Population dynamics of Bordetella pertussis in Finland and Sweden, neighbouring countries with different vaccination histories

Global spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis

As with other pathogens, competitive interactions between Bordetella pertussis strains drive infection risk. Vaccines are thought to perturb strain diversity through shifts in immune pressures; however, this has rarely been measured because of inadequate data and analytical tools. We used 3344 sequences from 23 countries to show that, on average, there are 28.1 transmission chains circulating within a subnational region, with the number of chains strongly associated with host population size. It took 5 to 10 years for B. pertussis to be homogeneously distributed throughout Europe, with the same time frame required for the United States. Increased fitness of pertactin-deficient strains after implementation of acellular vaccines, but reduced fitness otherwise, can explain long-term genotype dynamics. These findings highlight the role of vaccine policy in shifting local diversity of a pathogen that is responsible for 160,000 deaths annually.

High Prevalence of Macrolide-Resistant Bordetella pertussis and ptxP1 Genotype, Mainland China, 2014-2016

According to the government of China, reported cases of pertussis have increased remarkably and are still increasing. To determine the genetic relatedness of Bordetella pertussis strains, we compared multilocus variable-number tandem-repeat analysis (MLVA) results for isolates from China with those from Western countries. Among 335 isolates from China, the most common virulence-associated genotype was ptxA1/ptxC1/ptxP1/prn1/fim2–1/fim3A/tcfA2, which was more frequent among isolates from northern than southern China. Isolates of this genotype were highly resistant to erythromycin. We identified 36 ptxP3 strains mainly harboring ptxA1 and prn2 (35/36); ptxP3 strains were sensitive to erythromycin and were less frequently from northern China. For all isolates, the sulfamethoxazole/trimethoprim MIC was low, indicating that this drug should be recommended for patients infected with erythromycin-resistant B. pertussis. MLVA of 150 clinical isolates identified 13 MLVA types, including 3 predominant types. Our results show that isolates circulating in China differ from those in Western countries.

Genomic dissection of Australian Bordetella pertussis isolates from the 2008-2012 epidemic

OBJECTIVES

Despite high pertussis vaccination coverage, Australia experienced a prolonged epidemic in 2008-2012. The predominant Bordetella pertussis genotype harboured pertussis toxin promoter allele, ptxP3, and pertactin gene allele, prn2. The emergence and expansion of prn non-expressing isolates (Prn negative), were also observed. We aimed to investigate the microevolution and genomic diversity of epidemic B. pertussis isolates.

METHODS

We sequenced 22 B. pertussis isolates collected in 2008-2012 from two states of Australia which are geographically widely separated. Ten of the 22 were Prn negative isolates with three different modes of silencing of prn (prn::IS481F, prn::IS481R and prn::IS1002). Five pre-epidemic isolates were also sequenced for comparison.

RESULTS

Five single nucleotide polymorphisms were common in the epidemic isolates and differentiated them from pre-epidemic isolates. The Australian epidemic isolates can be divided into five lineages (EL1-EL5) with EL1 containing only Prn negative isolates. Comparison with global isolates showed that three lineages remained geographically and temporally distinct whereas two lineages mixed with isolates from 2012 UK outbreak.

CONCLUSION

Our results suggest significant diversification and the microevolution of B. pertussis within the 2008-2012 Australian epidemic.

