Development of real-time PCR assay for differential detection of Bordetella bronchiseptica and Bordetella parapertussis

Transient reemergence of Bordetella parapertussis in France in 2022

Between March and October 2022, a peak of detection of Bordetella parapertussis by qPCR, real-time PCR was observed in France.Hypothesis/Gap Statement. Whether this peak was due to resurgence from previous circulating lineages or reintroduction into the country was unknown.Objective. The objective of this study is to understand B. parapertussis-transient increase observed in France in 2022 whereas it had virtually stopped being reported since the start of the COVID-19 pandemic in 2020.Methods. We analysed real-time PCR (qPCR) data from the two largest French outpatient laboratories performing whooping cough diagnosis and characterized all B. parapertussis isolates collected in the 2016-2022 period by the French National Reference Centre for Whooping Cough.Results. Microbiological analyses reveal that 13 of 18 bacterial isolates collected in 2022 produce the vaccine antigen pertactin, whereas none of the 22 isolates collected in the 2016-2021 period did.Conclusion. We hypothesize a re-introduction of B. parapertussis from regions of the world where whole-cell vaccines are still in use.

Development and validation of multiplex one-step qPCR/RT-qPCR assays for simultaneous detection of SARS-CoV-2 and pathogens associated with feline respiratory disease complex

Feline respiratory disease complex (FRDC) is caused by a wide range of viral and bacterial pathogens. Both Influenza A virus (IAV) and Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) also induce respiratory diseases in cats. Two one-step multiplex qPCR/RT-qPCR assays were developed and validated: FRA_1 (Feline respiratory assay 1) for the detection of four viral targets and FRA_2 for the detection of three bacteria associated with FRDC. Both multiplex assays demonstrated high specificity, efficiency (93.51%-107.8%), linearity (> 0.998), analytical sensitivity (≤ 15 genome copies/μl), repeatability (coefficient of variation [CV] < 5%), and reproducibility (CV < 6%). Among the 63 clinical specimens collected from FRDC-suspected cats, 92.1% were positive for at least one pathogen and co-infection was detected in 57.1% of samples. Mycoplasma felis (61.9%) was the most found pathogen, followed by feline herpesvirus-1 (30.2%), Chlamydia felis (28.7%) and feline calicivirus (27.0%). SARS-CoV-2 was detected in two specimens. In summary, this new panel of qPCR/RT-qPCR assays constitutes a useful and reliable tool for the rapid detection of SARS-CoV-2 and viral and bacterial pathogens associated with FRDC in cats.

Development and Validation of a Panel of One-Step Four-Plex qPCR/RT-qPCR Assays for Simultaneous Detection of SARS-CoV-2 and Other Pathogens Associated with Canine Infectious Respiratory Disease Complex

Canine infectious respiratory disease complex (CIRDC) is the primary cause of respiratory disease in the canine population and is caused by a wide array of viruses and bacterial pathogens with coinfections being common. Since its recognition in late 2019, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been reported to cause respiratory disease in dogs. Therefore, the rapid detection and differentiation of SARS-CoV-2 from other common viral and bacterial agents is critical from a public health standpoint. Here, we developed and validated a panel of four one-step multiplex qPCR/RT-qPCR assays for the detection and identification of twelve pathogens associated with CIRDC (canine adenovirus-2, canine distemper virus, canine herpesvirus-1, canine influenza A virus, canine parainfluenza virus, canine pneumovirus, canine respiratory coronavirus, SARS-CoV-2, Bordetella bronchiseptica, Streptococcus equi subsp. zooepidemicus, Mycoplasma cynos, and M. canis), as well as the identification of three main CIV subtypes (i.e., H3N2, H3N8, and H1N1). All developed assays demonstrated high specificity and analytical sensitivity. This panel was used to test clinical specimens (n = 76) from CIRDC-suspected dogs. M. canis, M. cynos, and CRCoV were the most frequently identified pathogens (30.3%, 25.0%, and 19.7% of samples, respectively). The newly emerging pathogens CPnV and SARS-CoV-2 were detected in 5.3% of samples and coinfections were identified in 30.3%. This new multiplex qPCR/RT-qPCR panel is the most comprehensive panel developed thus far for identifying CIRDC pathogens, along with SARS-CoV-2.

