Molecular epidemiology of Bordetella pertussis in the Philippines in 2012-2014

Genotyping and macrolide-resistant mutation of Bordetella pertussis in East and South-East Asia

OBJECTIVES

Macrolide-resistant Bordetella pertussis (MRBP) has been emerging and prevailing in mainland China since 2011. In this study, we aimed to investigate the genotype and macrolide resistance of circulating B. pertussis in East and Southeast Asia using genetic analyses.

METHODS

A total of 302 DNA extracts from clinical specimens and isolates from 2010 to 2020 were analyzed: 145 from Vietnam, 76 from Cambodia, 48 from Taiwan, and 33 from Japan. Genotypes were determined by multilocus variable-number tandem-repeat analysis (MLVA). Macrolide-resistant A2047G mutation in B. pertussis 23S rRNA was investigated using the duplex Cycleave real-time polymerase chain reaction (PCR) assay. Whole-genome sequencing was performed on two MRBP isolates that were identified for the first time in Taiwan.

RESULTS

Overall, 286 DNA extracts (95%) generated a complete MLVA genotype and 283 DNA extracts (94%) yielded a complete result for the A2047G mutation analysis. The A2047G mutation was detected in 18 DNA extracts: fourteen from Vietnam, one from Cambodia, two from Taiwan, and one from Japan. Most of them (78%) showed the genotypes MT104 and MT195, which have previously been reported in Chinese MRBP isolates. Further, the Taiwanese MRBP isolates were classified into the MT104 clade of Chinese MRBP isolates.

CONCLUSION

After MRBP emerged and spread in mainland China, it may have spread to East and Southeast Asia in the 2010s. Continued surveillance targeting the A2047G mutation of MRBP is needed to prevent further spread of this emerging pathogen.

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.

Clinical characteristics, molecular epidemiology and antimicrobial susceptibility of pertussis among children in southern China

BACKGROUND

Increasing numbers of pertussis cases have been reported in recent years. The reported cases from Shenzhen Children's Hospital were close to one tenth of all cases in China. The epidemiology of antigenic genotype and antibiotic resistance of circulating strains in children have been unknown in Shenzhen, southern China. The aim of this study was to describe the clinical features and explore the genotypes and antimicrobial susceptibility of circulating Bordetella pertussis among children in Shenzhen.

METHODS

Data of hospitalized children with pertussis in Shenzhen Children's Hospital from August 2015 to April 2017 were collected. The genetic variability of isolates was investigated and Etest was performed for phenotypic susceptibility to erythromycin, azithromycin, clarithromycin, clindamycin, and trimethoprim/sulfamethoxazole.

RESULTS

469 children with pertussis confirmed by real-time quantitative polymerase chain reaction were hospitalized and strains were isolated from 105 patients. White blood cell count ≥ 20 × 10⁹/L and lymphocyte proportion ≥ 60% were observed in 39.29% of infants younger than 3 months. The two predominant profiles of virulence-associated allelic genes were ptxA1/ptxC1/ptxP1/prn1 (48.6%) and ptxA1/ptxC2/ptxP3/prn2 (44.8%). Among the isolates, 48.6% (51/105) were found resistant to macrolides.

CONCLUSIONS

These findings indicate that leukocytosis is not a sensitive indicator of pertussis. Isolates with the gene profile ptxP3/prn2 were highly circulating in Shenzhen and less resistant to macrolides, different from patterns observed in other parts of China.

Population dynamics and antigenic drift of Bordetella pertussis following whole cell vaccine replacement, Barcelona, Spain, 1986-2015

Among the factors associated with the resurgence of whooping cough, special emphasis has been given to pathogen adaptation after the introduction of the acellular vaccine (ACV). To assess the impact of the vaccine transition strategy from whole-cell vaccine (WCV) to ACV on population dynamics of Bordetella pertussis in Barcelona (Spain), we studied 339 isolates collected from 1986 to 2015 by PFGE and multi-locus variable-number tandem repeat analysis (MLVA). Additionally, allelic variants for the pertussis toxin and its promoter, pertactin, type 3 fimbriae and fimbrial serotyping were assessed to determine its antigenic drift. A shift was observed in the B. pertussis population as well as in its antigenic profile concurrently with the introduction of ACV in Barcelona. Four out of the five most prevalent PFGE profiles were replaced by new profiles following the ACV introduction. MLVA type 27 was the dominant genotype, and its frequency increased from 25% to 79.3% after WCV replacement. Antigen typing demonstrated the emergence of prn2, ptxP3, fim3-2 and a shift from the fimbriae 3 to the fimbriae 2 serotypes after the ACV introduction. Our findings support the presence of population and antigenic dynamic changes in B. pertussis likely driven by the introduction of ACV.

