<i>Haemophilus influenzae</i>
            : Genetic Variability and Natural Selection To Identify Virulence Factors

Gilsdorf, Janet R.; Marrs, Carl F.; Foxman, Betsy

doi:10.1128/iai.72.5.2457-2461.2004

Cited by 57 publications

(40 citation statements)

References 51 publications

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“…The ability to incorporate exogenous DNA facilitates horizontal gene exchange, considering also that multiple H. influenzae strains may colonize the nasopharynx. Several H. influenzae genes encoding virulence factors, such as hifA, hifE, and hap, exhibit intragenic mosaicism, an apparent mixing and matching of gene regions acquired from other H. influenzae strains, probably as a result of horizontal gene transfer through transformation and homologous recombination (6,13,18,21).…”

Section: Vol 74 2006 Variation In H Influenzae Hmw Binding Domainsmentioning

confidence: 99%

Conservation and Diversity of HMW1 and HMW2 Adhesin Binding Domains among Invasive Nontypeable Haemophilus influenzae Isolates

Giufrè¹,

Muscillo

Spigaglia³

et al. 2006

Infect Immun

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The pathogenesis of nontypeable Haemophilus influenzae (NTHi) begins with adhesion to the rhinopharyngeal mucosa. In almost 80% of NTHi clinical isolates, the HMW proteins are the major adhesins. The prototype HMW1 and HMW2 proteins, identified in NTHi strain 12, exhibit different binding specificities. The two binding domains have been localized in regions of maximal sequence dissimilarity (40% identity, 58% similarity). Two areas within these binding domains have been found essential for full level adhesive activity (designated the core-binding domains). To investigate the conservation and diversity of the HMW1 and HMW2 core-binding domains among isolates, PCR and DNA sequencing were used. First, we separately amplified the hmw1A-like and hmw2A-like structural genes in nine invasive NTHi isolates, discovering two new hmwA alleles, whose sequences are herein reported. Then, the hmw1A-like and hmw2A-like PCR products were used as the template in nested PCR to produce amplicons encompassing the encoding sequences of the two core-binding domains. In-depth sequence analysis was then performed among sequences of each group, with the support of specific computer programs. Overall, extensive sequence diversity among isolates was highlighted. However, similarity plots showed patterns consisting of peaks of relatively high similarity alternating with strongly divergent regions. The phylogenetic tree clearly indicated the HMW1-like and HMW2-like core-binding domain sequences as two clusters. Distinct sets of conserved amino acid motifs were identified within each group of sequences using the MEME/MOTIFSEARCH tool. Since HMW adhesins could represent candidates for future vaccines, identification of specific patterns of conserved motifs in otherwise highly variable regions is of great interest.Nontypeable Haemophilus influenzae (NTHi) is regarded as an important human pathogen, able to cause human respiratory tract disease and, especially in adults, invasive diseases such as meningitis and septicemia (11,12). The initial step in the pathogenesis of NTHi disease involves establishment of bacteria on the rhinopharyngeal respiratory mucosa followed by contiguous spread within the respiratory tract and, occasionally, to sterile sites. A number of adherence factors, including both pilus and nonpilus adhesins, have been identified (24). In almost 80% of NTHi clinical isolates, the HMW proteins are the major adhesins responsible for attachment to human epithelial cells (29). They were originally identified as a group of high-molecular-weight, surface-exposed proteins, predominant targets of human serum antibody response during acute otitis media (1).Given their functional role and their immunogenic character, HMW proteins have gained special consideration as NTHi vaccine candidates. The prototype proteins were detected in NTHi strain 12 and were designated HMW1 and HMW2 (2). They are encoded by separate chromosomal loci, hmw1 and hmw2, respectively, the hmwA gene encoding the structural protein, and two accessory genes, called hm...

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Section: Vol 74 2006 Variation In H Influenzae Hmw Binding Domainsmentioning

confidence: 99%

Conservation and Diversity of HMW1 and HMW2 Adhesin Binding Domains among Invasive Nontypeable Haemophilus influenzae Isolates

Giufrè¹,

Muscillo

Spigaglia³

et al. 2006

Infect Immun

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“…Two prior genomic studies have approached this problem by comparing an isolate from a diseased patient to an isolate from an asymptomatic carrier of G. vaginalis (29,78). Both studies identified differences in gene content, and yet the link between these differences and their pathogenic potential remains speculative, in part due to the fact that a pathogen may be present even in individuals who are not diseased, as is often seen in nasopharyngeal pathogens such as Haemophilus influenzae (15,23,43,50,77) and Streptococcus pneumoniae (60,61). In addition, individuals are often found to carry multiple strains of G. vaginalis, any of which might be responsible for pathogenicity (11).…”

