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

Sex bias in autism spectrum disorder in neurofibromatosis type 1

BACKGROUND: Despite extensive literature, little is known about the mechanisms underlying sex bias in autism spectrum disorder (ASD). This study investigates the sex differences in ASD associated with neurofibromatosis type 1, a single-gene model of syndromic autism. METHODS: We analysed data from n = 194 children aged 4–16 years with neurofibromatosis type 1. Sex differences were evaluated across the Autism Diagnostic Interview-Revised (ADI-R), Autism Diagnostic Observation Schedule (ADOS), verbal IQ, Social Responsiveness Scale (SRS) and Conners questionnaires. RESULTS: There was 2.68:1 male:female ratio in children meeting ASD criteria on the deep phenotyping measures. On symptom profile, males with neurofibromatosis type 1 (NF1) + ASD were more impaired on reciprocal social interaction and communication domains of the ADI-R but we found no differences on the restricted, repetitive behaviours (RRBs) domain of the ADI-R and no differences on the social on the ADOS. NF1 ASD males and females were comparable on verbal IQ, and the inattention/hyperactivity domains of the Conners questionnaire. CONCLUSIONS: There is a significant male bias in the prevalence of ASD in NF1. The phenotypic profile of NF1 + ASD cases includes greater social communication impairment in males. We discuss the implications of our findings and the rationale for using NF1 as a model for investigating sex bias in idiopathic ASD

Temporal trends in circulating Bordetella pertussis strains in Australia.

Australia experienced a resurgence of pertussis in the 1990s despite improved vaccine coverage. Although much of the increase was attributable to increased detection of cases in older persons with waning immunity by serology, vaccine changes or alterations in circulating Bordetella pertussis strains may also have contributed. We determined the frequency of variants of B. pertussis pertactin (prn), and pertussis toxin subunit 1 (ptxS1) genes, restriction fragment length polymorphism (RFLP) types and fimbrial serotypes prevalent in Australia prior to, and during the 1990s. Ampoules of the whole-cell vaccine in use prior to 1999 and 84 B. pertussis isolates stored between 1967 and 1998 by laboratories around Australia were analysed. One pertactin allele, Prn3, not detected before 1985, was found in 24 out of 57 (42%) isolates between 1989 and 1998 (P<0.0001). PtxS1A was found in all isolates. IS1002 type 29, found in 17 out of 31 (55%) isolates tested, was the predominant RFLP type. The only difference in fimbrial serotype distribution between the time-periods was an increase in serotype 3 (P=0.054). The whole-cell vaccine contained only the alleles prn1 and ptxS1A. Antigenic shift in B. pertussis may have contributed to the re-emergence of pertussis in Australia. Monitoring these trends will be important as acellular vaccines are introduced and changes are made to pertussis vaccine schedules

Small Mutations in <em>Bordetella pertussis</em> Are Associated with Selective Sweeps

<div><p><em>Bordetella pertussis</em> is the causative agent of pertussis, a highly contagious disease of the human respiratory tract. Despite high vaccination coverage, pertussis has resurged and has become one of the most prevalent vaccine-preventable diseases in developed countries. We have proposed that both waning immunity and pathogen adaptation have contributed to the persistence and resurgence of pertussis. Allelic variation has been found in virulence-associated genes coding for the pertussis toxin A subunit (<em>ptxA</em>), pertactin (<em>prn</em>), serotype 2 fimbriae (<em>fim2</em>), serotype 3 fimbriae (<em>fim3</em>) and the promoter for pertussis toxin (<em>ptxP</em>). In this study, we investigated how more than 60 years of vaccination has affected the Dutch <em>B. pertussis</em> population by combining data from phylogeny, genomics and temporal trends in strain frequencies. Our main focus was on the <em>ptxA</em>, <em>prn</em>, <em>fim3</em> and <em>ptxP</em> genes. However, we also compared the genomes of 11 Dutch strains belonging to successful lineages. Our results showed that, between 1949 and 2010, the Dutch <em>B. pertussis</em> population has undergone as least four selective sweeps that were associated with small mutations in <em>ptxA</em>, <em>prn</em>, <em>fim3</em> and <em>ptxP</em>. Phylogenetic analysis revealed a stepwise adaptation in which mutations accumulated clonally. Genomic analysis revealed a number of additional mutations which may have a contributed to the selective sweeps. Five large deletions were identified which were fixed in the pathogen population. However, only one was linked to a selective sweep. No evidence was found for a role of gene acquisition in pathogen adaptation. Our results suggest that the <em>B. pertussis</em> gene repertoire is already well adapted to its current niche and required only fine tuning to persist in the face of vaccination. Further, this work shows that small mutations, even single SNPs, can drive large changes in the populations of bacterial pathogens within a time span of six to 19 years.</p> </div