Determination of the cycle threshold value of the Xpert Xpress SARS-CoV-2/Flu/RSV test that corresponds to the presence of infectious SARS-CoV-2 in anterior nasal swabs

Despite having high analytical sensitivities and specificities, qualitative SARS-CoV-2 nucleic acid amplification tests (NAATs) cannot distinguish infectious from non-infectious virus in clinical samples. In this study, we determined the highest cycle threshold (Ct) value of the SARS-CoV-2 targets in the Xpert Xpress SARS-CoV-2/Flu/RSV (Xpert 4plex) test that corresponded to the presence of detectable infectious SARS-CoV-2 in anterior nasal swab samples. A total of 111 individuals with nasopharyngeal swab specimens that were initially tested by the Xpert Xpress SARS-CoV-2 test were enrolled. A healthcare worker subsequently collected anterior nasal swabs from all SARS-CoV-2-positive individuals, and those specimens were tested by the Xpert 4plex test, viral culture, and laboratory-developed assays for SARS-CoV-2 replication intermediates. SARS-CoV-2 Ct values from the Xpert 4plex test were correlated with data from culture and replication intermediate testing to determine the Xpert 4plex assay Ct value that corresponded to the presence of infectious virus. Ninety-eight of the 111 (88.3%) individuals initially tested positive by the Xpert Xpress SARS-CoV-2 test. An anterior nasal swab specimen collected from positive individuals a median of 2 days later (range, 0-9 days) tested positive for SARS-CoV-2 by the Xpert 4plex test in 39.8% (39/98) of cases. Of these samples, 13 (33.3%) were considered to contain infectious virus based on the presence of cultivable virus and replication intermediates, and the highest Ct value observed for the Xpert 4plex test in these instances was 26.3. Specimens that yielded Ct values of ≤26.3 when tested by the Xpert 4plex test had a likelihood of containing infectious SARS-CoV-2; however, no infectious virus was detected in specimens with higher Ct values.IMPORTANCEUnderstanding the correlation between real-time PCR test results and the presence of infectious SARS-CoV-2 may be useful for informing patient management and workforce return-to-work or -duty. Further studies in different patient populations are needed to correlate Ct values or other biomarkers of viral replication along with the presence of infectious virus in clinical samples.

Maintaining point of care testing capacity and pandemic preparedness in the post-COVID-19 era

INTRODUCTION

Testing at the point of care (we also refer to the 'point of need'), with rapid, actionable results reported to the patient and provider within hours can impact the individual as well as public health. Faster testing is good for patients and public health outcomes during 'peace time' (outside of the pandemic setting).

AREAS COVERED

Testing at the point of need was important during the COVID-19 pandemic to meet testing capacity demands, providing actionable results, and for providing testing within communities to increase access for all populations. Resources were acquired and built up dramatically during the pandemic as part of the response. With the end of the COVID-19 public health emergency and transition back to 'peace time' some testing sites have successfully shifted to using this capacity for testing for other critical needs, like sexually transmitted infection (STI) testing, and response to other seasonal diseases and for outbreak response.

EXPERT OPINION

The increased testing capacity added to handle unprecedented testing volume during the COVID-19 pandemic can be repurposed for other critical infectious diseases during 'peace time' (post-COVID-19 pandemic). This maintains testing capacity for the next pandemic.

Practical Challenges of Point-of-Care Testing

The practical challenges of point-of-care testing (POCT) include analytical performance and quality compared with testing performed in a central laboratory and higher cost per test compared with laboratory-based tests. These challenges can be addressed with new test technology, consensus, and practice guidelines for the use of POCT, instituting a quality management system and data connectivity in the POCT setting, and studies that demonstrate evidence of clinical and economic value of POCT.

The Traditional or Reverse Algorithm for Diagnosis of Syphilis: Pros and Cons

We reviewed relevant syphilis diagnostic literature to address the question “What diagnostic considerations should be taken into account when screening for syphilis using the traditional or reverse algorithm?” Improved laboratory diagnosis of syphilis is an important element of the effort to reduce syphilis rates. Screening for syphilis is performed using either a nontreponemal or treponemal test (part of the traditional or reverse algorithm, respectively). Both syphilis algorithms are used by laboratories. However, there are limited data on the performance and cost-effectiveness of the algorithms. An expert panel generated “key questions” in the laboratory diagnosis of syphilis. This paper pertains to the key factors that should be considered when deciding whether to screen for syphilis using either the traditional or the reverse algorithm. A systematic literature review was performed, and tables of evidence were created to address this question.

Point-of-Care Testing for Sexually Transmitted Infections: A Review of Recent Developments

CONTEXT.—

Sexually transmitted infections (STIs) are among the most common communicable diseases globally and are associated with significant morbidity and mortality worldwide. Point-of-care tests have the potential to revolutionize the prevention and control of STIs by enabling rapid diagnosis and early treatment of infections, thus interrupting transmission and preventing the sequelae of untreated infections. Currently, there are several point-of-care (POC) tests available for the diagnosis of Treponema pallidum, Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis infections, although these tests differ with regard to their performance, turnaround time, and cost.

