Genetic analysis of the capsule locus of Haemophilus influenzae serotype f

Direct Real-Time PCR for the Detection and Serotyping of Haemophilus influenzae without DNA Extraction

To monitor the burden and changes in Haemophilus influenzae (Hi) disease, direct real-time PCR (drt-PCR) assays have been developed for Hi detection in monoplex form and its six serotypes in triplex form, directly from cerebrospinal fluid (CSF) specimens. These assays target the phoB gene for the species detection (Hi-phoB) and serotype-specific genes in region II of the capsule biosynthesis locus (Hi-abf and Hi-cde), identified through comparative analysis of Hi and non-Hi whole-genome sequences. The lower limit of detection (LLD) is 293 CFU/mL for the Hi-phoB assay and ranged from 11 to 130 CFU/mL for the triplex serotyping assays. Using culture as a reference method, the sensitivity and specificity of Hi-phoB, Hi-abf, and Hi-cde were 100%. Triplex serotyping assays also showed 100% agreement for each serotype compared to their corresponding monoplex serotyping assay. These highly sensitive and specific drt-PCR assays do not require DNA extraction and thereby reduce the time, cost, and handling required to process CSF specimens. Furthermore, triplex drt-PCR assays combine the detection of three serotypes in a single reaction, further improving testing efficiency, which is critical for laboratories that process high volumes of Hi specimens for surveillance and diagnostic purposes.

An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim

BACKGROUND

The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occurrence of serotype b (Hib), the most virulent type of H. influenzae, has since decreased, reports of infections with other serotypes and non-typeable strains are on the rise. While non-typeable strains have been studied in-depth, very little is known of the pathogen's evolutionary history, and no genomes dating prior to 1940 were available.

RESULTS

We describe a Hib genome isolated from a 6-year-old Anglo-Saxon plague victim, from approximately 540 to 550 CE, Edix Hill, England, showing signs of invasive infection on its skeleton. We find that the genome clusters in phylogenetic division II with Hib strain NCTC8468, which also caused invasive disease. While the virulence profile of our genome was distinct, its genomic similarity to NCTC8468 points to mostly clonal evolution of the clade since the 6th century. We also reconstruct a partial Yersinia pestis genome, which is likely identical to a published first plague pandemic genome of Edix Hill.

CONCLUSIONS

Our study presents the earliest genomic evidence for H. influenzae, points to the potential presence of larger genomic diversity in the phylogenetic division II serotype b clade in the past, and allows the first insights into the evolutionary history of this major human pathogen. The identification of both plague and Hib opens questions on the effect of plague in immunocompromised individuals already affected by infectious diseases.

Global population structure of Haemophilus influenzae serotype a (Hia) and emergence of invasive Hia disease: capsule switching or capsule replacement?

The population structure of Hia was examined by interrogation of the H. influenzae MLST website. There were 196 entries of Hia with 55 sequence types (STs) identified (as of September 3, 2020). BURST analysis clustered related STs into four complexes with ST-23, ST-4, ST-21 and ST-62 identified as their ancestral STs. The majority of Hia entries (73.4%) and STs (65.5%) were identified as clonal division I (ST-23 and the ST-4 complexes). Only 43 (21.9%) entries and 14 STs (25.5%) were identified as clonal division II (ST-62 and ST-21 complexes). Current data suggested most invasive Hia belonged to clonal division I and the ST-23 complex while most clonal division II Hia were respiratory isolates with the exception of ST-62 which was common among invasive Hia in the U.S. southwest. Comparison of the capsule bexABCD genes from clonal divisions I and II strains showed sequence diversity with variations following the pattern of clonal divisions. Evidence from the literature and the current study suggests recent emergence of invasive Hia might be related to capsule replacement subsequent to the implementation of the Hib conjugate vaccine and possibly exacerbated by other conjugate vaccines that may have altered the microbial flora of the human respiratory tract.

Clinical and Molecular Epidemiology of Invasive Haemophilus influenzae Serotype a Infections in Utah Children

BACKGROUND

Following widespread use of the Haemophilus influenzae serotype b (Hib) vaccine, H. influenzae serotype a (Hia) has emerged as an important pathogen in children in some regions. We describe the clinical features and molecular epidemiology of invasive Hia disease in children in Utah over an 11-year period.

METHODS

We identified cases of invasive Hia disease, defined as detection of Hia from a normally sterile site, in children aged <18 years from Utah between 2007 and 2017. Medical records were reviewed to determine demographic characteristics and clinical outcomes. Available Hia isolates were genotyped using multilocus sequence typing, and phylogenetic division was determined using sodC polymerase chain reaction. Presence of the putative virulence-associated IS1016-bexA duplication-deletion was evaluated.

