The sodA gene as a target for phylogenetic dissection of the genus Haemophilus and accurate identification of human clinical isolates

Cattoir, Vincent; Lemenand, Olivier; Avril, J; Gaillot, Olivier

doi:10.1016/j.ijmm.2006.06.005

Cited by 13 publications

(11 citation statements)

References 28 publications

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“…Therefore, PCR tests should be developed and included since they are now available in non-specialist laboratories and are easily standardized and they demand less work than the classical phenotypic tests. The same holds true for methods using DNA sequencing (Gautier et al, 2005;Cattoir et al, 2006). In addition, some commercial laboratories now offer DNA sequencing at relatively low cost.…”

Section: Identificationmentioning

confidence: 87%

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

114

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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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Section: Identificationmentioning

confidence: 87%

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

114

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“…Different protein-coding genes have been studied and compared for species of Haemophilus and Aggregatibacter (8,98,101,(154)(155)(156)(157). The increased sequence variation of translated genes compared to rRNA genes confers more information for analysis, but this must be weighed against the increased probability of prior recombination events affecting the genes.…”

Section: Dna Sequencingmentioning

confidence: 99%

Classification, Identification, and Clinical Significance of Haemophilus and Aggregatibacter Species with Host Specificity for Humans

2014

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SUMMARY 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.

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“…Moreover, when expressed in E. coli, [Mn]-SOD from H. influenzae type b was regulated by the fumarate/nitrate reduction transcriptional regulator, Fnr and the ferric uptake regulator, Fur (Kroll et al, 1993). Using degenerate primers based on the sequences of sodA from H. influenzae strain Rd KW20 and NTHi strain 86-028NP, PCR analyses subsequently showed that homologues of sodA were present in all Haemophilus type strains tested (Cattoir et al, 2006). …”

Section: Haemophilus Influenzae's Response To Reactive Oxygen Speciesmentioning

confidence: 99%

Haemophilus influenzae and oxidative stress

Harrison¹,

Munson²

2012

Front. Cell. Inf. Microbio.

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Haemophilus influenzae is a commensal of the human upper respiratory tract. H. influenzae can, however, move out of its commensal niche and cause multiple respiratory tract diseases. Such diseases include otitis media in young children, as well as exacerbations of chronic obstructive pulmonary disease (COPD), sinusitis, conjunctivitis, and bronchitis. During the course of colonization and infection, H. influenzae must withstand oxidative stress generated by multiple reactive oxygen species produced endogenously, by other co-pathogens and by host cells. H. influenzae has, therefore, evolved multiple mechanisms that protect the cell against oxygen-generated stresses. In this review, we will describe these systems relative to the well-described systems in Escherichia coli. Moreover, we will compare how H. influenzae combats the effect of oxidative stress as a necessary phenotype for its roles as both a successful commensal and pathogen.

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The sodA gene as a target for phylogenetic dissection of the genus Haemophilus and accurate identification of human clinical isolates

Cited by 13 publications

References 28 publications

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

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

Classification, Identification, and Clinical Significance of Haemophilus and Aggregatibacter Species with Host Specificity for Humans

Haemophilus influenzae and oxidative stress

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