Are Bordetella bronchiseptica Siphoviruses (Genus Vojvodinavirus) Appropriate for Phage Therapy-Bacterial Allies or Foes?

Bordetella bronchiseptica is a respiratory animal pathogen that shows growing resistance to commonly used antibiotics, which has necessitated the examination of new antimicrobials, including bacteriophages. In this study, we examined the previously isolated and partially characterized B. bronchiseptica siphoviruses of the genus Vojvodinavirus (LK3, CN1, CN2, FP1 and MW2) for their ability to inhibit bacterial growth and biofilm, and we examined other therapeutically important properties through genomic analysis and lysogeny experiments. The phages inhibited bacterial growth at a low multiplicity of infection (MOI = 0.001) of up to 85% and at MOI = 1 for >99%. Similarly, depending on the phages and MOIs, biofilm formation inhibition ranged from 65 to 95%. The removal of biofilm by the phages was less efficient but still considerably high (40–75%). Complete genomic sequencing of Bordetella phage LK3 (59,831 bp; G + C 64.01%; 79 ORFs) showed integrase and repressor protein presence, indicating phage potential to lysogenize bacteria. Lysogeny experiments confirmed the presence of phage DNA in bacterial DNA upon infection using PCR, which showed that the LK3 phage forms more or less stable lysogens depending on the bacterial host. Bacterial infection with the LK3 phage enhanced biofilm production, sheep blood hemolysis, flagellar motility, and beta-lactam resistance. The examined phages showed considerable anti-B. bronchiseptica activity, but they are inappropriate for therapy because of their temperate nature and lysogenic conversion of the host bacterium.

Comparison of oral, nebulized and combination antibiotic treatment of Bordetella bronchiseptica in baboons (Papio spp.)

Incidence of Bordetella pertussis, the causative agent of whooping cough, is rising in some global human populations despite high vaccination rates, and significant research is underway to address the issue. Baboons are an established model for pertussis research, but like many mammals, they can be naturally infected with Bordetella bronchiseptica. Because B. bronchiseptica interferes with B. pertussis research, it must be excluded from baboons under consideration for enrollment in pertussis studies. In addition to research-related concerns, B. bronchiseptica can sometimes cause clinical disease in baboons and other nonhuman primates. This study examined the use of antibiotics to clear B. bronchiseptica in naturally infected baboons. Thirty-five juvenile baboons were divided into five treatment groups: oral sulfamethoxazole/trimethoprim (TMS), nebulized gentamicin (gentamicin), combination (TMS + gentamicin) in positive animals, combination (TMS + gentamicin) as a prophylactic in exposed animals and no treatment (control). Combination of oral TMS and nebulized gentamicin given to positive animals was most effective, producing long-term clearance in 11 out of 12 treated animals. To avoid unnecessary use of antibiotics, our primary management strategy is screening and separating to allow natural clearance and limiting exposure to non-infected animals, but this study investigates an antibiotic regimen that could be used in special circumstances.

Molecular detection of canine respiratory pathogens between 2017 and 2018 in Japan

A molecular survey was conducted to understand recent distribution of pathogens associated with canine infectious respiratory disease (CIRD) in Japan. Nasal and/or pharyngeal swabs were collected from asymptomatic dogs and those with CIRD, living in private house or in kennels. PCR-based examination was conducted for detecting nine pathogens. Among private household dogs, 50.8% with CIRD, 11.1% with respiratory disease other than CIRD, and 4.3% asymptomatic were positive for more than one pathogen, whereas in kennel-housed dogs, 42.9% with CIRD and 27.3% asymptomatic were positive. Bordetella bronchiseptica was most frequently detected, followed by canine herpesvirus 1, canine parainfluenza virus, canine pneumovirus, Mycoplasma cynos, and canine adenovirus type 2. In kennel environment, asymptomatic dogs might act as reservoirs carrying the respiratory pathogens.

