Diagnostic evaluation of polymerase chain reaction discriminative for Bordetella pertussis, B. parapertussis, and B. bronchiseptica

Analysis of the lung microbiota in dogs with Bordetella bronchiseptica infection and correlation with culture and quantitative polymerase chain reaction

Infection with Bordetella bronchiseptica (Bb), a pathogen involved in canine infectious respiratory disease complex, can be confirmed using culture or qPCR. Studies about the canine lung microbiota (LM) are recent, sparse, and only one paper has been published in canine lung infection. In this study, we aimed to compare the LM between Bb infected and healthy dogs, and to correlate sequencing with culture and qPCR results. Twenty Bb infected dogs diagnosed either by qPCR and/or culture and 4 healthy dogs were included. qPCR for Mycoplasma cynos (Mc) were also available in 18 diseased and all healthy dogs. Sequencing results, obtained from bronchoalveolar lavage fluid after DNA extraction, PCR targeting the V1–V3 region of the 16S rDNA and sequencing, showed the presence of Bb in all diseased dogs, about half being co-infected with Mc. In diseased compared with healthy dogs, the β-diversity changed (P = 0.0024); bacterial richness and α-diversity were lower (P = 0.012 and 0.0061), and bacterial load higher (P = 0.004). Bb qPCR classes and culture results correlated with the abundance of Bb (r = 0.71, P < 0.001 and r = 0.70, P = 0.0022). Mc qPCR classes also correlated with the abundance of Mc (r = 0.73, P < 0.001). Bb infection induced lung dysbiosis, characterized by high bacterial load, low richness and diversity and increased abundance of Bb, compared with healthy dogs. Sequencing results highly correlate with qPCR and culture results showing that sequencing can be reliable to identify microorganisms involved in lung infectious diseases.

Bordetella pertussis

Pertussis is a highly infectious vaccine-preventable cough illness that continues to be a significant source of morbidity and mortality around the world. The majority of human illness is caused by Bordetella pertussis, and some is caused by Bordetella parapertussis. Bordetella is a Gram-negative, pleomorphic, aerobic coccobacillus. In the past several years, even countries with high immunization rates in early childhood have experienced rises in pertussis cases. Reasons for the resurgence of reported pertussis may include molecular changes in the organism and increased awareness and diagnostic capabilities, as well as lessened vaccine efficacy and waning immunity. The most morbidity and mortality with pertussis infection is seen in infants too young to benefit from immunization. Severe infection requiring hospitalization, including in an intensive care setting, is mostly seen in those under 3 months of age. As a result, research and public health actions have been aimed at better understanding and reducing the spread of Bordetella pertussis. Studies comparing the cost benefit of cocooning strategies versus immunization of pregnant women have been favorable towards immunizing pregnant women. This strategy is expected to prevent a larger number of pertussis cases, hospitalizations, and deaths in infants <1 year old while also being cost-effective. Studies have demonstrated that the source of infection in infants usually is a family member. Efforts to immunize children and adults, in particular pregnant women, need to remain strong.

Quantitative PCR and Cytology of Bronchoalveolar Lavage Fluid in Dogs with Bordetella bronchiseptica Infection

Background

The use of quantitative PCR (qPCR) for detection of Bordetella bronchiseptica in bronchoalveolar lavage fluid (BALF) and demonstration of bacteria adhering to ciliated epithelial cells in BALF or bronchial brushing fluid (BBF) has not been assessed in a series of affected dogs. Coinfections can worsen the clinical severity in bordetellosis, but the specific association with Mycoplasma cynos has not been evaluated.

Objectives

To assess the utility of culture, qPCR and cytologic examination of cytospin preparations in the diagnosis of bordetellosis in dogs and the influence of coinfection by M. cynos on disease severity.

Animals

Twenty‐four referred dogs with B. bronchiseptica infection and 10 healthy dogs.

Methods

Retrospective case series. qPCR (B. bronchiseptica and M. cynos) and culture results from BALF were recorded. Cytospin preparations from BALF and BBF were reviewed. qPCR on BALF from 10 healthy dogs were used as negative control.

Results

The BALF culture and qPCR detected B. bronchiseptica in 14/24 and 18/18 dogs, respectively. Coccobacilli were found adhering to ciliated epithelial cells in 20 of the 21 BALF cytologic preparations where epithelial cells were found, and 2/3 BBF cytologic preparations. Quantitative PCR detected a low level of B. bronchiseptica in one healthy dog. The frequency of detection of M. cynos was not significantly different in B. bronchiseptica (9/17 dogs) compared with healthy dogs (2/10 dogs) (P = .09).

Conclusion and Clinical Importance

Quantitative PCR detection of B. bronchiseptica in BALF appears to be a useful diagnostic tool. Cytologic examination of BALF or BBF, when positive, allows a rapid and reliable diagnosis.

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.

