Evolution of Bordetella pertussis over a 23-year period in France, 1996 to 2018

BackgroundBordetella pertussis is the main agent of whooping cough. Vaccination with acellular pertussis vaccines has been largely implemented in high-income countries. These vaccines contain 1 to 5 antigens: pertussis toxin (PT), filamentous haemagglutinin (FHA), pertactin (PRN) and/or fimbrial proteins (FIM2 and FIM3). Monitoring the emergence of B. pertussis isolates that might partially escape vaccine-induced immunity is an essential component of public health strategies to control whooping cough.AimWe aimed to investigate temporal trends of fimbriae serotypes and vaccine antigen-expression in B. pertussis over a 23-year period in France (1996-2018).MethodsIsolates (n = 2,280) were collected through hospital surveillance, capturing one third of hospitalised paediatric pertussis cases. We assayed PT, FHA and PRN production by Western blot (n = 1,428) and fimbriae production by serotyping (n = 1,058). Molecular events underlying antigen deficiency were investigated by genomic sequencing.ResultsThe proportion of PRN-deficient B. pertussis isolates has increased steadily from 0% (0/38) in 2003 to 48.4% (31/64) in 2018 (chi-squared test for trend, p < 0.0001), whereas only 5 PT-, 5 FHA- and 9 FIM-deficient isolates were found. Impairment of PRN production was predominantly due to IS481 insertion within the prn gene or a 22 kb genomic inversion involving the prn promoter sequence, indicative of convergent evolution. FIM2-expressing isolates have emerged since 2011 at the expense of FIM3.ConclusionsB. pertussis is evolving through the rapid increase of PRN-deficient isolates and a recent shift from FIM3 to FIM2 expression. Excluding PRN, the loss of vaccine antigen expression by circulating B. pertussis isolates is epidemiologically insignificant.

Analysis of antibiotic sensitivity and resistance genes of Bordetella pertussis in Chinese children

OBJECTIVE

To understood the pathogen detection status and clinical characteristics of suspected pertussis in children and to observe the drug sensitivity and drug resistance genes of Bordetella pertussis (B. pertussis).

METHODS

Three hundred fifty-one cases were collected and their nasopharyngeal swab samples were analyzed by culture and fluorescent quantitative polymerase chain reaction. The susceptibility to erythromycin, clindamycin, ampicillin, levofloxacin, and sulfamethoxazole-trimethoprim were tested by E-test for the positive strains, and the susceptibility to erythromycin was also tested for the KB disk diffusion method. The 23S rRNA gene of the positive strains was amplified and sequenced, and statistical analysis was performed in conjunction with clinical data.

RESULTS

The positive rate of bacterial culture was 16.8% (59/351), and the positive rate of PCR was 62.4% (219/351). Two cases were positive about bacterial culture and negative for PCR. There were 221 confirmed cases of pertussis. The E-test results showed that the rate of the sensitivity of the 55 strains of pertussis to erythromycin and clindamycin was 50.9% (28/55), the minimum antibiotic concentration50 (MIC50) and MIC90 values were 0.094/>256 and 0.75/>256 mg/L, respectively, and the MIC50/MIC90 to ampicillin, levofloxacin, and sulfamethoxazole were 0.125/0.19, 0.38/0.5, and 0.125/0.25 mg/L, respectively. The KB disk diffusion method showed 27 of the 55 strains 49.1% (27/55) was resistant to erythromycin; all of the resistant strains had the 23S rRNA gene A2047G mutation, and their MIC of erythromycin was >256 mg/L.

CONCLUSION

The diagnosis of pertussis by a fluorescent quantitative polymerase chain reaction method is more sensitive than that of bacterial culture. The resistance of B. pertussis to erythromycin was prominent. All of the strains of B. pertussis resistant to erythromycin in our center had the A2047G mutation of the 23S rRNA gene.

Bordetella pertussis population dynamics and phylogeny in Japan after adoption of acellular pertussis vaccines

Bordetella pertussis, the causative agent of whooping cough, has experienced a resurgence in the past 15 years, despite the existence of both whole-cell and acellular vaccines. Here, we performed whole genome sequencing analysis of 149 clinical strains, provided by the National Institute of Infectious Diseases (NIID), Japan, isolated in 1982–2014, after Japan became the first country to adopt acellular vaccines against B. pertussis. Additionally, we sequenced 39 strains provided by the Konan Kosei Hospital in Aichi prefecture, Japan, isolated in 2008–2013. The genome sequences afforded insight into B. pertussis genome variability and population dynamics in Japan, and revealed that the B. pertussis population in Japan was characterized by two major clades that divided more than 40 years ago. The pertactin gene was disrupted in about 20 % of the 149 NIID isolates, by either a deletion within the signal sequence (ΔSS) or the insertion of IS element IS481 (prn :: IS481). Phylogeny suggests that the parent clones for these isolates originated in Japan. Divergence dating traced the first generation of the pertactin-deficient mutants in Japan to around 1990, and indicated that strains containing the alternative pertactin allele prn2 may have appeared in Japan around 1974. Molecular clock data suggested that observed fluctuations in B. pertussis population size may have coincided with changes in vaccine usage in the country. The continuing failure to eradicate the disease warrants an exploration of novel vaccine compositions.

Short-Read Whole-Genome Sequencing for Laboratory-Based Surveillance of Bordetella pertussis

Bordetella pertussis is a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance of B. pertussis acellular vaccine (aP) antigens is critical for understanding the interaction between evolutionary pressures, disease pathogenesis, and vaccine effectiveness. Methods currently used to characterize aP components are relatively labor-intensive and low throughput. To address this challenge, we sought to derive aP antigen genotypes from minimally processed short-read whole-genome sequencing data generated from 40 clinical B. pertussis isolates and analyzed using the SRST2 bioinformatic package. SRST2 was able to identify aP antigen genotypes for all antigens with the exception of pertactin, possibly due to low read coverage in GC-rich low-complexity regions of variation. Two main genotypes were observed in addition to a singular third genotype that contained an 84-bp deletion that was identified by SRST2 despite the issues in allele calling. This method has the potential to generate large pools of B. pertussis molecular data that can be linked to clinical and epidemiological information to facilitate research of vaccine effectiveness and disease severity in the context of emerging vaccine antigen-deficient strains.