Development of a one-run real-time PCR detection system for pathogens associated with porcine respiratory diseases

The etiology of Porcine respiratory disease complex is complicated by infections with multiple pathogens, and multiple infections increase the difficulty in identifying the causal pathogen. In this present study, we developed a detection system of microbes from porcine respiratory by using TaqMan real-time PCR (referred to as Dempo-PCR) to screen a broad range of pathogens associated with porcine respiratory diseases in a single run. We selected 17 porcine respiratory pathogens (Actinobacillus pleuropneumoniae, Boldetella bronchiseptica, Haemophilus parasuis, Pasteurella multocida, Pasteurella multocida toxin, Streptococcus suis, Mycoplasma hyopneumoniae, Mycoplasma hyorhinis, Mycoplasma hyosynovie, porcine circovirus 2, pseudorabies virus, porcine cytomegalovirus, swine influenza A virus, porcine reproductive and respiratory virus US strain, EU strain, porcine respiratory coronavirus and porcine hemagglutinating encephalomyelitis virus) as detection targets and designed novel specific primer-probe sets for seven of them. In sensitivity test by using standard curves from synthesized DNA, all primer-probe sets showed high sensitivity. However, porcine reproductive and respiratory virus is known to have a high frequency of genetic mutations, and the primer and probe sequences will need to be checked at a considerable frequency when performing Dempo-PCR from field samples. A total of 30 lung samples from swine showing respiratory symptoms on six farms were tested by the Dempo-PCR to validate the assay’s clinical performance. As the results, 12 pathogens (5 virus and 7 bacteria) were detected and porcine reproductive and respiratory virus US strain, Mycoplasma hyorhinis, Haemophilus parasuis, and porcine cytomegalovirus were detected at high frequency. These results suggest that Dempo-PCR assay can be applied as a screening system with wide detection targets.

Development and application of two multiplex real-time PCR assays for detection and speciation of bacterial pathogens in the koala

Infectious diseases have contributed to the decline in the health of koala ( Phascolarctos cinereus) populations in the wild in some regions of Australia. Herein we report the development and validation of 2 multiplex real-time PCR (rtPCR) panels for the simultaneous detection of Mycoplasma spp., Ureaplasma spp., Bordetella bronchiseptica, and Chlamydia, including speciation and quantification of Chlamydia, in ocular, reproductive, and nasal swab samples in addition to semen and male urogenital and reproductive tissues, from koalas. Each rtPCR panel was developed for use as a single-tube reaction using pathogen-specific primers and fluorescently labeled probe sets. DNA extracted from reference strains and isolates was used for validation of sequence gene targets for the multiplex rtPCR panels. Each panel was shown to be sensitive and specific in detecting and differentiating the bacterial pathogens. The multiplex rtPCR panels were used to screen clinical samples from free-ranging and hospitalized koalas for multiple pathogens simultaneously. The multiplex rtPCR will improve turnaround time compared to individual-pathogen rtPCR methods used, to date, for confirmation of diagnosis and will provide the wildlife clinician with the ability to make treatment decisions more rapidly.

Trends and costs of pertussis hospitalizations in Portugal, 2000 to 2015: from 0 to 95 years old

BACKGROUND

Pertussis has caused several outbreaks and concern worldwide. Despite high vaccination coverage, people of all ages are still affected with significant morbidity and mortality. We aimed to analyse all pertussis hospitalizations in Portugal to help to delineate preventive policies.

METHODS

Data were collected from a Portuguese administrative database, which contains all registered hospitalizations in mainland Portugal. Cases were identified using the ICD-9-CM code 033.x (whooping cough) as principal or secondary diagnosis, with hospital discharges between 2000 and 2015. Data were analysed by age groups.