Detection of respiratory viruses and Bordetella bronchiseptica in dogs with acute respiratory tract infections

Canine infectious respiratory disease (CIRD) is an acute, highly contagious disease complex caused by a variety of infectious agents. At present, the role of viral and bacterial components as primary or secondary pathogens in CIRD is not fully understood. The aim of this study was to investigate the prevalence of canine parainfluenza virus (CPIV), canine adenovirus type 2 (CAV-2), canine influenza virus (CIV), canine respiratory coronavirus (CRCoV), canine herpes virus-1 (CHV-1), canine distemper virus (CDV) and Bordetella bronchiseptica in dogs with CIRD and to compare the data with findings in healthy dogs. Sixty-one dogs with CIRD and 90 clinically healthy dogs from Southern Germany were prospectively enrolled in this study. Nasal and pharyngeal swabs were collected from all dogs and were analysed for CPIV, CAV-2, CIV, CRCoV, CHV-1, CDV, and B. bronchiseptica by real-time PCR.

In dogs with acute respiratory signs, 37.7% tested positive for CPIV, 9.8% for CRCoV and 78.7% for B. bronchiseptica. Co-infections with more than one agent were detected in 47.9% of B. bronchiseptica-positive, 82.6% of CPIV-positive, and 100% of CRCoV-positive dogs. In clinically healthy dogs, 1.1% tested positive for CAV-2, 7.8% for CPIV and 45.6% for B. bronchiseptica. CPIV and B. bronchiseptica were detected significantly more often in dogs with CIRD than in clinically healthy dogs (P < 0.001 for each pathogen) and were the most common infectious agents in dogs with CIRD in Southern Germany. Mixed infections with several pathogens were common. In conclusion, clinically healthy dogs can carry respiratory pathogens and could act as sources of infection for susceptible dogs.

Performance of Bordetella pertussis IS481 real-time PCR in a vaccine trial setting

A real-time PCR method targeting the Bordetella pertussis IS481 gene fragment was evaluated in a vaccine trial setting in which real-time PCR results could be validated against culture and serology results. Two commonly used DNA extraction methods, Amplicor Respiratory Preparation kit and the QIAamp DNA Mini Kit, were compared. An approximately 50-fold higher sensitivity was achieved using the Amplicor kit. 89 of 276 aspirates analysed with the IS481 real-time PCR were positive. Interestingly, six of these were culture negative and came from serology-negative patients. Defining true positive cases either as culture-positive or as PCR-positive cases that had been confirmed with a serology-positive result or verified with a newly constructed recA PCR, the sensitivity and specificity of the IS481 real-time PCR were 89% and 98%, respectively. This study confirms the specificity and high diagnostic sensitivity of IS481-based PCR methods for diagnosis of B. pertussis.

Multitarget PCR for diagnosis of pertussis and its clinical implications

PCR has greatly facilitated pertussis diagnosis due to the speed, sensitivity, and specificity of this assay compared to other detection methods. Various single-target PCR assays are currently utilized, but none is universally considered to be the "gold standard." Our aim was to assess the use of multitarget versus single-target PCR for the diagnosis of pertussis in clinical samples. PCR assays targeting insertion sequence IS481 (IS), pertussis toxin ptxA promoter region (PT), and outer membrane porin (PO), or recA (RA) were evaluated in respiratory specimens collected from 4,442 patients with suspected pertussis. The diagnosis of pertussis was confirmed in 309 (6.96%) patients by the 3-target IS-PT-PO/RA PCR versus 247 (5.56%) by the conventional single-target IS (P=0.007). Compared to single-target IS, the three-target combination increased the proportion of positive specimens by 1.25-fold, and two-target combinations increased the proportion of positive specimens by 1.10- to 1.24-fold. In addition, nine cases of B. parapertussis infection were also confirmed by using the discriminative features of this multitarget PCR. Of the 89 culture-proven pertussis cases, 17 (19.1%) and 5 of the 16 patients (31.3%) admitted to intensive care unit would have been missed had only the single-target IS PCR been applied. Patients with mild disease (P=0.004) and shorter hospitalization (P=0.006) were less likely to have positive cultures. This consensus generating real-time PCR approach permits a sensitive detection, as well as an accurate species identification of the causative Bordetella pathogens for the timely management of patients.

Defining pertussis epidemiology: clinical, microbiologic and serologic perspectives

In the past decade, numerous sources have noted an increase in reported pertussis in highly immunized populations. This has been accompanied by a perceived change in disease epidemiology, characterized by a significant increase in reported pertussis incidence among adolescents and adults. In populations where children are routinely immunized, adolescents and adults now constitute the main source of infection in infants. However, a range of factors makes delineation of these epidemiologic trends difficult. Reported cases of pertussis represent only a fraction of the actual number of Bordetella pertussis symptomatic infections, because underconsulting, underrecognition and underdiagnosis are widespread and are a particular problem in adolescents and adults. Possible explanations for failure to diagnose pertussis include the heterogeneity in pertussis disease expression and low physician awareness and index of suspicion. Consequently defining pertussis from a clinical perspective is difficult, and this is reflected by a lack of consistency between case definitions. Although case definitions for specific circumstances have been established by the World Health Organization and the United States Centers for Disease Control, these are not universally useful, making intercountry comparisons and global evaluation difficult. Less-than-optimal and poorly performed laboratory tests, or their lack of availability, also make confirmation of B. pertussis infection difficult. To overcome these problems, clinical case definitions should be standardized for outbreak and endemic situations. Rapid, easy-to-use and inexpensive laboratory diagnostic techniques also must be made available and be widely implemented. In particular, polymerase chain reaction and single serum serology are 2 techniques that should be more widely adopted.