OBJECTIVE.—

To provide an updated review of the POC tests available and under development for the diagnosis of T pallidum, C trachomatis, N gonorrhoeae, and T vaginalis infections, to discuss the context for which these tests might be used, and to highlight future directions for test development.

DATA SOURCES.—

We reviewed the literature pertaining to the recent development and performance evaluations of POC tests for the diagnosis of syphilis, chlamydia, gonorrhea, and trichomonas.

CONCLUSIONS.—

Recently, there has been rapid development of new POC tests for STIs. Although there are inexpensive, rapid, and accurate POC tests available for syphilis, there are few such tests available for the diagnosis of chlamydia, gonorrhea, or trichomonas, and currently none with the ability to detect antimicrobial resistance in N gonorrhoeae. Research evaluating implementation strategies for the currently available tests and the development of additional POC tests that are rapid, accurate, and affordable are urgently needed to address the rising number of STIs worldwide.

Meta-analysis of diagnostic performance of serology tests for COVID-19: impact of assay design and post-symptom-onset intervals

Serology detection is recognized for its sensitivity in convalescent patients with COVID-19, in comparison with nucleic acid amplification tests (NAATs). This article aimed to evaluate the diagnostic accuracy of serologic methods for COVID-19 based on assay design and post-symptom-onset intervals. Two authors independently searched PubMed, Cochrane library, Ovid, EBSCO for case-control, longitudinal and cohort studies that determined the diagnostic accuracy of serology tests in comparison with NAATs in COVID-19 cases and used QUADAS-2 for quality assessment. Pooled accuracy was analysed using INLA method. A total of 27 studies were included in this meta-analysis, with 4 cohort, 16 case-control and 7 longitudinal studies and 4565 participants. Serology tests had the lowest sensitivity at 0-7 days after symptom onset and the highest at >14 days. TAB had a better sensitivity than IgG or IgM only. Using combined nucleocapsid (N) and spike(S) protein had a better sensitivity compared to N or S protein only. Lateral flow immunoassay (LFIA) had a lower sensitivity than enzyme-linked immunoassay (ELISA) and chemiluminescent immunoassay (CLIA). Serology tests will play an important role in the clinical diagnosis for later stage COVID-19 patients. ELISA tests, detecting TAB or targeting combined N and S proteins had a higher diagnostic sensitivity compared to other methods.

Laboratory diagnosis of emerging human coronavirus infections - the state of the art

The three unprecedented outbreaks of emerging human coronavirus (HCoV) infections at the beginning of the twenty-first century have highlighted the necessity for readily available, accurate and fast diagnostic testing methods. The laboratory diagnostic methods for human coronavirus infections have evolved substantially, with the development of novel assays as well as the availability of updated tests for emerging ones. Newer laboratory methods are fast, highly sensitive and specific, and are gradually replacing the conventional gold standards. This presentation reviews the current laboratory methods available for testing coronaviruses by focusing on the coronavirus disease 2019 (COVID-19) outbreak going on in Wuhan. Viral pneumonias typically do not result in the production of purulent sputum. Thus, a nasopharyngeal swab is usually the collection method used to obtain a specimen for testing. Nasopharyngeal specimens may miss some infections; a deeper specimen may need to be obtained by bronchoscopy. Alternatively, repeated testing can be used because over time, the likelihood of the SARS-CoV-2 being present in the nasopharynx increases. Several integrated, random-access, point-of-care molecular devices are currently under development for fast and accurate diagnosis of SARS-CoV-2 infections. These assays are simple, fast and safe and can be used in the local hospitals and clinics bearing the burden of identifying and treating patients.

Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media

Background

Interferences between pathogenic bacteria and specific commensals are known. We determined the interactions between nasopharyngeal microbial pathogens and commensals during viral upper respiratory tract infection (URI) and acute otitis media (AOM) in infants.

Methods

We analyzed 971 specimens collected monthly and during URI and AOM episodes from 139 infants. The 16S rRNA V4 gene regions were sequenced on the Illumina MiSeq platform.

Results

Among the high abundant genus-level nasopharyngeal microbiota were Moraxella, Haemophilus, and Streptococcus (3 otopathogen genera), Corynebacterium, Dolosigranulum, Staphylococcus, Acinetobacter, Pseudomonas, and Bifidobacterium. Bacterial diversity was lower in culture-positive samples for Streptococcus pneumoniae, and Haemophilus influenzae, compared to cultured-negative samples. URI frequencies were positively associated with increasing trend in otopathogen colonization. AOM frequencies were associated with decreasing trend in Micrococcus colonization. During URI and AOM, there were increases in abundance of otopathogen genera and decreases in Pseudomonas, Myroides, Yersinia, and Sphingomonas. Otopathogen abundance was increased during symptomatic viral infection, but not during asymptomatic infection. The risk for AOM complicating URI was reduced by increased abundance of Staphylococcus and Sphingobium.