Genetic Variation of Bordetella pertussis in Austria

In Austria, vaccination coverage against Bordetella pertussis infections during infancy is estimated at around 90%. Within the last years, however, the number of pertussis cases has increased steadily, not only in children but also in adolescents and adults, indicating both insufficient herd immunity and vaccine coverage. Waning immunity in the host and/or adaptation of the bacterium to the immunised hosts could contribute to the observed re-emergence of pertussis. In this study we therefore addressed the genetic variability in B. pertussis strains from several Austrian cities. Between the years 2002 and 2008, 110 samples were collected from Vienna (n = 32), Linz (n = 63) and Graz (n = 15) by nasopharyngeal swabs. DNA was extracted from the swabs, and bacterial sequence polymorphisms were examined by MLVA (multiple-locus variable number of tandem repeat analysis) (n = 77), by PCR amplification and conventional Sanger sequencing of the polymorphic regions of the prn (pertactin) gene (n = 110), and by amplification refractory mutation system quantitative PCR (ARMS-qPCR) (n = 110) to directly address polymorphisms in the genes encoding two pertussis toxin subunits (ptxA and ptxB), a fimbrial adhesin (fimD), tracheal colonisation factor (tcfA), and the virulence sensor protein (bvgS). Finally, the ptxP promoter region was screened by ARMS-qPCR for the presence of the ptxP3 allele, which has been associated with elevated production of pertussis toxin. The MLVA analysis revealed the highest level of polymorphisms with an absence of MLVA Type 29, which is found outside Austria. Only Prn subtypes Prn1/7, Prn2 and Prn3 were found with a predominance of the non-vaccine type Prn2. The analysis of the ptxA, ptxB, fimD, tcfA and bvgS polymorphisms showed a genotype mixed between the vaccine strain Tohama I and a clinical isolate from 2006 (L517). The major part of the samples (93%) displayed the ptxP3 allele. The consequences for the vaccination strategy are discussed.

Immunization with the recombinant Cholera toxin B fused to Fimbria 2 protein protects against Bordetella pertussis infection

This study examined the immunogenic properties of the fusion protein fimbria 2 of Bordetella pertussis (Fim2)—cholera toxin B subunit (CTB) in the intranasal murine model of infection. To this end B. pertussis Fim2 coding sequence was cloned downstream of the cholera toxin B subunit coding sequence. The expression and assembly of the fusion protein into pentameric structures (CTB-Fim2) were evaluated by SDS-PAGE and monosialotetrahexosylgaglioside (GM1-ganglioside) enzyme-linked immunosorbent assay (ELISA). To evaluate the protective capacity of CTB-Fim2, an intraperitoneal or intranasal mouse immunization schedule was performed with 50 μg of CTB-Fim2. Recombinant (rFim2) or purified (BpFim2) Fim2, CTB, and phosphate-buffered saline (PBS) were used as controls. The results showed that mice immunized with BpFim2 or CTB-Fim2 intraperitoneally or intranasally presented a significant reduction in bacterial lung counts compared to control groups (P < 0.01 or P < 0.001 , resp.). Moreover, intranasal immunization with CTB-Fim2 induced significant levels of Fim2-specific IgG in serum and bronchoalveolar lavage (BAL) and Fim2-specific IgA in BAL. Analysis of IgG isotypes and cytokines mRNA levels showed that CTB-Fim2 results in a mixed Th1/Th2 (T-helper) response. The data presented here provide support for CTB-Fim2 as a promising recombinant antigen against Bordetella pertussis infection.

Perplexities of pertussis: recent global epidemiological trends and their potential causes

Recent much-publicized increases in pertussis case reports in some countries with high vaccine coverage have raised concerns about its current and future control. The ubiquity of this trend, however, remains unexamined. In an attempt to paint a global picture, we used case counts to determine which countries experienced statistically significant trends in incidence over the past two decades and to map changes in incidence during this period. These data reveal that pertussis resurgence is not a universal phenomenon. The heterogeneity in incidence trends, even in countries with superficially similar demography, socioeconomic conditions and vaccination programmes, is striking and requires explanation. In this opinion piece, we review and assess the multifaceted proposed explanations incorporating evolution, population dynamics, and the details of immunization programmes. While we do not solve the riddle that is pertussis epidemiology, we highlight critical aspects that are likely to hold the key to understanding its worldwide epidemiology.

Genetic analysis of Bordetella pertussis in Ontario, Canada reveals one predominant clone

OBJECTIVE

To characterize Bordetella pertussis isolates in Ontario, Canada in order to understand the clonal diversity of strains present in this province.

METHODS

A total of 521 isolates from the period 1998-2006 were analyzed by serotyping, pulsed-field gel electrophoresis (PFGE), and DNA sequencing of their virulence factors of pertactin, fimbriae 3, pertussis toxin subunit 1, and pertussis toxin gene promoter. Characteristics of the Ontario isolates were compared to those described for isolates from Europe and Australia.

