Development of a ribotyping scheme for Haemophilus influenzae type b

Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants

BACKGROUND

Haemophilus influenzae is an important human commensal pathogen associated with significant levels of disease. High-throughput DNA sequencing was used to investigate differences in genome content within this species.

RESULTS

Genomic DNA sequence was obtained from 85 strains of H. influenzae and from other related species, selected based on geographical site of isolation, disease association and documented genotypic and phenotypic differences. When compared by Mauve alignment these indicated groupings of H. influenzae that were consistent with previously published analyses; capsule expressing strains fell into two distinct groups and those of serotype b (Hib) were found in two closely positioned lineages. For 18 Hib strains representing both lineages we found many discrete regions (up to 40% of the total genome) displaying sequence variation when compared to a common reference strain. Evidence that this naturally occurring pattern of inter-strain variation in H. influenzae can be mediated by transformation was obtained through sequencing DNA obtained from a pool of 200 independent transformants of a recipient (strain Rd) using donor DNA from a heterologous Hib strain (Eagan).

CONCLUSION

Much of the inter-strain variation in genome sequence in H. influenzae is likely the result of inter-strain exchanges of DNA, most plausibly through transformation.

Genotyping of type b Haemophilus influenzae strains, comparison of strains collected before and during vaccine availability

OBJECTIVE AND METHOD

Five hundred and seventy-eight strains of type b Haemophilus influenzae (521 isolated in children, and 57 in adults) were compared using pulsed-field gel electrophoresis (PFGE) to assess strain evolution and to study the impact of the generalization of anti-Haemophilus b (anti-Hib) vaccination in France. Among these strains, 398 (including 342 from meningitis) were isolated in 1985-1992 (pre-vaccination era), 39 (including 31 from meningitis) in 1993 (year of the generalization of anti-Hib vaccination), and 141 (including 50 from CSF) in 1994-2001 (vaccination era).

RESULTS

A total of 102 PFGE patterns (patterns for 1-101 isolates) were obtained after SmaI restriction of the 578 strains. The strains isolated in children were distributed in 96 patterns, and those isolated in the adult in 34 patterns. The strains isolated during the pre-vaccination era presented 94 patterns. During the vaccination era, 50% of the patterns disappeared and 12 new patterns (11.7%) including 15 strains were observed. The strains belonging to the new patterns (including the two observed in 1993) were isolated in adults (n=7) from blood culture and bronchial secretions, and children (n=9) from CSF, blood culture, and bronchial secretions. In children, among the strains associated to vaccination failure, two presented with a new pulsotype.

CONCLUSION

There is no evidence that the vaccination program brought about any drastic modifications in the type b strains causing meningitis or in the other type b strains in circulation whether in adults or children.

Variability of outer membrane protein P1 and its evaluation as a vaccine candidate against experimental otitis media due to nontypeable Haemophilus influenzae: an unambiguous, multifaceted approach

Candidate vaccine antigens for preventing otitis media caused by nontypeable Haemophilus influenzae (NTHI) should possess one or more conserved epitopes. We sought to evaluate the candidacy of P1, a surface-expressed outer membrane protein knowing that this antigen is subject to diversifying selection. Therefore, we selected NTHI strains from among >500 phylogenically variant isolates representative of the diversity found in natural populations of H. influenzae. Twenty-three variants of P1 (</=95% similarity) were identified among 42 strains. When chinchillas were immunized with recombinant P1 (rP1) obtained from one of these isolates (BCH-3), all animals developed antibodies specific for rP1. Immunized animals were protected against disease when challenged with BCH-3, but not with an ompP1 mutant of BCH-3 or a strain (BCH-2) possessing a heterologous P1 (91% identity). We conclude that (i) while P1 induces protection against NTHI-mediated otitis media, development of a polyvalent vaccine reflecting the variability of P1 would be necessary to construct an efficacious vaccine and (ii) use of a phylogenically characterized collection of representative isolates in concert with gene sequencing, cloning, gene inactivation, and animal testing offers an efficient, rational, and rigorous strategy for evaluating the potential problems associated with variability of vaccine targets and specificity of related immune responses.

