Detection of adenoviruses (AdV) in culture-negative environmental samples by PCR during an AdV-associated respiratory disease outbreak

Since 1954, adenoviruses (AdV) have been recognized as an important cause of acute respiratory disease (ARD) among U.S. military recruits. Until recently, routine oral vaccination for AdV serotypes 4 and 7 eliminated epidemic AdV-associated ARD in this population. Now that the manufacturer has ceased production, vaccination has ended and AdV epidemics have reappeared. As part of a prospective epidemiological study during the high-risk ARD season, serial samples were obtained from ventilation system filters and tested for AdV by culture and PCR. An outbreak occurred during this surveillance. Of 59 air filters, 26 (44%) were AdV positive only by PCR. Sequence analysis confirmed the presence of AdV serotype 4, the implicated outbreak serotype. The number of AdV-related hospitalizations was directly correlated with the proportion of filters containing AdV; correlation coefficients were 0.86 (Pearson) and 0.90 (Spearman's rho). This is the first report describing a PCR method to detect airborne AdV during an ARD outbreak. It suggests that this technique can detect and quantify AdV-associated ARD exposure and may enable further definition of environmental effects on AdV-associated ARD spread.     

Evaluation of PCR testing of ethanol-fixed nasal swab specimens as an augmented surveillance strategy for influenza virus and adenovirus identification

Viral culture isolation has been widely accepted as the "gold standard" for laboratory confirmation of viral infection; however, it requires ultralow temperature specimen storage. Storage of specimens in ethanol at room temperature could expand our ability to conduct active surveillance and retrospective screenings of viruses with rapid and inexpensive real-time PCR tests, including isolates from remote regions where freezing specimens for culture is not feasible. Molecular methods allow for rapid identification of viral pathogens without the need to maintain viability. We hypothesized that ethanol, while inactivating viruses, can preserve DNA and RNA for PCR-based methods. To evaluate the use of ethanol-stored specimens for augmenting surveillance for detection of influenza viruses A and B and adenoviruses (AdV), paired nasal swab specimens were collected from 384 recruits with febrile respiratory illness at Fort Jackson, S.C., in a 2-year study. One swab was stored at ambient temperature in 100% ethanol for up to 6 months, and the other swab was stored at -70 degrees C in viral medium. For viral detection, frozen specimens were cultured for a variety of respiratory viruses, and ethanol-fixed specimens were tested with TaqMan (TM) probe and LightCycler SYBR green (SG) melting curve assays with at least two different PCR targets for each virus. The sensitivities of the TM and SG assays on specimens stored in ethanol for 1 month were 75% and 58% for influenza A, 89% and 67% for influenza B, and 93 to 98% and 57% for AdV, respectively. Lower specificities of the real-time assays corresponded to the increased detection of PCR-positive but culture-negative specimens. Influenza virus RNA was detected as well or better after 6 months of storage in ethanol.     

Detection of Meningococcal Carriage by Culture and PCR of Throat Swabs and Mouth Gargles

The standard method for detecting meningococcal carriage is culture of throat swabs on selective media, but the levels of carriage determined depend heavily on the skills of the individuals taking the swab and interpreting the cultures. This study aimed to determine the most sensitive detection method for meningococcal carriage. Throat swabs and saline mouth gargles, obtained from 89 university students, were processed in parallel by conventional culture and TaqMan ctrA PCR. Carriage of meningococci, as detected by the combined methods, was 20%. The sensitivities of throat swab culture, throat swab PCR, gargle culture, and gargle PCR were 72, 56, 56, and 50%, respectively, and the probabilities that these techniques would correctly identify the absence of carriage (negative predictive value [NPV]) were 93.4, 89.9, 89.9, and 88.8%. Culturing both throat swabs and gargles increased the NPV to 98.6%. The further addition of throat swab PCR increased this to 100%. Testing gargles by both culture and PCR was as sensitive as testing throat swabs by both methods, suggesting that gargles may be a suitable alternative for large-scale screening studies when throat swabs are difficult to obtain, although they required more lengthy laboratory processing. PCR was a useful adjunct to culture for detecting nasopharyngeal carriage, but it failed to detect some nongroupable strains. For maximum sensitivity, a combination of techniques was required. This study indicates the confidence with which health care professionals involved in meningococcal screening can regard laboratory results.     

Comparison of throat swabs with sputum specimens for the detection of Chlamydia pneumoniae antigen by direct immunofluorescence.