RESULTS

A single predominant clone was identified in Ontario, Canada, represented by 83.5% of the 521 isolates analyzed. This clone was characterized by the genotype fim3B, prn2, ptxS1A, and ptxP3 (sequence type (ST)-1), and 72.9% of this clone displayed three closely related PFGE profiles of BpSR11, BpSR5, and BpSR12. Pertussis isolates in Europe with these PFGE profiles and virulence factor genotype are reported as common. The Australian epidemic clone was previously reported to have the genotype prn2 and ptxP3.

CONCLUSION

The finding of one predominant B. pertussis clone in Ontario, Canada, with characteristics identical to strains involved in epidemics in Europe and Australia, suggests a potential link of this strain to the resurgence of pertussis in this province.

Selection and emergence of pertussis toxin promoter ptxP3 allele in the evolution of Bordetella pertussis

Evolutionary studies using single nucleotide polymorphisms (SNPs) have separated Bordetella pertussis isolates into six major clusters, with recent isolates forming cluster I. The expansion of cluster I isolates was characterised by changes in genes encoding antigenic components in acellular vaccines, including pertactin (Prn). Here, we determined the initial emergence of the pertussis toxin promoter allele, ptxP3, from an evolutionary perspective. This allele was previously shown in a study from the Netherlands to be associated with increased pertussis toxin production as a result of a single base mutation in the ptxP. The ptxP region of 313 worldwide isolates was sequenced, including 208 isolates from Australia collected over a 40 year period. Eight alleles were identified, of which only two predominated: ptxP1 and ptxP3. One novel allele was also found. ptxP3 was only found in SNP cluster I of B. pertussis and its emergence is concurrent with the change to the non-vaccine prn2 allele. Our results suggest that the globally distributed cluster I of B. pertussis has the ability to evade vaccine induced selection pressure.

SNP-based typing: a useful tool to study Bordetella pertussis populations

To monitor changes in Bordetella pertussis populations, mainly two typing methods are used; Pulsed-Field Gel Electrophoresis (PFGE) and Multiple-Locus Variable-Number Tandem Repeat Analysis (MLVA). In this study, a single nucleotide polymorphism (SNP) typing method, based on 87 SNPs, was developed and compared with PFGE and MLVA. The discriminatory indices of SNP typing, PFGE and MLVA were found to be 0.85, 0.95 and 0.83, respectively. Phylogenetic analysis, using SNP typing as Gold Standard, revealed false homoplasies in the PFGE and MLVA trees. Further, in contrast to the SNP-based tree, the PFGE- and MLVA-based trees did not reveal a positive correlation between root-to-tip distance and the isolation year of strains. Thus PFGE and MLVA do not allow an estimation of the relative age of the selected strains. In conclusion, SNP typing was found to be phylogenetically more informative than PFGE and more discriminative than MLVA. Further, in contrast to PFGE, it is readily standardized allowing interlaboratory comparisons. We applied SNP typing to study strains with a novel allele for the pertussis toxin promoter, ptxP3, which have a worldwide distribution and which have replaced the resident ptxP1 strains in the last 20 years. Previously, we showed that ptxP3 strains showed increased pertussis toxin expression and that their emergence was associated with increased notification in the Netherlands. SNP typing showed that the ptxP3 strains isolated in the Americas, Asia, Australia and Europe formed a monophyletic branch which recently diverged from ptxP1 strains. Two predominant ptxP3 SNP types were identified which spread worldwide. The widespread use of SNP typing will enhance our understanding of the evolution and global epidemiology of B. pertussis.

