Proficiency program for real-time PCR diagnosis of Bordetella pertussis infections in French hospital laboratories and at the French National Reference Center for Whooping Cough and other Bordetelloses

Follow-Up of External Quality Controls for PCR-Based Diagnosis of Whooping Cough in a Hospital Laboratory Network (Renacoq) and in Other Hospital and Private Laboratories in France

The French National Reference Centre (NRC) for Whooping Cough carried out an external quality control (QC) analysis in 2010 for the PCR diagnosis of whooping cough. The main objective of the study was to assess the impact of this QC in the participating laboratories through a repeat analysis in 2012.

Laboratory Diagnosis of Pertussis

The introduction of vaccination in the 1950s significantly reduced the morbidity and mortality of pertussis. However, since the 1990s, a resurgence of pertussis has been observed in vaccinated populations, and a number of causes have been proposed for this phenomenon, including improved diagnostics, increased awareness, waning immunity, and pathogen adaptation. The resurgence of pertussis highlights the importance of standardized, sensitive, and specific laboratory diagnoses, the lack of which is responsible for the large differences in pertussis notifications between countries. Accurate laboratory diagnosis is also important for distinguishing between the several etiologic agents of pertussis-like diseases, which involve both viruses and bacteria. If pertussis is diagnosed in a timely manner, antibiotic treatment of the patient can mitigate the symptoms and prevent transmission. During an outbreak, timely diagnosis of pertussis allows prophylactic treatment of infants too young to be (fully) vaccinated, for whom pertussis is a severe, sometimes fatal disease. Finally, reliable diagnosis of pertussis is required to reveal trends in the (age-specific) disease incidence, which may point to changes in vaccine efficacy, waning immunity, and the emergence of vaccine-adapted strains. Here we review current approaches to the diagnosis of pertussis and discuss their limitations and strengths. In particular, we emphasize that the optimal diagnostic procedure depends on the stage of the disease, the age of the patient, and the vaccination status of the patient.

Monitoring the Impact of Vaccination on Pertussis in Infants Using an Active Hospital-based Pediatric Surveillance Network: Results from 17 Years' Experience, 1996-2012, France

BACKGROUND

Despite a high vaccine coverage in France in children, a resurgence of pertussis in infants too young to be protected by vaccination was observed in the 1990 s, leading to additional vaccination strategies in older age groups. This article describes the epidemiologic trends and characteristics of cases among infants 0-5 months of age during 17 years of pertussis surveillance through Renacoq.

METHODS

Renacoq is a sentinel hospital-based voluntary surveillance network covering about 30% of hospitalized pertussis pediatric cases. It includes microbiologists and pediatricians from 42 large hospitals.

RESULTS

Since March 1996, the network has described 2227 cases of pertussis in infants aged 0-5 months of whom 67.7% were infants 0-2 months of age. Four epidemic peaks occurred. The estimated national average incidence rate for the children aged 0-2 months decreased significantly between 1996-1998 and 2008-2012 from 264 to 179 per 100,000. Globally, 18.4% of cases were admitted to an intensive care unit, and the average case fatality ratio was 1%. Two-thirds (67.1%) of infants aged 3-5 months were not correctly vaccinated according to age. Parents accounted for 41-57% of the infections and siblings for 17-24%.

CONCLUSIONS

Renacoq data confirmed the risk for young children and the need of timely pertussis vaccination. Parents and sibling remain the main source of infection, despite addition of boosters targeting sibling and parents. Improving vaccination coverage in adults in contact with young infants is needed. The continuation of Renacoq surveillance will allow monitoring the impact of additional vaccination strategies.

Evaluation of reported cases of pertussis: epidemiological study in a large city in Spain

We retrospectively analysed the incidence rate of reported cases of pertussis in Barcelona during 2009–2012 according to age, sex, type of medical centre and vaccination status. We included 748 confirmed or suspected cases, 613 (82.0 %) of which were confirmed by laboratory testing and the remaining 135 (18.0 %) by epidemiological evidence. The highest reported incidence of pertussis was amongst <1 year olds [96.1 per 100 000 person-years, 95 % confidence interval (CI): 84.3–109.1]. The majority of confirmed and suspected cases were reported in 2011 and 2012, and the total incidence (confirmed or suspected) was 6.3 (95 % CI: 5.6–6.9) and 4.2 (95 % CI: 3.6–4.7) per 100 000 person-years, respectively. Incidence increased significantly (P = 0.001) in 2011–2012 compared with 2009. Most confirmed cases occurred in children <1 year old (87.9 %). Cases were confirmed by real-time (RT)-PCR (87.5 %; 95 % CI: 81.3–87.6) and bacterial culture (13.7 %; 95 % CI: 11.0–17.1). We recommend performing RT-PCR in suspected cases with no epidemiological link to a confirmed case.

