Rapid multiplex nested PCR for detection of respiratory viruses

Development of Nested Polymerase Chain Reaction with Novel Specific Primers for Detection of Tritrichomonas muris Infection in Laboratory Mice

A variety of rodent ceca are parasitized by Tritrichomonas muris (T. muris), a flagellated protozoan. To date, there are no ideal methods for the detection of T. muris infections in laboratory mice; thus, new molecular methodologies for its specific detection need to be developed. In this study, using staining and SEM, it was observed that T. muris has a pear-shaped body and contains three anterior flagella. A nested PCR system with novel specific primers was designed based on the conserved regions of the SSU rRNA gene of T. muris. The nested PCR system for T. muris showed good specificity and high sensitivity for at least 100 T. muris trophozoites/mL and 0.1 ng/μL of fecal genomic DNA, which means that 176 trophozoites per gram of mouse feces could be detected. When using this nested PCR system, the detection rate was 18.96% (58/306), which was higher than the detection rate of 14.05% (43/306) detected via smear microscopy in fecal samples from five mouse strains. The sensitivity and specificity of nested PCR in detecting T. muris was found to be 100%, and it demonstrated a 26% increase in diagnostic sensitivity compared to the smear microscopy method in the present study. In conclusion, the nested PCR developed with novel primers based on the SSU rRNA gene of T. muris has good accuracy, specificity, and sensitivity for the detection of T. muris infections in laboratory mice.

Development of a diagnostic assay by three-tube multiplex real-time PCR for simultaneous detection of nine microorganisms causing acute respiratory infections

Acute respiratory infections are widespread in vulnerable populations of all ages and are characterized by a variety of symptoms. The underlying infection can be caused by a multitude of microorganisms, including viruses and bacteria. Early detection of respiratory infections through rapid pathogen screening is vital in averting infectious respiratory disease epidemics. This study utilized a multiplex real-time PCR system to develop a three-tube reverse transcription-PCR (RT-PCR) assay, enabling simultaneously detect nine respiratory pathogens, including: influenza A and B, adenovirus, respiratory syncytial virus (RSV), Streptococcus pneumoniae, Legionella pneumophila, Haemophilus influenzae, Chlamydia pneumoniae, and Mycoplasma pneumoniae. This technique utilizes a one-step assay, with specifically designed TaqMan primer-probe sets combined in the same tube. This assay provided rapid and simplified detection of the nine prevalent pathogens, as well as increased sensitivity and reduced cross-contamination. This assay was evaluated using 25 related viral/bacterial strains as positive references, the other 25 irrelevant strains as negative controls, and clinical specimens from 179 patients. All positive strains were detected with no amplification of the non-target microorganism mixtures and the assay's detection limits ranged between 250-500 copies/ml (1.25-2.5 copies/reaction). A total of 167 (93.3%) samples tested positive for at least one of the pathogens identified; 109 of these samples were from patients confirmed to have RSV infections. The diagnostic accuracy of our assay was further confirmed by matching results from classical direct immunofluorescence assay and nucleotide sequencing. These data demonstrate the innovative multiplex real-time PCR assay as a promising alternative to the current approaches used for early screening of acute respiratory infections.

Prevalence and Genotypes of Human Rhinoviruses among Iranian Hajj Pilgrims with Severe Acute Respiratory Infection

Background

Hajj is one of the main challenges of public health and infection control. Hajj-associated respiratory tract infections are very common during the pilgrimage. Studies have shown that human rhinovirus (HRV) is one of the most common causes of respiratory illnesses among pilgrims. The aim of this study was to investigate the prevalence and genotypes of HRV among Iranian pilgrims with severe acute respiratory infection (SARI) during the 2017 Hajj season.

Materials and Methods

Throat swabs or washes were collected from 104 pilgrims with SARI and transported to the National Influenza Center, School of Public Health, Tehran University of Medical Sciences. Specimens were screened for HRV by Nested PCR with primers for 5'UTR, and virus genotypes were determined using PCR with VP4-VP2 primers and sequencing method.

Results

Twenty-one cases were positive for HRV (20.19 %). The HRV species and types of 8 positive samples were: HRV-A21 (1/8, 12.5%), followed by HRV-B91 (3/8, 37.5%) and HRV-C (4/8, 50%) un-typed.

Conclusion

This study showed that HRV has a high prevalence in Iranian Hajj pilgrims. As there is no vaccine or antiviral therapy for HRV, prevention methods are the best way for infection control.

The prevalence of early- and late-onset bacterial, viral, and fungal respiratory superinfections in invasively ventilated COVID-19 patients

The role of respiratory superinfections in patients with coronavirus disease 2019 (COVID‐19) pneumonia remains unclear. We investigated the prevalence of early‐ and late‐onset superinfections in invasively ventilated patients with COVID‐19 pneumonia admitted to our department of intensive care medicine between March 2020 and November 2020. Of the 102 cases, 74 (72.5%) received invasive ventilation and were tested for viral, bacterial, and fungal pathogens on Days 0–7, 8–14, and 15–21 after the initiation of mechanical ventilation. Approximately 45% developed one or more respiratory superinfections. There was a clear correlation between the duration of invasive ventilation and the prevalence of coinfecting pathogens. Male patients with obesity and those suffering from chronic obstructive pulmonary disease and/or diabetes mellitus had a significantly higher probability to develop a respiratory superinfection. The prevalence of viral coinfections was high, with a predominance of the herpes simplex virus (HSV), followed by cytomegalovirus. No respiratory viruses or intracellular bacteria were detected in our cohort. We observed a high coincidence between Aspergillus fumigatus and HSV infection. Gram‐negative bacteria were the most frequent pathogen group. Klebsiella aerogenes was detected early after intubation, while Klebsiella pneumoniae and Pseudomonas aeruginosa were related to a prolonged respiratory weaning.

In our cohort, approximately 45% of the invasively ventilated COVID‐19 patients developed a respiratory bacterial, viral, and/or fungal superinfection within 3 weeks after intubation. The most prevalent group of pathogens were Gram‐negative bacteria.

Human Body Performance with COVID-19 Affectation According to Virus Specification Based on Biosensor Techniques

Life was once normal before the first announcement of COVID-19's first case in Wuhan, China, and what was slowly spreading became an overnight worldwide pandemic. Ever since the virus spread at the end of 2019, it has been morphing and rapidly adapting to human nature changes which cause difficult conundrums in the efforts of fighting it. Thus, researchers were steered to investigate the virus in order to contain the outbreak considering its novelty and there being no known cure. In contribution to that, this paper extensively reviewed, compared, and analyzed two main points; SARS-CoV-2 virus transmission in humans and detection methods of COVID-19 in the human body. SARS-CoV-2 human exchange transmission methods reviewed four modes of transmission which are Respiratory Transmission, Fecal-Oral Transmission, Ocular transmission, and Vertical Transmission. The latter point particularly sheds light on the latest discoveries and advancements in the aim of COVID-19 diagnosis and detection of SARS-CoV-2 virus associated with this disease in the human body. The methods in this review paper were classified into two categories which are RNA-based detection including RT-PCR, LAMP, CRISPR, and NGS and secondly, biosensors detection including, electrochemical biosensors, electronic biosensors, piezoelectric biosensors, and optical biosensors.

