Real-time polymerase chain reaction detection of Bordetella pertussis DNA in acellular pertussis vaccines

Asymptomatic Bordetella pertussis infections in a longitudinal cohort of young African infants and their mothers

Recent pertussis resurgence in numerous countries may be driven by asymptomatic infections. Most pertussis surveillance studies are cross-sectional and cannot distinguish asymptomatic from pre-symptomatic infections. Longitudinal surveillance could overcome this barrier, providing more information about the true burden of pertussis at the population level. Here we analyze 17,442 nasopharyngeal samples from a longitudinal cohort of 1320 Zambian mother/infant pairs. Our analysis has two elements. First, we demonstrate that the full range of IS481 qPCR CT values provides insight into pertussis epidemiology, showing concordance of low and high CT results over time, within mother/infant pairs, and in relation to symptomatology. Second, we exploit these full-range qPCR data to demonstrate a high incidence of asymptomatic pertussis, including among infants. Our results demonstrate a wider burden of pertussis infection than we anticipated in this population, and expose key limitations of threshold-based interpretation of qPCR results in infectious disease surveillance.

Asymptomatic Bordetella pertussis infections in young African infants and their mothers identified within a longitudinal cohort

Despite long-standing vaccination programs, pertussis incidence has increased in numerous countries; transmission by asymptomatic individuals is a suspected driver of this resurgence. However, unequivocal evidence documenting asymptomatic infections in adults and children is lacking due, in part, to the cross-sectional nature of most pertussis surveillance studies. In addition, modern pertussis surveillance relies on quantitative PCR (qPCR) using fixed diagnostic thresholds to identify cases. To address this gap, we present a longitudinal analysis of 17,442 nasopharyngeal samples collected from a cohort of 1,320 Zambian mother/infant pairs. Using full-range cycle threshold (CT) values from IS481 qPCR assays, we document widespread asymptomatic infections among mothers and also, surprisingly, among young infants. From an initial group of eight symptomatic infants who tested positive by qPCR, we identify frequent contemporaneous subclinical infections in mothers. Within the full cohort, we observe strong temporal correlation between low- and high-intensity qPCR signals. We compute a single time-averaged score for each individual summarizing the evidence for pertussis infection (EFI), and show that EFI strongly clusters within mother/infant pairs, and is strongly associated with clinical symptomatology and antibiotic use. Overall, the burden of pertussis here is substantially underestimated when restricting diagnostic criteria to IS481 CT≤35. Rather, we find that full-range CT values provide valuable insights into pertussis epidemiology in this population, and illuminate the infection arc within individuals. These findings have significant implications for quantifying asymptomatic pertussis prevalence and its contribution to overall transmission. Our results also expose limitations of threshold-based interpretations of qPCR assays in infectious disease surveillance.

Utilization of multiple real-time PCR assays for the diagnosis of Bordetella spp. in clinical specimens

Bordetella pertussis causes an upper respiratory infection in infants, adolescents, and adults. Diagnosis of pertussis, a vaccine-preventable disease, can be difficult, but recent implementation of real-time PCR assays in laboratories has hastened the ability of clinicians to make an accurate diagnosis. In this paper we describe the method of nasopharyngeal specimen collection, extraction of DNA, and real-time PCR assays that will allow the detection and identification of Bordetella spp. in clinical specimens.

The California Pertussis Epidemic 2010: A Review of 986 Pediatric Case Reports From San Diego County

BACKGROUND

The California Department of Public Health (CDPH) declared a pertussis epidemic on 23 June 2010. More cases were reported in 2010 (9146) than in any year since 1947. We describe the characteristics of pertussis epidemiology and disease from 986 reported cases in children in San Diego County (population 3.2 million).

METHODS

Descriptive statistics were abstracted from CDPH pertussis case report forms that were completed by public health nurses investigating reports of positive laboratory results for pertussis and reports of illnesses compatible with pertussis.

RESULTS

Of 1144 reported adult and pediatric cases, 753 (66%) were confirmed and 391 were probable/suspect. Children aged <19 years comprised 86% of all reported cases in San Diego County; of these, 22% were aged 11-18 years, 29% were aged 6-10 years, 27% were aged 1-5 years, and 22% were aged <1 year (with 70% aged <6 months). Case rates were highest in infants aged <6 months (651 per 100 000 population). Of those aged >1 year, the highest attack rates were in preschool children aged 1-5 years (114 per 100 000) and elementary school children aged 6-10 years (141 per 100 000). Of 51 children hospitalized, 82% were aged <6 months; 2 deaths occurred in these young infants. Paroxysmal cough was noted in over 70% of children in all age groups; post-tussive vomiting occurred in 36% (aged 11-18 years) to 57% (aged <6 months) of children.