Molecular pathogenesis, epidemiology, and clinical manifestations of respiratory infections due to Bordetella pertussis and other Bordetella subspecies

Bordetella respiratory infections are common in people (B. pertussis) and in animals (B. bronchiseptica). During the last two decades, much has been learned about the virulence determinants, pathogenesis, and immunity of Bordetella. Clinically, the full spectrum of disease due to B. pertussis infection is now understood, and infections in adolescents and adults are recognized as the reservoir for cyclic outbreaks of disease. DTaP vaccines, which are less reactogenic than DTP vaccines, are now in general use in many developed countries, and it is expected that the expansion of their use to adolescents and adults will have a significant impact on reducing pertussis and perhaps decrease the circulation of B. pertussis. Future studies should seek to determine the cause of the unique cough which is associated with Bordetella respiratory infections. It is also hoped that data gathered from molecular Bordetella research will lead to a new generation of DTaP vaccines which provide greater efficacy than is provided by today's vaccines.

Differential detection of B. pertussis from B. parapertussis using a polymerase chain reaction (PCR) in presence of SYBR green1 and amplicon melting analysis

Nucleic acid (DNA) from control stock strains of B. pertussis and B. parapertussis (B. pertussis strain # 9797 and B. parapertussis strain # 15234 from ATCC) was amplified by polymerase chain reaction (PCR) targeting pertussis toxin (PT) promotor region, in presence of SYBR green1 a dye that fluoresces on binding specifically to double stranded DNA; and fluorescent melting profile of amplicon (amplified DNA) was studied. Amplicon of B. pertussis and B. parapertussis generated distinctly different melting bands with melting temperature (Tm) at 89.8 and 91.7 degrees C, respectively. Melting profile and Tm of each randomly selected isolates of B. pertussis and B. parapertussis was identical to that of respective control strains. Distinct difference in Tm between B. pertussis and B. parapertussis specific amplicons allowed differential detection of the two Bordetella species based on a single PCR product. The amplified product of serial diluted control stock of bacteria was analyzed by both agarose gel electrophoresis and melting profile analysis. The analytical sensitivity of detection (1-10 CFU equivalent in the tested volume) by melting profile and Tm analysis was in agreement with that obtained by agarose gel analysis.

Comparison of culture and PCR for detection of Bordetella pertussis and Bordetella parapertussis under routine laboratory conditions

A PCR assay for the detection of Bordetella pertussis and Bordetella parapertussis was compared with the conventional culture method under routine laboratory conditions. Detection of B. pertussis was based on the amplification of a section of the IS481 insertion sequence and confirmation of positive results was based on a sequence of the pertussis toxin promoter region. Detection of B. parapertussis was based on the amplification of a section of the IS1001 insertion sequence. An internal control was included. Data were available for the period 28 November 2000 to 9 July 2003. In this period, 3096 patients were examined for infection with B. pertussis and B. parapertussis by culture and PCR on the same day. B. pertussis was found in 496 (16 %) patients; 208 (42 %) were diagnosed by PCR alone whereas 17 (3 %) were diagnosed by culture alone. B. parapertussis was found in 64 (2 %) patients. The sensitivity of the PCR was 97 % and of culture 58 %. The specificity of PCR was 93 % when regarding culture as 100 % sensitive. There was a significant relationship between laboratory method and age, as the superiority of PCR was most marked in the age group 0.5-3 years. The PCR assay proved highly sensitive for the diagnosis of pertussis. The specificity estimate of the PCR assay suffers from the influence of a gold-standard method with a low sensitivity. The PCR assay is considered highly specific due to the amplification of two different sequences in two separate assays.

Bordetella bronchiseptica infection in pediatric lung transplant recipients

Bordetella bronchiseptica are small, pleomorphic Gram-negative coccobacilli which are commensal organisms in the upper respiratory tract of many wild and domestic animals ('kennel cough' in dogs). While it is common for health care providers to ask about exposure to ill family/friends, most do not routinely inquire about the health or immunization status of household pets. We report two cases of B. bronchiseptica pneumonia in lung transplant recipients [cystic fibrosis (CF); ages 10 and 15 yr; one male] who contracted B. bronchiseptica from pet dogs. We compared their course and outcome to four children (two CF, one congenital heart disease and one Duchenne's muscular dystrophy; four males, age range 6 months to 14 yr) with B. bronchiseptica cultured from the respiratory tract. Two of the four patients also acquired their illnesses from pet dogs and two from unknown sources. One lung transplant recipient expired from progressive respiratory failure. We conclude that B. bronchiseptica can cause serious infections in both immunosuppressed and immunocompetent children. We speculate that a detailed history of exposure to ill pets (particularly dogs), and the immunization status of all pets should be included in the routine evaluation of all pediatric transplant recipients.