Appearance of Fim3 and ptxP3-Bordetella pertussis strains, in two regions of Sweden with different vaccination programs

After introduction of a mono-component vaccine, containing only pertussis toxoid (PT), the incidence of pertussis was significantly higher in the Gothenburg area among children during the period October 1, 1997 until end of 2006 compared to the Rest of Sweden where a vaccine containing PT and two other pertussis antigens was used. To investigate a possible cause of this difference, the Bordetella pertussis populations in both regions were compared by determining the fimbrial serotype (Fim), the PFGE-type and the pertussis toxin promoter allele type (ptxP). Strains with the ptxP1 allele were successively replaced by ptxP3 strains producing more pertussis toxin. In Gothenburg compared to the Rest of Sweden, Fim3 and ptxP3 strains were observed earlier and reached higher frequencies in the studied period. Since ptxP3 strains have been shown to be more virulent, their higher prevalence may have contributed to the higher incidence of pertussis in the Gothenburg area. In addition we found a high degree of linkage between PFGE-profile and ptxP3. Our results highlight the importance of strain typing to gain insight into the mechanisms of immunity-associated selection of microbial subtypes and the causes of changes in incidences of infectious diseases.

Effect of vaccination on Bordetella pertussis strains, China

Strains in China may differ from those in countries that have long histories of high vaccination coverage.

Whole-cell pertussis vaccine was introduced in China in the early 1960s. We used standard typing methods to compare 96 Bordetella pertussis isolates collected before and after introduction of vaccination, during 1953–2005. The following vaccine-type alleles of the pertussis toxin (ptx) gene were characteristic for all prevaccination strains: ptxA2, ptxA3, and ptxA4. The shift to ptxA1 occurred since 1963. All isolates collected since 1983 contained ptxA1. Pertactin (prn) allele 1, prn1, was predominant, although prn2 and prn3 have been detected since 2000. Serotypes fimbriae (Fim) 2 and Fim2,3 were found in all isolates collected before 1986. During 1997–2005, Fim3 became prevalent. Although changes in electrophoresis profiles over time were observed, the predominant profiles during 1997–2005 resembled those during the prevaccine era and those found in Europe before the 1990s. B. pertussis strains in China may differ from those in countries that have a long history of high vaccine coverage.

Insight into evolution of Bordetella pertussis from comparative genomic analysis: evidence of vaccine-driven selection

Despite high vaccine coverage, pertussis incidence has increased substantially in recent years in many countries. A significant factor that may be contributing to this increase is adaptation to the vaccine by Bordetella pertussis, the causative agent of pertussis. In this study, we first assessed the genetic diversity of B. pertussis by microarray-based comparative genome sequencing of 10 isolates representing diverse genotypes and different years of isolation. We discovered 171 single nucleotide polymorphisms (SNPs) in a total of 1.4 Mb genome analyzed. The frequency of base changes was estimated as one per 32 kb per isolate, confirming that B. pertussis is one of the least variable bacterial pathogens. We then analyzed an international collection of 316 B. pertussis isolates using a subset of 65 of the SNPs and identified 42 distinct SNP profiles (SPs). Phylogenetic analysis grouped the SPs into six clusters. The majority of recent isolates belonged to clusters I-IV and were descendants of a single prevaccine lineage. Cluster I appeared to be a major clone with a worldwide distribution. Typing of genes encoding acellular vaccine (ACV) antigens, ptxA, prn, fhaB, fim2, and fim3 revealed the emergence and increasing incidence of non-ACV alleles occurring in clusters I and IV, which may have been driven by ACV immune selection. Our findings suggest that B. pertussis, despite its high population homogeneity, is evolving in response to vaccination pressure with recent expansion of clones carrying variants of genes encoding ACV antigens.

Bordetella pertussis strains with increased toxin production associated with pertussis resurgence

A more virulent strain of the disease is emerging.

Before childhood vaccination was introduced in the 1940s, pertussis was a major cause of infant death worldwide. Widespread vaccination of children succeeded in reducing illness and death. In the 1990s, a resurgence of pertussis was observed in a number of countries with highly vaccinated populations, and pertussis has become the most prevalent vaccine-preventable disease in industrialized countries. We present evidence that in the Netherlands the dramatic increase in pertussis is temporally associated with the emergence of Bordetella pertussis strains carrying a novel allele for the pertussis toxin promoter, which confers increased pertussis toxin (Ptx) production. Epidemiologic data suggest that these strains are more virulent in humans. We discuss changes in the ecology of B. pertussis that may have driven this adaptation. Our results underline the importance of Ptx in transmission, suggest that vaccination may select for increased virulence, and indicate ways to control pertussis more effectively.

