多重PCR检测儿童呼吸道感染常见病毒

目的 对深圳、粤东地区儿童呼吸道病毒感染进行监测、分析,探讨其流行规律.方法 2006年6月-2008年6月,于汕头大学附属医院、深圳市第四人民医院、揭阳市人民医院采集毛细支气管炎、支气管肺炎、喘息支气管炎等的患儿咽拭子或鼻咽分泌物标本686份,多重PCR进行9种呼吸道病毒检测.结果 在686例标本中病毒阳性362例(52.77%),其中呼吸道感染患儿中呼吸道合胞病毒(RSV)感染占首位,达到31.22%(113/362),其次是鼻病毒(RHV)为16.85%(61/362),最低是流感病毒B型(IVB)占0.83%(3/362),流感病毒A型(IVA)占14.36%(52/362),副流感病毒1型(PIV1)和副流感病毒3型(PIV3)分别占7.73%(28/362)和8.29%(30/362),腺病毒(AdV)达到9.67%(35/362),而人博卡病毒(hBOV)和人偏肺病毒(hMPV)分别占6.08%(22/362)和4.97%(18/362).结论 RSV、RHV及IVA是华南地区儿童呼吸道感染的主要病毒病原,混合感染以RSV、IVA联合其他病毒感染为主,诊治时应根据所感染病原体制定有针对性的措施.     

Detection of respiratory viruses in adults with respiratory tract infection using a multiplex PCR assay at a tertiary center

BackgroundRespiratory viruses (RVs) are among the most common pathogens for both upper and lower respiratory tract infections (RTIs). However, the viral epidemiology of RV-associated RTIs in adults has long been under-recognized. Through a sensitive molecular assay, it would be possible to have a better understanding of the epidemiology of RV-associated RTIs.Material and methodsRespiratory tract (RT) specimens from adults hospitalized due to RTIs were tested for RVs, using the multiplex PCR-based Luminex xTAG® Respiratory Viral Panel assay. A total of nineteen RVs, including influenza viruses and non-influenza respiratory viruses (NIRVs) were detected. Positive rates were compared using a chi-square test.ResultsA total of 2292 samples from adult patients hospitalized with RTIs were screened for RVs. The overall positive rate was 22%, with 17.8% samples positive for at least one NIRV. NIRVs had a higher positive rate in non-winter seasons. As many as 12.7% (46/363) of the samples collected through broncho-alveolar lavage and 20.5% (176/859) of the samples collected in ICUs were positive for RVs. Distribution of corona virus (CoV), human metapneumovirus (hMPV) and parainfluenza virus (PIV) demonstrated seasonal variation. Also, temperature was associated with the positive rates of specific viruses, including CoV, respiratory syncytial virus (RSV), hMPV and PIV.ConclusionRespiratory viruses, notably NIRVs, were frequently detected in adults hospitalized with RTIs. Several RVs were detected with distinctive seasonal variations. A substantial number of RVs were identified in lower RT specimens or from patients admitted to ICU, highlighting their important role in causing severe respiratory infection.     

Efficacy and safety of discontinuing antibiotic treatment for uncomplicated respiratory tract infections when deemed unnecessary. A multicentre,randomized clinical trial in primary care