Issues associated with and recommendations for using PCR to detect outbreaks of pertussis

Two outbreaks of respiratory tract illness associated with prolonged cough occurring in 1998 and 1999 in New York State were investigated. A PCR test for Bordetella pertussis was primarily used by a private laboratory to confirm 680 pertussis cases. Several clinical specimens had positive culture results for B. pertussis during both outbreaks, which confirmed that B. pertussis was circulating during the outbreaks. However, testing by the New York State Department of Health reference laboratory suggested that some of the PCR results may have been falsely positive. In addition, features of the outbreak that suggested that B. pertussis may not have been the primary agent of infection included a low attack rate among incompletely vaccinated children and a significant amount of illness among patients testing PCR negative for B. pertussis. These investigations highlight the importance of appropriate clinical laboratory quality assurance programs, of the limitations of the PCR test, and of interpreting laboratory results in context of clinical disease.

Tetanus toxin fragment C-specific priming by intranasal infection with recombinant Bordetella pertussis

As an alternative to parenteral administration, mucosal administration offers several advantages including the ease of administration, safety and the ability to induce mucosal immunity. As a first step towards nasal administration of important childhood vaccines, we have previously developed attenuated Bordetella pertussis strains able to protect mice against pertussis upon nasal vaccination. Since pertussis vaccines are generally combined with tetanus and diphtheria vaccines, we constructed recombinant B. pertussis strains producing the non-toxic protective tetanus toxin fragment C (TTFC). TTFC was genetically fused to the N-terminal domain of the B. pertussis filamentous haemagglutinin. The hybrid gene was introduced into B. pertussis both on a multi-copy replicative plasmid and as a single copy inserted into the chromosome of a pertussis toxin-producing strain and a toxin-deficient attenuated strain. The hybrid protein was secreted by the recombinant strains. However, the recombinant multi-copy plasmid was unstable in vivo, and immunisation could only be carried out with the strains containing the single-copy chromosomal integration. Both the toxin-producing and the toxin-deficient recombinant B. pertussis strains were able to prime mice for the production of anti-TTFC serum antibodies upon intranasal administration, suggesting the feasibility of using recombinant attenuated B. pertussis for the development of combined childhood vaccines.

Clinical validation of a polymerase chain reaction assay for the diagnosis of pertussis by comparison with serology, culture, and symptoms during a large pertussis vaccine efficacy trial

OBJECTIVE

To assess the diagnostic sensitivity and specificity of a Bordetella pertussis polymerase chain reaction (PCR) assay using nasopharyngeal (NP) specimens from subjects with cough illnesses participating in a large pertussis vaccine efficacy trial.

DESIGN

From 1991 to 1994, we conducted a large pertussis vaccine efficacy trial in Germany to determine the efficacy of the Lederle/Takeda acellular pertussis component diphtheria-tetanus toxoids in comparison with the Lederle whole-cell component diphtheria-tetanus toxoids vaccine. In the final year of the follow-up period of this trial, a second NP specimen for PCR, in addition to a culture specimen and blood for specific serology (enzyme-linked immunosorbent assay), was collected by use of a Dacron swab in subjects or family members with cough illnesses >/=7 days duration or in subjects with exposure to a cough illness in a household member to establish a diagnosis of B pertussis infection. Oligonucleotide primers (pTp1 and pTp2) that amplify a 191-bp-sized DNA fragment from the pertussis toxin operon, which is specific for B pertussis, were used. The PCR-amplified products were visualized by dot blot analysis followed by hybridization with a digoxigenin labeled probe and rated as 1+, 2+, or 3+ in comparison with positive controls representing approximately 1 to 10, 11 to 50, and >50 B pertussis organisms, respectively. In the present analysis, we compare PCR findings with those of serology, culture, positive household contact, and clinical characteristics of cough illnesses.

RESULTS

Of 392 subjects with NP specimens obtained for PCR, 376 also had NP specimens collected for culture and 282 had serum specimens. PCR and culture were positive in 86 (22%) and 23 (6%) subjects, respectively. Of the positive PCR specimens, 40 were rated 3+, 32 were rated 2+, and 14 were rated 1+; 3+ positive specimens were more prevalent among DT recipients compared with pertussis vaccine recipients. Illnesses in subjects with 3+ positive PCR results were more typical of pertussis than were those in subjects with 2+ and 1+ positive results with a mean duration of cough of 48 days versus 43 and 42 days, respectively; presence of paroxysms, whoop or vomiting in 38% versus 17% and 10%, respectively; and a clinical diagnosis of definite or probable pertussis by the investigators of 26% versus 7% and 4%, respectively. Using serologic evidence of infection as the standard, sensitivity of PCR was 61%, and specificity was 88%. For 3+ positive PCR results, the respective values were 42% and 97%.