Efficacy and Safety of Ergoferon in Children from 6 Months to 6 Years Old with Acute Respiratory Viral Infections in Contemporary Outpatient Practice: A Multicenter, Double-Blind, Placebo-Controlled Randomized Trial

To evaluate the efficacy and safety of Ergoferon in combination with symptomatic therapy in children from 6 months to 6 years old with acute respiratory infections (ARI) in contemporary outpatient practice, an international, multicenter, double-blind, placebo-controlled, randomized, parallel-group clinical trial was performed. Derived by technological treatment of antibodies to interferon gamma, histamine, and CD4, Ergoferon was previously proved to modulate its molecular targets promoting effective antiviral protection. The data of 282 patients with oral temperature ≥38.0°C plus mild to moderate severity of flu-like nonspecific and nasal/throat/chest symptoms were included in intention-to-treat analysis (n = 140, Ergoferon group; n = 142, placebo group). Time to alleviation of all ARI symptoms was the primary endpoint, and 8 outcome measures were estimated as the secondary endpoints. Respiratory viruses were confirmed in 57.1% (Ergoferon) and 54.9% (Placebo) of patients. Compared to placebo, Ergoferon reduced time to alleviation of all ARI symptoms (4.5 ± 1.7 versus 5.2 ± 2.2 days in placebo; p=0.026) including fever (2.8 ± 1.5 vs 3.4 ± 2.0; p=0.031), flu-like nonspecific (4.0 ± 1.8 vs 4.7 ± 2.2, p=0.022), and nasal/throat/chest (4.3 ± 2.0 versus 5.0 ± 2.3; p=0.024) symptoms. Ergoferon add-on therapy decreased the mean total symptom severity score (according to 4-point scale for each symptom), ARI severity, frequency of antipyretic use, and percentage of complication requiring antibiotics and increased the percentage of recovered patients. The incidence of adverse events (AEs) in the Ergoferon group was significantly lower compared to the placebo group (7.0% versus 18.8%; p=0.004) including infectious diseases (3.5% vs 12.5%; p=0.008). In the Ergoferon group, AEs were mild or moderate. In 8 (57.1%) cases, AEs were unrelated to Ergoferon, in 5 (35.7%), the relationship was uncertain, and in 1 (7.1%), it was possible (mild rash on the face). Ergoferon treatment is beneficial for infants and young children with ARI in contemporary outpatient practice. Being well-tolerated, Ergoferon increases the symptomatic therapy effectiveness and improves the patient condition and disease outcomes.

Environmental contamination with SARS-CoV-2 in COVID-19 hospitals in Wuhan, China, 2020

Coronavirus disease 2019 (COVID-19) pandemic has caused high number of infections and deaths of healthcare workers globally. Distribution and possible transmission route of SARS-CoV-2 in hospital environment should be clarified. We herein collected 431 environmental (391 surface and 40 air) samples in the intensive care unit (ICU) and general wards (GWs) of three hospitals in Wuhan, China from February 21 to March 4, 2020, and detected SARS-CoV-2 RNA by real-time quantitative PCR. The viral positive rate in the contaminated areas was 17.8% (28/157), whereas there was no virus detected in the clean areas. Higher positive rate (22/59, 37.3%) was found in ICU than that in GWs (3/63, 4.8%). The surfaces of computer keyboards and mouse in the ICU were the most contaminated (8/10, 80.0%), followed by the ground (6/9, 66.7%) and outer glove (2/5, 40.0%). From 17 air samples in the contaminated areas, only one sample collected at a distance of around 30 cm from the patient was positive. Enhanced surface disinfection and hand hygiene effectively decontaminated the virus from the environment. This finding might help understand the transmission route and contamination risk of SARS-CoV-2 and evaluate the effectiveness of infection prevention and control measures in healthcare facilities.

Laboratory detection methods for the human coronaviruses

Coronaviruses are a group of envelop viruses which lead to diseases in birds and mammals as well as human. Seven coronaviruses have been discovered in humans that can cause mild to lethal respiratory tract infections. HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 are the low-risk members of this family and the reason for some common colds. Besides, SARS-CoV, MERS-CoV, and newly identified SARS-CoV-2, which is also known as 2019-nCoV, are the more dangerous viruses. Due to the rapid spread of this novel coronavirus and its related disease, COVID-19, a reliable, simple, fast, and low-cost detection method is necessary for patient diagnosis and tracking worldwide. Human coronaviruses detection methods were classified and presented in this article. The laboratory detection techniques include RT-PCR, RT-LAMP, electrochemical and optical biosensors for RNA detection, and whole virus or viral proteins detection assays.

Development and evaluation of a panel of multiplex one-tube nested real time PCR assay for simultaneous detection of 14 respiratory viruses in five reactions

Multiplex real-time quantitative polymerase chain reaction (mRT-qPCR) assay is commonly used to detect respiratory viruses, however, the sensitivity is limited for most reports. A panel of locked nucleic acid based multiplex closed one-tube nested real-time PCR (mOTNRT-PCR) assay consisting of five separate internally controlled RT-qPCR assays was developed for detection of 14 respiratory viruses. The sensitivity and reproducibility of mOTNRT-PCR panel were evaluated using plasmid standards and the specificity was evaluated using clinical samples. The clinical performance of mOTNRT-PCR panel was further evaluated with 468 samples collected from patients with an acute respiratory infection and compared with individual real-time PCR (RT-qPCR) assay. The analytical sensitivities of mOTNRT-PCR panel ranged from 2 to 20 copies/reaction, and no cross-reaction with common respiratory viruses was observed. The coefficients of variation of intra-assay and inter-assay were between 0.35% and 8.29%. Totally 35 clinical samples detected by mOTNRT-PCR assay panel were missed by RT-qPCR and confirmed true positive by sequencing of nested PCR products. The mOTNRT-PCR assay panel provides a more sensitive and high-throughput method for the detection of 14 respiratory viruses.

Bacterial pneumonia and its associated factors in children from a developing country: A prospective cohort study

Introduction

Pneumonia in children is a common disease yet determining its aetiology remains elusive.

Objectives

To determine the a) aetiology, b) factors associated with bacterial pneumonia and c) association between co-infections (bacteria + virus) and severity of disease, in children admitted with severe pneumonia.

Methods

A prospective cohort study involving children aged 1-month to 5-years admitted with very severe pneumonia, as per the WHO definition, over 2 years. Induced sputum and blood obtained within 24 hrs of admission were examined via PCR, immunofluorescence and culture to detect 17 bacteria/viruses. A designated radiologist read the chest radiographs.

Results

Three hundred patients with a mean (SD) age of 14 (±15) months old were recruited. Significant pathogens were detected in 62% of patients (n = 186). Viruses alone were detected in 23.7% (n = 71) with rhinovirus (31%), human metapneumovirus (HMP) [22.5%] and respiratory syncytial virus (RSV) [16.9%] being the commonest. Bacteria alone was detected in 25% (n = 75) with Haemophilus influenzae (29.3%), Staphylococcus aureus (24%) and Streptococcus pneumoniae (22.7%) being the commonest. Co-infections were seen in 13.3% (n = 40) of patients. Male gender (AdjOR 1.84 [95% CI 1.10, 3.05]) and presence of crepitations (AdjOR 2.27 [95% CI 1.12, 4.60]) were associated with bacterial infection. C-reactive protein (CRP) [p = 0.007]) was significantly higher in patients with co-infections but duration of hospitalization (p = 0.77) and requirement for supplemental respiratory support (p = 0.26) were not associated with co-infection.

Conclusions

Bacteria remain an important cause of very severe pneumonia in developing countries with one in four children admitted isolating bacteria alone. Male gender and presence of crepitations were significantly associated with bacterial aetiology. Co-infection was associated with a higher CRP but no other parameters of severe clinical illness.

Pathogenic viruses: Molecular detection and characterization

Pathogenic viruses are viruses that can infect and replicate within human cells and cause diseases. The continuous emergence and re-emergence of pathogenic viruses has become a major threat to public health. Whenever pathogenic viruses emerge, their rapid detection is critical to enable implementation of specific control measures and the limitation of virus spread. Further molecular characterization to better understand these viruses is required for the development of diagnostic tests and countermeasures. Advances in molecular biology techniques have revolutionized the procedures for detection and characterization of pathogenic viruses. The development of PCR-based techniques together with DNA sequencing technology, have provided highly sensitive and specific methods to determine virus circulation. Pathogenic viruses potentially having global catastrophic consequences may emerge in regions where capacity for their detection and characterization is limited. Development of a local capacity to rapidly identify new viruses is therefore critical. This article reviews the molecular biology of pathogenic viruses and the basic principles of molecular techniques commonly used for their detection and characterization. The principles of good laboratory practices for handling pathogenic viruses are also discussed. This review aims at providing researchers and laboratory personnel with an overview of the molecular biology of pathogenic viruses and the principles of molecular techniques and good laboratory practices commonly implemented for their detection and characterization.

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The continous emergence and re-emergence of pathogenic viruses has become a major threat to public health.

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PCR-based techniques together with DNA sequencing technology have provided highly sensitive and specific methods to determine virus circulation.

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Southeast Asia is considered to be vulnerable to potential outbreaks of pathogenic viruses. A number of pathogenic viruses have been reported to circulate in this region. The 2019 novel coronavirus has also been identified in Southeast Asia.

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Development of local capacity to rapidly identify new viruses is very important.