RESULTS

We identified 51 children with invasive Hia. The average annual incidence was 1.7 cases per 100 000 children aged <5 years; 4.8 cases per 100 000 children aged <1 year. The median age was 11.3 months. The most common clinical presentation was meningitis (53%), followed by pneumonia (14%) and septic arthritis (14%). Twenty-two children (43%) required admission to an intensive care unit; 1 died. Sequence type (ST) 62, phylogenetic division II isolates caused 75% (21/28) of disease. No isolates contained the virulence-associated IS1016-bexA duplication-deletion.

CONCLUSIONS

Hia is a significant cause of severe invasive bacterial infection in Utah. The majority of infections were caused by ST62 isolates, a phylogenetic division II Hia type that lacks the IS1016-bexA duplication-deletion. Hia ST62 has not been commonly reported elsewhere, suggesting a unique molecular epidemiology in our population.

Genomic characterization of Haemophilus influenzae: a focus on the capsule locus

Background

Haemophilus influenzae (Hi) can cause invasive diseases such as meningitis, pneumonia, or sepsis. Typeable Hi includes six serotypes (a through f), each expressing a unique capsular polysaccharide. The capsule, encoded by the genes within the capsule locus, is a major virulence factor of typeable Hi. Non-typeable (NTHi) does not express capsule and is associated with invasive and non-invasive diseases.

Methods

A total of 395 typeable and 293 NTHi isolates were characterized by whole genome sequencing (WGS). Phylogenetic analysis and multilocus sequence typing were used to characterize the overall genetic diversity. Pair-wise comparisons were used to evaluate the capsule loci. A WGS serotyping method was developed to predict the Hi serotype. WGS serotyping results were compared to slide agglutination (SAST) or real-time PCR (rt-PCR) serotyping.

Results

Isolates of each Hi serotype clustered into one or two subclades, with each subclade being associated with a distinct sequence type (ST). NTHi isolates were genetically diverse, with seven subclades and 125 STs being detected. Regions I and III of the capsule locus were conserved among the six serotypes (≥82% nucleotide identity). In contrast, genes in Region II were less conserved, with only six gene pairs from all serotypes showing ≥56% nucleotide identity. The WGS serotyping method was 99.9% concordant with SAST and 100% concordant with rt-PCR in determining the Hi serotype.

Conclusions

Genomic analysis revealed a higher degree of genetic diversity among NTHi compared to typeable Hi. The WGS serotyping method accurately predicted the Hi capsule type and can serve as an alternative method for Hi serotyping.

hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus

Haemophilus influenzae exclusively colonizes the human nasopharynx and can cause a variety of respiratory infections as well as invasive diseases, including meningitis and sepsis. A key virulence determinant of H. influenzae is the polysaccharide capsule, of which six serotypes are known, each encoded by a distinct variation of the capsule biosynthesis locus (cap-a to cap-f).

Haemophilus influenzae exclusively colonizes the human nasopharynx and can cause a variety of respiratory infections as well as invasive diseases, including meningitis and sepsis. A key virulence determinant of H. influenzae is the polysaccharide capsule, of which six serotypes are known, each encoded by a distinct variation of the capsule biosynthesis locus (cap-a to cap-f). H. influenzae type b (Hib) was historically responsible for the majority of invasive H. influenzae disease, and its prevalence has been markedly reduced in countries that have implemented vaccination programs targeting this serotype. In the postvaccine era, nontypeable H. influenzae emerged as the most dominant group causing disease, but in recent years a resurgence of encapsulated H. influenzae strains has also been observed, most notably serotype a. Given the increasing incidence of encapsulated strains and the high frequency of Hib in countries without vaccination programs, there is growing interest in genomic epidemiology of H. influenzae. Here we present hicap, a software tool for rapid in silico serotype prediction from H. influenzae genome sequences. hicap is written using Python3 and is freely available at https://github.com/scwatts/hicap under the GNU General Public License v3 (GPL3). To demonstrate the utility of hicap, we used it to investigate the cap locus diversity and distribution in 691 high-quality H. influenzae genomes from GenBank. These analyses identified cap loci in 95 genomes and confirmed the general association of each serotype with a unique clonal lineage, and they also identified occasional recombination between lineages that gave rise to hybrid cap loci (2% of encapsulated strains).