RESULTS

Of 2281 hospitalizations, 94% occurred in infants (<1 year). The mean and median ages were 20 and 2 months, respectively. A seasonal pattern was observed, with higher number of hospitalizations during the winter for infants, and during the summer for other age groups. Higher hospitalization rates were registered in the Southern regions. The mean and median lengths of hospital stay were 8 and 6 days, respectively. The main complications were acute respiratory failure and pneumonia. Invasive or non-invasive ventilation, or both, was required in 2.4, 1.8 and 0.6% of hospitalized cases, respectively. The overall inpatient case fatality rate was 0.7%; 0.8, 11.5 and 17.4% for the age groups 0-1 months, 18-64 years and ≥65 years, respectively. Total hospitalization costs were estimated to be 2,698,995€.

CONCLUSION

Our study emphasizes the need to adopt new preventive strategies mainly focused on infants, to reduce morbidity and costs of hospitalizations related to pertussis.

Incidence of pertussis in subjects aged 50years and older in France in 2013-2014

OBJECTIVE

To assess the incidence of pertussis (whooping cough) in subjects aged 50years and older in France.

METHODS

Participating family physicians (FPs) using the patient record management software AxiSanté^® included patients aged 50years and older, who had signed an informed consent form, presenting with persistent cough for 7 to 21days. Bordetella genetic material was detected by polymerase chain reaction (PCR) on nasopharyngeal samples collected at the FP's discretion.

RESULTS

A total of 42 FPs included 129 patients from June 2013 to August 2014 (large cities: 38; medium-sized cities: 57; rural areas: 34); 106 samples were analyzed. Overall, 30 pertussis cases were diagnosed: 10 cases confirmed by PCR, 18 purely clinical cases, and two direct epidemiological cases. The crude incidence rate per 100,000 patients aged≥50years was 103.6 (95% CI: 69.9-47.9): 77.1 in large cities, 103.1 in medium-sized cities, and 143.9 in rural areas. The extrapolated incidence rate per 100,000 persons aged≥50years was 187.1 (95% CI: 126.2-67.1): 131.1 in large cities, 256.1 in medium-sized cities, and 242.2 in rural areas.

CONCLUSION

The population aged 50years and older can serve as a reservoir. Its role in Bordetella pertussis circulation should be taken into account for pertussis booster vaccination programs.

Whooping cough surveillance in France in pediatric private practice in 2006-2015

BACKGROUND

Increasing incidence of whooping cough (pertussis) has been reported in many countries, attributed to a switch from whole-cell pertussis-containing vaccine (wPV) to acellular PV (aPV) and circulation of the pertactin non-producing Bordetella pertussis. The present study aimed to estimate the duration of immunity conferred by PVs in children in France with data from an ongoing pediatric ambulatory surveillance of pertussis.

METHODS

A total of 64 pediatricians throughout France enrolled children with suspected pertussis. A standardized data form was used to collect data on age sex, vaccination status, brand of wPV or aPV and source of infection. Confirmed cases were positive on culture and/or real-time Polymerase Chain Reaction (for B.-non-classified or B. pertussis or B. parapertussis) and/or pertussis serology.

RESULTS

Between October 2006 and December 2015, 149 cases of confirmed Bordetella infections were reported, 86 infected with B. pertussis and 55 B. non-classified. Fifteen children (10.1%) were not vaccinated, and 26 (17.4%) were partially vaccinated. The mean age was greater for children who received 4 doses of wPV (11.3±2.2, p<0.001) or a combination of wPV and aPV (10.5±3.3, p<0.001) than only aPV (7.2±2.4years). The mean duration of cough before a visit to a pediatrician was longer for children with wPV or a combination of wPV and aPV than only aPV (23.8±10.1 and 25.0±25.6vs 13.6±10.0days).