ObjectivesTo determine the benefits and harms of discontinuing unnecessary antibiotic therapy for uncomplicated respiratory tract infections (RTI) when antibiotics are considered no longer necessary.MethodsMulticentre, open-label, randomized controlled clinical trial in primary care centres from 2017 to 2020 (ClinicalTrials.gov, NCT02900820). Adults with RTIs—acute rhinosinusitis, sore throat, influenza or acute bronchitis—who had previously taken any dose of antibiotic for less than 3 days, which physicians no longer deemed necessary were recruited. The patients were randomly assigned in a 1:1 ratio to discontinuing antibiotic therapy or the usual strategy of continuing antibiotic treatment. The primary outcome was the duration of severe symptoms (number of days scoring 5 or 6 on a six-item Likert scale). Secondary outcomes included days with symptoms, moderate symptoms (scores of 3 or 4), antibiotics taken, adverse events, patient satisfaction and complications within the first 3 months.ResultsA total of 467 patients were randomized, out of which 409 were considered valid for the analysis. The mean (SD) duration of severe symptoms was 3.0 (1.5) days for the patients assigned to discontinuation and 2.8 (1.3) days for those allocated to the control group (mean difference 0.2 days; 95% CI –0.1 to 0.4 days). Patients randomized to the discontinuation group used fewer antibiotics after the baseline visit (52/207 (25.1%) versus 182/202 (90.1%); p 0.001). Patients assigned to antibiotic continuation presented a relative risk of adverse events of 1.47 (95% CI 0.80–2.71), but the need for further health-care contact in the following 3 months was slightly lower (RR 0.61; 95% CI 0.28–1.37).ConclusionsDiscontinuing antibiotic treatment for uncomplicated RTIs when clinicians consider it unnecessary is safe and notably reduces antibiotic consumption.     

多重实时PCR检测三种呼吸道病毒

目的建立多重实时PCR检测体系可同时快速检测引起人呼吸道感染的甲型流感病毒（IAV）、呼吸道合胞病毒（RSV）和SARS冠状病毒（SARS-CoV）。方法通过对PCR反应条件的优化，建立了同时检测IAV、RSV和SARS-CoV的多重实时PCR方法。结果经熔解曲线分析，证实了该法可同时或分别检测3种重要呼吸道病毒。检测灵敏度分别为10^0.7 TCID50／ml、1 TCID50／ml和10^-0.5 TCID50／ml。采用相同的反应体系和条件，分别对其他7种呼吸道病毒（包括乙型流感病毒，副流感病毒2型，柯萨奇病毒B3和B5血清型及腺病毒2、3和7血清型）进行扩增，均未检测出扩增产物。此种方法可在4h内完成。结论建立的多重实时PCR检测方法适用于3种重要呼吸道病毒的快速检测。     

Simultaneous detection of respiratory viruses in children with acute respiratory infection using two different multiplex reverse transcription-PCR assays

A 4-tube multiplex RT-PCR (mRT-PCR), which showed higher sensitivity over conventional methods, was previously developed for the diagnosis of 14 viral pathogens of the respiratory tract. Herein the mRT-PCR was compared to the commercial Luminex mPCR-microsphere flow cytometry assay (Resplex II) which allows the detection of 12 different viruses. Eleven different viruses were identified in 91 nasopharyngeal swabs of children with acute respiratory infection, influenza A (IAV) and B, respiratory syncytial virus (RSV), human rhinovirus (hRhV), human echovirus, parainfluenza viruses (PIV) 1, 2, 3 and 4, human metapneumovirus (hMPV), and human coronavirus NL63. The results of the two techniques showed 53 and 40 positive patients by the Resplex II assay and mRT-PCR, respectively, with a concordance in 35 positive and 33 negative patients (74.7%). Individual RT-PCR tests were performed to control viruses not simultaneously detected by the two multiplex assays. The major virus misdiagnosed by mRT-PCR was IAV whereas the major viruses misdiagnosed by Resplex II were PIV1, 3 and 4. The mRT-PCR remains a simple, rapid, and specific assay for the specific detection of respiratory viruses, and can be easily implemented with standards in clinical laboratories at a low cost.     

Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis

ObjectivesTo provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)—BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test (Verigene RV+) and Hologic Gen-Probe Prodesse assays—on the detection of viral respiratory infections.MethodsA comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RV+ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay.ResultsTwenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RV+ and ProFlu+ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848–0.949), 0.949 (95% confidence interval, 0.882–0.979) and 0.954 (95% confidence interval, 0.871–0.985), respectively. The three mPCRs were comparable in terms of detection of FluA.ConclusionsPoint estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RV+ and ProFlu+) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments.     