Optimal Timing of Repeat Multiplex Molecular Testing for Respiratory Viruses

Determining whether and when multiplex nucleic acid amplification tests (NAATs) for respiratory viruses should be repeated is difficult. We analyzed 5 years of results for a multiplex NAAT targeting 14 respiratory viruses, to determine how often repeat tests were ordered and the time period in which results were likely to change. Results for NAATs performed on nasopharyngeal specimens and repeated within 90 days after initial testing were analyzed. Logistic regression models were used to compare time periods between tests with respect to the odds of a change in the sample result. During the study period, 21,819 nasopharyngeal specimens from 16,779 individuals were submitted. Of these, 8,807 samples (40%) were positive for at least one viral pathogen. Among this cohort, 2,583 specimens (12%) collected from 1,473 patients (9%) were repeat tests performed within 90 days after an initial test. If repeated within 90 days, 71% of tests (1,833 tests) did not have a change in result. Initially negative tests typically remained negative, whereas initially positive tests mostly remained positive until 11 to 15 days. The odds of result change plateaued after 20 days. The odds of result change for tests repeated within 20 days were only 0.52 times the odds (95% confidence interval, 0.43 to 0.62) for those repeated at 21 to 90 days (P < 0.001). Multiplex tests for respiratory viruses that are repeated within short periods lead to redundant results at additional costs. Repeat testing of nasopharyngeal specimens before 20 days demonstrates little change. These results provide a vital component for use in laboratory stewardship to curtail unnecessary respiratory viral testing.

Association of time-to-treatment with outcomes of Pneumocystis pneumonia with respiratory failure in HIV-negative patients

Background

The prevalence of pneumocystis pneumonia (PCP) and associated hypoxic respiratory failure is increasing in human immunodeficiency virus (HIV)-negative patients. However, no prior studies have evaluated the effect of early anti-PCP treatment on clinical outcomes in HIV-negative patient with severe PCP. Therefore, this study investigated the association between the time to anti-PCP treatment and the clinical outcomes in HIV-negative patients with PCP who presented with hypoxemic respiratory failure.

Methods

A retrospective observational study was performed involving 51 HIV-negative patients with PCP who presented in respiratory failure and were admitted to the intensive care unit between October 2005 and July 2018. A logistic regression model was used to adjust for potential confounding factors in the association between the time to anti-PCP treatment and in-hospital mortality.

Results

All patients were treated with appropriate anti-PCP treatment, primarily involving trimethoprim/sulfamethoxazole. The median time to anti-PCP treatment was 58.0 (28.0–97.8) hours. Thirty-one (60.8%) patients were treated empirically prior to confirmation of the microbiological diagnosis. However, the hospital mortality rates were not associated with increasing quartiles of time until anti-PCP treatment (P = 0.818, test for trend). In addition, hospital mortality of patients received early empiric treatment was not better than those of patients received definitive treatment after microbiologic diagnosis (48.4% vs. 40.0%, P = 0.765). In a multiple logistic regression model, the time to anti-PCP treatment was not associated with increased mortality. However, age (adjusted OR 1.07, 95% CI 1.01–1.14) and failure to initial treatment (adjusted OR 13.03, 95% CI 2.34–72.65) were independently associated with increased mortality.

Conclusions

There was no association between the time to anti-PCP treatment and treatment outcomes in HIV-negative patients with PCP who presented in hypoxemic respiratory failure.

Detection of Intraspinal Spirocerca lupi in Canine Cerebrospinal Fluid by Polymerase Chain Reaction

Aberrant migration of Spirocerca lupi into the spinal cord is an important cause of severe progressive neurological dysfunction in dogs. Although early diagnosis is essential to prevent deterioration, ante-mortem diagnosis of this condition remains challenging. The aim of this study was to evaluate the detection of the 18S ribosomal DNA (rDNA) S. lupi gene in the cerebrospinal fluid (CSF) of presumptively-affected dogs using polymerase chain reaction (PCR). Dogs with a non-compressive spinal cord lesion, pleocytosis with presence of eosinophils in the CSF and a characteristic clinical presentation were included. CSF samples from eight dogs were available for the study, of which seven were definitively diagnosed with intraspinal spirocercosis by PCR of either the CSF samples (6/7) or tissue samples obtained at necropsy examination (3/7), or both (2/7). Of these seven positive cases, only one dog had a negative CSF PCR, indicating a sensitivity of 86% for detecting nematode DNA in the CSF of infected dogs using this PCR protocol. The nematode DNA sequences obtained from the CSF of six dogs and the spinal cord tissue of three dogs were 98-100% identical to the publicly available sequences of S. lupi, confirming the diagnosis. These findings indicate that PCR targeting the 18S rDNA of S. lupi in CSF is useful for the ante-mortem diagnosis of canine intraspinal spirocercosis.

Screening nested-PCR primer for 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing and application in Hunan, China

Citrus Huanglongbing (HLB) is one of the most devastating citrus diseases worldwide. Sensitive and accurate assays are vital for efficient prevention of the spread of HLB-associated "Candidatus Liberibacter spp". "Candidatus Liberibacter spp" that infect Citrus includes "Candidatus Liberibacter asiaticus" (Las), "Candidatus Liberibacter africanus" (Laf) and "Candidatus Liberibacter americanus" (Lam). Of them, Las is the most widespread species. In this study, a set of nested PCR primer pairs were screened to diagnose Las, and the nested PCR method greatly enhanced the sensitivity to detect Las up to 10 times and 100 times compared to qPCR and conventional PCR, respectively. Totally, 1112 samples from 5 different citrus cultivars in 39 different counties and cities were assayed by nested PCR. The results show that 384 samples were HLB-infected; the highest positive detection rate was 79.7% from the lopsided fruit samples, and the lowest positive detection rate was 16.3% from the apical dieback samples. The results indicate that the designed nested PCR primer pairs can detect Las from different symptomatic tissues, different citrus cultivars and different geographic regions. The set of nested PCR primers designed in the present study will provide a very useful supplementation to the current approaches for Las detection.

Viral respiratory infections diagnosed by multiplex polymerase chain reaction in pediatric patients

Syndromic diagnosis by multiplex nucleic acid amplification tests is the most practical approach to respiratory tract infections since the symptoms are rarely agent‐specific. The aim of this study was to investigate the respiratory viruses in children admitted to a university hospital with acute respiratory tract infection during the last 8 years by a multiplex polymerase chain reaction (PCR) assay. A total of 3162 respiratory samples collected from children between April 2011 and April 2018 tested by a multiplex real‐time PCR assay. Two different commercial assays were used during the study period, "AusDiagnostics/Respiratory Pathogens 12 (AusDiagnostics)" used between April 2011 and December 2015, which changed to "Fast Track Diagnostics/Respiratory Pathogens 21 (Fast Track Diagnostics)" after January 2016 to cover more viruses. Nucleic acid extraction was done by EZ1 Advanced XL platform (QIAGEN). Respiratory pathogens detected in 1857 of the 3162 (58.7%) samples. The most prevalent viruses during the 8‐year period were rhinovirus/enterovirus (RV/EV; 36.2%), respiratory syncytial virus (RSV; 19%), and influenza virus A/B (14.7%). Rhinovirus was the main contributor to the RV/EV group as shown by the assay used during the 2016‐2018 period. RV/EV and adenoviruses detected throughout the year. Influenza virus was most frequently detected during January to March when both RSV and metapneumovirus were also in circulation. The coinfection percentage was 10.2%. Rhinovirus was the most common virus in coinfections while RSV plus rhinovirus/enterovirus were the most frequent combination. RSV and metapneumovirus showed a similar seasonal distribution to the influenza virus, which made it necessary to use a virological diagnostic assay during the influenza season.

Association of specific viral infections with childhood asthma exacerbations

Introduction

Asthma exacerbations may occur due to a variety of triggers including respiratory viruses. The aim of this study was to determine the role of particular viral infections in asthma exacerbations in children.

Materials and methods

The study was performed at Dr. Daneshvari Hospital Pediatric Emergency Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran between 2014 and 2015. A nasopharyngeal aspirate or swab was obtained from each patient during admission. All samples were maintained at 4 °C until submission to the virology laboratory and were tested for respiratory viruses by nucleic acid testing.

Results

A total of 60 patients with asthma exacerbations were recruited for this study. Of the 60 samples collected from the patients with acute asthma exacerbations, rhinovirus was detected in 12 patients (20%), respiratory syncytial virus in 5 (8%), adenovirus in 5 (8%), and influenza virus in 1 (1.6%). Respiratory pathogens were not detected in 37 (61%) samples. All the samples investigated showed single viral infection.