Status of pertussis in iran

BACKGROUND

Pertussis is a respiratory and contagious disease which is mostly caused by Bordetella pertussis and B. parapertussis. It usually spreads from person to personduring the incubation or catarrhal phase of the disease. Despite of large-scale vaccination, whooping cough is still an endemic disease with several outbreaks.

OBJECTIVES

The aim of this study was to determine the prevalence of pertussis and identify its causative agents, B. pertussis or B. parapertussis, from specimens collected from Iranian patients from 2004 to 2008.

PATIENTS AND METHODS

Nasopharyngeal swab samples from 347 suspected pertussis cases were collected from 18 provinces of Iran. The patients were in different age groups and were either unvaccinated or vaccinated for pertussis with whole cell vaccine (WCV). Bacterial culture, agglutination tests and quantitative PCR (qPCR) targeting IS481 and IS1001 for B. pertussis and B. parapertussis were done for every specimen, respectively.

RESULTS

The results showed that seven nasopharyngeal swab samples (2%) were positive for B. pertussis (1.7%) and B. parapertussis (0.3%) by culture and agglutination test and 30 patients had positive qPCR test results (9%).

CONCLUSIONS

Despite the fact that bacterial culture is the golden standard for the detection of B. pertussis, direct detection of bacteria from nasopharyngeal specimens can be performed by a rapid qPCR assay. In this study, high percentage of positive qPCR cases may indicate that the patients might have recovered from pertussis following antibiotic treatment before samples were collected. Rapid detection by qPCR could be important for immediate diagnosis and treatment of patients with pertussis.

Harmonization of Bordetella pertussis real-time PCR diagnostics in the United States in 2012

Real-time PCR (rt-PCR) is an important diagnostic tool for the identification of Bordetella pertussis, Bordetella holmesii, and Bordetella parapertussis. Most U.S. public health laboratories (USPHLs) target IS481, present in 218 to 238 copies in the B. pertussis genome and 32 to 65 copies in B. holmesii. The CDC developed a multitarget PCR assay to differentiate B. pertussis, B. holmesii, and B. parapertussis and provided protocols and training to 19 USPHLs. The 2012 performance exercise (PE) assessed the capability of USPHLs to detect these three Bordetella species in clinical samples. Laboratories were recruited by the Wisconsin State Proficiency Testing program through the Association of Public Health Laboratories, in partnership with the CDC. Spring and fall PE panels contained 12 samples each of viable Bordetella and non-Bordetella species in saline. Fifty and 53 USPHLs participated in the spring and fall PEs, respectively, using a variety of nucleic acid extraction methods, PCR platforms, and assays. Ninety-six percent and 94% of laboratories targeted IS481 in spring and fall, respectively, in either singleplex or multiplex assays. In spring and fall, respectively, 72% and 79% of USPHLs differentiated B. pertussis and B. holmesii and 68% and 72% identified B. parapertussis. IS481 cycle threshold (CT) values for B. pertussis samples had coefficients of variation (CV) ranging from 10% to 28%. Of the USPHLs that differentiated B. pertussis and B. holmesii, sensitivity was 96% and specificity was 95% for the combined panels. The 2012 PE demonstrated increased harmonization of rt-PCR Bordetella diagnostic protocols in USPHLs compared to that of the previous survey.

Qualitative assessment of pertussis diagnostics in United States laboratories

BACKGROUND

United States national surveillance data show that the use of culture for pertussis diagnostics has sharply declined, whereas polymerase chain reaction (PCR) is now the most common testing method. PCR testing for pertussis is rapid and sensitive, but the lack of standardization and variable specificity is concerning.

METHODS

A web-based survey containing 12 questions was sent to public health, commercial and hospital-based US laboratories performing clinical diagnostics to determine the pertussis diagnostics used. An extensive real-time PCR (RT-PCR) questionnaire accompanied a proficiency panel assessing the types of extraction methods, RT-PCR methods and current quality control in place at the laboratories. The proficiency panel of 12 specimens containing Bordetella pertussis at various concentrations and negative controls was created to detect cross-contamination and assess the lower limit of detection.

RESULTS

One hundred twenty-three (35%) of 355 respondents from the web-based survey performed diagnostic tests for the presence of B. pertussis. Eighty-three (71%) labs reported performing culture, whereas 67 (54%) labs used PCR. All 41 laboratories that consented to participate in the proficiency exercise used the IS481 RT-PCR target; however, a variety of extraction and RT-PCR methods were employed. The laboratories correctly identified 92% of the B. pertussis specimens, and 5% of the laboratories (1.8% of the panel specimens) reported at least 1 false-positive.