CONCLUSION

Our findings demonstrate that PCR is more sensitive than conventional culture for the diagnosis of pertussis. They also demonstrate a high specificity of PCR when serology with or without other confirmative criteria (culture and household contact) is used as the reference. Analysis of semiquantitative PCR results revealed that subjects with a 3+ PCR more frequently experienced typical illness compared with patients with 1+ or 2+ PCR. Although specific serologic study remains a necessity in pertussis research its modification for diagnosis in the clinical setting results in low sensitivity and specificity. Therefore, because PCR is more sensitive than culture and is easy to perform, it is a useful addition in the clinical setting.

Polymorphism in the pertussis toxin promoter region affecting the DNA-based diagnosis of Bordetella infection

The pertussis toxin (PT) promoter region is a frequently used target for DNA-based diagnosis of pertussis and parapertussis infections. The reported polymorphism in this region has also allowed discrimination of species in mixtures with several Bordetella species by their specific PCR amplicon restriction patterns. In the present study, we investigated the degree of polymorphism in order to confirm the reliability of the assay. Five different sequence types of the amplified 239- or 249-bp region were found among the 33 Bordetella pertussis, B. parapertussis, and B. bronchiseptica American Type Culture Collection reference strains and patient isolates analyzed. According to the sequences that were obtained and according to the PT promoter sequences already available in the databases, restriction enzyme analysis with TaqI, BglI, and HaeII, which gave four different patterns, can be performed to reliably identify B. pertussis, B. parapertussis, and B. bronchiseptica.

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.

Detection of Bordetella bronchiseptica by the polymerase chain reaction

Polymerase chain reaction (PCR) assays were developed that enabled not only discriminative detection of three Bordetella species, B. pertussis, B. parapertussis, and B. bronchiseptica (Bspp PCR), but also specific detection of B. bronchiseptica (Bb PCR). An upstream sequence of the flagellin gene was used as a target DNA region. This sequence contained differences in B. pertussis, B. parapertussis, and B. bronchiseptica DNA. These species could then be differentiated using two different sets of primers, Bspp and Bb. When oligonucleotide Bspp primers were used, PCR products were obtained from the three species of Bordetella. A fragment of the expected size (164 bp) was amplified using B. bronchiseptica and B. parapertussis DNA, but a fragment with a distinct molecular weight was amplified with B. pertussis DNA (195 bp). This Bspp PCR was specific and sensitive, but it could not differentiate between B. parapertussis and B. bronchiseptica. When Bb primers were used, a 237-bp PCR product was detected only from B. bronchiseptica DNA. No PCR products were identified after Bb PCR amplification of DNAs either from B. parapertussis isolates or B. pertussis isolates, nor from other respiratory pathogen DNAs tested. This second PCR assay had a sensitivity limit of less than 10 organisms of B. bronchiseptica after detection with a specific probe. The specificity and the sensitivity of the fla PCR assay were evaluated with purified DNA, as was its capacity for detecting the bacteria in human clinical samples and in lungs of infected mice.

Simultaneous amplification of Bordetella repeated insertion sequences and toxin promoter region gene by polymerase chain reaction

A polymerase chain reaction was devised to simultaneously detect repeated insertion sequences and the pertussis toxin promoter gene for the diagnostic identification of Bordetella pertussis, B. parapertussis, and B. bronchiseptica. The sensitivity of this method was sufficient to detect one B. pertussis organism using the following cycles and temperatures: 95 degrees C for 15 min, followed by 32 amplification cycles (1 min at 95 degrees C, 1 min at 66 degrees C, 1 min at 72 degrees C), and finally 5 min at 72 degrees C. Using the primers as a combined set did not affect sensitivity, but required an increased temperature for optimal annealing compared with a single-sequence assay. As nasopharyngeal aspirate and swab materials sometimes contain hemoglobin, we also tested the inhibitory effect of hemoglobin on this assay, which was inhibited completely when using DNA extracts from samples containing hemoglobin at a final concentration >0.015 g/L: this inhibition was reversed by addition of bovine serum albumin to the buffer. Our assay shows promising sensitivity and specificity for clinical use.

The rationale and method for constructing internal control DNA used in pertussis polymerase chain reaction

The inclusion of an appropriate internal control DNA in polymerase chain reaction (PCR) is a rapid and simple method for the detection of PCR failure. Two PCR coamplification internal control DNAs (ICD I and ICD II) with the same primer-binding sequences as the target DNA for the detection of Bordetella pertussis and Bordetella parapertussis were produced using an overlap extension technique and a PCR MIMIC construction kit, respectively. The ICD II was further evaluated in a prospective clinical study in 360 patients with a clinical diagnosis of pertussis. From 360 nasopharyngeal swabs the internal control was positive in 318 (88%) samples, but was negative in 42 (12%). After phenol-chloroform extraction an additional 10 internal controls became positive. For the detection of PCR failure, the use of internal control DNA is highly recommended for PCR-based identification of B. pertussis and B. parapertussis organisms from nasopharyngeal swabs and aspirates.