Conclusions

To conclude, the most common viruses detected were rhinovirus followed by respiratory syncytial virus (RSV) and adenovirus. RSV was more commonly associated with more severe attacks. Both the study design (e.g., time of sampling, age of the patients, etc.) and also the method used for viral detection influence the frequency of detection of the respiratory viruses.

A highly sensitive 1-tube nested real-time RT-PCR assay using LNA-modified primers for detection of respiratory syncytial virus

Respiratory syncytial virus (RSV) causes serious respiratory tract infection worldwide. The relatively low RSV load makes it difficult to detect in frail, elderly, and severely immune-compromised patients. In the present study, we developed a locked nucleic acid–-based 1-tube nested real-time RT-PCR (OTNRT-PCR) assay with the advantages of extremely high sensitivity, facile operability, and less likelihood of cross-contamination. The sensitivity, specificity, and clinical performance of the OTNRT-PCR assay were compared in parallel with a conventional TaqMan probe-based real-time PCR (qRT-PCR) assay and a traditional 2-step nested RT-PCR assay. The limit of detection of the OTNRT-PCR assay was 1.02 × 10⁻¹ TCID50/mL, equivalent to the traditional 2-step nested RT-PCR assay and 25-fold lower than the qRT-PCR assay. Of 616 nasopharyngeal aspirates tested, 143 RSV-negative samples by qRT-PCR were confirmed as positive by sequencing the OTNRT-PCR products. We therefore conclude that OTNRT-PCR is more sensitive than qRT-PCR for detection of RSV in clinical samples.

Development of Multiplex Nested PCR for Simultaneous Detection of Ectoparasitic Fungi Laboulbeniopsis termitarius and Antennopsis gallica on Reticulitermes speratus (Blattodea: Rhinotermitidae)

Laboulbeniopsis termitarius (Thaxt) and Antennopsis gallica (Buchli and Heim) are two of the most common ectoparasitic fungi found on the body surface of termites. While visual observation under a dissecting microscope is a common method used to screen for such fungi, it generally requires a large number of termites and is thus very time consuming. In this study, we develop a fast, efficient protocol to detect fungal infection on the termite Reticulitermes speratus (Kolbe). Species-specific primers were designed based on sequence data and amplified using a number of universal fungus primer pairs that target partial sequences of the 18s rRNA gene of the two fungi. To detect these fungi in a robust yet economic manner, we then developed a multiplex nested polymerase chain reaction assay using species-specific primers. Results suggested that both fungi could be successfully detected, even in cases where L. termitarius was at low titer (e.g., a single thallus per termite). The new method described here is recommended for future surveys of these two fungi, as it is more sensitive, species specific, and faster than visual observation, and is likely to facilitate a better understanding of these fungi and their dynamics in host populations.

Detailed genetic analyses of the HN gene in human respirovirus 3 detected in children with acute respiratory illness in the Iwate Prefecture, Japan

We performed detailed genetic analyses of the partial hemagglutinin-neuraminidase (HN) gene in 34 human respirovirus 3 (HRV3) strains from children with acute respiratory illness during 2013-2015 in Iwate Prefecture, Japan. In addition, we performed analyses of the evolutionary timescale of the gene using the Bayesian Markov chain Monte Carlo (MCMC) method. Furthermore, we analyzed pairwise distances and performed selective pressure analyses followed by linear B-cell epitope mapping and N-glycosylation and phylodynamic analyses. A phylogenetic tree showed that the strains diversified at around 1939, and the rate of molecular evolution was 7.6 × 10^-4 substitutions/site/year. Although the pairwise distances were relatively short (0.03 ± 0.018 [mean ± standard deviation, SD]), two positive selection sites (Cys544Trp and Leu555Ser) and no amino acid substitutions were found in the active/catalytic sites. Six epitopes were estimated in this study, and three mouse monoclonal antibody binding sites (amino acid positions 278, 281, and 461) overlapped with two epitopes belonging to subcluster C3 strains. Bayesian skyline plot analyses indicated that subcluster C3 strains have been increasing from 2004, whereas subcluster C1 strains have declined from 2004. Based on these results, Iwate strains were divided into two subclusters and each subcluster evolved independently. Moreover, our results suggested that some predicted linear epitopes (epitopes 3 and 5) are candidates for an HRV3 vaccine motif. To better understand the details of the molecular evolution of HRV, further studies are needed.

Risk factors of respiratory syncytial virus infection among pediatric influenza-like illness and severe acute respiratory infections in Suzhou, China

The characteristics and risk factors of respiratory syncytial virus (RSV) infection among children has not yet been fully understood. To address the characteristics of RSV-associated illness and risk factors of RSV infection among children under 5 years of age in Suzhou, China. From April 2011 to March 2014, we conducted a prospective surveillance among children in Suzhou, China. Nasal or throat swabs were collected from outpatients with influenza-like illness (ILI) and inpatients with severe acute respiratory infections (SARI). RSV was detected by reverse-transcriptase polymerase chain reaction and direct fluorescent antibody assay for children with ILI and SARI, respectively. Multivariable logistic-regression models were constructed to explore risk factors and symptoms of RSV infection. Of 3267 ILI and 1838 SARI children enrolled in the study, 192 (5.9%) and 287 (15.6%) tested positive for RSV, respectively. Among ILI patients, children with RSV infections visited clinics more often (P = 0.005) and had longer duration of fever (P = 0.032) than those without RSV infection. All RSV-positive children had an increased risk of having cough (OR = 2.9), rhinorrhea (OR = 1.6), breathing difficulty (OR = 3.4), wheezing (OR = 3.3), and irritability (OR = 2.7). Children aged <2 years, had history of prematurity (OR = 2.0) and recent respiratory infections (OR = 1.3) were more likely to get infected by RSV. Children with SARI had higher positive rate of RSV than those with ILI. Cough, rhinorrhea, and wheezing were the most common symptoms in RSV infection. Children aged <2 years, had history of prematurity and recent respiratory infections were the potential risk factors for RSV infection.

Detection and quantification of Spirocerca lupi by HRM qPCR in fecal samples from dogs with spirocercosis

Background

Spirocerca lupi, the dog oesophageal nematode, causes a potentially fatal disease in domestic dogs, and is currently clinically diagnosed by coproscopy and oesophagoscopy. To date, a single molecular method, a semi-nested PCR, targeting the cox1 gene, has been developed to aid in the diagnosis of spirocercosis. The present study describes three novel high-resolution melt (HRM) quantitative PCR (qPCR) assays targeting fragments of the ITS1, 18S and cytb loci of S. lupi. The performance of these molecular assays in feces was compared to fecal flotation and to the previously described cox1 gene semi-nested PCR in 18 fecal samples from dogs with clinical oesophageal spirocercosis diagnosed by oesophagoscopy.

Results

The HRM qPCR for ITS1 and 18S were both able to detect 0.2 S. lupi eggs per gram (epg), while the HRM qPCR for the cytb and the semi-nested PCR for the cox1 detected 6 epg and 526 epg, respectively. Spirocerca lupi was detected in 61.1%, 44.4%, 27.8%, 11.1% and 5.6% of the fecal samples of dogs diagnosed with spirocercosis by using the ITS1 and 18S HRM qPCR assays, fecal flotation, cytb HRM qPCR and cox1 semi-nested PCR, respectively. All dogs positive by fecal flotation were also positive by ITS1 and 18S HRM qPCRs. Quantification of S. lupi eggs was successfully achieved in the HRM qPCRs and compared to the fecal flotation with no significant difference in the calculated concentrations between the HRM qPCRs that detected the 18S and ITS1 loci and the fecal flotation. The HRM qPCR for the 18S cross-amplified DNA from Toxocara canis and Toxascaris leonina. In contrast, the HRM qPCR for ITS1 did not cross-amplify DNA from other canine gastrointestinal parasites.

Conclusions

This study presents two new molecular assays with significantly increased sensitivity for confirming and quantifying fecal S. lupi eggs. Of these, the HRM qPCR for ITS1 showed the best performance in terms of the limit of detection and absence of cross-amplification with other parasites. These assays will be useful in detecting infection and for follow-up during therapy.

Electronic supplementary material

The online version of this article (10.1186/s13071-017-2374-3) contains supplementary material, which is available to authorized users.