CONCLUSION

Despite the use of a more sensitive diagnostic method and emergence of pertactin non producing B. pertussis, in France context, aPV-induced immunity still protects against pertussis; however, the mean duration of immunity is about 6 to 7years, compared to 9years for wPV vaccine, after the primary vaccination and one booster (3+1 doses).

Cilia-associated bacteria in fatal Bordetella bronchiseptica pneumonia of dogs and cats

Bordetella bronchiseptica frequently causes nonfatal tracheobronchitis, but its role in fatal pneumonia is less recognized. Our study evaluated histologic identification of cilia-associated bacteria as a method for diagnosis of B. bronchiseptica pneumonia. Cases of fatal bronchopneumonia were studied retrospectively, excluding neonates and cases of aspiration pneumonia, minor lung lesions, or autolysis. The study population comprised 36 canine and 31 feline cases of bronchopneumonia. B. bronchiseptica was identified in 8 of 36 canine and 14 of 31 feline cases based on immunohistochemistry (IHC) using serum from a rabbit hyperimmunized with pertactin, PCR testing (Fla2/Fla12), and/or bacterial culture data when available. Of these, IHC was positive in 4 canine and 7 feline cases, PCR was positive in 8 canine and 14 feline cases, and B. bronchiseptica was isolated in 2 of 5 canine and 3 of 9 feline cases tested. Examination of histologic sections stained with hematoxylin and eosin revealed bronchial cilia-associated bacteria in 4 of 36 canine and 5 of 31 feline cases; these were all positive by IHC and PCR. The presence of cilia-associated bacteria had been noted in the pathology report for only 2 of these 9 cases. Thus, the presence of cilia-associated bacteria seems frequently overlooked by pathologists, but is a diagnostically significant feature of B. bronchiseptica pneumonia. A specific diagnosis of B. bronchiseptica pneumonia is important because it suggests primary or opportunistic bacterial pneumonia rather than aspiration pneumonia, and because of the risk of animal-to-animal transmission of B. bronchiseptica, the availability of vaccines for disease prevention, and the potential zoonotic risk to immunocompromised pet owners.

Increasing incidence of pertussis in Brazil: a retrospective study using surveillance data

BACKGROUND

Many countries have reported an increase in the incidence of pertussis, which has become a global public health concern.

METHODS

In this study, the epidemiology of pertussis in Brazil was assessed retrospectively using surveillance data gathered from case notification forms from 2007 to 2014.

RESULTS

From 2007 to 2014, 80,068 suspected cases of pertussis were reported in Brazil. Of these, 24,612 (32 %) were confirmed by various criteria. The annual distribution of confirmed cases demonstrated a significant increase in incidence rate since 2012. A seasonal pattern in which cases occur most frequently between the end of spring and midsummer has been identified. Among the confirmed cases, 34.5 % occurred in infants aged 0-2 months, 22.4 % occurred in infants aged 3-6 months, 21 % occurred in children aged 7 months to 4 years, and 8 % were reported in adults >21 years. Of the confirmed cases, 47.2 % met only clinical criteria, 15.5 % met clinical and epidemiological criteria, and 36.6 % were confirmed in a laboratory. The overall case fatality rate was 2.1 %, reaching 4.7 % among infants aged 0-2 months. The complications most commonly reported in the notification forms were pneumonia, encephalitis, dehydration, otitis, and malnutrition. Of the confirmed cases, 23.1 % occurred in subjects who received at least 3 doses of the pertussis vaccine. Within this group, there were 1098 infants aged 7 to 15 months and 2079 children aged 16 months to 4 years. In 2012, 18 states did not achieve 95 % immunization coverage, a number that dropped to 10 and 6 in 2013 and 2014, respectively.

CONCLUSIONS

Brazil's main challenges in facing pertussis resurgence will be to offer the best quality medical attention to reduce mortality, to improve the infrastructure for laboratory diagnosis and to increase vaccination coverage. Additional studies to assess the effectiveness of the current vaccination schedule and basic research on the genetics and evolution of circulating B. pertussis strains are also needed.