Impact of multiplex polymerase chain reaction syndromic panel on antibiotic use among hospitalized children with respiratory tract illness during COVID-19 pandemic

Background/PurposePrecise detection of respiratory pathogens by molecular method potentially may shorten the time to diagnose and reduce unnecessary antibiotic use.MethodsMedical records of hospitalized children from January 2020 to June 2021 with acute respiratory illness who received a FilmArray RP for respiratory pathogens were reviewed and compared with data from diagnosis-matched patients without receiving the test.ResultsIn total, 283 patients and 150 diagnosis-matched controls were included. Single pathogen was detected in 84.3% (193/229) of the patients. The most common pathogen was human rhinovirus/enterovirus (31.6%, 84/266), followed by respiratory syncytial virus (18.8%, 50/266) and adenovirus (15%, 40/266). Although antimicrobial days of therapy (DOT) was significantly longer in FilmArray group than the control [7.1 ± 4.9 days vs 5.7 ± 2.7 days, P = 0.002], the former showed a higher intensive care unit (ICU) admission rate (3.9% vs 0%; P = 0.010). All ICU admissions were in FilmArray RP-positive group. There was no difference in antimicrobial DOT between FilmArray RP-positive and the negative groups, in all admissions, even after excluding ICU admissions. Antimicrobial DOT was shorter in the positive than negative group in patients with lower respiratory tract infections without admission to ICU [median (IQR): 6 (4–9) days vs 9 (4–12) days, P = 0.047].ConclusionsShorter antimicrobial DOTs were identified in children with lower respiratory tract infection admitted to general pediatric ward and with an identifiable respiratory pathogen, indicating a role of the multiplex PCR in reducing antimicrobial use for children with respiratory tract infection.     

Saliva as a diagnostic specimen for testing respiratory virus by a point-of-care molecular assay: a diagnostic validity study

Objectives

Automated point-of-care molecular assays have greatly shortened the turnaround time of respiratory virus testing. One of the major bottlenecks now lies at the specimen collection step, especially in a busy clinical setting. Saliva is a convenient specimen type that can be provided easily by adult patients. This study assessed the diagnostic validity, specimen collection time and cost associated with the use of saliva.

登革病毒悬液芯片分型检测方法的建立

目的 建立一种基于悬液芯片的登革病毒(dengue virus,DV)检测方法,可对四种血清型登革病毒进行快速检测和鉴定.方法 依据GenBank上4种病毒的基因序列信息,设计并合成相关引物及探针序列.抽提病毒RNA,经反转录后对目的基因进行PCR扩增,产物与核酸探针微球组杂交后于Bio-PlexTM 200系统检测荧光信号值.结果 DV1的悬液芯片检测敏感性约9 DNA拷贝,DV2、DV3、DV4的悬液芯片检测敏感性约90 DNA拷贝.进而将本方法用于检测15份临床标本,其检测结果与分型荧光RT-PCR一致.结论 建立了可同时检测四种血清型登革病毒的悬液芯片检测方法,为快速筛查和鉴定登革病毒提供了新的手段.     

Respiratory etiological surveillance among quarantined patients with suspected lower respiratory tract infection at a medical center in southern Taiwan during COVID-19 pandemic

BackgroundA comprehensive study of respiratory pathogens was conducted in an area with a low prevalence of COVID-19 among the adults quarantined at a tertiary hospital.MethodsFrom March to May 2020, 201 patients suspected lower respiratory tract infection (LRTI) were surveyed for etiologies by multiplex polymerase chain reaction (PCR: FilmArray TM Respiratory Panel) test combination with cultural method, viral antigen detection and serologic surveys.ResultsTotal 201 patients tested with FilmArray TM Respiratory Panel were enrolled, of which 68.2% had sputum bacterial culture, 86.1% had pneumococcus and Legionella urine antigen test. Their median age was 72.0 year-old with multiple comorbidities, and 11.4% were nursing home residents. Bacteria accounted for 59.7% of identified pathogens. Atypical pathogens were identified in 31.3% of total pathogens, of which viruses accounted for 23.9%. In comparison to patients with bacterial infection, patients with atypical pathogens were younger (median= 77.2 vs 67.1, years, P = 0.017) and had shorter length of hospital (8.0 vs 4.5, days, P = 0.007).ConclusionsPatients with LRTI caused by atypical pathogens was indistinguishable from those with bacterial pathogens by clinical manifestations or biomarkers. Multiplex PCR providing rapid diagnosis of atypical pathogens enhance patient care and decision making when rate of sputum culture sampling was low in quarantine ward during pandemic.     