Bordetella pertussis and vaccination: the persistence of a genetically monomorphic pathogen

Before childhood vaccination was introduced in the 1950s, pertussis or whooping cough was a major cause of infant death worldwide. Widespread vaccination of children was successful in significantly reducing morbidity and mortality. However, despite vaccination, pertussis has persisted and, in the 1990s, resurged in a number of countries with highly vaccinated populations. Indeed, pertussis has become the most prevalent vaccine-preventable disease in developed countries with estimated infection frequencies of 1-6%. Recently vaccinated children are well protected against pertussis disease and its increase is mainly seen in adolescents and adults in which disease symptoms are often mild. The etiologic agent of pertussis, Bordetella pertussis, is extremely monomorphic and its ability to persist in the face of intensive vaccination is intriguing. Numerous studies have shown that B. pertussis populations changed after the introduction of vaccination suggesting adaptation. These adaptations did not involve the acquisition of novel genes but small genetic changes, mainly SNPs, and occurred in successive steps in a period of 40 years. The earliest adaptations resulted in antigenic divergence with vaccine strains. More recently, strains emerged with increased pertussis toxin (Ptx) production. Here I argue that the resurgence of pertussis is the compound effect of pathogen adaptation and waning immunity. I propose that the removal by vaccination of naïve infants as the major source for transmission was the crucial event which has driven the changes in B. pertussis populations. This has selected for strains which are more efficiently transmitted by primed hosts in which immunity has waned. The adaptation of B. pertussis to primed hosts involved delaying an effective immune response by antigenic divergence with vaccine strains and by increasing immune suppression through higher levels of Ptx production. Higher levels of Ptx may also benefit transmission by enhancing clinical symptoms. The study of B. pertussis populations has not only increased our understanding of pathogen evolution, but also suggests way to improve pertussis vaccines, underlining the public health significance of population-based studies of pathogens.

Analysis of Swedish Bordetella pertussis isolates with three typing methods: characterization of an epidemic lineage

Three Bordetella pertussis typing methods, pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and multi-locus variable number tandem repeat analysis (MLVA) were compared using a collection of Swedish strains. Of the three typing methods used, PFGE was found to be the most discriminatory. MLVA and MLST were less discriminatory, but may be valuable for strain discrimination when culture is not possible as they are based on PCR. The combination of MLVA/MLST was found to be equally discriminatory as PFGE and should therefore also be considered. The relationship between predominant lineages in Sweden and The Netherlands, characterized by the PFGE type BpSR11 and the allele for the pertussis toxin promoter ptxP3, respectively, was investigated. Linkage was found between the PFGE type BpSR11 and ptxP3 in that all BpSR11 strains carried ptxP3. On the other hand ptxP3 was found in several other PFGE-types. The presence of the ptxP3 allele in different genetic backgrounds may indicate horizontal gene transfer within B. pertussis or homoplasy. Alternatively, this observation may be due to convergence of PFGE types.

Rapid and accurate typing of Bordetella pertussis targeting genes encoding acellular vaccine antigens using real time PCR and High Resolution Melt analysis

Real Time-PCR (RT-PCR) and high resolution melt (HRM) analyses were used for rapid typing of genes encoding components of the pertussis acellular vaccine, namely prn, ptxA, fhaB, fim2 and fim3. The length polymorphisms in prn were detected by RT-PCR followed by HRM; single nucleotide polymorphisms in prn and other genes were detected by hairpin primer RT-PCR. These rapid methods are suitable for large-scale studies of vaccine-driven evolution of Bordetella pertussis.