Polymerase chain reaction (PCR) compared with conventional identification in culture for detection of Bordetella pertussis in 7153 children

OBJECTIVE: To compare the polymerase chain reaction (PCR) results with conventional culture results for the diagnosis of Bordetella pertussis infections. METHODS: PCR and culture were performed in the course of a large vaccine efficacy trial in Germany on specimens taken from 7153 children less-than-or-equal2 years of age with cough illness lasting >6 days, and laboratory results were compared with clinical data also obtained from the patients. Calcium alginate nasopharyngeal swabs were taken for culture and clinical data were obtained from patients. Swabs were inoculated on charcoal horse blood agar plates containing cephalexin, and then discarded. The agar plates were preincubated for 2 days at the physician's office and then shipped to the culture laboratory at the University Children's Hospital in Munich, Germany, for diagnosis of B. pertussis and B. parapertussis infections. In this laboratory, Dacron swabs for PCR were taken from each culture by a wide sweep over the culture. Swabs for PCR were stored in NaCl and sent weekly to the PCR laboratory at the University Children's Hospital in Basel, Switzerland, for PCR diagnosis of B. pertussis infections. RESULTS: B. pertussis was identified by culture in 3% (213/7153) and by PCR in 7.6% (546/7153) of the specimens. Therefore, PCR increased the identification rate of subjects with B. pertussis infection 2.6-fold. Clinical characteristics were considered according to the type of laboratory findings: group 1 consisted of 209 culture-positive and PCR-positive subjects, and group 2 of 337 culture-negative but PCR-positive subjects. Group 2 subjects were significantly more likely to have mild or atypical clinical symptoms of whooping cough than were group 1 subjects. By analyzing the PCR results of group 2 subjects semiquantitatively, it could be shown that the degree of PCR positivity correlated with the severity of the clinical symptoms of whooping cough in the patient. CONCLUSIONS: PCR identified many pertussis cases with mild or atypical clinical symptoms that were not identified by culture. Semiquantification of PCR products revealed that the less positive the PCR result, the higher was the failure rate in diagnosing pertussis by culture, and, in addition, the less typical were the clinical symptoms in the patient.

Detection of Bordetella pertussis in clinical specimens by PCR and a microtiter plate-based DNA hybridization assay

In order to improve detection of Bordetella pertussis in nasopharyngeal aspirates (NPAs) in our laboratory, a PCR-based assay was optimized, and a study was designed (i) to compare results obtained by PCR to those obtained by culture and (ii) to evaluate a novel microtiter plate-based DNA hybridization assay (PCR-plate) by comparing it to agarose gel electrophoresis (PCR-gel) for detection of the PCR product. DNA for the PCR was extracted with a guanidine thiocyanate buffer and used in a PCR mixture containing primers directed against a reiterated gene sequence in B. pertussis (Q. He, J. Mertsola, H. Soini, M. Skurnik, O. Ruuskanen, and M. K. Viljanen, J. Clin, Microbiol. 31:642-645, 1993). Of 96 NPAs submitted from a targeted study group, 23 were positive by culture, 27 were positive by PCR-gel, and 31 were positive by PCR-plate. All culture-positive specimens were also positive by PCR. Of nine patients with culture-negative-PCR-positive results, six had discharge diagnoses of pertussis. Thus, PCR with plate-based product detection is a sensitive method for the laboratory detection of B. pertussis in NPAs. Additional advantages of the plate assay include rapidity, objectivity in reading results, specificity, and the capability of being adapted to a high-volume, automated system.

Direct PCR analysis for toxigenic Pasteurella multocida

A more rapid, accurate method to detect toxigenic Pasteurella multocida is needed for improved clinical diagnosis, farm biosecurity, and epidemiological studies. Toxigenic and nontoxigenic P. multocida isolates cannot be differentiated by morphology or standard biochemical reactions. The feasibility of using PCR for accurate, rapid detection of toxigenic P. multocida from swabs was investigated. A PCR protocol which results in amplification of an 846-nucleotide segment of the toxA gene was developed. The PCR amplification protocol is specific for toxigenic P. multocida and can detect fewer than 100 bacteria. There was concordance of PCR results with (i) detection of toxA gene with colony blot hybridization, (ii) detection of ToxA protein with colony immunoblot analysis, and (iii) lethal toxicity of sonicate in mice in a test set of 40 swine diagnostic isolates. Results of an enzyme-linked immunosorbent assay for ToxA agreed with the other assays except for a negative reaction in one of the 19 isolates that the other assays identified as toxigenic. In addition to accuracy, as required for a rapid direct specimen assay, toxigenic P. multocida was recovered efficiently from inoculated swabs without inhibition of the PCR. The results show that PCR detection of toxigenic P. multocida directly from clinical swab specimens should be feasible.

