Molecular epidemiology of Bordetella pertussis in Greece, 2010-2015

Real-time polymerase chain reaction on filter paper spotted samples: a gateway to molecular diagnosis of invasive bacterial diseases for rural areas in low-income countries

BACKGROUND

Bacterial culture is the gold standard for the diagnosis of invasive bacterial diseases (IBDs) but molecular methods are more specific and sensitive. Fresh liquid samples (FLSs) show patent limitations for shipping and storage. We aimed to evaluate the sensitivity and specificity of real-time polymerase chain reaction (PCR) performed on dried sample spots (DSSs) obtained from different biological fluids compared with real-time PCR or culture performed on FLSs.

METHODS

FLSs positive for Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Escherichia coli, Streptococcus pyogenes, Staphylococcus aureus, Bordetella pertussis and/or Pseudomonas aeruginosa were spotted on filter paper. Real-time PCR was performed on both FLSs and DSSs and results were compared. The stability of the DSS results over time was evaluated.

RESULTS

Real-time PCR performed on 114 DSSs showed a specificity of 99.1% and a sensitivity of 91.2% for IBD diagnosis. A positive correlation was found between FLS cycle threshold (Ct) and DSS Ct (r=0.84; r2=0.71) with the Pearson statistical test and Bland-Altman analysis showing that 95% of the specimens were within agreeable limits. Although we observed a trend towards signal reduction over time in the DSSs, there was no statistical evidence of an increase in Ct values. Real-time PCR on DSSs was 2.2 times more sensitive than culture.

CONCLUSIONS

Real-time PCR applied to DSSs may be a useful approach in different situations, such as IBD diagnosis, both for rural areas of low-income countries and family practitioners in various settings.

Rapid and simple SNP genotyping for Bordetella pertussis epidemic strain MT27 based on a multiplexed single-base extension assay

Multilocus variable-number tandem repeat analysis (MLVA) is widely used for genotyping of Bordetella pertussis, the causative bacteria for pertussis. However, MLVA genotyping is losing its discriminate power because prevalence of the epidemic MT27 strain (MLVA-27) is increasing worldwide. To address this, we developed a single nucleotide polymorphism (SNP) genotyping method for MT27 based on multiplexed single-base extension (SBE) assay. A total of 237 MT27 isolates collected in Japan during 1999–2018 were genotyped and classified into ten SNP genotypes (SG1 to SG10) with a Simpson’s diversity index (DI) of 0.79 (95% CI 0.76–0.82). Temporal trends showed a marked increase in the genotypic diversity in the 2010s: Simpson’s DI was zero in 1999–2004, 0.16 in 2005–2009, 0.83 in 2010–2014, and 0.76 in 2015–2018. This indicates that the SNP genotyping is applicable to the recently circulating MT27 strain. Additionally, almost all outbreak-associated MT27 isolates were classified into the same SNP genotypes for each outbreak. Multiplexed SBE assay allows for rapid and simple genotyping, indicating that the SNP genotyping can potentially be a useful tool for subtyping the B. pertussis MT27 strain in routine surveillance and outbreak investigations.

Severe Bordetella pertussis infection and vaccine issue in Chongqing, from 2012 to 2018

OBJECTIVE

Pertussis is a highly contagious respiratory illness mainly caused by the Gram-negative bacterium Bordetella pertussis. The infection of B. pertussis has been increasing and the current diagnosis of pertussis in children is challenging; little is known of B. pertussis infection in Chongqing.

METHODS

There were 25,441 children (14,863 male and 10,578 female) with suspected pertussis enrolled in our retrospective study from December 2012 to November 2018. Then 800 children with suspected B. pertussis infection were randomly chosen to be evaluated by simultaneous amplification and testing in this prospective study.

RESULTS

Infants younger than 12 months had the greatest burden of pertussis, and the incidence of pertussis in Chongqing appeared to have a periodic pattern. The problem of vaccine quality in China was more serious than previously reported based on the fluctuation of infection rates from 2012 to 2018. Simultaneous amplification and testing to detect B. pertussis RNA (Area Under Curve: 0.900 and Kappa value: 0.831) had better diagnostic performance than real-time PCR for B. pertussis DNA (Area Under Curve: 0.869 and Kappa value: 0.690).

CONCLUSIONS

We revealed the characteristics of B. pertussis infection and vaccine issues in Chongqing. Simultaneous amplification and testing could be a potential novel assay for measuring B. pertussis infection in the future.

Bordetella pertussis Infection in Infants and Young Children in Shanghai, China, 2016-2017: Clinical Features, Genotype Variations of Antigenic Genes and Macrolides Resistance

BACKGROUND

The global resurgence of pertussis in countries with high vaccination coverage has been a concern of public health.

METHODS

Nasopharyngeal swabs were collected for Bordetella pertussis culture from children with suspected pertussis. Clinical and vaccination information were reviewed through electronic medical chart and immunization record. Antibiotics susceptibility was evaluated using E-test for erythromycin, azithromycin, clarithromycin and sulfamethoxazole/trimethoprim. The MLST genotypes and 7 antigenic genes (ptxP, ptxA, ptxC, Prn, fim3, fim2 and tcfA) of Bordetella pertussis were identified by polymerase chain reaction amplification and sequencing.

RESULTS

During January 2016 to September 2017, a total of 141 children 1-48 months of age were culture-confirmed with pertussis, of whom 98 (69.5%) were younger than 6 months, 25 (17.7%) had completed at least 3 doses of DTaP and 75 (53.2%) had a clear exposure to household members with persistent cough. Fully vaccinated cases manifested milder disease than unvaccinated and not-fully vaccinated cases. All strains were MLST2. High-virulent strains characteristic of ptxP3/prn2/ptxC2 constituted 41.1% (58/141) and were all susceptible to macrolides while low-virulent strains characteristic of ptxP1/prn1/ptxC1 constituted 58.9% (83/141) and 97.6% (81/83), respectively, were highly resistant to macrolides.

CONCLUSIONS

Pertussis is resurging among infants and young children in Shanghai, and household transmission is the main exposure pathway. The high-virulent strains harboring ptxP3/prn2/ptxC2 and the macrolide-resistant Bordetella pertussis strains are quite prevalent. These issues impose a public health concern in Shanghai. Our findings are important to modify the DTaP vaccination strategy and the management guideline of pertussis in China.

Molecular Epidemiology of Bordetella pertussis

Although vaccination has been effective, Bordetella pertussis is increasingly causing epidemics, especially in industrialized countries using acellular vaccines (aPs). One factor behind the increased circulation is the molecular changes on the pathogen level. After pertussis vaccinations were introduced, changes in the fimbrial (Fim) serotype of the circulating strains was observed. When bacterial typing methods improved, further changes between the vaccine and circulating strains, especially among the common virulence genes including pertussis toxin (PT) and pertactin (PRN) were noticed. Moreover, development of genome based techniques including pulsed-field gel electrophoresis (PFGE), multiple-locus variable number tandem repeat analysis (MLVA) and whole-genome sequencing (WGS) have offered a better resolution to monitor B. pertussis strains. After the introduction of aP vaccines, B. pertussis strains that are deficient to vaccine antigens, especially PRN, have appeared widely. On the other hand, antimicrobial resistance to first line drugs (macrolides) against B. pertussis is still low in many countries and therefore no globally evaluated antimicrobial susceptibility test values have been recommended. In this review, we focus on the molecular changes in the bacteria, which have or may have affected the past and current epidemiology of pertussis.