coagulase-negative staphylococcus (CNS) were identified in all 10 subjects. One or more bacterial sinus/otitis pathogens were identified by microarray in 6 of the 10 volunteers. The microarray identified a few bacteria not included in traditional bacterial cultures.

CONCLUSION

Our pilot study showed that each of the 10 volunteers had a unique bacterial profile in the nose by microarray analysis and that bacterial load did not change during experimental rhinovirus colds. Larger scale studies are warranted.

Controlled human infection and rechallenge with Streptococcus pneumoniae reveals the protective efficacy of carriage in healthy adults

RATIONALE

The immunological and protective role of pneumococcal carriage in healthy adults is not known, but high rates of disease and death in the elderly are associated with low carriage prevalence.

OBJECTIVES

We employed an experimental human pneumococcal carriage model to investigate the immunizing effect of a single carriage episode.

METHODS

Seventy healthy adults were challenged, and of those with carriage, 10 were rechallenged intranasally with live 6B Streptococcus pneumoniae up to 11 months after clearance of the first carriage episode. Serum and nasal wash antibody responses were measured before and after each challenge.

MEASUREMENTS AND MAIN RESULTS

A total of 29 subjects were experimentally colonized. No subjects were colonized by experimental rechallenge, demonstrating the protective effect of initial carriage against subsequent infection. Carriage increased both mucosal and serum IgG levels to pneumococcal proteins and polysaccharide, resulting in a fourfold increase in opsonophagocytic activity. Importantly, passive transfer of postcarriage sera from colonized subjects conferred 70% protection against lethal challenge by a heterologous strain in a murine model of invasive pneumococcal pneumonia. These levels were significantly higher than the protection conferred by either precarriage sera (30%) or saline (10%).

CONCLUSIONS

Experimental human carriage resulted in mucosal and systemic immunological responses that conferred protection against recolonization and invasive pneumococcal disease. These data suggest that mucosal pneumococcal vaccination strategies may be important for vulnerable patient groups, particularly the elderly, who do not sustain carriage.

Experimental human pneumococcal carriage

Experimental human pneumococcal carriage (EHPC) is scientifically important because nasopharyngeal carriage of Streptococcus pneumoniae is both the major source of transmission and the prerequisite of invasive disease. A model of carriage will allow accurate determination of the immunological correlates of protection, the immunizing effect of carriage and the effect of host pressure on the pathogen in the nasopharyngeal niche. Further, methods of carriage detection useful in epidemiologic studies, including vaccine studies, can be compared.

Detection of respiratory viruses in asymptomatic children undergoing allogeneic hematopoietic cell transplantation

Detection of respiratory viruses by molecular methods, in children without respiratory symptoms undergoing hematopoietic cell transplantation (HCT), has not been well described. A prospective study of 33 asymptomatic children detected respiratory viruses in 8 of 33 (24%) patients before HCT. Human rhinovirus (HRV) was detected in five patients, and human adenovirus (hADV) in three patients. Two additional patients shed HRV, and one shed human coronavirus (hCoV), post-HCT. Two patients had co-infections. Of the 11 asymptomatic patients where respiratory virus was detected, 3 (27%) later developed an upper respiratory tract infection, from the same virus.

Human nasal challenge with Streptococcus pneumoniae is immunising in the absence of carriage

Infectious challenge of the human nasal mucosa elicits immune responses that determine the fate of the host-bacterial interaction; leading either to clearance, colonisation and/or disease. Persistent antigenic exposure from pneumococcal colonisation can induce both humoral and cellular defences that are protective against carriage and disease. We challenged healthy adults intra-nasally with live 23F or 6B Streptococcus pneumoniae in two sequential cohorts and collected nasal wash, bronchoalveolar lavage (BAL) and blood before and 6 weeks after challenge. We hypothesised that both cohorts would successfully become colonised but this did not occur except for one volunteer. The effect of bacterial challenge without colonisation in healthy adults has not been previously assessed. We measured the antigen-specific humoral and cellular immune responses in challenged but not colonised volunteers by ELISA and Flow Cytometry. Antigen-specific responses were seen in each compartment both before and after bacterial challenge for both cohorts. Antigen-specific IgG and IgA levels were significantly elevated in nasal wash 6 weeks after challenge compared to baseline. Immunoglobulin responses to pneumococci were directed towards various protein targets but not capsular polysaccharide. 23F but not 6B challenge elevated IgG anti-PspA in BAL. Serum immunoglobulins did not increase in response to challenge. In neither challenge cohort was there any alteration in the frequencies of TNF, IL-17 or IFNγ producing CD4 T cells before or after challenge in BAL or blood. We show that simple, low dose mucosal exposure with pneumococci may immunise mucosal surfaces by augmenting anti-protein immunoglobulin responses; but not capsular or cellular responses. We hypothesise that mucosal exposure alone may not replicate the systemic immunising effect of experimental or natural carriage in humans.

Exposure to respiratory pathogens such as Streptococcus pneumoniae (pneumococcus) is a frequent event that can result in immediate clearance, nasal colonisation or disease for the host. Human and mouse studies have shown that natural colonisation is an immunising event. Colonisation is prevalent in children but rare in human adults (<10%), suggesting that despite high pneumococcal exposure adult mucosal defences are sufficient to prevent colonisation. We exposed healthy adults to pneumococci in the nose in order to achieve colonisation and mimic a natural colonisation event. In most volunteers, however, we were not able to obtain colonisation using this protocol. In exposed but not colonised volunteers we measured antibody and cellular responses in nose, lung and blood samples. The mucosal defences elicited during acute pneumococcal exposure are poorly described but these data will shed light on the mechanisms that prevent colonisation in healthy adults and inform future vaccine design. Live bacterial exposure increases specific antibody and innate responses at mucosal surfaces such as the nose and lung. Systemic responses were not increased. These data suggest that acute bacterial exposure per se augments mucosal but not systemic defences. Natural or experimental colonisation may be required for systemic immunisation.