Anti-inflammatory effects of adjunctive macrolide treatment in adults hospitalized with influenza: A randomized controlled trial

INTRODUCTION

- Macrolides can ameliorate inflammation in respiratory diseases, providing clinical benefits. Data in influenza is lacking.

METHOD

- A randomized, open-label, multicenter trial among adults hospitalized for laboratory-confirmed influenza was conducted. Study treatments of oseltamivir and azithromycin (500 mg/day), or oseltamivir alone, both for 5 days, were allocated at 1:1 ratio. The primary outcome was plasma cytokine/chemokine concentration change over time (Day 0-10); secondary outcomes were viral load and symptom score changes. Generalized Estimating Equation (GEE) models were used to analyze longitudinal data.

RESULTS

- Fifty patients were randomized to the oseltamivir-azithromycin or oseltamivir groups, with comparable baseline characteristics (age, 57 ± 18 years; A/H3N2, 70%), complications (72%), and viral load. Pro-inflammatory cytokines IL-6 (GEE: β -0.037, 95%CI-0.067,-0.007, P = 0.016; reduction from baseline -83.4% vs -59.5%), CXCL8/IL-8 (β -0.018, 95%CI-0.037,0.000, P = 0.056; -80.5% vs -58.0%), IL-17 (β -0.064, 95%CI-0.117,-0.012, P = 0.015; -74.0% vs -34.3%), CXCL9/MIG (β -0.010, 95%CI-0.020,0.000, P = 0.043; -71.3% vs -56.0%), sTNFR-1, IL-18, and CRP declined faster in the oseltamivir-azithromycin group. There was a trend toward faster symptom resolution (β -0.463, 95%CI-1.297,0.371). Viral RNA decline (P = 0.777) and culture-negativity rates were unaffected. Additional ex vivo studies confirmed reduced induction of IL-6 (P = 0.017) and CXCL8/IL-8 (P = 0.005) with azithromycin.

CONCLUSION

- We found significant anti-inflammatory effects with adjunctive macrolide treatment in adults with severe influenza infections. Virus control was unimpaired. Clinical benefits of a macrolide-containing regimen deserve further study. [ClinicalTrials.gov NCT01779570].

Diagnosis of Viral Infections

Accurate diagnosis of viral infections enhances the ability of the clinician to make decisions on appropriate treatment of patients, evaluate disease progression and prevent misuse of antibiotics. Knowledge of the pathogen involved also allow implementation of infection control and monitoring of success of antiviral treatments that may affect the prognosis of patients. Epidemiological data collected through accurate diagnostics play an important role in public health through identification and control of outbreaks, implementation of appropriate diagnostic tests, vaccination programs and treatment but also to recognize common and emerging pathogens in a community. It is key that the clinician have an understanding of appropriate specimens to send to the laboratory and the value of specific nucleic acid and serological testing for different viral pathogens. Molecular techniques have revolutionized viral diagnoses over the past decade and enhanced both the sensitivity and specificity of tests and the speed by which a diagnosis can be made and new tests be developed. The continued use of serology for viruses with a short viremia, or for chronic infections should however complement these tests. This chapter aims to provide an overview of the available tests, the principles of testing and appropriate tests to select for different viruses and syndromes. Also provided is a glimpse of new developments in diagnostics that may further enhance the capacity to make a conclusive diagnosis in the near future.

Bacterial Pathogens Associated with Community-acquired Pneumonia in Children Aged Below Five Years

OBJECTIVE

To determine the spectrum of bacterial pathogens causing community-acquired pneumonia in children below 5 years of age.

METHODS

Children aged below 5 years satisfying the WHO criteria for pneumonia, severe pneumonia or very severe pneumonia, and with the presence of lung infiltrates on chest X-ray were enrolled. Two respiratory samples, one for culture and the other for PCR analysis, and a blood sample for culture were collected from every child.

RESULTS

Of the 180 samples processed, bacterial pathogens were detected in 64.4%. Streptococcus pneumoniae and Hemophilus influenzae were most frequently detected. The performance of PCR analysis and culture were identical for the typical bacterial pathogens; atypical pathogens were detected by PCR analysis only.

CONCLUSION

S. pneumoniae and H. influenza were the most commonly detected organisms from respiratory secretions of children with community acquired pneumonia.

Sensitive and specific nested PCR assay for detection of rotavirus A in samples with a low viral load

Techniques such as the real-time reverse transcription-polymerase chain reaction (qRT-PCR) can detect RNA in samples with a low viral load. However, these amplicons typically are either too short or at insufficient concentrations for use in subsequent sequencing reactions for genotyping and detection confirmation. The assay developed in this study detects rotavirus G genotypes and P genotypes with viral loads as low as 6.2 and 8.2 copies per reaction, respectively. The assay was validated using a panel of 91 stool samples, 32 reference rotavirus strains, and 6 non-target enteric virus samples.

The use of multiplex PCR for the diagnosis of viral severe acute respiratory infection in children: a high rate of co-detection during the winter season

Respiratory tract infection is a major cause of hospitalization in children. Although most such infections are viral in origin, it is difficult to differentiate bacterial and viral infections, as the clinical symptoms are similar. Multiplex polymerase chain reaction (PCR) methods allow testing for multiple pathogens simultaneously and are, therefore, gaining interest. This prospective case-control study was conducted from October 2013 to February 2014. Nasopharyngeal (NP) and oropharyngeal (throat) swabs were obtained from children admitted with severe acute respiratory infection (SARI) at a tertiary hospital. A control group of 40 asymptomatic children was included. Testing for 16 viruses was done by real-time multiplex PCR. Multiplex PCR detected a viral pathogen in 159/177 (89.9 %) patients admitted with SARI. There was a high rate of co-infection (46.9 %). Dual detections were observed in 64 (36.2 %), triple detections in 17 (9.6 %), and quadruple detections in 2 (1.1 %) of 177 samples. Seventy-eight patients required intensive care unit (ICU) admission, of whom 28 (35.8 %) had co-infection with multiple viruses. AdV, HBoV, HRV, HEV, and HCoV-OC43 were also detected among asymptomatic children. This study confirms the high rate of detection of viral nucleic acids by multiplex PCR among hospitalized children admitted with SARI, as well as the high rate of co-detection of multiple viruses. AdV, HBoV, HRV, HEV, and HCoV-OC43 were also detected in asymptomatic children, resulting in challenges in clinical interpretation. Studies are required to provide quantitative conclusions that will facilitate clinical interpretation and application of the results in the clinical setting.

Pathogen profiles and molecular epidemiology of respiratory viruses in Japanese inpatients with community-acquired pneumonia

Background

The etiological profile of viruses among adult patients with community-acquired pneumonia (CAP) has not been characterized yet. The aim of this study was twofold: first, investigate the pathogen profiles and the molecular epidemiology of respiratory viruses among Japanese CAP patients; and second, explore the clinical significance of viral infections.

Methods

A cross-sectional observational study was conducted at Kyorin University Hospital. To identify respiratory pathogens, hospitalized CAP patients were enrolled, and reverse transcriptase–polymerase chain reaction technology was applied alongside conventional microbiological methods. Phylogenetic and pairwise distance analyses of 10 viruses were performed. CAP patients were divided into four etiological groups (virus alone, bacteria alone, co-detection of virus and bacteria, and not detected) and the clinical findings were compared.

Results

Seventy-six patients were enrolled. Bacteria alone were detected in 39.5% (n=30) of CAP patients. Virus alone or co-detection were found in 10.5% (n=8) and 11.8% (n=9) of cases, respectively. Streptococcus pneumoniae and human metapneumovirus were the most frequently detected bacterium and virus, respectively. Phylogenetic analyses of human metapneumovirus, human rhinovirus, and human respiratory syncytial virus showed that different subgroups and genotypes might be associated with CAP. Respiratory failure was more common when a virus was detected (both virus alone and co-detection groups; n=17, 100%, p<0.05) than when a bacteria alone was detected (n=17, 56.7%).

Conclusion

Prevalence of respiratory virus infection in CAP inpatients was 22.3%. The detected viruses display high genetic divergence and correlate with increased respiratory failure.