AIM: To compare throat swabs with sputum specimens for Chlamydia pneumoniae antigen detection. METHODS: During a one year period, sputum and throat swabs from 50 patients over 15 years of age with acute or persisting lower respiratory tract infection were examined for C pneumoniae antigen by direct immunofluorescence. RESULTS: C pneumoniae antigen was detected in 18/50 patients (36.0%) from sputum, throat swab, or both. Paired sputum and throat swabs were received from 35/50 patients (70.0%). C pneumoniae antigen was detected in either or both specimens from 14/35 patients (40.0%). Of the 14 positive patients, both specimens were positive in nine (64.3%), throat swab only in four (28.6%), and sputum only in one (7.1%). Of the remaining 15 patients from whom only a single specimen was sent, a further three of eight throat swabs and one of seven sputum specimens were positive. There was no statistically significant difference between the results obtained from the two types of specimen. CONCLUSIONS: Throat swabs may be as good as sputum for the detection of C pneumoniae antigen.     

2011-2012年深圳市呼吸道腺病毒分子分型及其流行特征

目的了解2011—2012年深圳地区致病性呼吸道腺病毒（AdV）的病原体基因亚型和遗传进化及其流行特征．分析深圳地区呼吸道腺病毒的流行规律和传播途径。方法收集2011年1月至2012年12月深圳地区31个流感样病例监测哨点2822份样本,先用荧光定量PCR方法筛查流感样病例,筛查后的阴性样本进一步进行呼吸道腺病毒等13种常见呼吸道病毒的核酸检测。对检测出的109份腺病毒阳性标本进行病毒分离,感染Hep-2受体细胞后共获得71份AdV稳定细胞毒株,用腺病毒六邻体基因作为靶基因,扩增其中的50份腺病毒阳性标本,纯化扩增产物后直接用于序列分析,在GenBank上进行序列比较,确定其病毒亚型并进行系统进化分析。结果2011—2012年深圳市腺病毒感染患者的高发年龄段人群为小于7岁的儿童,1～2岁婴幼儿发病率最高;4-6月和10—12月为每年发病高峰期。在2822份流感样病例咽拭子标本中,经定量PCR方法确定为AdV核酸阳性共109份,核酸阳性率为3．86％,从109份核酸阳性样本中分离病毒7l份,病毒分离率为68．93％。50份分离的呼吸道腺病毒分子分型结果为1型AdV6例,占12％;2型AdV4例,占8％;3型AdV27例,占54％;4型AdV3例,占6％;5型AdV4例,占8％;7型AdV5例,占10％;另外有复合型AdV（HAdV—un）1例,占2％。结论近两年来深圳地区呼吸道Adv感染以3型为主,腺病毒引起的呼吸道疾病主要发生在每年的4—6月,感染人群主要是1~2岁婴幼儿。     

Rapid detection and identification of human adenovirus species by adenoplex, a multiplex PCR-enzyme hybridization assay

Human adenoviruses (AdV) have been implicated in a wide variety of diseases and are ubiquitous in populations worldwide. These agents are of concern particularly in immunocompromised patients, children, and military recruits, resulting in severe disease or death. Clinical diagnosis of AdV is usually achieved through routine viral cell culture, which can take weeks for results. Immunofluorescence and enzyme-linked immunosorbent assay-based techniques are more timely but lack sensitivity. The ability to distinguish between the six different AdV species (A to F) is diagnostically relevant, as infections with specific AdV species are often associated with unique clinical outcomes and epidemiological features. Therefore, we developed a multiplex PCR-enzyme hybridization assay, the Adenoplex, using primers to the fiber gene that can simultaneously detect all six AdV species A through F in a single test. The limit of detection (LOD) based on the viral 50% tissue culture infective dose/ml for AdV A, B, C, D, E, and F was 10(-2), 10(-1), 10(-1), 10(-2), 10(-1), and 10(-2), respectively. Similarly, the LOD for the six DNA controls ranged from 10(2) to 10(3) copies/ml. Twelve common respiratory pathogens were tested with the Adenoplex, and no cross-reactivity was observed. We also validated our assay using clinical specimens spiked with different concentrations of AdV strains of each species type and tested by multiplex PCR and culture. The results demonstrated an overall sensitivity and specificity of Adenoplex of 100%. This assay can be completed in as few as 5 h and provides a rapid, specific, and sensitive method to detect and subtype AdV species A through F.     