Conclusion

Otopathogen genera played the key roles in URI and AOM occurrences. Staphylococcus counteracts otopathogens thus Staphylococcal colonization may be beneficial, rather than harmful. While Sphingobium may play a role in preventing AOM complicating URI, the commonly used probiotic Bifidobacterium did not play a significant role during URI or AOM. The role of less common commensals in counteracting the deleterious effects of otopathogens requires further studies.

Comparison of the Alere i and BD Veritor Assays for the Rapid Detection of Influenza A and B Viruses

BACKGROUND

The use of point-of care testing (POCT) in patient management decisions is becoming increasingly common. Our goal was to evaluate the diagnostic performance of 2 commercially available rapid POCT devices for influenza viruses A and B: the Alere™ i Instrument (Alere, Scarborough) and the BD Veritor™ System (BD Diagnostics).

METHODS

Paired nasopharyngeal swabs were collected from patients (18-71 years) presenting with influenza-like symptoms at 3 outpatient clinics. A total of 65 samples were obtained. The Alere i and BD Veritor were performed according to the manufacturers' instructions. Discordant results were resolved using real-time reverse transcription PCR (RT-PCR).

RESULTS

In a head-to-head comparison involving symptomatic adult patients visiting outpatient clinics during the 2014-2015 and 2015-2016 influenza seasons, the Alere i and BD Veritor had 90.63% agreement in the detection of influenza A virus and a statistically significant observed κ coefficient of 0.754 (P <0.0001). Discordant results between the Alere i and BD Veritor were further investigated using RT-PCR, showing that the BD Veritor missed 5 positive influenza A virus results (false negatives) and detected 1 false positive, while the Alere i results agreed with all RT-PCR results. There were no discordant results between the Alere i and BD Veritor in the detection of influenza B virus.

CONCLUSIONS

Our data suggest that the Alere i has higher sensitivity and specificity than the BD Veritor in the detection of influenza A virus. Both assays showed equal performance in the detection of influenza B virus.

A Rapid Zika Diagnostic Assay to Measure Neutralizing Antibodies in Patients

The potential association of microcephaly and other congenital abnormalities with Zika virus (ZIKV) infection during pregnancy underlines the critical need for a rapid and accurate diagnosis. Due to the short duration of ZIKV viremia in infected patients, a serologic assay that detects antibody responses to viral infection plays an essential role in diagnosing patient specimens. The current serologic diagnosis of ZIKV infection relies heavily on the labor-intensive Plaque Reduction Neutralization Test (PRNT) that requires more than one-week turnaround time and represents a major bottleneck for patient diagnosis. To overcome this limitation, we have developed a high-throughput assay for ZIKV and dengue virus (DENV) diagnosis that can attain the "gold standard" of the current PRNT assay. The new assay is homogeneous and utilizes luciferase viruses to quantify the neutralizing antibody titers in a 96-well format. Using 91 human specimens, we showed that the reporter diagnostic assay has a higher dynamic range and maintains the relative specificity of the traditional PRNT assay. Besides the improvement of assay throughput, the reporter virus technology has also shortened the turnaround time to less than two days. Collectively, our results suggest that, along with the viral RT-PCR assay, the reporter virus-based serologic assay could be potentially used as the first-line test for clinical diagnosis of ZIKV infection as well as for vaccine clinical trials.

Acute Otitis Media and Other Complications of Viral Respiratory Infection

BACKGROUND

Viral upper and lower respiratory tract infections (URI, LRI) are common in infants. We determined the prevalence of viral URI and its complications, including acute otitis media (AOM) and LRI, and assessed the effect of bacterial-viral interactions, and genetic and environmental risks on AOM development.

METHODS

Healthy infants were enrolled from near birth and followed to the first episode of AOM up to 12 months of age. Nasopharyngeal specimens were collected at monthly intervals (months 1-6, 9) and during viral URI episodes for bacterial culture and viral polymerase chain reaction studies. Subjects were followed closely for AOM development.

RESULTS

A total of 367 infants were followed for 286 child-years; 887 URI (305 infants) and 180 AOM episodes (143 infants) were documented. Prevalence of URI, LRI, and AOM in the first year was 3.2, 0.25, and 0.67 per child-year, respectively. Cumulative AOM incidence by ages 3, 6, and 12 months was 6%, 23%, and 46%. Infants with and without AOM had 4.7 and 2.3 URI episodes per child-year, respectively (P < .002). Pathogenic bacterial colonization rates by month were significantly higher in infants with AOM (P < .005). Breastfeeding reduced both URI and AOM risks (P < .05). Significant bacterial-viral interactions occurred with Moraxella catarrhalis and a variety of respiratory viruses and altered URI and AOM risks.

CONCLUSIONS

Almost half of infants experienced AOM by age 1. Important AOM risk factors included frequent viral URI, pathogenic bacterial colonization, and lack of breastfeeding. Bacterial-viral interactions may play a significant role in AOM pathogenesis and deserve further investigation.