Epidemiological analysis and rapid detection by one-step multiplex PCR assay of Haemophilus influenzae in children with respiratory tract infections in Zhejiang Province, China

Background

Haemophilus influenzae (H. influenzae) is one of the most important pathogenic bacteria causing respiratory tract infection diseases in children. There are two main types of H. influenzae, encapsulated H. influenzae and nontypeable H. influenzae (NTHi). Serotype b of H. influenzae (Hib) used to be the main epidemic type of H. influenzae, causing the invasive infection. However, the epidemiology of invasive H. influenzae disease has changed substantially, and most invasive diseases are now caused by NTHi and other serotypes of H. influenzae. The aim of this study was to determine the main epidemic strains of H. influenzae in Zhejiang Province in China, and establish a one-step multiplex PCR assay to distinguish H. influenzae from other bacteria associated with respiratory tract infections, and distinguish encapsulated H. influenzae from NTHi.

Method

In this study, bacterial culture and serum agglutination testing were used to determine the most prevalent serotype of H. influenzae, and the results have served as a gold standard for clinical diagnosis. We also designed a one-step multiplex PCR assay using several kinds of standard strains of respiratory tract infection bacteria, to examine the stability, specificity, and detection limit of the PCR assays. We then used 1514 nasopharyngeal secretion (NPS) samples collected from children with respiratory tract infections to verify the specificity and sensitivity of the PCR assay.

Results

The bacterial culture and serum agglutination test results showed that the positive rates of H. influenzae and encapsulated H. influenzae were 18.49 and 1.18%, respectively. The PCR results showed that the detection limit of the multiplex PCR assay was 1.89 × 10³ copies /μL, the ompP6 positive rate was 19.35%, and the bexA positive rate was 1.32%. The sensitivity and specificity of the multiplex PCR were 100 and 99.86%, respectively.

Conclusions

According to our study, the most prevalent H. influenzae subtype in Zhejiang Province was NTHi, account for 93.57%; the one-step multiplex PCR assay we established can be used as the differential detection of clinical H. influenzae strains, replacing routine bacterial culture and serum agglutination testing.

The capsule polymerase CslB of Neisseria meningitidis serogroup L catalyzes the synthesis of a complex trimeric repeating unit comprising glycosidic and phosphodiester linkages

Neisseria meningitidis is a human pathogen causing bacterial meningitis and sepsis. The capsular polysaccharide surrounding N. meningitidis is a major virulence factor. The capsular polysaccharide consists of polyhexosamine phosphates in N. meningitidis serogroups A and X. The capsule polymerases (CPs) of these serogroups are members of the Stealth protein family comprising d-hexose-1-phosphate transferases from bacterial and protozoan pathogens. CslA, one of two putative CPs of the pathophysiologically less relevant N. meningitidis serogroup L, is one of the smallest known Stealth proteins and caught our attention for structure-function analyses. Because the N. meningitidis serogroup L capsule polymer consists of a trimeric repeating unit ([→3)-β-d-GlcNAc-(1→3)-β-d-GlcNAc-(1→3)-α-d-GlcNAc-(1→OPO3→]n), we speculated that the two predicted CPs (CslA and CslB) work together in polymer production. Consequently, both enzymes were cloned, overexpressed, and purified as recombinant proteins. Contrary to our expectation, enzymatic testing identified CslB to be sufficient to catalyze the synthesis of the complex trimeric N. meningitidis serogroup L capsule polymer repeating unit. No polymerase activity was detected for CslA, although the enzyme facilitated the hydrolysis of UDP-GlcNAc. Bioinformatics analyses identified two glycosyltransferase (GT) domains in CslB. The N-terminal domain modeled with 100% confidence onto a number of GT-A folded proteins, whereas the C-terminal domain modeled with 100% confidence onto TagF, a GT-B folded teichoic acid polymerase from Staphylococcus epidermidis. Amino acid positions known to have critical catalytic functions in the template proteins were conserved in CslB, and their point mutation abolished enzyme activity. CslB represents an enzyme of so far unique complexity regarding both the catalyzed reaction and enzyme architecture.

