Positive predictive value of the UK clinical case definition for H1N1/09 (‘swine’) influenza

For the purpose of surveillance of the acquired immunodeficiency syndrome (AIDS) in developing countries, the World Health Organization (WHO) has recommended criteria for the clinical case definition of AIDS in adults and children. In a preliminary examination of children in Zambia a number of patients with obvious AIDS did not fit the published WHO case definition for paediatric AIDS. Based on this the Zambia National AIDS Surveillance Committee designed local criteria for the clinical case definition of paediatric AIDS. We compared the Zambian criteria with the WHO criteria for the diagnosis of paediatric AIDS by studying 134 consecutively admitted children to one of the paediatric wards at the University Teaching Hospital in Lusaka. Twenty-nine of the patients were HIV-1 seropositive and 105 were HIV-1 seronegative. Among the 29 HIV-seropositive patients, the Zambian criteria identified 23, and the WHO criteria identified 20 children as having AIDS. The 105 HIV-seronegative children were classified as having AIDS in 9 cases by the Zambian criteria and in 38 cases by the WHO criteria. These results give the Zambian criteria for the diagnosis of AIDS a sensitivity of 79.3%, a specificity of 91.4% and a positive predictive value of 86.8% compared to a sensitivity of 69%, specificity of 64% and a positive predictive value of 38% for the WHO criteria. The current WHO criteria are inadequate for the diagnosis of paediatric AIDS. The need to refine the WHO criteria for the diagnosis of paediatric AIDS is discussed.

Download Full-text

MEASLES IN LARUT, MATANG AND SELAMA: ANALYSIS AND EVALUATION OF CLINICAL CASE DEFINITIONS FOR 2015-2019

Malaysian Journal of Public Health Medicine ◽

10.37268/mjphm/vol.20/no.1/art.440 ◽

2020 ◽

Vol 20 (1) ◽

pp. 130-140

Author(s):

Asraf Ahmad Qamruddin ◽

Afiq Malek ◽

Asnita Rozali ◽

Norsihimah Wahid

Keyword(s):

Positive Predictive Value ◽

Incidence Rate ◽

Negative Predictive Value ◽

Predictive Value ◽

Clinical Case ◽

Case Definition ◽

Case Definitions ◽

Cross Sectional ◽

Sensitivity Specificity ◽

Clinical Case Definition

An accurate system of identifying measles cases is critical for the measles surveillance system. The objectives were: 1) To determine the incidence rate of measles in Larut, Matang and Selama district in Perak from 2015 to 2019 2) To evaluate the measles clinical case definition by comparing the performance of the measles clinical case definition in predicting laboratory-confirmed measles case. A cross-sectional analysis was carried out looking at all suspected and laboratory-confirmed measles cases in Larut, Matang and Selama District registered on the online measles surveillance reporting system between 2015 to 2019. The sensitivity, specificity, positive predictive value and negative predictive value of the clinical case definition as confirmed by the laboratory result were calculated. The incidence rate for suspected measles showed an increasing trend from 3.96 per 100,000 population in 2015 to 28.82 per 100,000 population in 2019. For laboratory-confirmed measles cases, the incidence rate showed more variation with an increase to 36.11 per million population in 2017 from 5.67 per million population in 2015. The incidence rate later decreased to 10.99 per million population in 2018 and increased again to 24.47 per million population in 2019. The sensitivity of the clinical case definition in confirming measles was 86.67% (95% CI: 69.28%, 96.24%) , specificity 47.52% (95% CI: 41.56%, 53.52%), positive predictive value 14.95% (95% CI 12.81%, 17.36%) and negative predictive value 97.10% (93.03%, 98.83%). Measles incidence is increasing in trend. The clinical case definition is an effective tool to rule out measles in cases that failed to meet the criteria due to the high negative predictive value of the definition. However, for cases that meet the clinical case definition, laboratory confirmation or epidemiological link to a confirmed case is needed.