CONCLUSIONS

The small percentage of false-positives suggests that adequate procedures are in place to prevent cross-contamination. Differing extraction and PCR methods as well as variable analytic sensitivity emphasize the necessity for an external well-defined quality control program and interlaboratory pertussis PCR harmonization.

Real-time PCR as a diagnostic tool for bacterial diseases

In recent years, quantitative real-time PCR tests have been extensively developed in clinical microbiology laboratories for routine diagnosis of infectious diseases, particularly bacterial diseases. This molecular tool is well-suited for the rapid detection of bacteria directly in clinical specimens, allowing early, sensitive and specific laboratory confirmation of related diseases. It is particularly suitable for the diagnosis of infections caused by fastidious growth species, and the number of these pathogens has increased recently. This method also allows a rapid assessment of the presence of antibiotic resistance genes or gene mutations. Although this genetic approach is not always predictive of phenotypic resistances, in specific situations it may help to optimize the therapeutic management of patients. Finally, an approach combining the detection of pathogens, their mechanisms of antibiotic resistance, their virulence factors and bacterial load in clinical samples could lead to profound changes in the care of these infected patients.

Prevalence of Bordetella pertussis and Bordetella parapertussis infections in Tunisian hospitalized infants: results of a 4-year prospective study

The prevalence of pertussis in Tunisia remains undetermined essentially because of the unavailability of a basic laboratory diagnostic service. Specific diagnostic tools were applied for the first time in a Tunisian prospective study in order to get a first estimation of the prevalence of Bordetella pertussis/parapertussis infections and to evaluate their use to determine the epidemiologic characteristics of these infections in Tunisian infants. Between 2007 and 2011, a total of 626 samples from 599 infants aged <1 year with and without pertussoid cough were investigated for the presence of B. pertussis/parapertussis using culture and real-time polymerase chain reaction (PCR). The real-time PCR (RT-PCR) targets include IS481 commonly found in B. pertussis, B. bronchiseptica, and B. holmesii; IS1001 specific of B. parapertussis, in combination with the pertussis toxin promoter region gene (ptx) of B. pertussis; and the recA gene specific of B. holmesii. When possible, patients' household contacts provided nasopharyngeal aspirates (NPAs) for RT-PCR detection of B. pertussis/parapertussis or single-serum samples for anti-PT IgG quantification. All except 1 NPAs were negative by conventional culture, whereas PCR gave positive signals for 126 specimens (21%): B. pertussis, B. parapertussis, and Bordetella spp. were detected in 82%, 6%, and 4% of the samples, respectively. The simultaneous presence of B. pertussis and B. parapertussis was noted in 8% of the cases. Pertussis was reported throughout the year with a peak during the summer of the year 2009. The prevalence of Bordetella infection was 20% between 2007 and 2011. Most of these cases corresponded to patients younger than 6 months who received <3 doses of pertussis vaccine. Among the household contacts enrolled in the study, mothers seemed to be the likely source of infection. This study showed that pertussis is still prevalent in Tunisia and that the disease remains a public health problem affecting not only infants but also adults. Given this situation, sensitive and specific laboratory tests are needed to improve the accuracy of pertussis diagnosis.

The diagnosis of pertussis: which method to choose?

Despite the introduction of routine vaccination against pertussis for more than a half century, leading to a drastic decline in the number of reported cases, pertussis continues to be an important respiratory disease afflicting unvaccinated infants and previously vaccinated children as well as adults in whom immunity has waned. The diagnosis of pertussis is challenging and accurate laboratory identification of Bordetella infections remains problematic. Common laboratory diagnostic methods used for pertussis diagnosis include culture, direct-fluorescent-antibody testing (DFA), serology and polymerase chain reaction (PCR). Culture of Bordetella pertussis is highly specific but fastidious and has limited sensitivity. DFA provides a much more rapid result, but has the disadvantage of poor sensitivity and specificity. Serology is not useful in infants. In older persons, it is hampered by the limitations of paired sera and it provides mainly a retrospective diagnosis. Such limitations of conventional diagnosis testing have led to the development of PCR assays. Notwithstanding its lack of standardization, PCR has been found to be more sensitive and more specific than other methods. In this report, we aimed to review current knowledge about the available diagnostic methods and tests that accurately diagnose pertussis.

Evaluation of four commercial real-time PCR assays for detection of Bordetella spp. in nasopharyngeal aspirates

We evaluated the performances of 4 commercial real-time PCR kits for Bordetella pertussis IS481 sequence detection in nasopharyngeal aspirates by comparison with an in-house real-time PCR assay. Among them, the Simplexa Bordetella pertussis/parapertussis assay (Focus Diagnostics), the SmartCycler Bordetella pertussis/parapertussis assay (Cepheid), and Bordetella R-gene (Argene) present sensitivities over 90%. One kit proved unsuitable for routine clinical use.