A cluster of Legionella-associated pneumonia cases in a population of military recruits

A Legionella cluster was identified through retrospective PCR analysis of 240 throat swab samples from X-ray-confirmed pneumonia cases. These were identified among young and otherwise healthy U.S. military recruits during population-based surveillance for pneumonia pathogens. Results were confirmed by sequence analysis. Cases clustered tightly, suggesting a local environmental etiology.     

Viral agents responsible for febrile respiratory illnesses among military recruits training in tropical Singapore

BackgroundMilitary personnel are highly susceptible to febrile respiratory illnesses (FRI), likely due to crowding, stress and other risk factors present in the military environment.ObjectiveOur objective was to investigate the viral etiological agents responsible for FRI among military recruits training in a tropical climate in Singapore.Study designFrom March 2006 through April 2007, a total of 1354 oropharyngeal (throat) swabs were collected from military recruits who reported sick with an oral temperature of ≥38 °C and a cough and/or sore throat. Real-time polymerase chain reaction (PCR) was used to assay for the presence of influenza A and B viruses and adenoviruses (H-AdV), and conventional PCR used for the remaining respiratory viruses in all specimens.ResultsInfluenza A virus was the dominant infection with a laboratory-confirmed incidence of 24% (326/1354) and a predominance of the H3N2 subtype. The temporal pattern for influenza A virus infections coincided with the nation-wide pattern in the civilian community. Detection rates of 12% (159/1354) and 2.7% (5/1354) were obtained for influenza B virus and other respiratory viruses, respectively.ConclusionsThe laboratory findings identified influenza A virus as the primary causative viral agent for FRI in the Singapore military, in strong contrast to findings from temperate countries and countries where recruits are often vaccinated for influenza. Our results suggest that influenza vaccination should be considered as a requirement to reduce the incidence of influenza infections. This is the first report describing respiratory infections in a tropical military setting, in a developed country in Asia.     

Clinical use of capillary PCR to diagnose Mycoplasma pneumonia

In the present study, serologic data were compared with data obtained by capillary PCR to establish the efficacy of capillary PCR for the determination of Mycoplasma infection in samples obtained from throat swabs, bronchoalveolar lavage fluids (BALF), and sputum of patients with Mycoplasma pneumonia. We performed PCR analysis for Mycoplasma DNA on a total of 325 samples from 197 patients with community-acquired pneumonia and in whom Mycoplasma pneumonia was suspected. There were 68 PCR-positive specimens. Review of the differences in PCR positivity rates based on the site of specimen collection showed the highest rate of detection (28.6%) from throat swabs. From among the 31 patients with significantly elevated titers of serum Mycoplasma antibodies, the PCR results were positive for 25 patients. Thus, capillary PCR had a sensitivity of 80.6% (25 of 31). Five of the six false-negative results were from throat swab specimens. Moreover, testing (PCR) had been performed only once for these five patients with false-negative results. From among the PCR-positive findings from BALF specimens, there were no false-positive results. BALF specimens were very useful, except for the technical procedures and increased patient burden required to obtain these specimens. We suggest that the use of throat swab specimens in capillary PCR is much more suitable for diagnosing Mycoplasma pneumonia in routine clinical practice; however, careful throat swab specimen collection and an increase in the number of times that the PCR is performed are necessary to reduce the rate of false-negative results.     

Use of oligonucleotide microarrays for rapid detection and serotyping of acute respiratory disease-associated adenoviruses

The cessation of the adenovirus vaccination program for military trainees has resulted in several recent acute respiratory disease (ARD) outbreaks. In the absence of vaccination, rapid detection methods are necessary for the timely implementation of measures to prevent adenovirus transmission within military training facilities. To this end, we have combined a fluorogenic real-time multiplex PCR assay with four sets of degenerate PCR primers that target the E1A, fiber, and hexon genes with a long oligonucleotide microarray capable of identifying the most common adenovirus serotypes associated with adult respiratory tract infections (serotypes 3, 4, 7, 16, and 21) and a representative member of adenovirus subgroup C (serotype 6) that is a common cause of childhood ARD and that often persists into adulthood. Analyses with prototype strains demonstrated unique hybridization patterns for representative members of adenovirus subgroups B(1), B(2), C, and E, thus allowing serotype determination. Microarray-based sensitivity assessments revealed lower detection limits (between 1 and 100 genomic copies) for adenovirus serotype 4 (Ad4) and Ad7 cell culture lysates, clinical nasal washes, and throat swabs and purified DNA from clinical samples. When adenovirus was detected from coded clinical samples, the results obtained by this approach demonstrated an excellent concordance with those obtained by the more established method of adenovirus identification as well as by cell culture with fluorescent-antibody staining. Finally, the utility of this method was further supported by its ability to detect adenoviral coinfections, contamination, and, potentially, recombination events. Taken together, the results demonstrate the usefulness of the simple and rapid diagnostic method developed for the unequivocal identification of ARD-associated adenoviral serotypes from laboratory or clinical samples that can be completed in 1.5 to 4.0 h.     