Detection of Bordetella pertussis by rapid-cycle PCR and colorimetric microwell hybridization

The use of rapid-cycle PCR combined with colorimetric microwell hybridization for detecting Bordetella pertussis was investigated. Rapid cycling was performed with an air thermocycler (model 1605; Idaho Technology, Idaho Falls, Idaho). Although the instrument was originally designed to be used with capillary tubes, an adapter that allows this instrument to be used with PCR tubes has recently been introduced. Because of the low heat capacity of air, the thermocycler has rapid transition rates between temperatures. The combination of a rapid temperature transition rate, small sample volume (10 microliters), and overshooting or undershooting of the temperature set points allowed the cycles to be reduced to 5 s for denaturation and 10 s for extension and annealing. Thus, the amplification could be completed in a total of approximately 35 min. Amplified DNA was detected with biotin-labeled primers and by hybridization to a capture probe immobilized in microwell plates. When simulated clinical specimens consisting of pooled nasopharyngeal washes with known numbers of B. pertussis organisms were examined by this procedure, as little as one organism per 5 microliters of sample could be detected. Six nasopharyngeal aspirates or washes from culture-positive patients were positive by PCR, as were two of seven specimens obtained from patients that were negative by culture and direct fluorescent-antibody assay. The two patients who were PCR positive but culture and direct fluorescent-antibody assay negative had clinical disease compatible with pertussis. This method appears to be a sensitive, convenient means of detecting B. pertussis in clinical specimens. The total time required for specimen processing, amplification, and detection is about 2.5 h.

Immunomagnetic separation and solid-phase detection of Bordetella pertussis

In the present study, novel solid-phase methods were used for both sample preparation and PCR detection of Bordetella pertussis. The sample preparation was performed by immunomagnetic separation with paramagnetic beads coated with polyclonal antibodies directed toward the surface antigens of the bacteria. The precoated immunobeads were directly used on nasopharyngeal aspirates to capture the bacteria on the solid support and were subsequently transferred to the PCR tube with no further manipulations. The region encompassing the pertussis toxin promoter was analyzed to allow direct discrimination between the three major Bordetella species (B. pertussis, B. parapertussis, and B. bronchiseptica). The resulting amplicons were captured on a second magnetic solid phase, allowing detection and restriction analysis of the target sequence. A colorimetric detection system based on a DNA binding fusion protein enabled the use of standardized enzyme-linked immunosorbent format tests both for the detection of Bordetella spp. and for species evaluation. When the optimized system was evaluated on 55 clinical aspirate samples, 21 of 22 (95%) culture-positive samples were positive by the system that we developed. In addition, two samples were positive by the PCR-based assay, while the culture assay was negative. The implications of these results are discussed.

Validation of nested Bordetella PCR in pertussis vaccine trial

A nested PCR, using a 239-bp sequence in the pertussis toxin promoter region, was developed and evaluated. The assay differentiates Bordetella pertussis, Bordetella parapertussis, and Bordetella bronchiseptica by restriction enzyme analysis of the amplified fragments. The diagnostic performance of the PCR was evaluated in a Swedish pertussis vaccine efficacy trial which took place from 1992 to 1995, including study children and household members and using culture and serology for laboratory confirmation of suspected cases. In total 2,421 nasopharyngeal aspirates were analyzed. The total diagnostic sensitivity for B. pertussis was 90.2% (194 of 215). During the study period samples were processed with and without the cation-exchange resin Chelex. The PCR diagnostic sensitivity for B. pertussis among the Chelex-treated aspirates was 94.9% (75 of 79), and that for B. pertussis among 124 aspirates in a consecutive non-Chelex-treated material was 89.5% (111 of 124). After Chelex treatment of the 13 PCR-negative samples, an additional six became PCR positive, giving a final sensitivity of 94.3%. In addition, PCR was positive for B. pertussis with 57 of 1,744 samples negative by culture but with available serological data. The specificity of PCR with these samples was supported by a significant increase in antibody levels between acute and convalescent sera in 45 cases and by epidemiological or clinical data in all but two of the remaining cases. PCR was also positive for B. pertussis with 26 of 415 aspirates from episodes lacking serology. The diagnostic sensitivity of PCR for B. parapertussis was 74.0% (37 of 50). There were an additional seven culture-negative B. parapertussis PCR findings, six from cases with significant antibody increases against filamentous hemagglutinin only and one from a case lacking serology. There were no samples positive for B. bronchiseptica. In conclusion, PCR detection of B. pertussis and/or B. parapertussis enabled us to identify 90 positive nasopharyngeal aspirates, in addition to the 262 culture-positive samples (an increase of 34%). Relating these cases to serology and clinical data indicated a PCR specificity approaching 100%.

Polymerase chain reaction for the identification of Bordetella pertussis and Bordetella parapertussis

The polymerase chain reaction (PCR) for the detection of Bordetella pertussis and Bordetella parapertussis DNA in clinical samples was well documented by recent studies. Different regions in Bordetella pertussis DNA have been successfully used as targets for this method by various authors. In this work we report the usefulness of the PCR assay also for speciating Bordetellae isolates in those cases where the biochemical and serological tests gave inconclusive results.

A controlled trial of a two-component acellular, a five-component acellular, and a whole-cell pertussis vaccine

BACKGROUND

Because of concern about safety and efficacy, no pertussis vaccine has been included in the vaccination program in Sweden since 1979. To provide data that might permit the reintroduction of a pertussis vaccine, we conducted a placebo-controlled trial of two acellular and one whole-cell pertussis vaccines.