Proteomics in medical microbiology

The techniques of proteomics (high resolution two-dimensional electrophoresis and protein characterisation) are widely used for microbiological research to analyse global protein synthesis as an indicator of gene expression. The rapid progress in microbial proteomics has been achieved through the wide availability of whole genome sequences for a number of bacterial groups. Beyond providing a basic understanding of microbial gene expression, proteomics has also played a role in medical areas of microbiology. Progress has been made in the use of the techniques for investigating the epidemiology and taxonomy of human microbial pathogens, the identification of novel pathogenic mechanisms and the analysis of drug resistance. In each of these areas, proteomics has provided new insights that complement genomic-based investigations. This review describes the current progress in these research fields and highlights some of the technical challenges existing for the application of proteomics in medical microbiology. The latter concern the analysis of genetically heterogeneous bacterial populations and the integration of the proteomic and genomic data for these bacteria. The characterisation of the proteomes of bacterial pathogens growing in their natural hosts remains a future challenge.

Molecular epidemiological study of Haemophilus influenzae serotype b strains obtained from children with meningitis in Japan

We report an epidemiological study of 30 Haemophilus influenzae serotype b (Hib) strains derived from the cerebrospinal fluid of children with meningitis. The Hib strains were biotyped, tested for beta-lactamase production, and genotyped by long PCR-ribotyping, random amplified polymorphic DNA (RAPD) analysis, and genomic DNA restriction fragment length polymorphism (RFLP) analysis by pulsed-field gel electrophoresis (PFGE). The phenotypic study characterized 22 of the strains (73%) as biotype I. A genotypic study using long PCR-ribotyping with HaeIII restriction digestion showed no polymorphisms among these 30 Hib strains, but RAPD analysis with two sets of primers demonstrated two distinctive subtypes: one typical of the strains of biotype group II and the second characteristic of the strains of biotype groups I and IV. Each RAPD group was subtyped into several genotypic groups by PFGE-RFLP with SmaI digestion. The genotyping of clinically isolated Hib strains may help to elucidate transmission routes in community infections, endemicity, and the reasons for vaccine failure.

Evaluation and application of ribotyping for epidemiological studies of Actinobacillus pleuropneumoniae in Denmark

The aim of the present study was to evaluate ribotyping as an epidemiological tool for Actinobacillus pleuropneumoniae and apply the method in studies of A. pleuropneumoniae infections in Danish pig herds. The evaluation of ribotyping was based on the 13 international reference strains and 106 epidemiologically unrelated Danish field strains representing the nine serotypes of biotype 1 (1, 2, 5A/B, 6, 7, 8, 10, 12, and K2:O7) and one serotype 14 of biotype 2. Enzymes CfoI and HindIII were chosen for generation of ribotype patterns. Ribotyping of the reference strains resulted in 10 CfoI types and 11 HindIII types. Ribotyping of the Danish strains resulted in 17 different CfoI ribotypes and 24 different HindIII ribotypes. Combining HindIII- and CfoI-ribotyping divided the Danish strains into 26 different types. The stability, reproducibility and typability of ribotype patterns were good, and the discriminatory power was between 0.85-0.89. The relatively low discriminatory power was caused by four predominant types, containing 61% of the isolates. The typing system was applied in studies of routes of infection of specific pathogen-free (SPF) pig herds and included 112 strains of A. pleuropneumoniae. Airborne transmission from neighboring conventional pig farms was investigated in 12 cases of infected SPF herds. Transmission via vehicles transporting pigs between SPF herds was investigated in nine cases while transmission by trading of pigs between SPF herds was investigated in two cases. Serotype 2 was isolated from all SPF herds included in this study, except one, emphasizing the high prevalence of this serotype in Denmark. By ribotyping, airborne transmission was indicated in five of 12 cases, transmission via pig transporting vehicle was indicated in six of nine cases, and transmission via trading was indicated in one of two cases. In many cases findings of predominant ribotypes made interpretations of suspected routes of transmission difficult. The relationship of strains based on ribotypes was calculated using Dices coefficient and clustered by UPGMA. HindIII ribotypes of serotype 2 strains were closely related, though only showing 43% similarity to HindIII ribotypes of remaining serotypes.