呼吸道合胞病毒下呼吸道感染对机体细胞免疫的影响

为研究呼吸道合胞病毒（ＲＳＶ）急性下呼吸道感染（ＡＬＲＩ）的细胞免疫变化，对２５例病儿外周血白细胞介素２（ＩＬ－２）和可溶性白细胞介素２受体（ｓＩＬ－２Ｒ）水平、Ｔ细胞白细胞介素２受体（ＩＬ－２Ｒ）表达率和Ｔ细胞亚群百分率进行检测。结果显示，急性期病儿外周血ＩＬ－２水平明显低于恢复期和正常对照组，Ｔ细胞ＩＬ－２Ｒ表达率亦明显降低，而ｓＩＬ－２Ｒ水平却显著增高。急性期病儿ＩＬ－２水平与Ｔ细胞ＩＬ－２Ｒ表达率和ＣＤ＋４细胞百分率呈正相关，与ｓＩＬ－２Ｒ水平和ＣＤ＋８细胞百分率呈负相关；ｓＩＬ－２Ｒ水平与Ｔ细胞ＩＬ－２Ｒ表达率呈负相关，与临床严重程度呈正相关。上述各项免疫指标异常均提示ＲＳＶ感染时机体存在细胞免疫功能紊乱。     

Enhanced antimicrobial stewardship based on rapid phenotypic antimicrobial susceptibility testing for bacteraemia in patients with haematological malignancies: a randomized controlled trial

ObjectivesRecently, rapid phenotypic antimicrobial susceptibility testing (AST) based on microscopic imaging analysis has been developed. The aim of this study was to determine whether implementation of antimicrobial stewardship programmes (ASP) based on rapid phenotypic AST can increase the proportion of patients with haematological malignancies who receive optimal targeted antibiotics during early periods of bacteraemia.MethodsThis randomized controlled trial enrolled patients with haematological malignancies and at least one positive blood culture. Patients were randomly assigned 1:1 to conventional (n = 60) or rapid phenotypic (n = 56) AST. The primary outcome was the proportion of patients receiving optimal targeted antibiotics 72 hr after blood collection for culture.ResultsThe percentage receiving optimal targeted antibiotics at 72 hr was significantly higher in the rapid phenotypic AST group (45/56, 80.4%) than in conventional AST group (34/60, 56.7%) (relative risk (RR) 1.42, 95% confidence interval (CI) 1.09–1.83). The percentage receiving unnecessary broad-spectrum antibiotics at 72 hr was significantly lower (7/26, 12.5% vs 18/60, 30.0%; RR 0.42, 95% CI 0.19–0.92) and the mean time to optimal targeted antibiotic treatment was significantly shorter (38.1, standard deviation (SD) 38.2 vs 72.8, SD 93.0 hr; p < 0.001) in the rapid phenotypic AST group. The mean time from blood collection to the AST result was significantly shorter in the rapid phenotypic AST group (48.3, SD 17.6 vs 83.1, SD 22.2 hr).DiscussionASP based on rapid phenotypic AST can rapidly optimize antibiotic treatment for bacteraemia in patients with haematological malignancy. Rapid phenotypic AST can improve antimicrobial stewardship in immunocompromised patients.     

A prospective study of prevalence of respiratory viruses causing acute respiratory infection in pediatric in-patients during pre- COVID times