The capsule biosynthesis locus of Haemophilus influenzae shows conspicuous similarity to the corresponding locus in Haemophilus sputorum and may have been recruited from this species by horizontal gene transfer

The newly described species Haemophilus sputorum has been cultured from the upper respiratory tract of humans and appears to have little pathogenic potential. The species encodes a capsular biosynthesis locus of approximately 12  kb composed of three distinct regions. Region I and III genes, involved in export and processing of the capsular material, show high similarity to the corresponding genes in capsulate lineages of the pathogenic species Haemophilus influenzae; indeed, standard bexA and bexB PCRs for detection of capsulated strains of H. influenzae give positive results with strains of H. sputorum. Three ORFs are present in region II of the sequenced strain of H. sputorum, of which a putative phosphotransferase showed homology with corresponding genes from H. influenzae serotype c and f. Phylogenetic analysis of housekeeping genes from 24 Pasteurellaceae species showed that H. sputorum was only distantly related to H. influenzae. In contrast to H. influenzae, the capsule locus in H. sputorum is not associated with transposases or other transposable elements. Our data suggest that the capsule locus of capsulate lineages of H. influenzae may have been recruited relatively recently from the commensal species H. sputorum by horizontal gene transfer.

Classification, identification, and clinical significance of Haemophilus and Aggregatibacter species with host specificity for humans

The aim of this review is to provide a comprehensive update on the current classification and identification of Haemophilus and Aggregatibacter species with exclusive or predominant host specificity for humans. Haemophilus influenzae and some of the other Haemophilus species are commonly encountered in the clinical microbiology laboratory and demonstrate a wide range of pathogenicity, from life-threatening invasive disease to respiratory infections to a nonpathogenic, commensal lifestyle. New species of Haemophilus have been described (Haemophilus pittmaniae and Haemophilus sputorum), and the new genus Aggregatibacter was created to accommodate some former Haemophilus and Actinobacillus species (Aggregatibacter aphrophilus, Aggregatibacter segnis, and Aggregatibacter actinomycetemcomitans). Aggregatibacter species are now a dominant etiology of infective endocarditis caused by fastidious organisms (HACEK endocarditis), and A. aphrophilus has emerged as an important cause of brain abscesses. Correct identification of Haemophilus and Aggregatibacter species based on phenotypic characterization can be challenging. It has become clear that 15 to 20% of presumptive H. influenzae isolates from the respiratory tracts of healthy individuals do not belong to this species but represent nonhemolytic variants of Haemophilus haemolyticus. Due to the limited pathogenicity of H. haemolyticus, the proportion of misidentified strains may be lower in clinical samples, but even among invasive strains, a misidentification rate of 0.5 to 2% can be found. Several methods have been investigated for differentiation of H. influenzae from its less pathogenic relatives, but a simple method for reliable discrimination is not available. With the implementation of identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry, the more rarely encountered species of Haemophilus and Aggregatibacter will increasingly be identified in clinical microbiology practice. However, identification of some strains will still be problematic, necessitating DNA sequencing of multiple housekeeping gene fragments or full-length 16S rRNA genes.

Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f

BACKGROUND

The incidence of invasive disease caused by encapsulated Haemophilus influenzae type f (Hif) has increased in the post-H. influenzae type b (Hib) vaccine era. We previously annotated the first complete Hif genome from a clinical isolate (KR494) that caused septic shock and necrotizing myositis. Here, the full genome of Hif KR494 was compared to sequenced reference strains Hib 10810, capsule type d (Hid) Rd Kw20, and finally nontypeable H. influenzae 3655. The goal was to identify possible genomic characteristics that may shed light upon the pathogenesis of Hif.

RESULTS

The Hif KR494 genome exhibited large regions of synteny with other H. influenzae, but also distinct genome rearrangements. A predicted Hif core genome of 1390 genes was shared with the reference strains, and 6 unique genomic regions comprising half of the 191 unique coding sequences were revealed. The majority of these regions were inserted genetic fragments, most likely derived from the closely-related Haemophilus spp. including H. aegyptius, H. haemolyticus and H. parainfluenzae. Importantly, the KR494 genome possessed several putative virulence genes that were distinct from non-type f strains. These included the sap2 operon, aef3 fimbriae, and genes for kanamycin nucleotidyltranserase, iron-utilization proteins, and putative YadA-like trimeric autotransporters that may increase the bacterial virulence. Furthermore, Hif KR494 lacked a hisABCDEFGH operon for de novo histidine biosynthesis, hmg locus for lipooligosaccharide biosynthesis and biofilm formation, the Haemophilus antibiotic resistance island and a Haemophilus secondary molybdate transport system. We confirmed the histidine auxotrophy and kanamycin resistance in Hif by functional experiments. Moreover, the pattern of unique or missing genes of Hif KR494 was similar in 20 Hif clinical isolates obtained from different years and geographical areas. A cross-species comparison revealed that the Hif genome shared more characteristics with H. aegyptius than Hid and NTHi.

