Multilocus sequence phylogenetic study of the genus Haemophilus with description of Haemophilus pittmaniae sp. nov.

Nørskov‐Lauritsen, Niels; Bruun, Brita; Kilian, Mogens

doi:10.1099/ijs.0.63325-0

Cited by 60 publications

(62 citation statements)

References 26 publications

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“…Recently, Nørskov-Lauritsen et al (42) defined the relationships of human-specific haemophili within the family Pasteurellaceae by performing MLSA with partial, concatenated adk, pgi, recA, and infB gene sequences. Since this approach revealed that both H. influenzae and H. haemolyticus were present in an Haemophilus sensu stricto phylogenetic cluster and were separate from other members of the family, we have used it to determine if the NT H. influenzae and H. haemolyticus (hemolytic and nonhemolytic) strains in our study also maintain the same relationships.…”

Section: Resultsmentioning

confidence: 99%

“…Partial DNA sequences of the adk, pgi, recA, and infB genes were generated for MLSA according to the strategy used by Nørskov-Lauritsen et al (42), with the exception that the oligonucleotides used for PCR amplification of these genes in the present study were based on sequences from H. influenzae strain Rd ( Table 2). The oligonucleotides used for PCR amplification of the partial 16S rRNA gene sequences for the differentiation of Haemophilus species have been described previously (32) ( (42) and for infB (20). The 16S rRNA gene sequences for a subset of these strains ( Fig.…”

Section: Methodsmentioning

confidence: 99%

“…Initial phylogenetic studies performed by using DNA-DNA hybridization revealed that H. haemolyticus associated with H. influenzae in a cluster of the family Pasteurellaceae termed Haemophilus sensu stricto (6,41,47), and these results were substantiated by analysis of the 16S rRNA gene (8,9,43), analysis of the infB gene (20), or multilocus sequence analysis (MLSA) (42).…”

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Relationships of Nontypeable Haemophilus influenzae Strains to Hemolytic and Nonhemolytic Haemophilus haemolyticus Strains

et al. 2008

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Haemophilus influenzae is both a human respiratory pathogen and pharyngeal commensal, while H. haemolyticus, the closest phylogenetic relative of H. influenzae, is arguably a strict pharyngeal commensal. A hemolytic phenotype has historically differentiated H. haemolyticus from H. influenzae, but the recent recognition of significant nonhemolytic H. haemolyticus colonization has decreased this trait's resolvability. Given this and the potential of recombination between the species, we examined the distribution of microbiologic and molecular traits between collections of H. influenzae and H. haemolyticus strains separated within a dendrogram obtained by multilocus sequence analysis (MLSA). All strains hybridizing with a probe to iga, a gene encoding an immunoglobulin A protease of H. influenzae, clustered apart from strains that did not hybridize with the probe. Other traits also segregated significantly along this division, suggesting a separation of the species. Of note, the LOS genes licA, lic2A, and lgtC of H. influenzae were approximately 2, 6, and 54 times, respectively, more prevalent in H. influenzae than in H. haemolyticus. In contrast to species separation, interspecies recombination was evidenced by the inability of single gene sequences to phylogenetically separate the species and by the "fuzzy" distribution of some species-specific traits across the species dividing line. Together, these data support the historically accurate and pragmatic division of these species while recognizing their potential for recombination. Future comparative genomic studies identifying common and distinctive genes could be useful in evaluating their role in the commensal or virulent growth, respectively, of H. influenzae.Haemophilus influenzae is one of eight Haemophilus species that reside as commensal organisms in the pharyngeal cavity of humans. These other commensal Haemophilus species include H. parainfluenzae, H. haemolyticus, H. parahaemolyticus, H. paraphrohaemolyticus, H. segnis, H. aphrophilus, and H. paraphrophilus. H. influenzae is by far the most pathogenic member of the genus in humans. Strains possessing a type b capsule are often associated with invasive diseases, such as meningitis, sepsis, and pneumonia; and strains lacking a capsule (referred to as nontypeable [NT]) are associated with localized mucosal diseases, such as otitis media, sinusitis, and bronchitis. Other haemophili are considered to be rarely associated with disease, and H. haemolyticus has never been implicated as an infectious disease agent (1).In contrast to other haemophili, H. haemolyticus and H. influenzae both depend on X (hemin) and V (NAD) growth factors, both lack the ability to ferment sucrose, both share similar GϩC contents, and both are nearly indistinguishable by their colony and cellular morphologies (25). Initial phylogenetic studies performed by using DNA-DNA hybridization revealed that H. haemolyticus associated with H. influenzae in a cluster of the family Pasteurellaceae termed Haemophilus sensu stricto (6,41,47), and t...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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confidence: 99%

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Relationships of Nontypeable Haemophilus influenzae Strains to Hemolytic and Nonhemolytic Haemophilus haemolyticus Strains

et al. 2008

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“…In the study of Nørskov-Lauritsen et al (2005), four genes were used for MLSA comparison to describe the novel species Haemophilus pittmaniae, supporting DNA-DNA hybridization results. Three of the housekeeping genes were selected from the multilocus sequence typing (MLST) study of Haemophilus influenzae (Meats et al, 2003).…”