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confidence: 99%

Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with Subspeciation into Genovars

et al. 2012

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Gardnerella vaginalis is associated with a spectrum of clinical conditions, suggesting high degrees of genetic heterogeneity among stains. Seventeen G. vaginalis isolates were subjected to a battery of comparative genomic analyses to determine their level of relatedness. For each measure, the degree of difference among the G. vaginalis strains was the highest observed among 23 pathogenic bacterial species for which at least eight genomes are available. Genome sizes ranged from 1.491 to 1.716 Mb; GC contents ranged from 41.18% to 43.40%; and the core genome, consisting of only 746 genes, makes up only 51.6% of each strain's genome on average and accounts for only 27% of the species supragenome. Neighbor-grouping analyses, using both distributed gene possession data and core gene allelic data, each identified two major sets of strains, each of which is composed of two groups. Each of the four groups has its own characteristic genome size, GC ratio, and greatly expanded core gene content, making the genomic diversity of each group within the range for other bacterial species. To test whether these 4 groups corresponded to genetically isolated clades, we inferred the phylogeny of each distributed gene that was present in at least two strains and absent in at least two strains; this analysis identified frequent homologous recombination within groups but not between groups or sets. G. vaginalis appears to include four nonrecombining groups/clades of organisms with distinct gene pools and genomic properties, which may confer distinct ecological properties. Consequently, it may be appropriate to treat these four groups as separate species.

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“…These sequences include genes encoding virulence-associated autotransporters (14,48), hemagglutinating pili (66), novel NTHi sequences expressed during interaction with human epithelial cell lines (67), genes that are upregulated in the middle ear in a chinchilla model of acute otitis media (42), and uncharacterized sequences predicted to encode hypothetical or phage-like proteins (47). Such sequences have come to be recognized as components of a set of contingency genes that are available to H. influenzae at a population level and are distributed among the clinical strains; however, no single strain has the full complement of genes present in the population-based supragenome (15,21,24).…”

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confidence: 99%

Identification, Distribution, and Expression of Novel Genes in 10 Clinical Isolates of Nontypeable Haemophilus influenzae

et al. 2005

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We hypothesize that Haemophilus influenzae, as a species, possesses a much greater number of genes than that found in any single H. influenzae genome. This supragenome is distributed throughout naturally occurring infectious populations, and new strains arise through autocompetence and autotransformation systems. The effect is that H. influenzae populations can readily adapt to environmental stressors. The supragenome hypothesis predicts that significant differences exist between and among the genomes of individual infectious strains of nontypeable H. influenzae (NTHi). To test this prediction, we obtained 10 low-passage NTHi clinical isolates from the middle ear effusions of patients with chronic otitis media. DNA sequencing was performed with 771 clones chosen at random from a pooled genomic library. Homology searching demonstrated that ϳ10% of these clones were novel compared to the H. influenzae Rd KW20 genome, and most of them did not match any DNA sequence in GenBank. Amino acid homology searches using hypothetical translations of the open reading frames revealed homologies to a variety of proteins, including bacterial virulence factors not previously identified in the NTHi isolates. The distribution and expression of 53 of these genes among the 10 strains were determined by PCR-and reverse transcription PCR-based analyses. These unique genes were nonuniformly distributed among the 10 isolates, and transcription of these genes in planktonic cultures was detected in 50% (177 of 352) of the occurrences. All of the novel sequences were transcribed in one or more of the NTHi isolates. Seventeen percent (9 of 53) of the novel genes were identified in all 10 NTHi strains, with each of the remaining 44 being present in only a subset of the strains. These genic distribution analyses were more effective as a strain discrimination tool than either multilocus sequence typing or 23S ribosomal gene typing methods.

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Haemophilus influenzae : Genetic Variability and Natural Selection To Identify Virulence Factors

Cited by 57 publications

References 51 publications

Conservation and Diversity of HMW1 and HMW2 Adhesin Binding Domains among Invasive Nontypeable Haemophilus influenzae Isolates

Conservation and Diversity of HMW1 and HMW2 Adhesin Binding Domains among Invasive Nontypeable Haemophilus influenzae Isolates

Comparative Genomic Analyses of 17 Clinical Isolates of Gardnerella vaginalis Provide Evidence of Multiple Genetically Isolated Clades Consistent with Subspeciation into Genovars

Identification, Distribution, and Expression of Novel Genes in 10 Clinical Isolates of Nontypeable Haemophilus influenzae

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