PurposeTo find out the prevalence of respiratory viruses causing Acute Respiratory Infection in pediatric in-patients during Pre-COVID times.MethodsNasal swabs were collected from children in the age group of 1 month–16 years who were admitted at our hospital with Acute Respiratory Infection. Samples were subjected to nucleic acid extraction and Real time polymerase chain reaction to detect 16 RNA viruses and 2 DNA viruses. The results were interpreted in context of most prevalent viruses detected, their seasonal distribution, co-infecting viruses, co-morbidities in patients with effect thereof and use and effect of antibiotics in those positive for viral etiology.ResultsOf the 250 children recruited in the study, viral pathogen was detected in 74% cases. RSV was the most common virus detected with 36.2% positivity (92/254) followed by rhino/entero (19.2%, 49/254), PIV 1,2,3,4 (9.4%, 24/254), Influenza A,B,C (8.2%, 21/254), adenovirus & HBoV (6.2%, 16/254), coronavirus HKU1, NL63, OC43, 229E (4.3%, 11/254), H1N1 (4.7%, 12/254) and hMPV (0.7%, 2/254). Co-infection with 2 or more viruses was seen in 34% cases. Among the cases on whom antibiotics were started, they were withdrawn following test results in 42.3% of the cases.ConclusionThe prevalence of viral etiology is high amongst children especially ≤2 years. RSV, rhino/enterovirus, PIV 1,2,3,4 and Influenza virus were more prevalent than others. Rapid, early detection of virus with multiplex PCR will help in early cohorting of the patients thus reducing nosocomial spread of these viruses and prevent injudicious use of antibiotics.     

Evaluation of a molecular point-of-care testing for viral and atypical pathogens on intravenous antibiotic duration in hospitalized adults with lower respiratory tract infection: a randomized clinical trial

ObjectivesThe primary objective was to evaluate whether a molecular point-of-care test (POCT) for viral and atypical pathogens added to routine real-time PCR could reduce duration of intravenous antibiotics in hospitalized patients with lower respiratory tract infection (LRTI) compared with routine real-time PCR.MethodsIn this single-centre, open-label, randomized controlled study, we enrolled hospitalized adults diagnosed with LRTI. Patients were randomized to an intervention group (POCT FilmArray Panel for 20 viruses, atypical pathogens and bacteria plus routine real-time PCR) or a control group (routine real-time PCR for ten pathogens). The primary outcome was duration of intravenous antibiotics during hospitalization. The secondary outcomes included length of stay, cost of hospitalization and de-escalation within 72 hours and between 72 hours and 7 days. Intention-to-treat analysis was used.ResultsBetween October 2017 and July 2018, we enrolled 800 eligible patients (398 in the intervention group and 402 in the control group). Duration of intravenous antibiotics in the intervention group was shorter than in the control (7.0 days (interquartile range (IQR) 5.0–9.0) versus 8.0 days (IQR 6.0–11.0); p <0.001). Length of hospital stay in the intervention group was significantly shorter (8.0 days (IQR 7.0–11.0) versus 9.0 days (IQR 7.0–12.0; p <0.001) and the cost of hospitalization in the intervention group was significantly lower ($1804.7 (IQR 1298.4–2633.8) versus $2042.5 (IQR 1427.4–2926.2); p 0.002) than control group. More patients in the intervention group achieved de-escalation within 72 hours (7.9%, 29/367 versus 3.2%, 12/377; p 0.005) and between 72 hours and 7 days (29.7%, 109/367 versus 22.0%, 83/377; p 0.024).ConclusionsUse of molecular POCT testing for respiratory viruses and atypical pathogens might help to reduce intravenous antibiotic use in hospitalized LRTI patients.Clinical Trial Registrationclinicaltrials.gov Identifier: NCT03391076.     

Comparison of multiplex PCR assays and conventional techniques for the diagnostic of respiratory virus infections in children admitted to hospital with an acute respiratory illness