A CAPS-based binding assay provides semi-quantitative validation of protein-DNA interactions

Investigation of protein-DNA interactions provides crucial information for understanding the mechanisms of gene regulation. Current methods for studying protein-DNA interactions, such as DNaseI footprinting or gel shift assays, involve labeling DNA with radioactive or fluorescent tags, making these methods costly, laborious, and potentially damaging to the environment. Here, we describe a novel cleaved amplified polymorphic sequence (CAPS)-based binding assay (CBA), which is a label-free method that can simplify the semi-quantitative validation of protein-DNA interactions. The CBA tests the interaction between a protein and its target DNA, based on the CAPS pattern produced due to differences in the accessibility of a restriction endonuclease site (intrinsic or artificial) in amplified DNA in the presence and absence of the protein of interest. Thus, the CBA can produce a semi-quantitative readout of the interaction strength based on the dose of the binding protein. We demonstrate the principle and feasibility of CBA using B3, MADS3 proteins and the corresponding RY or CArG-box containing DNAs.

Application of Multiplex PCR Coupled with Matrix-Assisted Laser Desorption Ionization-Time of Flight Analysis for Simultaneous Detection of 21 Common Respiratory Viruses

Respiratory infections continue to pose a significant threat to human health. It is important to accurately and rapidly detect respiratory viruses. To compensate for the limits of current respiratory virus detection methods, we developed a 24-plex analysis (common respiratory virus-mass spectrometry [CRV-MS]) that can simultaneously detect and identify 21 common respiratory viruses based on a matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system. To evaluate the efficacy of the CRV-MS method, we used 102 samples that were confirmed positive for these common respiratory viruses. All tests using the CRV-MS method were effective, with no cross-reactivity observed with other common respiratory viruses. To confirm the usefulness of the CRV-MS method, we screened 336 nasal and throat swabs that were collected from adults or children with suspected viral acute respiratory tract infections using the CRV-MS method and consensus PCR/reverse transcription-PCR (RT-PCR) methods. Excluding four RNase P-negative samples, the CRV-MS and consensus PCR/RT-PCR methods detected respiratory viruses in 92.5% (307/332) and 89.5% (297/332) of the samples, respectively. The two methods yielded identical results for 306 (92.2%) samples, including negative results for 25 samples (7.5%) and positive results for 281 samples (84.6%). Differences between the two methods may reflect their different sensitivities. The CRV-MS method proved to be sensitive and robust, and it can be used in large-scale epidemiological studies of common respiratory virus infections.

Respiratory viral pathogens among Singapore military servicemen 2009-2012: epidemiology and clinical characteristics

Background

Few studies have comprehensively described tropical respiratory disease surveillance in military populations. There is also a lack of studies comparing clinical characteristics of the non-influenza pathogens with influenza and amongst themselves.

Methods

From May 2009 through October 2012, 7733 consenting cases of febrile respiratory illness (FRI) (temperature [greater than or equal to]37.5degreesC with cough or sorethroat) and controls in the Singapore military had clinical data and nasal washes collected prospectively. Nasal washes underwent multiplex PCR, and the analysis was limited to viral mono-infections.

Results

49% of cases tested positive for at least one virus, of whom 10% had multiple infections. 53% of the FRI cases fulfilled the definition of influenza-like illness (ILI), of whom 52% were positive for at least one virus. The most frequent etiologies for mono-infections among FRI cases were Influenza A(H1N1)pdm09 (13%), Influenza B (13%) and coxsackevirus (9%). The sensitivity, specificity, positive predictive value and negative predictive value of ILI for influenza among FRI cases were 72%, 48%, 40% and 69% respectively. On logistic regression, there were marked differences in the prevalence of different symptoms and signs between viruses with fever more prevalent amongst influenza and adenovirus infections than other viruses.

Conclusion

There are multiple viral etiologies for FRI and ILI with differing clinical symptoms in the Singapore military. Influenza and coxsackevirus were the most common etiology for FRI, while influenza and adenoviruses displayed the most febrile symptoms. Further studies should explore these differences and possible interventions.

Evaluation of the AdvanSure™ real-time RT-PCR compared with culture and Seeplex RV15 for simultaneous detection of respiratory viruses

Recently, AdvanSure™ kit based on multiplex real-time PCR was developed for simultaneous detection of 14 respiratory viruses (RVs). We compared the performance of AdvanSure with those of Seeplex® RV 15 ACE and culture by determining their sensitivities and specificities against a composite reference standard. Four hundred thirty-seven respiratory samples were tested by modified shell vial culture method, RV 15 ACE, and AdvanSure. One hundred fourteen samples (26.2%) out of 437 samples were positive by culture, while additional 91 (20.8%) were positive by AdvanSure or RV15. One hundred twelve of 114 culture-positive samples were positive by AdvanSure except 2 samples (1 adenovirus, 1 respiratory syncytial virus [RSV]). Overall, the sensitivities of culture, RV15, and AdvanSure were 74.5%, 89.8%, and 95.1%, respectively. Sensitivities of culture, RV15, and AdvanSure for each virus tested were as follows: 91/100/96% for influenza A, 60/0/100% for influenza B, 63/95/97% for RSV, 69/81/89% for adenovirus, and 87/93/93% for parainfluenza virus. For viruses not covered by culture, sensitivities of RV15 and AdvanSure were as follows: 77/88% for rhinovirus, 100/100% for coronavirus OC43, 40/100% for coronavirus 229E/NL63, 13/100% for metapneumovirus, and 44/100% for bocavirus. The overall specificities of culture, RV15, and AdvanSure were 100/98.9/99.5%, respectively. Of 45 coinfected specimens, AdvanSure detected 41 specimens (91.1%) as coinfected, while RV15 detected 27 specimens (60.0%) as coinfected. AdvanSure assay demonstrated exquisite performance for the detection of RVs and will be a valuable tool for the management of RV infection.

Phylogenetic analysis and seroprevalence of influenza C virus in Mie Prefecture, Japan in 2012

Reverse transcription polymerase chain reaction (RT-PCR) and real-time RT-PCR were used to detect 14 (6.6%) influenza C virus (InfC) among 213 clinical samples collected from children with respiratory symptoms in Mie Prefecture, Japan, between January 2012 and December 2012. Virus isolation using Madin-Darby canine kidney cells and/or embryonated chicken eggs was also successful for 3 of the 14 PCR-positive samples. Eleven patients (78.6%) were aged <3 years. Phylogenetic analysis of the hemagglutinin-esterase gene showed that the InfC detected in Mie Prefecture belonged to the C/Sao Paulo/82-related lineage. To determine the seroprevalence of InfC, a total of 575 serum samples from patients aged 1 month to 69 years in Mie Prefecture were screened by hemagglutination inhibition test using the C/Mie/199/2012 (C/Sao Paulo/82-related lineage) strain as the antigen. The samples with an antibody titer of ≥1:16 were designated as antibody-positive. The results showed that 53.7% of the 296 serum samples collected in 2011 and 85.3% of the 279 samples collected in 2012 were positive for antibodies against InfC, suggesting that an outbreak of InfC infection occurred in Mie Prefecture in 2012. Therefore, continuous and proactive monitoring is important to determine the number of InfC-infections and to better understand the epidemiology.

Outcomes of Pneumocystis pneumonia with respiratory failure in HIV-negative patients

PURPOSE

The outcomes and predictors of mortality from Pneumocystis pneumonia (PCP) in HIV-negative patients requiring mechanical ventilation (MV) for respiratory failure were evaluated.

MATERIALS AND METHODS

This retrospective observational study enrolled 48 patients with PCP requiring MV in the medical intensive care unit (ICU). Multiple logistic regression analysis was used to identify independent predictors of in-hospital mortality.

RESULTS

The main conditions underlying the PCP were malignancies (60%) or post solid organ transplant (35%). Excluding four patients whose initial treatment was changed due to adverse reactions, 21 (44%) of 44 patients did not respond to the initial treatment. During the ICU stay, additional complications developed: shock in 22 (46%), ventilator-associated pneumonia in 16 (33%), and acute kidney injury in 15 (31%). Ultimately, 31 (65%) patients died while hospitalised. In multivariate analysis, hospital mortality was independently associated with severity of illness on ICU admission, failure of initial antimicrobial treatment for PCP, and newly developed shock during ICU stay.

CONCLUSIONS

PCP in HIV-negative patients requiring MV for respiratory failure remains a serious illness with high mortality. Failure of the initial antimicrobial treatment for PCP as well as severity of illness was independent predictors of poor outcomes.