Duration of rhinovirus shedding in the upper respiratory tract in the first year of life

BACKGROUND

Current molecular diagnostic methods have detected rhinovirus RNA in a high proportion of asymptomatic infants and children, raising the question of the clinical significance of these findings. This study investigates the prevalence of prolonged rhinovirus RNA presence in the upper respiratory tract of infants during the first year of life.

METHODS

In a longitudinal study, infants were followed from birth up to 12 months. Nasopharyngeal specimens were collected monthly (months 1-6 and month 9) and during an upper respiratory infection. Rhinoviruses were detected by quantitative reverse-transcription polymerase chain reaction. Presence of repeated rhinovirus RNA was evaluated by nucleotide sequence analysis.

RESULTS

A total of 2153 specimens from 362 infants were studied; 341 distinct rhinovirus infections in 216 infants were identified. Follow-up specimens were available within 30 days for 179 infections, creating the sample set to assess prolonged rhinovirus presence. Of the 179 infections, 46 involved the detection of the same rhinovirus strain in repeated specimens, including 8 events of prolonged presence of the same strain (detected in specimens collected >30 days apart), representing 4.5% of the evaluable rhinovirus infections. There were 26 events in which a rhinovirus strain was replaced by a different strain within a 30-day interval, representing 14.5% of the 179 infections.

CONCLUSIONS

Although rhinovirus infections are common in healthy infants, prolonged presence of rhinovirus RNA in the respiratory tract after an upper respiratory infection was uncommon (<5%). Detection of rhinovirus RNA in an infant most likely represents an infection within a 30-day period.

Purpura fulminans and late onset group B streptococcal sepsis in a premature twin

INTRODUCTION

 Purpura fulminans (PF) is a skin manifestation due to hemorrhagic infarction caused by intravascular thrombosis secondary to bacterial infections or deficiency of anticoagulants such as protein C and protein S. Neonatal PF is a rare but potentially disabling disorder associated with a high mortality and severe long term morbidity in those who survive.

CASE DESCRIPTION

 We report a case of a premature infant who developed extensive PF due to late onset group B streptococcus sepsis. Despite early identification and initiation of antibiotic therapy in our patient, PF progressed rapidly, leading to autoamputation of fingers and toes and severe brain injury.

CONCLUSION

 In conclusion, our case highlights the severe sequelae of PF due to late onset GBS sepsis in a premature infant.

Symptomatic and asymptomatic respiratory viral infections in the first year of life: association with acute otitis media development

Sensitive viral diagnostic methods have identified increasing prevalence of asymptomatic viral infection. This study determined the epidemiologic characteristics and etiology of asymptomatic upper respiratory tract infection in the first year of life and the association with acute otitis media complication.

Background. Sensitive diagnostic assays have increased the detection of viruses in asymptomatic individuals. The clinical significance of asymptomatic respiratory viral infection in infants is unknown.

Methods. High-throughput, quantitative polymerase chain reaction assays were used to detect 13 common respiratory viruses from nasopharyngeal specimens collected during 2028 visits from 362 infants followed from near birth up to 12 months of age. Specimens were collected at monthly interval (months 1–6 and month 9) and during upper respiratory tract infection (URTI) episodes. Subjects were followed closely for acute otitis media (AOM) development.

Results. Viruses were detected in 76% of 394 URTI specimens and 27% of asymptomatic monthly specimens. Rhinovirus was detected most often; multiple viruses were detected in 29% of the specimens. Generalized mixed-model analyses associated symptoms with increasing age and female sex; detection of respiratory syncytial virus (RSV), influenza, rhinovirus, metapneumovirus, and adenovirus was highly associated with symptoms. Increasing age was also associated with multiple virus detection. Overall, 403 asymptomatic viral infections in 237 infants were identified. Viral load was significantly higher in URTI specimens than asymptomatic specimens but did not differentiate cases of URTI with and without AOM complication. The rate of AOM complicating URTI was 27%; no AOM occurred following asymptomatic viral infections. AOM development was associated with increasing age and infection with RSV, rhinovirus, enterovirus, adenovirus, and bocavirus.

Conclusions. Compared to symptomatic infection, asymptomatic viral infection in infants is associated with young age, male sex, low viral load, specific viruses, and single virus detection. Asymptomatic viral infection did not result in AOM.

The pattern of indeterminate human immunodeficiency virus test and follow-up evaluation in pregnant women

We studied the pattern of indeterminate HIV serological tests among pregnant women with follow-up testing in the postpartum period. Medical records of pregnant women were reviewed over a 2-year period. Of 16,596 pregnant women, 127 (0.8%) had positive HIV enzyme-linked immunoassay (ELISA) result. With Western blot (WB) test, 54 (0.33%) were positive, 43 (0.26%) were negative, and 30 (0.18%) were indeterminate. One of the 30 women (3.3%) with indeterminate WB converted to positive WB during pregnancy. White and black women were more likely to have an unconfirmed positive ELISA (indeterminate or negative WB) than Hispanics ( P = 0.021). The positive WB rate for black women was significantly higher ( P < 0.001) than other racial/ethnic groups. The postpartum follow-up testing of 14 women with indeterminate WB varied between 4 to 20 weeks; 16 did not have any postpartum follow-up test. The common bands in indeterminate WB were P24, P18, and nonviral proteins. The pattern of indeterminate WB result and its follow-up was variable during pregnancy and postpartum period. There is a need for development of national standards of care for indeterminate WB mothers and their infants in the postpartum period. Additional studies are needed to determine the cause of indeterminate tests, reducing their occurrence in the testing process, and the optimum time for testing in the postpartum period.