CONCLUSIONS

The genomic comparative analyses facilitated identification of genotypic characteristics that may be related to the specific virulence of Hif. In relation to non-type f H. influenzae strains, the Hif genome contains differences in components involved in metabolism and survival that may contribute to its invasiveness.

Haemophilus influenzae serotype a as a cause of serious invasive infections

Haemophilus influenzae, particularly H influenzae serotype b (Hib), is an important pathogen that causes serious diseases like meningitis and septicaemia. Since the introduction of Hib conjugate vaccines in the 1990s, the epidemiology of invasive H influenzae disease has changed substantially, with most infections now caused by non-Hib strains. We discuss the importance of H influenzae serotype a (Hia) as a cause of serious morbidity and mortality and its global epidemiology, clinical presentation, microbiology, immunology, prevention, and control. Much like Hib, the capsule of Hia is an important virulence factor contributing to the development of invasive disease. Molecular typing of Hia has identified distinct clonal groups, with some linked to severe disease and high case-fatality rates. Similarities between Hia and Hib capsules, their clinical presentation, and immunology of infection suggest that a bivalent Hia-Hib capsular polysaccharide-protein conjugate vaccine could offer protection against these two important serotypes of H influenzae.

Real-time polymerase chain reaction for detection of encapsulated Haemophilus influenzae using degenerate primers to target the capsule transport gene bexA

A real-time polymerase chain reaction assay that uses degenerate primers and a dual-labelled probe was developed to detect the bexA gene of Haemophilus influenzae, including those belonging to non-b serotypes as well as clonal division II strains. This assay is sensitive and specific, detecting 20 copies of the gene, but negative with a variety of bacteria associated with meningitis and bacteremia or septicemia.

Use of bexB to detect the capsule locus in Haemophilus influenzae

Haemophilus influenzae strains are classified as typeable or nontypeable H. influenzae (NTHI) based upon the presence or absence of capsule. In addition to serotyping, which is subject to false-positive results, typeable strains can be identified through the detection of the capsular export gene bexA and one of six capsule-specific genes, but this method is resource intensive, especially in characterizing large numbers of strains. To address these challenges, we developed a bexB-based method to differentiate true NTHI strains from typeable strains. We validated a PCR-based method to detect bexB in 10 strains whose capsule status was well defined. Among 40 strains that were previously serotype positive in clinical microbiology laboratories, 5 lacked bexA, bexB, and capsule type-specific genes by PCR analysis and thus likely represent false-positive serotyping results. Among 94 additional otitis media, commensal, and serotype b-negative invasive strains, 85 were bexA and bexB negative and 9 contained either a complete or partial capsule locus, i.e., 8 were bexA and bexB positive and 1 was bexA negative but bexB positive. Finally, we adapted the method for use in a high-throughput DNA hybridization-based microarray method, which showed 98.75 and 97.5% concordance to the PCR methods for bexA and bexB, respectively. In addition, bexB showed 84% or greater nucleotide identity among strains containing the capsule locus. In this study, we demonstrate that bexB is a reliable proxy for the capsule locus and that its detection provides a simple and reliable method for differentiating strains that lack the entire capsule locus from those containing a partial or complete capsule locus.

Sequence analysis of serotype-specific synthesis regions II of Haemophilus influenzae serotypes c and d: evidence for common ancestry of capsule synthesis in Pasteurellaceae and Neisseria meningitidis

Sequencing of yet unknown Haemophilus influenzae serotype c (Hic) and d (Hid) capsule synthesis regions II revealed four (ccs1-4) and five (dcs1-5) open reading frames, respectively. The inferred gene functions were in line with capsular polysaccharide structures. One or more proteins encoded by the Hic capsule synthesis region II showed similarity to Actinobacillus pleuropneumoniae serotype 1 and Actinobacillus suis K1 enzymes. Orthologues to the complete operon were observed in Actinobacillus minor strain 202, where even the gene order was conserved. Furthermore, Ccs4 was related to the capsule O-acetyltransferase of Neisseria meningitidis serogroup W-135. For the Hid locus, similarities to Hie, Mannheimia haemolytica A1 and N. meningitidis serogroup A were identified and the succession of genes was similar in the different species. The resemblance of genes and gene organization found for Hic and Hid with other species suggested horizontal gene transfer during capsule evolution across the bacterial classes.

Genetic characterization of the capsulation locus of Haemophilus influenzae serotype e

The capsulation (cap) locus of Haemophilus influenzae type e (Hie) was characterized and sequenced. No IS1016 element was found to flank the locus. The 18.2-kb locus included 14 open reading frames (ORFs), which were grouped into three functional regions. Eight new ORFs (named ecs1 to ecs8) were identified in the Hie capsule-specific region II.