Diagnosis of Chlamydia trachomatis infections in asymptomatic men and women by PCR assay.

A PCR assay was evaluated for its ability to detect genital chlamydial infection in asymptomatic men and women. Urethral swab specimens were collected from 472 men for culture and PCR assay, and first-void urine (FVU) specimens were collected from 379 of these men for enzyme immunoassay (EIA) and PCR assay. Cervical swab specimens were collected from 242 women for culture, EIA, and PCR assay. Patients were considered infected if they were culture positive or positive by PCR with both plasmid- and major outer membrane protein-based primers. By using this extended "gold standard," the prevalence of infection in this population was 7.6% for men and 7.9% for women. For men, the sensitivities of urethral swab specimen culture and PCR and FVU specimen EIA and PCR were 61, 72, 55, and 91%, respectively. All assays had specificities of > or = 99.8%. The positive and negative predictive values for PCR testing of FVU specimens were 100 and 99.4%, respectively, compared with values of 96.3 and 97.8%, respectively, for PCR of urethral swab specimens. The sensitivities of cervical swab specimen culture and PCR testing were 42 and 90%, respectively, with corresponding specificities of 100 and 99.3%. All cervical swabs were negative by EIA. Molecular techniques such as PCR assays are valuable tools for the detection of symptomatic genital chlamydial infection. In particular, PCR assays of FVU specimens from men offer a highly sensitive, noninvasive screening tool that will likely improve patient compliance for diagnostic testing.     

Use of immunofluorescence to identify measles virus infections.

Monoclonal antibody to measles virus was used successfully to identify measles virus antigen directly in clinical specimens, as well as in cell cultures. Pooled nasopharyngeal-throat swab specimens had a higher yield than throat swabs or urine samples for virus detection. Use of A549 cell cultures in the spin amplification vial assay proved to be highly efficient, allowing virus recognition within 1 to 2 days of inoculation. A combination of appropriately collected specimens, which includes a nasopharyngeal-throat swab, direct antigen detection with monoclonal antibody to measles in an indirect immunofluorescence system, and the spin amplification vial assay using A549 cells provides a sensitive and rapid system for isolation and/or identification of measles virus infections.     

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.     

四例咽拭子检测阳性发热伴血小板减少综合征重症患者的临床特征分析?

通过疑似发热伴血小板减少综合征（ Severe fever with thrombocytopenia syndrome, SFTS）病例咽拭子的新型布尼亚病毒（SFTSV）检出情况,探讨SFTSV通过呼吸道传播的可能性。按照国家卫生部颁发的《发热伴血小板减少综合征防治指南（2010版）》中疑似病例的纳入标准,于2013年5～9月在SFTS高发区河南信阳的监测哨点医院收集72例疑似 SFTS 病例的血清和咽拭子标本,采用实时 RT?PCR 方法和ELISA方法检测SFTSV。结果显示,在72例疑似SFTS病例中,52（72?2％）例检测是SFTSV阳性,其中46例核酸RT?PCR检测阳性,6例血清ELISA检测阳性。在52例SFTSV阳性病例中,4（7?7％）例咽拭子核酸检测SFTSV阳性;在20例SFTSV阴性病例中,咽拭子核酸均未检测到SFTSV。4例咽拭子SFTSV阳性病例均为重症,同时都伴有咳嗽症状,其病毒载量最高可达108 copies／mL。 SFTSV在患者的咽拭子中可以检测到,咽拭子核酸检测SFTSV阳性检出率远低于血清标本,其作为检测SFTSV的可行性值得商榷。咽拭子检测SFTSV阳性患者体内病毒载量高且伴有咳嗽症状,加大了SFTSV通过呼吸道传播的风险。     

Ten-minute detection of group A streptococci in pediatric throat swabs.