CONCLUSIONS

Pertussis vaccine efficacy may decrease more rapidly than previously believed, facilitating spread of pertussis in elementary school-aged children. The highest case rates and the only mortality occurred in infants aged <6 months.

Pertussis Pseudo-outbreak linked to specimens contaminated by Bordetella pertussis DNA From clinic surfaces

BACKGROUND AND OBJECTIVES

We investigated a pertussis outbreak characterized by atypical cases, confirmed by polymerase chain reaction (PCR) alone at a single laboratory, which persisted despite high vaccine coverage and routine control measures. We aimed to determine whether Bordetella pertussis was the causative agent and advise on control interventions.

METHODS

We conducted case ascertainment, confirmatory testing for pertussis and other pathogens, and an assessment for possible sources of specimen contamination, including a survey of clinic practices, sampling clinics for B pertussis DNA, and review of laboratory quality indicators.

RESULTS

Between November 28, 2008, and September 4, 2009, 125 cases were reported, of which 92 (74%) were PCR positive. Cases occurring after April 2009 (n = 79; 63%) had fewer classic pertussis symptoms (63% vs 98%; P < .01), smaller amounts of B pertussis DNA (mean PCR cycle threshold value: 40.9 vs 33.1; P < .01), and a greater proportion of PCR-positive results (34% vs 6%; P < .01). Cultures and serology for B pertussis were negative. Other common respiratory pathogens were detected. We identified factors that likely resulted in specimen contamination at the point of collection: environmentally present B pertussis DNA in clinics from vaccine, clinic standard specimen collection practices, use of liquid transport medium, and lack of clinically relevant PCR cutoffs.

CONCLUSIONS

A summer pertussis pseudo-outbreak, multifactorial in cause, likely occurred. Recommendations beyond standard practice were made to providers on specimen collection and environmental cleaning, and to laboratories on standardizing PCR protocols and reporting results, to minimize false-positive results from contaminated clinical specimens.

Aerosolized vaccine as an unexpected source of false-positive Bordetella pertussis PCR results

When 13 of 13 nasal wash specimens from a single pediatrician's office tested positive for low quantities of Bordetella pertussis DNA, we suspected prelaboratory contamination. Investigation revealed that Pentacel and Adacel vaccines contain high copy numbers of B. pertussis DNA, which can be aerosolized, causing false-positive B. pertussis PCR results.

Novel multitarget real-time PCR assay for rapid detection of Bordetella species in clinical specimens

A novel multitarget real-time PCR (RT-PCR) assay for the rapid identification of Bordetella pertussis, B. parapertussis, and B. holmesii was developed using multicopy insertion sequences (ISs) in combination with the pertussis toxin subunit S1 (ptxS1) singleplex assay. The RT-PCR targets for the multiplex assay include IS481, commonly found in B. pertussis and B. holmesii; IS1001 of B. parapertussis; and the IS1001-like sequence of B. holmesii. Overall, 402 Bordetella species and 66 non-Bordetella species isolates were tested in the multitarget assay. Cross-reactivity was found only with 5 B. bronchiseptica isolates, which were positive with IS1001 of B. parapertussis. The lower limit of detection (LLOD) of the multiplex assay was similar to the LLOD of each target in an individual assay format, which was approximately 1 genomic equivalent per reaction for all targets. A total of 197 human clinical specimens obtained during cough-illness outbreak investigations were used to evaluate the multitarget RT-PCR assay. The multiplex assay results from 87 clinical specimens were compared to the individual RT-PCR assay and culture results. The multitarget assay is useful as a diagnostic tool to confirm B. pertussis infections and to rapidly identify other Bordetella species. In conclusion, the use of this multitarget RT-PCR approach increases specificity, while it decreases the amount of time, reagents, and specimen necessary for RT-PCRs used for accurate diagnosis of pertussis-like illness.

Development and evaluation of dual-target real-time polymerase chain reaction assays to detect Bordetella spp

Novel, highly specific, and sensitive real-time polymerase chain reaction (PCR) assays using 2 targets, insertion sequence (IS481) and pertussis toxin subunit 1 (ptxS1), were developed to detect Bordetella pertussis and to differentiate between relevant Bordetella spp. Sixty-four non-Bordetella isolates were negative by both assays, demonstrating the specificity of the assays. B. pertussis, Bordetella parapertussis, and Bordetella holmesii isolates were specifically identified using the assays. The lower limit of detection was less than 10 genomic equivalents per reaction for the IS481 and ptxS1 assays. These assays were evaluated using 145 human clinical specimens obtained during cough-illness outbreak investigations, and PCR results were compared with Bordetella spp. culture results. Twenty-seven (18.6%) specimens had late positive cycle threshold (Ct) values (35 <or= Ct < 40) using the IS481 assay with corresponding negative results using the ptxS1 assay and culture and were considered indeterminate. Guidelines for use of PCR testing and interpretation of results during cough-illness outbreaks are discussed.