Prevalence of the sodC gene in nontypeable Haemophilus influenzae and Haemophilus haemolyticus by microarray-based hybridization

The sodC gene has been reported to be a useful marker for differentiating nontypeable (NT) Haemophilus influenzae from Haemophilus haemolyticus in respiratory-tract samples, but discrepancies exist as to the prevalence of sodC in NT H. influenzae. Therefore, we used a microarray-based, "library-on-a-slide" method to differentiate the species and found that 21 of 169 (12.4%) NT H. influenzae strains and all 110 (100%) H. haemolyticus strains possessed the sodC gene. Multilocus sequence analysis confirmed that the 21 NT H. influenzae strains were H. influenzae and not H. haemolyticus. An inactive sodC gene has been reported in encapsulated H. influenzae strains belonging to phylogenetic division II. Capsule-specific Southern hybridization and PCR and a lack of copper/zinc-cofactored superoxide dismutase (CuZnSOD) expression indicated that 6 of the 21 sodC-containing NT H. influenzae strains in our study were likely capsule-deficient mutants belonging to phylogenetic division II. DNA sequence comparisons of the 21 H. influenzae sodC genes with sodC from H. haemolyticus or encapsulated H. influenzae demonstrated that the sodC genes of the six H. influenzae capsule-deficient mutants were, on average, 99% identical to sodC from encapsulated H. influenzae but only 85% identical to sodC from H. haemolyticus. The sodC genes from 2/15 NT H. influenzae strains were similarly more closely related to sodC from encapsulated strains, while sodC genes from 13 NT H. influenzae strains were almost 95% identical to sodC genes from H. haemolyticus, suggesting the possibility of interspecies recombination in these strains. In summary, this study demonstrates that sodC is not completely absent (9.2%) in true NT H. influenzae strains.

Detection of cryptic genospecies misidentified as Haemophilus influenzae in routine clinical samples by assessment of marker genes fucK, hap, and sodC

Clinical isolates of Haemophilus influenzae were assessed for the presence of fucK, hap, and sodC by hybridization with gene-specific probes, and isolates diverging from the expected H. influenzae genotype were characterized by phenotype and 16S rRNA gene sequencing. Two of 480 isolates were finally classified as variant strains ("nonhemolytic Haemophilus haemolyticus").

Nanoscale structural and mechanical properties of nontypeable Haemophilus influenzae biofilms

Nontypeable Haemophilus influenzae (NTHI) bacteria are commensals in the human nasopharynx, as well as pathogens associated with a spectrum of acute and chronic infections. Two important factors that influence NTHI pathogenicity are their ability to adhere to human tissue and their ability to form biofilms. Extracellular polymeric substances (EPS) and bacterial appendages such as pili critically influence cell adhesion and intercellular cohesion during biofilm formation. Structural components in the outer cell membrane, such as lipopolysaccharides, also play a fundamental role in infection of the host organism. In spite of their importance, these pathogenic factors are not yet well characterized at the nanoscale. Here, atomic force microscopy (AFM) was used in aqueous environments to visualize structural details, including probable Hif-type pili, of live NTHI bacteria at the early stages of biofilm formation. Using single-molecule AFM-based spectroscopy, the molecular elasticities of lipooligosaccharides present on NTHI cell surfaces were analyzed and compared between two strains (PittEE and PittGG) with very different pathogenicity profiles. Furthermore, the stiffness of single cells of both strains was measured and subsequently their turgor pressure was estimated.

Genome-based vaccine development: a short cut for the future

Bacterial infectious diseases remain a major cause of deaths and disabilities in the world. Although conventional vaccinology approaches were successful in conferring protection against several diseases, they failed in providing efficient vaccines against many others. Together to the sequencing of the first genome, a new chapter in the vaccinology history started to be written. Reverse vaccinology changed the way to think about vaccine development, using the information provided by the microorganisms' genome against themselves. Since then, reverse vaccinology has evolved and helped researchers to overcome the limits of the conventional vaccinology approaches and led to the discovery and development of novel vaccines concerning emerging diseases, like Neisseria meningitidis B and Streptococcus agalactiae. A lot of work must be done, but deciphering the information provided by genome sequences and using it to better understand the host-pathogen interactions has proved to be the key for protection.