A 10-min latex agglutination test kit, Culturette Brand Ten-Minute Group A Strep ID (Marion Scientific, Div. of Marion Laboratories, Inc., Kansas City, Mo.), was assessed for the rapid detection of group A beta-hemolytic streptococcus directly from a throat swab. Four hundred and thirty-five throat swab specimens from children with suspected group A streptococcal infection were tested by the Ten-Minute Group A Strep ID and by concurrent conventional culture. The strep test was effective in detecting group A streptococcal infection; 90% (63/70) of culture-positive specimens gave positive latex tests. The specificity of the test was 99.2% (362/365). The predictive values were 95.5% for positives and 98.1% for negatives. Overall agreement with culture was 98% (425/435). This test offers a sensitive and specific method for the early detection of group A beta-hemolytic streptococci in throat swabs of children and would be most useful in a hospital laboratory or pediatrician's office.     

Comparison of nasopharyngeal aspirates and throat swab specimens in a polymerase chain reaction-based test forMycoplasma pneumoniae

Nasopharyngeal aspirates and throat swab specimens were compared in a polymerase chain reaction (PCR)-based test forMycoplasma pneumoniae. The pathogen was detected in 50 % and 45 % of throat swab specimens and aspirates, respectively. However, in specimens negative forMycoplasma pneumoniae by PCR, amplification inhibitors were detected in 0 % and 36 % of throat specimens and aspirates, respectively. Further investigations confirmed that no throat specimens, but one-quarter of aspirates, are likely to be rejected for containing inadequate respiratory material or excess amplification inhibitors. Because rejection of most of the unsuitable specimens is possible only after PCR, the use of aspirates is less cost-effective. This, and the reluctance to subject patients to aspiration, make the aspirate an inferior specimen for detection ofMycoplasma pneumoniae by PCR.     

The use of TaqMan PCR assay for detection of Bordetella pertussis infection from clinical specimens

OBJECTIVE: The routine clinical laboratory detection of Bordetella pertussis is through culture, which can require 5 to 7 days for the bacteria to grow. Using a polymerase chain reaction (PCR) assay can shorten this detection time while increasing the sensitivity of detection with similar specificity. This study compared culture with TaqMan PCR for detection of B pertussis in clinical specimens and the turnaround time for each assay during the pertussis season. MATERIALS AND METHODS: Nasopharyngeal swabs in Regan-Lowe transport media were collected from 1556 persons who had symptoms of whooping cough or who had had contact with infected persons; the swabs were submitted for B pertussis detection during the pertussis season. A single nasopharyngeal swab from each patient was submitted for both culture and TaqMan PCR detection. Upon receipt of the specimens, the swabs were inoculated onto Regan-Lowe agar for culture and incubated for up to 7 days. The same swab was processed for PCR detection using TaqMan PCR assay. A second nested PCR was used on positive specimens for resolution purposes. The TaqMan PCR assay was performed 3 to 5 days a week, whereas the culture was performed 6 days a week. All specimens were processed on the same day or earliest possible working day for TaqMan or culture, and specimens queued for resolution by nested PCR were batched. RESULTS: There were a total of 275 PCR positives and 28 culture positives. After resolution with the second nested PCR, the sensitivity, specificity, positive predictive value, and negative predictive value were 100%, 97.4%, 87.6%, and 100% for TaqMan PCR and 11.6%, 100%, 100%, and 85.7% for culture. The average turnaround time for positive culture was 5.1 days, and the average turnaround time for PCR was 2.3 days. CONCLUSION: The TaqMan PCR assay has superior sensitivity and shorter turnaround time over culture because it can be finished within one working day. Furthermore, the same swab can be used for culture of the bacteria for antibiotic susceptibility testing. The early detection of pertussis using TaqMan PCR assay allows early intervention on the spread of the disease and the ability to culture the bacteria from the same swab, thereby eliminating the need for a second swab and allowing for detection of antibiotic resistance.     

Rapid diagnosis of respiratory syncytial virus infection by using Pernasal swabs.

The sensitivity and specificity of direct immunofluorescence microscopy performed on Pernasal swab specimens and compared with those of nasopharyngeal aspirates were 93 and 99%, respectively. Posterior nasopharyngeal swabs applied immediately to microscope slides allow a rapid and simple screening procedure for the diagnosis of acute respiratory syncytial virus infections.