Analysis of the prevaccine population of noncapsulate Haemophilus influenzae and identification of a putative epidemic clone

For six months prior to the introduction of Haemophilus influenzae serotype b vaccines, all noncapsulate Haemophilus influenzae received by our laboratory were characterised by biotyping, antibiogram, outer-membrane protein profiling, and ribotyping. Simpson's index of diversity (SID) showed the population was heterogeneous with multiple clones. The study identified a clone within noncapsulate Haemophilus influenzae biotype II that caused more disease than other strains. This clone was shown to have previously caused two outbreaks of respiratory disease and to possess a small extrachromosomal plasmid encoding ampicillin resistance. The study shows that describing the diversity within a bacterial population with SID may negate the need for retrospective subtyping comparisons.

Molecular characteristics of Haemophilus influenzae causing invasive disease during the period of vaccination in Switzerland: analysis of strains isolated between 1986 and 1993

The broad use of conjugated vaccines against Haemophilus influenzae type b may select for strains to which the polysaccharide vaccine does not provide immunity. We analyzed 392 consecutive H. influenzae isolates from Swiss children 0 to 16 years of age with invasive disease during the years 1986 to 1993. Bacterial strains were characterized by serotyping, capsular genotyping, outer membrane protein (OMP) subtyping, and ribotyping. Of 392 strains, 372 were serotype b, 1 was serotype a, 3 were serotype f, and 16 were nontypeable H. influenzae. After the introduction of Haemophilus conjugate vaccines in 1990, there was a relative increase of nontypeable strains from 3 to 6.6% (P = 0.27). Of the type b strains, 281 (75.5%) had the same OMP subtype and ribotype pattern. This clone predominated in the pre- and postvaccine periods. After the year 1990, the proportions of OMP subtype 1c and OMP subtype 3 tended to increase. Isolates from previously vaccinated (n = 10) and nonvaccinated patients did not differ in their subtype distributions. We conclude that the administration of conjugated vaccines decreased invasive disease caused by the most prevalent H. influenzae type b clone. However, further surveillance of circulating H. influenzae strains during the period of vaccination is indicated.

Haemophilus influenzae: then and now

Haemophilus influenzae has long been recognised as a major cause of serious infection and mortality in children less than 5 years old. Prior to the introduction of Haemophilus influenzae type b (Hib) immunisation, the incidence of a child suffering an invasive Haemophilus infection was 20-50/100,000 in industrialised countries and up to ten times higher in developing regions. The introduction of a Hib vaccine programme results in a rapid and dramatic decline in the incidence of Hib infection in the susceptible childhood population. For example, within two years of the introduction of routine Hib vaccination of infants in the UK, the risk of serious Hib infection had fallen from 1:600 to 1:30,000 by 5 years of age. Many other European countries have introduced, or are in the process of introducing, a routine Hib immunisation programme. Because the epidemiology of Haemophilus influenzae infection is changing so dramatically, it is opportune to review Haemophilus influenzae as it was perceived in the pre-vaccine era (the past) and during vaccine implementation (the present), and how its role may change in the post-vaccination era (the future). This review will summarise the historical landmarks that have led to our present-day understanding of Haemophilus influenzae pathogenicity, the concerns about antibiotic resistance, the features of the host immune response to Haemophilus influenzae, and the introduction of the Hib vaccine. Furthermore, the possible importance of this organism in the future will be discussed.