Section: Taxonomic Investigation At the Species Levelmentioning

confidence: 99%

Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae

Christensen

Kuhnert

Busse

et al. 2007

International Journal of Systematic and Evolutionary Microbiology

115

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4Rødding Tvaervej 3, 6630 Rødding, DenmarkPrinciples and guidelines are presented to ensure a solid scientific standard of papers dealing with the taxonomy of taxa of Pasteurellaceae Pohl 1981. The classification of the Pasteurellaceae is in principle based on a polyphasic approach. DNA sequencing of certain genes is very important for defining the borders of a taxon. However, the characteristics that are common to all members of the taxon and which might be helpful for separating it from related taxa must also be identified. Descriptions have to be based on as many strains as possible (inclusion of at least five strains is highly desirable), representing different sources with respect to geography and ecology, to allow proper characterization both phenotypically and genotypically, to establish the extent of diversity of the cluster to be named. A genus must be monophyletic based on 16S rRNA gene sequence-based phylogenetic analysis. Only in very rare cases is it acceptable that monophyly can not be achieved by 16S rRNA gene sequence comparison. Recently, the monophyly of genera has been confirmed by sequence comparison of housekeeping genes. In principle, a new genus should be recognized by a distinct phenotype, and characters that separate the new genus from its neighbours should be given clearly. Due to the overall importance of accurate classification of species, at least two genotypic methods are needed to show coherence and for separation at the species level. The main criterion for the classification of a novel species is that it forms a monophyletic group based on 16S rRNA gene sequence-based phylogenetic analysis. However, some groups might also include closely related species. In these cases, more sensitive tools for genetic recognition of species should be applied, such as DNA-DNA hybridizations. The comparison of housekeeping gene sequences has recently been used for genotypic definition of species. In order to separate species, phenotypic characters must also be identified to recognize them, and at least two phenotypic differences from existing species should be identified if possible. We recommend the use of the subspecies category only for subgroups associated with disease or similar biological characteristics. At the subspecies level, the genotypic groups must always be nested within the boundaries of an existing species. Phenotypic cohesion must be documented at the subspecies level and separation between subspecies and related species must be fully documented, as well as association with particular disease and host. An overview of methods previously used to characterize isolates of the Pasteurellaceae has been given. Genotypic and phenotypic methods are separated in relation to tests for investigating diversity and cohesion and to separate taxa at the level of genus as well as species and subspecies. et al., 1992). However, it makes no sense to name a novel taxon without having considered its specific properties and evaluated how it differs from related taxa. To ensure the optimal circumscript...

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“…As a result of improved sequencing technologies, identification based on sequence comparisons of multiple housekeeping genes has become technically and economically feasible. Multilocus sequence analysis (MLSA) eliminates the potential problems resulting from homologous recombination and has been applied with success in the identification of several bacterial species that are difficult to differentiate by simpler methods (5,13,17,18,23,29,25,33). Schemes based on four to seven gene loci have proven valuable in differentiation of Streptococcus species (5, 17, 18).…”

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Novel Molecular Method for Identification of Streptococcus pneumoniae Applicable to Clinical Microbiology and 16S rRNA Sequence-Based Microbiome Studies

2012

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The close phylogenetic relationship of the important pathogen Streptococcus pneumoniae and several species of commensal streptococci, particularly Streptococcus mitis and Streptococcus pseudopneumoniae , and the recently demonstrated sharing of genes and phenotypic traits previously considered specific for S. pneumoniae hamper the exact identification of S. pneumoniae . Based on sequence analysis of 16S rRNA genes of a collection of 634 streptococcal strains, identified by multilocus sequence analysis, we detected a cytosine at position 203 present in all 440 strains of S. pneumoniae but replaced by an adenosine residue in all strains representing other species of mitis group streptococci. The S. pneumoniae -specific sequence signature could be demonstrated by sequence analysis or indirectly by restriction endonuclease digestion of a PCR amplicon covering the site. The S. pneumoniae -specific signature offers an inexpensive means for validation of the identity of clinical isolates and should be used as an integrated marker in the annotation procedure employed in 16S rRNA-based molecular studies of complex human microbiotas. This may avoid frequent misidentifications such as those we demonstrate to have occurred in previous reports and in reference sequence databases.

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Multilocus sequence phylogenetic study of the genus Haemophilus with description of Haemophilus pittmaniae sp. nov.

Cited by 60 publications

References 26 publications

Relationships of Nontypeable Haemophilus influenzae Strains to Hemolytic and Nonhemolytic Haemophilus haemolyticus Strains

Relationships of Nontypeable Haemophilus influenzae Strains to Hemolytic and Nonhemolytic Haemophilus haemolyticus Strains

Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae

Novel Molecular Method for Identification of Streptococcus pneumoniae Applicable to Clinical Microbiology and 16S rRNA Sequence-Based Microbiome Studies

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