Effect of endocervical specimen adequacy on ligase chain reaction detection of Chlamydia trachomatis

Several studies have demonstrated that the sensitivity of a commercially available PCR test for the detection of Chlamydia trachomatis (Roche Diagnostics) is affected by the cellular quality of the endocervical swab specimens. The cellular adequacies of 1,633 female endocervical swab specimens were assessed and compared with the results of C. trachomatis detection obtained by ligase chain reaction (LCR; Abbott Laboratories). Specimen adequacy studies and LCR were performed with samples from the same swab, after demonstration of the stability of human epithelial cells in LCR transport medium. Prior to heat treatment of the swab specimen, an aliquot was removed and cytocentrifuged onto a slide. Cell spots were stained and examined at x 400 magnification for endocervical (columnar epithelial or metaplastic) cells and erythrocytes. The overall rate of positivity of the LCR was 6.5% (106 of 1,633 specimens) with pooled specimens (pools of 4 specimens each; reduced cutoff). Of the 1,633 specimens examined, 655 (40.1%) were found to contain one or more endocervical cells. The rate of positivity for C. trachomatis was 10.8% (71 of 655 specimens) among specimens containing endocervical cells, whereas it was 3.6% (35 of 978 specimens) among specimens lacking endocervical cells (P < 0.0001). There was no linear trend between the rate of positivity for C. trachomatis and the number of endocervical cells (P = 0.24). The rate of positivity for C. trachomatis was 5.4% (8 of 147 specimens) among specimens containing large numbers of erythrocytes (> or =100 per high-power field), whereas it was 6.6% (98 of 1,486 specimens) among specimens containing less than 100 erythrocytes per high-power field (P = 0.59). These results show that the sensitivity of the Abbott C. trachomatis LCR test is affected by the presence of endocervical cells. Additionally, they indicate that the presence of a single endocervical cell is as good an indicator of specimen adequacy as the presence of many endocervical cells. The presence of a large number of erythrocytes was not associated with an increased rate of sensitivity of the LCR.

Real-time PCR assay targeting IS481 of Bordetella pertussis and molecular basis for detecting Bordetella holmesii

Detection of Bordetella holmesii by a real-time PCR assay targeting IS481 of Bordetella pertussis is reported. Sequencing of IS481-specific PCR products from B. pertussis and B. holmesii isolates revealed sequence homology. Restriction fragment length polymorphism demonstrated a low copy number of IS481-like sequences in B. holmesii. These results, and culture of B. holmesii from patients with cough, suggest that the specificity and predictive value of IS481-based PCR assays for pertussis may be compromised.

Rapid-cycle PCR method to detect Bordetella pertussis that fulfills all consensus recommendations for use of PCR in diagnosis of pertussis

No standardized PCR method is available for the laboratory diagnosis of the pertussis syndrome. Consensus recommendations for the use of PCR in the diagnosis of Bordetella pertussis infections have been proposed, and the aim of this study was to develop a method that fulfills all of these criteria. A rapid-cycle shared-primer PCR method with a microwell format and probe hybridization detection step (POR) was developed using novel oligonucleotides targeted to the outer membrane porin gene (Bordetella spp.). In specimens positive for Bordetella spp., B. pertussis was differentiated from Bordetella parapertussis and Bordetella bronchiseptica by hybridization with organism-specific oligonucleotide probes. An internal control was developed using overlap extension PCR and mouse beta-actin DNA. The analytical specificity was 100%. The analytical sensitivity was comparable to that of nested IS481 and IS1001 PCR ( approximately 1 organism per reaction). The clinical sensitivity and specificity were ascertained using 705 specimens (from 705 patients). The results were compared to those of a nested-PCR method targeting the insertion sequences IS481 and IS1001. Fifty-one specimens were positive for B. pertussis by POR and IS481 PCR. Two specimens which fulfilled a clinical definition of pertussis were positive by POR and negative by IS481 PCR. A total of 652 specimens were negative by both methods. B. parapertussis was not detected in any specimens. PCR inhibition was detected in 21 out of 705 specimens (2.98%). Thus, a rapid (4 h, including specimen preparation) PCR method which fulfills all of the consensus recommendations was developed and validated for the detection of B. pertussis.