Changes in genetic diversity of the Bordetella pertussis population in the United Kingdom between 1920 and 2006 reflect vaccination coverage and emergence of a single dominant clonal type

Pertussis (whooping cough) is a potentially fatal respiratory disease caused by the bacterium Bordetella pertussis. Despite effective vaccination programs, there has been concern in some developed countries that pertussis cases are on the increase. We characterized 703 clinical B. pertussis isolates collected in the United Kingdom between 1920 and 2006 using multilocus variable-number tandem repeat analysis (MLVA), pertactin (prnA) and pertussis toxin (ptxA) genotyping, and serotyping. The results showed that the genetic diversity of the bacterial population decreased during periods of high vaccine coverage. However, it was elevated between 1977 and 1986, when vaccine coverage in the United Kingdom was low and epidemics occurred. A high proportion of MLVA types during this epidemic period were novel, and the prnA(2) and prnA(3) alleles were seen for the first time in the United Kingdom. MLVA-27 appeared in 1982, was codominant during the 1998-to-2001 period, and comprised approximately 70% of isolates during both the 2002-to-2004 and the 2005-to-2006 periods. The United Kingdom is dominated currently by an MLVA-27 prnA(2) ptxA(1) serotype Fim3 clonal type. Even during recent periods dominated by MLVA-27, many novel types were found at low frequencies, suggesting that either there are a large number of uncommon MLVA types circulating at low frequencies or new types are constantly arising. This supports a hypothesis that MLVA-27 is under some form of positive selection conferring increased survival in a highly vaccinated population. There has been no significant change to the bacterial population in the first 2 years since the United Kingdom switched from a whole-cell to an acellular vaccine.

Genome-wide analysis of single nucleotide polymorphisms in Bordetella pertussis using comparative genomic sequencing

Bordetella pertussis is known to be a genotypically homogeneous pathogen but the extent of homogeneity at the genomic level is unknown. A currently circulating B. pertussis isolate from Australia was compared with the genome-sequenced Tohama I strain isolated in Japan in the 1950s from a distantly related lineage. Microarray-based comparative genome sequencing (CGS) was used to detect single nucleotide polymorphisms (SNPs) in a total of 1.4 Mb of the 4.09 Mb genome, including 1012 coding-regions, 217 pseudogenes and 268 intergenic regions. The CGS analysis, followed by validation using real-time PCR and DNA sequencing, identified 70 SNPs and five 1-3 bp indels, giving an overall frequency of base changes of 1 per 20 kb. Thirty-two of the 56 SNPs in coding regions were non-synonymous, including five located in virulence-associated genes. The data also allowed us to compare genomic diversity with other "clonal" human pathogens such as Mycobacterium tuberculosis and Yersinia pestis, showing that B. pertussis may be one of the least variable pathogenic bacterial species.

The re-emergence of pertussis: implications for diagnosis and surveillance

Pertussis, or whooping cough, a highly contagious disease caused by Bordetella pertussis, is making a comeback globally and nationally in spite of reasonable vaccination coverage. This paper provides an update on laboratory testing methods that assist the confirmation of clinical disease and investigation of outbreaks. Laboratory confirmation of the diagnosis by polymerase chain reaction or serology should be attempted, especially when atypical pertussis is suspected clinically. Genetic and antigenic variations in virulence factors of strains circulating in the population should also be monitored.

Factors contributing to pertussis resurgence

Despite extensive immunization, the disease pertussis remains one of the world’s leading causes of vaccine-preventable deaths. An estimated 50 million cases and 300,000 deaths occur every year. A resurgence of pertussis is observed in highly immunized populations. Increasing numbers of pertussis are reported in adolescents and adults who transmit bacteria to newborns and infants to whom pertussis may be a life-threatening disease. Many studies have shown that the causes for the resurgence are multiple, such as increased awareness of disease, use of better diagnostic tools, improved surveillance methods and waning vaccine-induced immunity. Recently, antigenic divergence has been found between vaccine strains and clinical isolates in many countries with high vaccination coverage. Here, we summarize these findings and discuss the factors contributing to pertussis resurgence in immunized populations.

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.