Pertussis in the Association of Southeast Asian Nations: epidemiology and challenges

Pertussis is a highly infectious respiratory disease caused by Bordetella pertussis. Infants and young children are particularly at risk of severe and life-threatening disease. Infectious older individuals may transmit Bordetella pertussis to unprotected infants. Pertussis control measures have even failed in some countries with high pertussis vaccination coverage rates, leading to increased incidence rates. In 2014, this caused the World Health Organization to declare pertussis resurgent in some countries and led to recommendations regarding pertussis surveillance and national immunization programs. Despite the resurgence of pertussis, epidemiology of the disease in Southeast Asia has received little attention. In this narrative review, we describe pertussis surveillance systems, control measures, epidemiologic trends, and region-specific pertussis research in Southeast Asia. We also make recommendations for the intensification of pertussis surveillance and research in the region.

How Genomics Is Changing What We Know About the Evolution and Genome of Bordetella pertussis

The evolution of Bordetella pertussis from a common ancestor similar to Bordetella bronchiseptica has occurred through large-scale gene loss, inactivation and rearrangements, largely driven by the spread of insertion sequence element repeats throughout the genome. B. pertussis is widely considered to be monomorphic, and recent evolution of the B. pertussis genome appears to, at least in part, be driven by vaccine-based selection. Given the recent global resurgence of whooping cough despite the wide-spread use of vaccination, a more thorough understanding of B. pertussis genomics could be highly informative. In this chapter we discuss the evolution of B. pertussis, including how vaccination is changing the circulating B. pertussis population at the gene-level, and how new sequencing technologies are revealing previously unknown levels of inter- and intra-strain variation at the genome-level.

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.

Pertactin-deficient Bordetella pertussis isolates in Poland-a country with whole-cell pertussis primary vaccination

The introduction of pertussis vaccination in the 1950s resulted in a significant decrease in the incidence of disease. However, since the 1990s many highly vaccinated countries have observed the re-emergence of the disease. One of the causes of this phenomenon might be related to the adaptation of Bordetella pertussis to vaccination. The purpose of the presented study was an investigation of the emergence and spread of vaccine antigen-deficient B. pertussis isolates in Poland and genomic characterization of the currently circulating pathogen population using PFGE, MLVA and MAST. The results revealed that all tested isolates expressed Ptx, FHA and ACT antigens but 15.4% (4/26) of isolates from 2010 to 2016 were Prn-deficient. Moreover, one TcfA-deficient isolate was collected in 2015. The genotyping showed a genetic distinction between the isolates circulating in 2010-2016 and isolates from previous periods. The majority of currently circulating isolates belonged to PFGE group IV (96.2%), type MT27 (73.1%), and carried ptxA1-ptxC2-ptxP3-prn2-tcfA2-fim2-1-fim3-1 alleles (61.5%). The unique genetic structure of the B. pertussis population in Poland has changed since 2010 and became similar to that observed in countries with aP vaccination. This could be a result of increasing use of aP vaccines (60% of primary vaccination in 2013) over wP vaccines, which have been broadly used for primary vaccination in Poland for decades.

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.

Molecular epidemiology of Bordetella pertussis in Greece, 2010-2015

Purpose

To determine the predominant strains of Bordetella pertussis in Greece during 2010–2015.

Methodology

Infants and children (n=1150) (15 days to 14 years) of Greek, Roma and immigrant origin with different vaccination statuses were hospitalized in Athens, Greece with suspected pertussis infection. IS481/IS1001 real-time PCR confirmed Bordetella spp./B. pertussis infection in 300 samples. A subset of samples (n=153) were analysed by multi-locus variable number tandem repeat analysis (MLVA) and (n=25) by sequence-based typing of the toxin promotor region (ptxP) on DNA extracted from clinical specimens.

Results/Key findings

A complete MLVA profile was determined in 66 out of 153 samples; the B. pertussis MLVA type 27 (n=55) was the dominant genotype and all tested samples (n=25) expressed the ptxP3 genotype. The vaccine coverage in the Greek population was 90 %; however, the study population expressed complete coverage in 2 out of 264 infants (0–11 months) and in 20 out of 36 children (1–14 years). Roma and immigrant minorities represent 7 % of the Greek population, but make up 50 % of the study population, indicating a low vaccine coverage among these groups.