Comparison of PCR, culture, and direct fluorescent-antibody testing for detection of Bordetella pertussis

We prospectively compared the performance of culture, direct fluorescent-antibody testing (DFA), and an in-house-developed PCR test targeting the repeated insertion sequence IS481 for the detection of Bordetella pertussis in nasopharyngeal swab specimens. We tested 319 consecutive paired specimens on which all three tests were performed. A total of 59 specimens were positive by one or more tests. Of these, 5 were positive by all three tests, 2 were positive by culture and PCR, 16 were positive by PCR and DFA, 28 were positive by PCR only, and 8 were positive by DFA only. Any specimen positive by culture was considered to be a true positive, as were specimens positive by both PCR and DFA. Specimens positive only by PCR or DFA were considered discrepant, and their status was resolved by review of patient histories. Patients with symptoms meeting the Centers for Disease Control and Prevention clinical case definition for pertussis and who had a specimen positive by PCR or DFA were considered to have true B. pertussis infections. Of the 28 patients positive by PCR only, 20 met the clinical case definition for pertussis, while 3 of the 8 patients positive by DFA only met the clinical case definition. After resolution of the status of discrepant specimens, the sensitivity, specificity, positive predictive value, and negative predictive value were 15.2, 100, 100, and 87.5%, respectively, for culture; 93.5, 97.1, 84.3, and 98.9%, respectively, for PCR; and 52.2, 98.2, 82.8, and 92.4%, respectively, for DFA. The actual positive predictive value of PCR was probably greater, as several PCR-positive patients who did not meet the clinical case definition had symptoms consistent with typical or atypical pertussis. PCR is a sensitive and specific method for the detection of B. pertussis.

Insertion element IS3-based PCR method for subtyping Escherichia coli O157:H7

An Escherichia coli O157:H7 subtyping method based on PCR amplification of variable DNA sequences between the repetitive element IS3 was developed. Template DNA was prepared by boiling cells in Chelex. Two separate IS3 PCR amplifications were performed for each isolate: one with a single primer (primer IS3A) and one with two primers (primers IS3A and IS3B). The IS3 PCR subtyping method was applied to 35 epidemiologically related and unrelated E. coli O157:H7 isolates that had been previously characterized by pulsed-field gel electrophoresis (PFGE). PFGE identified 25 different subtypes (difference of one or more bands). PCR with single primer IS3A and primer pair IS3A-IS3B identified 6 and 14 different subtypes, respectively. By combining the results of the two PCR amplifications, 15 different IS3 PCR subtypes were identified. While not as sensitive as PFGE, IS3 PCR subtyping grouped all outbreak-related isolates. IS3 PCR banding patterns were reproducible between amplifications and between subcultures. IS3 PCR could serve as a simple, rapid screening method for the identification of unrelated E. coli O157:H7 isolates.

Polymerase chain reaction typing of nonviable Mycobacterium tuberculosis isolates

Repetitive element polymerase chain reaction (PCR) typing was applied to two Mycobacterium tuberculosis isolates for which both viable and nonviable cultures were available. DNA extracted from the nonviable cultures and from fresh subcultures of the viable cultures was amplified with primers directed against the insertion sequence IS6110 and the polymorphic GC-rich repetitive sequence. For both isolates, the nonviable cultures generated PCR-banding patterns identical to those generated by the fresh subcultures.

Prospective comparison of culture vs genome detection for diagnosis of enteroviral meningitis in childhood

OBJECTIVE

To assess the sensitivity and specificity of a new polymerase chain reaction (PCR) assay with uninterrupted reverse transcription and complementary DNA amplification (RT-PCR) for the diagnosis of enteroviral (EV) meningitis in children.

DESIGN

A prospective, cohort study.

SETTINGS

Two medical centers: 1 university hospital and 1 children's hospital in San Diego County, California, during a 5-week period.

PATIENTS

All pediatric patients younger than 16 years who underwent a lumbar puncture for evaluation of possible meningitis.

MAIN OUTCOME MEASURES

The results of cerebrospinal fluid (CSF) RT-PCR were compared with viral cultures and clinical histories.

RESULTS

During the 5-week period, 90 patients were entered into the study. Nonpolio EVs were cultured from 10% (9/90) of the patients from the following sites: CSF, 6.7% (6/90) of the patients; stool, 19% (4/21) of the patients; and throat swabs, 5.6% (1/18) of the patients. The EV genome was detected in the CSF by using RT-PCR in 7 of 9 EV culture-positive patients. The sensitivity and specificity of the CSF RT-PCR assay to detect EV meningitis were 77.8% and 100%, respectively. This compared with a sensitivity of 66.7% for detection of EV in CSF by viral culture alone.

CONCLUSION

The new RT-PCR assay is a rapid and reliable method for the detection of EV infection in childhood.

Direct and uninterrupted RNA amplification of enteroviruses with colorimetric microwell detection

BACKGROUND

Enteroviruses (EV) cause a broad spectrum of human diseases, of which aseptic meningitis is among the most common and most clinically vexing. While the clinical symptoms of meningitis caused by bacteria, fungi and viruses are similar, the diagnosis, therapy and outcome of disease caused by these agents vary greatly. In order to appropriately manage meningitis patients, rapid and reliable diagnosis of EV meningitis impacts significantly on patient management.