Etiologies, diagnostic strategies, and outcomes of diffuse pulmonary infiltrates causing acute respiratory failure in cancer patients: a retrospective observational study

Introduction

Although previous studies have reported etiologies, diagnostic strategies, and outcomes of acute respiratory failure (ARF) in cancer patients, few studies investigated ARF in cancer patients presenting with diffuse pulmonary infiltrates.

Methods

This was a retrospective observational study of 214 consecutive cancer patients with diffuse pulmonary infiltrates on chest radiography admitted to the oncology medical intensive care unit for acute respiratory failure between July 2009 and June 2011.

Results

After diagnostic investigations including bronchoalveolar lavage in 160 (75%) patients, transbronchial lung biopsy in 75 (35%), and surgical lung biopsy in 6 (3%), the etiologies of diffuse pulmonary infiltrates causing ARF were identified in 187 (87%) patients. The most common etiology was infection (138, 64%), followed by drug-induced pneumonitis (13, 6%) and metastasis (12, 6%). Based on the etiologic diagnoses, therapies for diffuse pulmonary infiltrates were subsequently modified in 99 (46%) patients. Diagnostic yield (46%, 62%, 85%, and 100%; P for trend < 0.001) and frequency of therapeutic modifications (14%, 37%, 52%, and 100%; P for trend < 0.001) were significantly increased with additional invasive tests. Patients with therapeutic modification had a 34% lower in-hospital mortality rate than patients without therapeutic modification (38% versus 58%, P = 0.004) and a similar difference in mortality rate was observed up to 90 days (55% versus 73%, Log-rank P = 0.004). After adjusting for potential confounding factors, therapeutic modification was still significantly associated with reduced in-hospital mortality (adjusted OR 0.509, 95% CI 0.281-0.920).

Conclusions

Invasive diagnostic tests, including lung biopsy, increased diagnostic yield and caused therapeutic modification that was significantly associated with better outcomes for diffuse pulmonary infiltrates causing ARF in cancer patients.

Clinical characteristics and outcomes of influenza and other influenza-like illnesses in Mexico City

BACKGROUND

Influenza-like illnesses (ILI) are estimated to cause millions of deaths annually. Despite this disease burden, the etiologic causes of ILI are poorly described for many geographical regions.

METHODS

Beginning in April 2010, we conducted an observational cohort study at five hospitals in Mexico City, enrolling subjects who met the criteria for ILI. Evaluations were conducted at enrollment and on day 28, with the collection of clinical data and a nasopharyngeal swab (or nasal aspirate in children). Swabs were tested by multiplex PCR for 15 viral pathogens and real-time PCR for influenza.

RESULTS

During the first year, 1065 subjects were enrolled in this study, 55% of whom were hospitalized; 24% of all subjects were children. One or more pathogens were detected by PCR in 64% of subjects, most commonly rhinovirus (25% of all isolates) and influenza (24% of isolates). Six percent of subjects died, and of those, 54% had no pathogen identified. Rhinovirus was the most common pathogen among those who died, although it did not have the highest case fatality rate.

CONCLUSIONS

Multiple respiratory viruses beyond influenza are associated with significant morbidity and mortality among adults and children in Mexico City. Detection of these agents could be useful for the adjustment of antibiotic treatment in severe cases.

Molecular evolution of attachment glycoprotein (G) gene in human respiratory syncytial virus detected in Japan 2008-2011

We investigated the evolution of the C-terminal 3rd hypervariable region of G gene in the prevalent human respiratory syncytial virus (RSV) subgroups A (RSV-A) and B (RSV-B) in Japan in 2008-2011. Phylogenetic analysis and the evolutionary timescale was obtained by the Bayesian Markov Chain Monte Carlo method. All 38 RSV-A strains detected were classified into genotype NA1 and the 17 RSV-B strains detected belonged to genotypes BA and GB2. NA1 subdivided around 1998 in the present phylogenetic tree. Genotype BA subdivided around 1994. The evolutionary rates for RSV-A and RSV-B were estimated at 3.63×10⁻³ and 4.56×10⁻³ substitutions/site/year, respectively. The mean evolutionary rate of RSV-B was significantly faster than that of RSV-A during all seasons. The pairwise distance was relatively short (less than 0.06). In addition, some unique sites under positive selection were found. The results suggested that this region of the RSV strains rapidly evolved with some unique amino acid substitutions due to positive pressure.

Viral etiology of acute respiratory infection in Gansu Province, China, 2011

Background

Acute respiratory infections (ARIs) are the leading cause of children and their leading killer. ARIs are responsible for at least six percent of the world's disability and death. Viruses are one of the most common agents causing ARIs. Few studies on the viral etiology and clinical characteristics of ARIs have been performed in the northwest region of China, including Gansu Province.

Methods

Clinical and demographic information and throat swabs were collected from 279 patients from January 1st to December 30st, 2011. Multiplex RT-PCR was performed to detect 16 respiratory viral pathogens.

Results

279 patients were admitted for ARIs. The patients aged from 1 month to 12 years, with the median age of 2 years. Of which, 105 (37.6%) were positive for at least one pathogen. A total of 136 respiratory viral pathogens were identified from the 105 patients. Respiratory syncytial virus (RSV) was the most frequently detected pathogen (26.5%, 36/136), followed by parainfluenza virus (PIV) 1–3 (22.1%, 30/136), human rhinovirus (HRV) (21.3%, 29/136), human coronavirus (CoV) (10.3%, 14/136) and human adenovirus (HAdV) (9.6%, 13/136). Influenza A (Flu A), human metapneumovirus (hMPV) and human bocavirus (BoCA) were found 4.4%, 3.7% and 2.2%, respectively. Influenza B (Flu B) and seasonal influenza A H1N1(sH1N1) were not detected. Single-infections were detected in 30.5% (85/279) of cases. RSV was the most common pathogens in patients under 1 year and showed seasonal variation with peaks during winter and spring.

Conclusions

This paper presents data on the epidemiology of viral pathogens associated with ARIs among children in Gansu Province, China. RSV is most frequently detected in our study. The findings could serve as a reference for local CDC in drawing up further plans to prevent and control ARIs.

Diagnostics and surveillance for Swine influenza

Collective knowledge regarding the occurrence of influenza among swine is incomplete due to inconsistent surveillance of swine populations. In this chapter, we review what surveillance activities exist and some of the practical challenges encountered. Furthermore, to support robust surveillance activities, accurate laboratory assays are needed for the detection of the virus and viral nucleic acids within clinical samples, or for antiviral antibodies in serum samples. The most common influenza diagnostic assays used for swine are explained and their use as surveillance tools evaluated.

Multiplex nested RT-PCR for detecting avian influenza virus, infectious bronchitis virus and Newcastle disease virus

In this study, multiplex nested RT-PCR (mnRT-PCR) was applied to simultaneous detect multiplex PCR with the higher sensitivity of nested PCR that is required for avian influenza, infectious bronchitis and Newcastle disease virus using two steps of amplification. For the first PCR, primers that were specific for each virus were newly designed from the nucleoprotein gene of AIV, the nucleocapsid protein gene of IBV and the fusion protein gene of NDV to amplify products of 665, 386 and 236 nucleotides, respectively. The multiplex PCR step provides mass amplification using common primers, which increased markedly the sensitivity of the test. Non-specific reactions were not observed when other viruses and bacteria were used for evaluating the mnRT-PCR. As a field application, 172 samples were tested by RT-PCR and mnRT-PCR. Among these samples, the concordance rates for mnRT-PCR and the single conventional RT-PCR showed 98.9% (kappa=0.98) and 98.8% (kappa=0.96) similarity for IBV and AIV, respectively. As a result, it is recommended the multiplex nested PCR as an effective tool for detecting and studying the molecular epidemiology of various mixed infections of one or more of these viruses in poultry.

Role of atypical pathogens in nursing home-acquired pneumonia

Objectives

No international consensus has been reached on the empirical use of antibiotics with atypical coverage in nursing home–acquired pneumonia (NHAP). Aspiration is an important cause of NHAP, but it may not require antimicrobial treatment. This study aimed to investigate the prevalence and clinical characteristics of AP infections and review the need for empirical antibiotics with atypical coverage in NHAP.

Design

A prospective cohort study.

Setting

Four nursing homes with a total number of 772 residents.

Participants

Patients were aged ≥ 65 years, hospitalized for NHAP, which was defined as the presence of respiratory symptoms and abnormal chest radiographs, from April 2006 to March 2007.