Conclusions

The B. pertussis MT27 and ptxP3 genotype is dominant in Greek, Roma and immigrant infants and children hospitalized in Greece. Thus, the predominant MLVA genotype in Greece is similar to other countries using acellular vaccines.

Molecular epidemiology of Bordetella pertussis in Cambodia determined by direct genotyping of clinical specimens

OBJECTIVES

This study sought to determine the genotypes of circulating Bordetella pertussis, the causative agent of pertussis, in Cambodia by direct molecular typing of clinical specimens.

METHODS

DNA extracts from nasopharyngeal swabs obtained from 82 pertussis patients in 2008-2016 were analyzed by multilocus variable-number tandem repeat analysis (MLVA). B. pertussis virulence-associated allelic genes (ptxA, prn, and fim3) and the pertussis toxin promoter ptxP were also investigated by DNA sequence-based typing.

RESULTS

Forty-four DNA extracts (54%) yielded a complete MLVA profile, and these were sorted into 8 MLVA types (MT18, MT26, MT27, MT29, MT43, MT72, MT95, and MT200). MT27 and MT29, which are common in developed countries, were the predominant strain types (total 73%). The predominant profile of virulence-associated allelic genes was the combination of ptxP3/ptxA1/prn2/fim3A (48%). MT27 strains were detected during the entire study period, whereas MT29 strains were only found in 2014-2016.

CONCLUSIONS

The B. pertussis population in Cambodia, where a whole-cell pertussis vaccine (WCV) has been continuously used, resembled those observed previously in developed countries where acellular pertussis vaccines are used. Circulating B. pertussis strains in Cambodia were distinct from those in other countries using WCVs.

Multi-locus variable-number tandem repeat analysis of Bordetella pertussis isolates circulating in Poland in the period 1959-2013

PURPOSE

Despite the long history of pertussis vaccination and high vaccination coverage in Poland and many other developed countries, pertussis incidence rates have increased substantially, making whooping cough one of the most prevalent vaccine-preventable diseases. Among the factors potentially involved in pertussis resurgence, the adaptation of the Bordetella pertussis population to country-specific vaccine-induced immunity through selection of non-vaccine-type strains still needs detailed studies.

METHODOLOGY

Multi-locus variable-number tandem repeat analysis (MLVA), also linked to MLST and PFGE profiling, was applied to trace the genetic changes in the B. pertussis population circulating in Poland in the period 1959-2013 versus country-specific vaccine strains.

RESULTS

Generally, among 174 B. pertussis isolates, 31 MLVA types were detected, of which 11 were not described previously. The predominant MLVA types of recent isolates in Poland were different from those of the typical isolates circulating in other European countries. The MT27 type, currently predominant in Europe, was rarely seen and detected in only five isolates among all studied. The features of the vaccine strains used for production of the pertussis component of a national whole-cell diphtheria-tetanus-pertussis (DTP) vaccine, as studied by MLVA and MLST tools, were found to not match those observed in the currently circulating B. pertussis isolates in Poland.

CONCLUSIONS

Differences traced by MLVA in relation to the MLST and PFGE profiling confirmed that the B. pertussis strain types currently observed elsewhere in Europe, even if appearing in Poland, were not able to successfully disseminate within a human population in Poland that has been vaccinated with a whole-cell pertussis vaccine not used in other countries.

Bordetella pertussis infection in children with severe pneumonia, Philippines, 2012-2015

A case-comparison study was conducted based on an observational study of severe pneumonia among hospitalized children in the Philippines. The children, from 8days to 13years old and hospitalized with clinical diagnosis of severe or very severe pneumonia from August 2012 to February 2015, were recruited. Nasopharyngeal swabs were collected from 1152 cases and B. pertussis were detected from 34 cases by PCR. Pertussis-positive cases were more likely to have no fever, more than one week of coughing and breathing difficulty, decreased breathing sounds, and central cyanosis than pertussis- negative cases. The percentage of underweight was significantly higher in pertussis-positive cases than pertussis-negative cases. Pertussis-positive cases showed remarkably higher fatality rate than pertussis-negative cases. All of the fatal cases among pertussis-positive cases were less than 6months old. More attention should be given to protect young infants from pertussis.