Delineation of the species Haemophilus influenzae by phenotype, multilocus sequence phylogeny, and detection of marker genes

To obtain more information on the much-debated definition of prokaryotic species, we investigated the borders of Haemophilus influenzae by comparative analysis of H. influenzae reference strains with closely related bacteria including strains assigned to Haemophilus haemolyticus, cryptic genospecies biotype IV, and the never formally validated species "Haemophilus intermedius". Multilocus sequence phylogeny based on six housekeeping genes separated a cluster encompassing the type and the reference strains of H. influenzae from 31 more distantly related strains. Comparison of 16S rRNA gene sequences supported this delineation but was obscured by a conspicuously high number of polymorphic sites in many of the strains that did not belong to the core group of H. influenzae strains. The division was corroborated by the differential presence of genes encoding H. influenzae adhesion and penetration protein, fuculokinase, and Cu,Zn-superoxide dismutase, whereas immunoglobulin A1 protease activity or the presence of the iga gene was of limited discriminatory value. The existence of porphyrin-synthesizing strains ("H. intermedius") closely related to H. influenzae was confirmed. Several chromosomally encoded hemin biosynthesis genes were identified, and sequence analysis showed these genes to represent an ancestral genotype rather than recent transfers from, e.g., Haemophilus parainfluenzae. Strains previously assigned to H. haemolyticus formed several separate lineages within a distinct but deeply branching cluster, intermingled with strains of "H. intermedius" and cryptic genospecies biotype IV. Although H. influenzae is phenotypically more homogenous than some other Haemophilus species, the genetic diversity and multicluster structure of strains traditionally associated with H. influenzae make it difficult to define the natural borders of that species.

Two variants among Haemophilus influenzae serotype b strains with distinct bcs4, hcsA and hcsB genes display differences in expression of the polysaccharide capsule

Background

Despite nearly complete vaccine coverage, a small number of fully vaccinated children in the Netherlands have experienced invasive disease caused by Haemophilus influenzae serotype b (Hib). This increase started in 2002, nine years after the introduction of nationwide vaccination in the Netherlands. The capsular polysaccharide of Hib is used as a conjugate vaccine to protect against Hib disease. To evaluate the possible rise of escape variants, explaining the increased number of vaccine failures we analyzed the composition of the capsular genes and the expressed polysaccharide of Dutch Hib strains collected before and after the introduction of Hib vaccination.

Results

The DNA sequences of the complete capsular gene clusters of 9 Dutch Hib strains were assessed and two variants, designated type I and type II were found. The two variants displayed considerable sequence divergence in the hcsA and hcsB genes, involved in transport of capsular polysaccharide to the cell surface. Application of hcsA type specific PCRs on 670 Hib strains collected from Dutch patients with invasive Hib disease showed that 5% of the strains collected before 1996 were type II. No endogenous type II Hib strains were isolated after 1995 and all type II strains were isolated from 0–4 year old, non-vaccinated children only. Analysis of a worldwide collection of Hib strains from the pre-vaccination era revealed considerable geographic differences in the distribution of the type I and type II strains with up to 73% of type II strains in the USA. NMR analysis of type I and type II capsule polysaccharides did not reveal structural differences. However, type I strains were shown to produce twice as much surface bound capsular polysaccharide.

Conclusion

Type II strains were only isolated during the pre-vaccination era from young, non-vaccinated individuals and displayed a lower expression of capsular polysaccharide than type I strains. The higher polysaccharide expression may have provided a selective advantage for type I strains resulting in the rapid elimination of type II from the Dutch Hib population after introduction of nationwide Hib vaccination. However, this phenomenon does not explain the increase in the number of Hib vaccine failures in the Netherlands.

Molecular characterization of four Haemophilus influenzae serotype a strains isolated from patients in Quebec, Canada

Four epidemiologically unrelated Haemophilus influenzae serotype a (Hia) strains from patients in Quebec, Canada, were characterized and found to represent 3 distinct groups. One isolate, found to be biotype I and sequence type (ST)-62 by multilocus sequence typing, was shown to possess the copper- and zinc-containing superoxide dismutase gene, sodC, and was suspected to belong to clonal division II. The other 3 isolates were classified as clonal division I based on the absence of the sodC gene. Among the 3 sodC-negative Hia strains, 2 were biotype II and had related STs (ST-23 and ST-403) and highly similar DNA fingerprints, similar to a group of previously described Hia isolates causing invasive disease in Manitoba, Canada. The remaining sodC-negative strain belonged to biotype I and ST-4 and shared no common allele with ST-23, ST-403, or ST-62. This isolate also possessed the IS1016-bexA partial deletion, which is often associated with increased virulence. Despite the small number of isolates used in this study, our finding of 3 distinct groups shows the existence of a potential genetic diversity not previously described for Hia. Whether this genetic diversity is related to the severity and epidemiology of Hia disease requires further studies.