Measurements

Demographics, clinical parameters, and investigation results were recorded. Microbial investigations comprised sputum routine and mycobacterial cultures, blood and urine cultures, serology, and nasopharyngeal aspirate viral culture and polymerase chain reaction tests. Suspected aspiration pneumonitis was arbitrarily defined as NHAP without pathogens identified.

Results

After excluding lone bacteriuria, 108 episodes of NHAP in 94 patients were included. Twelve APs were detected in 11 patients. There was no clinical feature to distinguish between infections caused by APs and other pathogens. The commonest APs were Mycoplasma pneumoniae (6) and Chlamydophila pneumoniae (3). No Legionella pneumophila was detected by urinary antigen test. None of the patients with AP infection received antibiotics indicated for AP infections. However, AP infections did not result in mortality. No pathogen was isolated in 31.5% of cases. Patients without pathogens isolated were less likely to have purulent sputum and crepitations on chest auscultation, compared with those with pneumonia caused by identified pathogens.

Conclusions

Atypical pathogens (APs) were not associated with mortality even in cases where the prescribed antibiotics did not cover APs. NHAP may not necessarily be treated with empirical antibiotics covering APs.

The Evolving Threat of Influenza Viruses of Animal Origin and the Challenges in Developing Appropriate Diagnostics

BACKGROUND

An H1N1 subtype of swine origin caused the first influenza pandemic in this century. This pandemic strain was a reassortant of avian, swine, and human influenza viruses. Many diagnostic laboratories were overwhelmed by the testing demands related to this pandemic. Nevertheless, there remains the threat of other animal influenza viruses, such as highly pathogenic H5N1. As a part of pandemic preparedness, it is essential to identify the diagnostic challenges that will accompany the next pandemic.

CONTENT

We discuss the natural reservoir of influenza viruses and the possible role of livestock in the emergence of pandemic strains. The current commonly used molecular tests for influenza diagnosis or surveillance are also briefly reviewed. Some of these approaches are also used to detect animal viruses. Unfortunately, owing to a lack of systematic surveillance of animal influenza viruses, established tests may not be able to detect pandemic strains that have yet to emerge from the animal reservoir. Thus, multiple strategies need to be developed for better identification of influenza viruses. In addition, molecular assays for detection of mutations associated with antiviral resistance and for viral segment reassortments should also be encouraged.

SUMMARY

Influenza viruses are highly dynamic viruses. Regular and systematic influenza surveillance in both humans and animals is essential to provide a more comprehensive picture of the prevalent influenza viruses. To better prepare for the next pandemic, we should develop some simple and easy-to-use tests for characterizing newly emerging influenza viruses.

Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens

BACKGROUND

In this study, we evaluated the analytical performance and clinical potential of a one-step multiplex real-time PCR assay for the simultaneous detection of 14 types of respiratory viruses using the AdvanSure RV real-time PCR Kit (LG Life Sciences, Korea).

METHODS

Three hundred and twenty clinical specimens were tested with the AdvanSure RV real-time PCR Kit and conventional multiplex reverse transcription (RT)-PCR assay. The assay results were analyzed and the one-step AdvanSure RV real-time PCR Kit was compared with the conventional multiplex RT-PCR assay with respect to the sensitivity and specificity of the detection of respiratory viruses.

RESULTS

The limit of detection (LOD) was 1.31 plaque-forming units (PFU)/mL for human rhinoviruses (hRVs), 4.93 PFU/mL for human coronavirus HCoV-229E/NL63, 2.67 PFU/mL for human coronavirus HCoV-OC43, 18.20 PFU/mL for parainfluenza virus 1 (PIV)-1, 24.57 PFU/mL for PIV-2, 1.73 PFU/mL for PIV-3, 1.79 PFU/mL for influenza virus group (Flu) A, 59.51 PFU/mL for FluB, 5.46 PFU/mL for human respiratory syncytial virus (hRSV)-A, 17.23 PFU/mL for hRSV-B, 9.99 PFU/mL for human adenovirus (ADVs). The cross-reactivity test for this assay against 23 types of non-respiratory viruses showed negative results for all viruses tested. The agreement between the one-step AdvanSure multiplex real-time PCR assay and the conventional multiplex RT-PCR assay was 98%.

CONCLUSIONS

The one-step AdvanSure RV multiplex real-time PCR assay is a simple assay with high potential for specific, rapid and sensitive laboratory diagnosis of respiratory viruses compared to conventional multiplex RT-PCR.

High incidence of multiple viral infections identified in upper respiratory tract infected children under three years of age in Shanghai, China

Background

Upper respiratory tract infection (URTI) is a major reason for hospitalization in childhood. More than 80% of URTIs are viral. Etiological diagnosis of URTIs is important to make correct clinical decisions on treatment methods. However, data for viral spectrum of URTIs are very limited in Shanghai children.

Methods

Nasopharyngeal swabs were collected from a group of 164 children aged below 3 years who were hospitalized due to acute respiratory infection from May 2009 to July 2010 in Shanghai. A VRDAL multiplex PCR for 10 common respiratory viruses was performed on collected specimens compared with the Seeplex® RV15 ACE Detection kit for 15 respiratory viruses.

Results

Viruses were detected in 84 (51.2%) patients by VRDAL multiplex PCR, and 8 (4.9%) of cases were mixed infections. Using the Seeplex® RV15 ACE Detection kit, viruses were detected in 129 (78.7%) patients, 49 (29.9%) were co-infected cases. Identified viruses included 37 of human rhinovirus (22.6% of cases), 32 of influenza A virus (19.5%), 30 of parainfluenzavirus-2 (18.3%), 23 of parainfluenzavirus-3 (14.0%), 15 of human enterovirus (9.1%), 14 each of parainfluenzavirus-1, respiratory syncytial virus B and adenovirus (8.5%), 8 of coronavirus 229E/NL63 (4.9%), 6 of human bocavirus (3.7%), 5 each of influenza B virus and respiratory syncytial virus A (3.0%), 3 of parainfluenzavirus-4 (1.8%), 2 of coronavirus OC43/HKU1 (1.2%), and 1 human metapneumovirus (0.6%).

Conclusions

A high frequency of respiratory infections (78.7%) and co-infections (29.9%) was detected in children with acute respiratory infection symptoms in Shanghai. The Seeplex® RV15 ACE detection method was found to be a more reliable high throughput tool than VRDAL method to simultaneously detect multiple respiratory viruses.

Validation of a multiplex reverse transcriptase PCR ELISA for the detection of 19 respiratory tract pathogens

INTRODUCTION

Since acute respiratory tract infections inflict a high burden of disease in children worldwide, a multiplex reverse transcription polymerase chain reaction combined with a microwell hybridization assay (m-RT-PCR-ELISA) to detect 19 different respiratory pathogens was developed and validated.

METHODS

A total of 430 respiratory specimens were retrospectively tested in parallel by both the advanced 19-valent m-RT-PCR-ELISA as well as by culture or individual RT-PCR assays used in clinical routine.

RESULTS

The mean (median) sensitivity of the m-RT-PCR-ELISA in the retrospective test was 93.3% (95.1%; range 83.3-100 %), and the mean (median) specificity was 99.8 and 100 % (range 98.6-100 %), respectively. The mean positive predictive value was 99.3 % (range 93.4-100 %) and the mean negative predictive value was 95.3 % (range 98.4-100 %). Feasibility and clinical value of the 19-valent method was prospectively shown on 16,231 incoming clinical specimens from patients between 0 and 16 years of age with acute respiratory tract infections admitted to pediatric hospitals or private practices from October 2003 to June 2010 in three regions in Germany (Kiel, Mainz, Freiburg; Freiburg to June 2007 only). At least one microorganism was detected in 10,765 of 16,231 (66.3 %) clinical specimens: 5,044 RV, 1,999 RSV, 1,286 AV, 944 EV, 737 seasonal IVA, 173 pandemic IVA H1N1-2009, 899 MPV, 518 CV, 383 PIV3, 268 PIV1, 259 Mpn, 205 IVB, 164 PIV2, 144 PIV4, 103 Bp, 29 Cpn and 29 Bpp, while reovirus and Lpn were not present in these specimens from a pediatric population. More than one organism could be detected in 13.4 % of the specimens.

CONCLUSIONS

The m-RT-PCR-ELISA evaluated here improves the spectrum for diagnosing respiratory infections and is a feasible instrument for individual diagnostic and epidemiological studies.