The performances of four multiplex PCR (m-PCR) were compared to direct immunofluorescence assay (DFA) and HuH7 cell culture for the detection of viruses in 263 children admitted to hospital with an acute respiratory illness. One hundred fifty (57.6%) nasal aspirates were found DFA-positive; 188 (72.3%) were found positive by both DFA and HuH7 cell culture, and 242 (92%) were PCR-positive. The m-PCR detected 124 viruses which were not found by conventional methods: 68 rhinovirus, 17 human metapneumovirus, 15 respiratory syncytial virus (RSV), 8 parainfluenza virus (PIV), 5 coronavirus 229E, 3 OC43 and 3 NL63, 4 enterovirus, 2 influenza virus B and C virus. The m-PCR were more sensitive, had the advantages of a shorter delay in specific diagnosis, and a lower cost than DFA and culture. Using these m-PCR, the prevalence of each virus was compared between in-patient and out-patient groups of children attending the emergency unit of the hospital. Nasal aspirates from 411 (91.5%) children were found positive by the PCRs. RSV, rhinovirus, and influenza virus were the most frequent viruses detected in this population, representing 43.6%, 31.8%, and 8.8% of the virus found, respectively, followed by human metapneumovirus (4.4%), coronavirus (3.4%), parainfluenza virus (3.2%), adenovirus (2.3%), and enterovirus (2.1%). RSVs were detected more significantly in the in-patient group than in the out-patient group, and influenza viruses were detected more frequently in the out-patient group than in the in-patient group. Moreover, the use of m-PCR pointed out the frequency of rhinovirus and mixed viral detections in these patients. In conclusion, according to the requirements of speed and low cost of the methods, and to achieve the highest rate of detection of respiratory viruses, the combined use of DFA and m-PCR is today likely to be the best way to improve diagnosis of respiratory illnesses in children.     

Effectiveness of a brief advance directive intervention in primary care: a randomized clinical trial

ObjectiveTo measure the effectiveness of a brief intervention aimed at increasing interest in and use of advanced directives (AD) among primary care patients.MethodsRandomized controlled trial. In the intervention arm, patients were given brief oral information and a leaflet on AD by General Practitioners (GPs), in the control group were briefly informed about the study’s purpose. Outcome variables were the proportion of patients who expressed interest in AD and those who completed one. Covariates were sex, age, education, race, Charlson comorbidity index (CCI), religion, and possession of financial will.ResultsOverall, 332 patients were recruited; 58 in the intervention and 36 in the control group expressed interest in AD (p = 0.033) and 18 (5.4 %) made an AD (nine in each group). Variables associated with interest were Caucasian race (odds ratio [OR], 1.88), the intervention (OR, 1.86), and CCI extreme scores (OR, 0.36). Variables associated with AD completion were primary education/no schooling (OR, 5.69) and fewer children (OR, 0.57).ConclusionsA brief oral and written intervention delivered by GP significantly increased interest in AD and achieved a completion rate of 5.4 %, without differences with the control group.Practice ImplicationsAD interventions should focus on individuals already likely to be motivated.     

Prevalence and clinical characteristics of human respiratory syncytial virus in Chinese adults with acute respiratory tract infection

Respiratory syncytial virus (RSV) is a leading cause of respiratory tract illnesses worldwide. Although the prevalence and clinical manifestations of the two subtypes, RSV‐A and RSV‐B, have been studied in some detail in infants and young children, they have not been determined in adults. To evaluate the prevalence of the RSV subtypes and disease severity between RSV‐A and RSV‐B infections in adults, nasal and throat swabs that were collected from patients ≥15 years old who sought medical care for acute respiratory infections at the Fever Clinic of the Peking Union Medical College Hospital in Beijing, China between May 2005 and April 2010. The samples were tested for RSV infection using PCR and sequencing analysis. RSV was detected in 95 (1%) of the adult patients, of whom 53 (55.8%) were positive for RSV‐A and 42 (44.2%) for RSV‐B. The incidence of RSV infections increased with age (χ² = 37.17, P = 1.66E?07). Demographic data and clinical manifestations of RSV‐A were similar to those of RSV‐B. Although RSV‐A and RSV‐B co‐circulated during the 2005–2006 and 2008–2009 seasons, RSV‐A was predominant in the 2006–2008 seasons, whereas RSV‐B was predominant in the 2009–2010 season. Upper respiratory tract infections were diagnosed in most RSV‐infected patients (n = 80, 84.2%), and three patients suffered from pulmonary infection. This is the first study to provide data on the prevalence and clinical manifestations of RSV subgroups among Chinese adults with fever and acute illness, over five successive epidemic seasons. J. Med. Virol. 85:348–353, 2013. © 2012 Wiley Periodicals, Inc.