Antigenic variation in Bordetella pertussis isolates recovered from adults and children in Japan

Recently, the incidence of reported pertussis cases of adults has dramatically increased in Japan. In the present study, we analyzed seven Bordetella pertussis isolates recovered from adults in Japan using pulsed-field gel electrophoresis (PFGE) and sequencing of their antigenic and virulence-associated proteins, compared with those from children. PFGE analysis demonstrated that the adult strains were closely related to the child strains (78-100% genetic similarity). On the other hand, the genotyping revealed that 71% (5/7) of the adult strains and 47% (25/53) of the child strains had the same combination of antigenic/virulence-associated allelic variants (ptxS1B/prn1/fim2-1/fim3A/fhaB1/tcfA2) as the Japanese vaccine strain Tohama, respectively. In comparison to the child strains, there was no apparent antigenic and genetic shift in the adult strains. Our result suggests that (i) there is no B. pertussis circulating strain specific to adults and (ii) the antigenic/virulence-associated proteins are unrelated to the rise in adult pertussis incidence in Japan.

Bordetella pertussis strains circulating in Europe in 1999 to 2004 as determined by pulsed-field gel electrophoresis

Clinical isolates of Bordetella pertussis collected during the year 2004 (n = 153) in eight European countries, Denmark, Finland, France, Germany, The Netherlands, Poland, Sweden, and United Kingdom, were analyzed by pulsed-field gel electrophoresis (PFGE), and their PFGE profiles were compared with those of isolates collected in 1999 (n = 102). The 255 isolates produced 59 distinct PFGE profiles. Among the 153 isolates from 2004, 36 profiles were found, while within the 102 isolates from 1999, 33 profiles were detected. One PFGE profile, BpSR11, was dominant (30% to 50%) in all countries except Denmark (10%) and Poland (0%). In comparison with 1999, there was an increase in BpSR11 prevalence in Finland in 2004 from 5% to 40%, coinciding with a major incidence peak. Some other PFGE profiles seemed to be associated with limited dissemination. Poland was the only country in which the most common actual European PFGE profiles were not found. In a dendrogram analysis, all common PFGE profiles were identified within PFGE group IV, and BpSR11 clustered together with PFGE subgroup IVbeta. Compared to the 1999 isolates, PFGE group V representative for pertactin variant prn3 strains had disappeared, and a new cluster was seen. In conclusion, some PFGE profiles, such as BpSR11, evidently have a higher capacity to spread, suggesting increased fitness to the present immunological environment. It is therefore of major interest to continue with surveillance programs of B. pertussis isolates, as both waning vaccine-derived immunity and strain variation may play a role in the persistence of pertussis.

Comparative genomics of Bordetella pertussis reveals progressive gene loss in Finnish strains

Background

Bordetella pertussis is a Gram-negative bacterium that infects the human respiratory tract and causes pertussis or whooping cough. The disease has resurged in many countries including Finland where the whole-cell pertussis vaccine has been used for more than 50 years. Antigenic divergence has been observed between vaccine strains and clinical isolates in Finland. To better understand genome evolution in B. pertussis circulating in the immunized population, we developed an oligonucleotide-based microarray for comparative genomic analysis of Finnish strains isolated during the period of 50 years.

Methodology/Principal Findings

The microarray consisted of 3,582 oligonucleotides (70-mer) and covered 94% of 3,816 ORFs of Tohama I, the strain of which the genome has been sequenced [1]. Twenty isolates from 1953 to 2004 were studied together with two Finnish vaccine strains and two international reference strains. The isolates were selected according to their characteristics, e.g. the year and place of isolation and pulsed-field gel electrophoresis profiles. Genomic DNA of the tested strains, along with reference DNA of Tohama I strain, was labelled and hybridized. The absence of genes as established with microarrays, was confirmed by PCR. Compared with the Tohama I strain, Finnish isolates lost 7 (8.6 kb) to 49 (55.3 kb) genes, clustered in one to four distinct loci. The number of lost genes increased with time, and one third of lost genes had functions related to inorganic ion transport and metabolism, or energy production and conversion. All four loci of lost genes were flanked by the insertion sequence element IS481.

Conclusion/Significance

Our results showed that the progressive gene loss occurred in Finnish B. pertussis strains isolated during a period of 50 years and confirmed that B. pertussis is dynamic and is continuously evolving, suggesting that the bacterium may use gene loss as one strategy to adapt to highly immunized populations.