Download Full-text

Comparison of PCR, Culture, and Direct Fluorescent-Antibody Testing for Detection of Bordetella pertussis

Journal of Clinical Microbiology ◽

10.1128/jcm.37.9.2872-2876.1999 ◽

1999 ◽

Vol 37 (9) ◽

pp. 2872-2876 ◽

Cited By ~ 82

Author(s):

Mike J. Loeffelholz ◽

Curt J. Thompson ◽

Karla S. Long ◽

Mary J. R. Gilchrist

Keyword(s):

Positive Predictive Value ◽

Bordetella Pertussis ◽

Predictive Value ◽

Clinical Case ◽

Fluorescent Antibody ◽

Case Definition ◽

Specific Method ◽

Antibody Testing ◽

Direct Fluorescent Antibody ◽

Clinical Case Definition

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.

Download Full-text

Enhancing the predictive value of throat swabs in virological influenza surveillance

Eurosurveillance ◽

10.2807/esm.07.12.00389-en ◽

2002 ◽

Vol 7 (12) ◽

pp. 180-183 ◽

Cited By ~ 8

Author(s):

K Leitmeyer ◽

U Buchholz ◽

M. Kramer ◽

B Schweiger

Keyword(s):

National Survey ◽

Predictive Value ◽

Clinical Case ◽

Disease Onset ◽

Case Definition ◽

Influenza Viruses ◽

Influenza Surveillance ◽

Definition Of ◽

Virological Surveillance ◽

Clinical Case Definition

According to a national survey in Germany, the influenza virological surveillance can be improved when sentinel practitioners take throat swabs specimens only from patients who consult early after the disease onset (ie, within 48 hours), and when they use the strict clinical case definition of influenza-like illness. PCR should be used for primary detection of influenza viruses.

Download Full-text

Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation

BMJ ◽

10.1136/bmj.n214 ◽

2021 ◽

pp. n214

Author(s):

Weedon MN ◽

Jackson L ◽

Harrison JW ◽

Ruth KS ◽

Tyrrell J ◽

...

Keyword(s):

Positive Predictive Value ◽

Predictive Value ◽

Population Based ◽

Genome Project ◽

Personal Genome ◽

Uk Biobank ◽

Sequencing Data ◽

Snp Chip ◽

Pathogenic Variants ◽

The Uk

Abstract Objective To determine whether the sensitivity and specificity of SNP chips are adequate for detecting rare pathogenic variants in a clinically unselected population. Design Retrospective, population based diagnostic evaluation. Participants 49 908 people recruited to the UK Biobank with SNP chip and next generation sequencing data, and an additional 21 people who purchased consumer genetic tests and shared their data online via the Personal Genome Project. Main outcome measures Genotyping (that is, identification of the correct DNA base at a specific genomic location) using SNP chips versus sequencing, with results split by frequency of that genotype in the population. Rare pathogenic variants in the BRCA1 and BRCA2 genes were selected as an exemplar for detailed analysis of clinically actionable variants in the UK Biobank, and BRCA related cancers (breast, ovarian, prostate, and pancreatic) were assessed in participants through use of cancer registry data. Results Overall, genotyping using SNP chips performed well compared with sequencing; sensitivity, specificity, positive predictive value, and negative predictive value were all above 99% for 108 574 common variants directly genotyped on the SNP chips and sequenced in the UK Biobank. However, the likelihood of a true positive result decreased dramatically with decreasing variant frequency; for variants that are very rare in the population, with a frequency below 0.001% in UK Biobank, the positive predictive value was very low and only 16% of 4757 heterozygous genotypes from the SNP chips were confirmed with sequencing data. Results were similar for SNP chip data from the Personal Genome Project, and 20/21 individuals analysed had at least one false positive rare pathogenic variant that had been incorrectly genotyped. For pathogenic variants in the BRCA1 and BRCA2 genes, which are individually very rare, the overall performance metrics for the SNP chips versus sequencing in the UK Biobank were: sensitivity 34.6%, specificity 98.3%, positive predictive value 4.2%, and negative predictive value 99.9%. Rates of BRCA related cancers in UK Biobank participants with a positive SNP chip result were similar to those for age matched controls (odds ratio 1.31, 95% confidence interval 0.99 to 1.71) because the vast majority of variants were false positives, whereas sequence positive participants had a significantly increased risk (odds ratio 4.05, 2.72 to 6.03). Conclusions SNP chips are extremely unreliable for genotyping very rare pathogenic variants and should not be used to guide health decisions without validation.

Download Full-text