METHODS

After informed consent was obtained, 9829 children born in 1992 were randomly assigned to receive one of four vaccines: a two-component acellular diphtheria-tetanus-pertussis (DTP) vaccine (2566 children), a five-component acellular DTP vaccine (2587 children), a whole-cell DTP vaccine licensed in the United States (2102 children), or (as a control) a vaccine containing diphtheria and tetanus toxoids (DT) alone (2574 children). The vaccines were given at 2, 4, and 6 months of age, and the children were then followed for signs of pertussis for an additional 2 years (to a mean age of 21/2 years).

RESULTS

The whole-cell vaccine was associated with significantly higher rates of protracted crying, cyanosis, fever, and local reactions than the other three vaccines. The rates of adverse events were similar for the acellular vaccines and the control DT vaccine. After three doses, the efficacy of the vaccines with respect to pertussis linked to a laboratory-confirmed case of pertussis or contact with an infected household member with paroxysmal cough for > or = 21 days was 58.9 percent for the two-component vaccine (95 percent confidence interval, 50.9 to 65.9 percent), 85.2 percent for the five-component vaccine (95 percent confidence interval, 80.6 to 88.8 percent), and 48.3 percent for the whole-cell vaccine (95 percent confidence interval, 37.0 to 57.6 percent).

CONCLUSIONS

The five-component acellular pertussis vaccine we evaluated can be recommended for general use, since it has a favorable safety profile and confers sustained protection against pertussis. The two-component acellular vaccine and the whole-cell vaccine were less efficacious.

Nonradioactive colony lift-hybridization assay for detection of Bordetella bronchiseptica infection in swine

Current methods for the isolation and identification of Bordetella bronchiseptica from clinical samples are time-consuming and are based, in part, on subjective observations. We describe the use of a Bordetella-specific DNA probe in a nonradioactive colony lift-hybridization assay for the identification of B. bronchiseptica. Eleven of 82 clinical specimens were found to contain B. bronchiseptica by this method, while only 5 of these were reported to contain the organism when the specimens were analyzed by traditional methods. The chromosomal fragment containing a sequence complementary to the probe appeared to be conserved in B. bronchiseptica isolates from swine from a variety of sources. The assay is more rapid than culture and biochemical testing since it can be performed directly on primary culture plates, even when they are heavily contaminated with other bacterial species. Only minimal training is required to accomplish the assay successfully, and the results are easy to interpret.

A competitive polymerase chain reaction assay for reliable identification of Bordetella pertussis in nasopharyngeal swabs

In order to optimize the identification of clinically relevant quantities of Bordetella pertussis in nasopharyngeal swabs, an automated assay introducing competitive polymerase chain reaction was established. A 183 base pair DNA fragment from a repetitive region of the Bordetella pertussis genome was amplified in a polymerase chain reaction. An internal control DNA with nine base substitutions was coamplified in the same reaction. The differentiation between the amplified B. pertussis DNA and the internal control was based on hybridisation against two different probes using Enzymun Test DNA Detection (Boehringer Mannheim). Nasopharyngeal swabs from serologically positive patients, clinically diagnosed with whooping cough, serologically negative patients after contact with B. pertussis and a negative group were compared. The advantages of competitive PCR are a reduced risk of false-positive and false-negative results and the possibility to differentiate between the different PCR positive groups.

Applications of DNA amplification techniques in veterinary diagnostics

An overview of the principles of the polymerase chain reaction, ligase chain reaction, self-sustained sequence replication and Q beta replicase is given. The application of these methods for the diagnosis of veterinary infectious and hereditary diseases as well as for other diagnostic purposes is discussed and comprehensive tables of reported assays are provided. Specific areas where these DNA-based amplification methods provide substantial advantages over traditional approaches are also highlighted. With regard to PCR-based assays for the detection of viral pathogens, this article is an update of a previous review by Belák and Ballagi-Pordány (1993).

Nested PCR optimized for detection of Bordetella pertussis in clinical nasopharyngeal samples

Several genes and sequences in Bordetella pertussis have been used as targets in diagnostic PCR assays. A previously developed single-step PCR assay for the detection of B. pertussis was based on an insertion sequence, IS480, that is present in about 70 to 80 copies in each genome. The diagnostic sensitivity, specificity, and reliability of this assay with aspirated and heat-treated samples from the nasopharynx of patients and their contacts was improved by the use of a nested PCR configuration. The nested PCR assay produced a 205-bp fragment with all of the 115 B. pertussis strains tested and was negative with all strains belonging to other Bordetella species (n = 44) as well as other bacteria commonly found in the upper respiratory tract (n = 115). The diagnostic value of the assay was verified by giving positive results for B. pertussis in all the 51 nasopharyngeal aspirates from culture-positive patients. The assay also detected 18 positive aspirates from a total of 196 culture-negative patients. A confirmatory cleavage of the 205-bp nested PCR product by MvaI gave in all cases two bands of 88 and 117 bp. In conclusion, this newly developed nested PCR assay was shown to be reasonably fast and uncomplicated, with an optimal sensitivity and a high degree of specificity for the diagnosis of B. pertussis in aspirated nasopharyngeal samples processed simply by heat treatment. The detection level in the nested PCR was about 10 bacteria per ml, or seven to eight insertion sequence copies per 10 microliters of boiled sample.