OBJECTIVE

To develop a direct and uninterrupted RNA amplification of enteroviruses using rTth DNA polymerase.

STUDY DESIGN

Purified coxsackievirus B6 RNA of various concentrations was amplified by rTth DNA polymerase-mediated amplification to determine analytic sensitivity. The specificity of the EV amplification was examined with a panel of nucleic acids from 36 EV serotypes, 15 non-EV pathogens and 10 coded clinical specimens of cerebrospinal fluid (CSF).

RESULTS

All EV serotypes tested were detected successfully by this method at a sensitivity of 1 TCID(50) with the exception of echoviruses 1, 5, 22 and 23. Echovirus 5 was detected at 10 TCID(50), and echovirus 1 was detected at 100 TCID(50). Echoviruses 22 and 23 were not detectable at 100 TCID(50). Cross-reactivity of EV RT-PCR assay with 15 known non-EV meningitis pathogens has not been observed. Results of 10 CSF tested with this system correlated well with tissue culture.

CONCLUSIONS

We have developed an EV amplification assay which has several important advantages over previously reported methods. This assay employs rTth DNA polymerase which possesses both reverse transcriptase and DNA polymerase activities, simplifying RNA reverse transcription and DNA amplification to an uninterrupted reaction. Additionally, potential carryover contamination and enhanced amplification specificity is provided by substituting dUTP for dTTP and adding uracil N-glycosylase (UNG) in the amplification reaction. Finally, the detection of amplified product is via a colorimetric, microwell format permitting the use of readily available instrumentation.

Diagnosis of Chlamydia trachomatis urethritis in men by polymerase chain reaction assay of first-catch urine

To determine the accuracy of a recently developed polymerase chain reaction (PCR) urine assay to detect Chlamydia trachomatis urethral infection in men, we obtained urethral swabs and first-catch urine from 365 men attending a sexually transmitted diseases clinic. Thirty-three (9%) of the 365 men were infected with C. trachomatis as defined by urethral culture. Thirty-two of the 33 men with culture-positive urethral swabs also had PCR-positive urine assays. Of 332 patients with culture-negative urethral swabs, 325 had PCR-negative urine. Compared with chlamydia culture of urethral specimens, PCR assay of urine samples thus had a sensitivity of 97% and a specificity of 98%. The positive predictive value of the urine PCR assay was 82%, and the negative predictive value was 99%. Analysis of discrepant results indicated that six of seven PCR-positive, urethral culture-negative patients probably had chlamydial urethritis. All six patients had symptoms of urethritis and had either a positive urethral swab PCR or a positive urine PCR with a different amplification target. After resolution of discrepant results, (defining true positives as the 33 culture-positive patients and the 6 PCR-positive, culture-negative patients just described), the sensitivity and specificity of culture were 85% (33 of 39) and 100% (326 of 326), respectively. The revised sensitivity and specificity of PCR were 97% (38 of 39) and 99.7% (325 of 326), respectively. We conclude that this urine PCR assay provides a highly sensitive, noninvasive alternative method for the detection of C. trachomatis urethral infection in high-risk men attending a sexually transmitted diseases clinic. This assay could greatly facilitate the testing of larger numbers of male patients for chlamydial infection and should be studied in other settings.

Detection of Chlamydia trachomatis in endocervical specimens by polymerase chain reaction

A rapid and sensitive polymerase chain reaction (PCR)-based assay for detection of Chlamydia trachomatis in cervical specimens is described. This assay consists of (i) sample preparation which avoids the use of heat, centrifugation, or organic extractions; (ii) rapid, two-temperature PCR amplification of C. trachomatis cryptic plasmid sequences; and (iii) capture and colorimetric detection of amplified DNA in microwell plates. PCR was compared with culture by using 503 cervical specimens. After resolution of discrepant specimens with a confirmatory PCR assay directed against the chlamydial major outer membrane protein gene, PCR had a sensitivity of 97% and a specificity of 99.7% while culture had a sensitivity of 85.7% and a specificity of 100%. In a separate study, PCR was compared with a direct specimen enzyme immunoassay (Chlamydiazyme; Abbott Diagnostics) by using 375 cervical specimens. After resolution of discrepant specimens, PCR had a sensitivity and specificity of 100%, while the enzyme immunoassay had a sensitivity of 58.8% and a specificity of 100%.

Method for improved extraction of DNA from Nocardia asteroides

In a variation of standard DNA extraction methods, Nocardia asteroides was repeatedly exposed to sodium dodecyl sulfate at 60 degrees C for 30 min; each extraction was followed by centrifugation, removal of the nucleic acid-rich supernatant, and suspension of the cell pellet in fresh sodium dodecyl sulfate. The pooled supernatants contained a substantially higher amount of DNA than the first supernatant alone. The possible implications of this procedure on the development of DNA probes are discussed.