Real-time PCR for determining capsular serotypes of Haemophilus influenzae

A two-step real-time PCR assay targeting all six capsulation loci of Haemophilus influenzae (i.e., serotypes a to f) was developed and compared with a previously published qualitative PCR assay by using 131 H. influenzae clinical isolates. There was a 98.5% concordance between the two tests. The sensitivity of detection of capsular type-specific reference strains of H. influenzae a to c (10(1) CFU/PCR) was higher than that for type e (10(3) CFU/PCR) and types d and f (10(4) CFU/PCR), and a broader dynamic range was obtained (5 to 8 log(10) units). No cross-reaction was observed with bacteria commonly isolated from the respiratory tract. We showed that both PCR assays are more reliable than slide agglutination serotyping. The real-time PCR-based assay seems to be an alternative of choice for the epidemiological follow-up of H. influenzae invasive infections.

Nucleotide sequence diversity of the bexA gene in serotypeable Haemophilus influenzae strains recovered from invasive disease patients in Canada

The bexA genes of 36 Haemophilus influenzae isolates were sequenced to reveal their nucleotide sequence diversity, which divided them into two groups, similar to clonal divisions I and II. This sequence diversity may lead to false-negative PCR results for H. influenzae infections if bexA is the chosen gene target.

Commensals upon us

A battle to control and curtail bacterial infectious diseases is being waged in our hospitals and communities through antibiotic therapies and vaccines targeting specific species. But what effects do these interventions have on the epidemiology of infections caused by the organisms that are part of our natural microbial flora? Gram-positive and gram-negative bacteria appear as new disease agents from among commensal flora. These include vancomycin resistant enterococci (VRE), community-associated methicillin resistant Staphylococcus aureus (CA-MRSA), non-vaccine invasive serotypes of Streptococcus pneumoniae, new strains of non-type b Haemophilus influenzae and multi-drug resistant Escherichia coli. These examples illustrate how clinical improvements and widespread use and misuse of antibiotics have pushed evolution, allowing normally non-pathogenic strains to become infectious disease threats to human health.

Stealth proteins: in silico identification of a novel protein family rendering bacterial pathogens invisible to host immune defense

There are a variety of bacterial defense strategies to survive in a hostile environment. Generation of extracellular polysaccharides has proved to be a simple but effective strategy against the host's innate immune system. A comparative genomics approach led us to identify a new protein family termed Stealth, most likely involved in the synthesis of extracellular polysaccharides. This protein family is characterized by a series of domains conserved across phylogeny from bacteria to eukaryotes. In bacteria, Stealth (previously characterized as SacB, XcbA, or WefC) is encoded by subsets of strains mainly colonizing multicellular organisms, with evidence for a protective effect against the host innate immune defense. More specifically, integrating all the available information about Stealth proteins in bacteria, we propose that Stealth is a D-hexose-1-phosphoryl transferase involved in the synthesis of polysaccharides. In the animal kingdom, Stealth is strongly conserved across evolution from social amoebas to simple and complex multicellular organisms, such as Dictyostelium discoideum, hydra, and human. Based on the occurrence of Stealth in most Eukaryotes and a subset of Prokaryotes together with its potential role in extracellular polysaccharide synthesis, we propose that metazoan Stealth functions to regulate the innate immune system. Moreover, there is good reason to speculate that the acquisition and spread of Stealth could be responsible for future epidemic outbreaks of infectious diseases caused by a large variety of eubacterial pathogens. Our in silico identification of a homologous protein in the human host will help to elucidate the causes of Stealth-dependent virulence. At a more basic level, the characterization of the molecular and cellular function of Stealth proteins may shed light on fundamental mechanisms of innate immune defense against microbial invasion.

Failure to detect capsule gene bexA in Haemophilus influenzae types e and f by real-time PCR due to sequence variation within probe binding sites

Detection of the conserved capsule gene bexA is used to distinguish capsulate from non-capsulate Haemophilus influenzae. While developing a real-time PCR assay to detect bexA, it was found that bexA probes produced a detectable signal for H. influenzae types a to d, but failed to do so for H. influenzae types e and f. Sequencing revealed differences compared with H. influenzae types a to d within probe binding sites. To prevent misclassification of strains as non-capsulate, assays must detect all capsular types.