Antimicrobial mechanisms against Acinetobacter calcoaceticus of rat polymorphonuclear leukocyte granule extract

The antimicrobial mechanisms of rat polymorphonuclear leukocyte granule extract and isolated extract fractions against Acinetobacter calcoaceticus were examined. Crude granule extract and a fraction containing low-molecular-weight cationic peptides (peak D) reduced the viability of A. calcoaceticus and inhibited the uptake of radiolabeled macromolecule precursors by cells. The inhibitory activity observed with peak D was not as great as that of crude granule extract containing equivalent amounts of peak D protein. Crude extract also inhibited incorporation of uracil into trichloroacetic acid-precipitable material, while no isolated fraction, including peak D, had any substantial effect on incorporation. The antimicrobial activities of crude granule extract were more sensitive to boiling than those of isolated peak D. Preincubation of A. calcoaceticus with either crude granule extract or a fraction (peak B) possessing proteolytic activity but lacking any antimicrobial activity caused cells to become sensitive to a subinhibitory concentration of actinomycin D, suggesting that granule extract and peak B increase the outer membrane permeability of A. calcoaceticus. The antimicrobial granule extract fraction, peak D, did not affect outer membrane permeability. These results suggest that rat polymorphonuclear leukocyte granule extract reduces the viability of A. calcoaceticus by inhibiting the transport and incorporation of macromolecule precursors and that either whole granule extract is required for complete antimicrobial activity or an unidentified component is responsible for antimicrobial activity in addition to peak D. The granule extract activity that increases outer membrane permeability does not appear to be directly responsible for the observed decrease in viability.

Effect of plasmid RP1 on phase changes in inner and outer membranes and lipopolysaccharide from Acinetobacter calcoaceticus: a Fourier transform infrared study

The successful transfer of the resistance plasmid RP1 into the Gram-negative bacterium Acinetobacter calcoaceticus resulted in increased resistance of this microorganism to the antibiotics kanamycin and tetracycline. Microorganisms harboring the RP1 plasmid showed altered fatty acid composition in the lipopolysaccharide fraction and increased outer membrane permeability compared to organisms without the plasmid. Thermotropic gel to liquid crystal lipid phase changes were detected in both inner and outer membranes and purified lipopolysaccharide by Fourier transform infrared spectroscopy. The phase transition temperatures observed in the outer membranes and isolated lipopolysaccharide of the plasmid-containing cells were significantly higher than those of the plasmid-free organisms, while little difference was observed for the inner membranes. The plasmid-induced decrease in outer membrane fluidity may play a mediating role in the mechanisms of antibiotic resistance and susceptibility to host immune cells in Gram-negative microorganisms.

Outer membrane permeability of Acinetobacter calcoaceticus mediates susceptibility to rat polymorphonuclear leukocyte granule contents

Growth of Acinetobacter calcoaceticus on specific alkanes altered the outer membrane permeability of the organism, as indicated by a change in sensitivity to the antibiotic actinomycin D. As the carbon length of the alkane energy source decreased, outer membrane permeability and susceptibility to actinomycin D increased. Concomitant with the increase in outer membrane permeability, A. calcoaceticus became more susceptible to the oxygen-independent antimicrobial activity of extracted contents from rat polymorphonuclear leukocyte granules. Individual fractions of granule extract possessed no antimicrobial activity against A. calcoaceticus. The alkane-induced change in outer membrane permeability was not associated with alterations of lipopolysaccharide O antigen. An outer membrane permeability mechanism, independent of changes in lipopolysaccharide content, mediating susceptibility to the oxygen-independent antimicrobial activity of rat polymorphonuclear leukocyte granule contents is suggested.

Plasmid RP1-mediated susceptibility of Acinetobacter calcoaceticus to rat polymorphonuclear leukocyte granule contents

The resistance plasmid RP1 was transferred by conjugation to a plasmidless strain of Acinetobacter calcoaceticus. Acquisition and expression of RP1 by A. calcoaceticus HO1-N was associated with an increase in sensitivity to the antimicrobial activity of extracted contents from rat polymorphonuclear leukocyte granules. Plasmid RP1-associated antibiotic resistance and sensitivity to granule contents were cured by exposure to acridine orange. Assays with granule extract fractions separated by fast protein liquid chromatography showed myeloperoxidase, protease, and lysozyme fractions to possess little or no antimicrobial activity against the A. calcoaceticus strains. A protein fraction designated peak D, containing two low-molecular-weight cationic peptides (M. J. Loeffelholz and M. C. Modrzakowski, Anal. Biochem., in press), did possess antimicrobial activity against both HO1-N and Ho1-N(RP1) strains, with the HO1-N(RP1) strain being significantly more sensitive.

Isolation of cationic peptides from rat polymorphonuclear leukocyte granule contents using fast protein liquid chromatography

Separation of extracted rat polymorphonuclear leukocyte (PMN) granule contents using fast protein liquid chromatography yielded four major protein fractions. These fractions consisted of myeloperoxidase (peak A), neutral protease (peak B), lysozyme (peak C), and low molecular weight, cationic peptides (peak D). This study represents the first noted purification of the cationic peptides of rat PMN granules.