Increased level of intragenomic 16S rRNA gene heterogeneity in commensal strains closely related to Haemophilus influenzae

Nørskov‐Lauritsen, Niels

doi:10.1099/mic.0.047233-0

Cited by 9 publications

(14 citation statements)

References 30 publications

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“…6). However, seven other strains harbored two separate helix 18 types; depending on the combination, the mixture of helix types resulted in 8, 9, or 11 polymorphic positions within the region of 23 nt that comprises the outer stem of helix 18 (153). These findings emphasize that even rRNA genes may be subject to interspecies recombination among members of the H. influenzae group.…”

Section: Differentiation Of Haemophilus Influenzae From Haemophilus Hmentioning

confidence: 69%

“…In comparison with MLSA, the inferior resolution of the 16S rRNA gene analysis is caused by less variability, a shorter fragment length, and the presence of polymorphic positions in the multiple copies of the 16S rRNA gene. An unexpectedly high level of 16S rRNA gene polymorphism was recently described for a collection of strains of H. haemolyticus and related organisms (153). The average frequency of 16S rRNA gene polymorphic nucleotide positions was approximately 10 times the level observed in H. influenzae.…”

Section: Differentiation Of Haemophilus Influenzae From Haemophilus Hmentioning

confidence: 99%

“…Six copies of the 16S rRNA gene are usually present in the genomes of Haemophilus and Aggregatibacter (41,(149)(150)(151)(152), but little 16S rRNA gene heterogeneity is observed in these genomes. Recently, an unexpected and conspicuously large number of polymorphic positions was observed in a collection of H. haemolyticus strains and related organisms (see below) (153), and such a degree of heterogeneity may seriously interfere with 16S rRNA gene-based identification.…”

Section: Dna Sequencingmentioning

confidence: 99%

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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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Section: Differentiation Of Haemophilus Influenzae From Haemophilus Hmentioning

confidence: 69%

Section: Differentiation Of Haemophilus Influenzae From Haemophilus Hmentioning

confidence: 99%

Section: Dna Sequencingmentioning

confidence: 99%

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

2014

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“…A mixture of H. influenzae and H. haemolyticus 16S rRNA genes in the genomes of strains H43 and H56 is indicated by their position in the dendrogram (Fig. 1A), and such mixtures have previously been documented for other strains of H. haemolyticus by sequencing of individual RNA operons (25). However, an exclusive presence of 16S rRNA genes from a different species, to our knowledge, has not been de Gier et al…”

Section: Discussionmentioning

confidence: 82%

“…Identification of polymorphic nucleotide positions and 16S rRNA gene sequencing were carried out as previously described (25). A 1,362-nt fragment corresponding to nucleotides 27 to 1,388 of the 16S rRNA gene in H. influenzae strain Rd was obtained from all 54 strains and used for analysis.…”

Section: Methodsmentioning

confidence: 99%

Complete Deletion of the Fucose Operon in Haemophilus influenzae Is Associated with a Cluster in Multilocus Sequence Analysis-Based Phylogenetic Group II Related to Haemophilus haemolyticus: Implications for Identification and Typing

2015

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bNonhemolytic variants of Haemophilus haemolyticus are difficult to differentiate from Haemophilus influenzae despite a wide difference in pathogenic potential. A previous investigation characterized a challenging set of 60 clinical strains using multiple PCRs for marker genes and described strains that could not be unequivocally identified as either species. We have analyzed the same set of strains by multilocus sequence analysis (MLSA) and near-full-length 16S rRNA gene sequencing. MLSA unambiguously allocated all study strains to either of the two species, while identification by 16S rRNA sequence was inconclusive for three strains. Notably, the two methods yielded conflicting identifications for two strains. Most of the "fuzzy species" strains were identified as H. influenzae that had undergone complete deletion of the fucose operon. Such strains, which are untypeable by the H. influenzae multilocus sequence type (MLST) scheme, have sporadically been reported and predominantly belong to a single branch of H. influenzae MLSA phylogenetic group II. We also found evidence of interspecies recombination between H. influenzae and H. haemolyticus within the 16S rRNA genes. Establishing an accurate method for rapid and inexpensive identification of H. influenzae is important for disease surveillance and treatment. Haemophilus influenzae is an important human pathogen involved in respiratory tract infections, such as sinusitis, acute otitis media, pneumonia, and exacerbations in chronic obstructive pulmonary disease (1-5). The majority of these infections are caused by unencapsulated H. influenzae, traditionally designated nontypeable H. influenzae (NTHi). Haemophilus haemolyticus is a close relative of H. influenzae, and the two species colonize the upper respiratory tract of humans. Although H. haemolyticus has, on rare occasion, been isolated from invasive infections (6), several lines of evidence indicate that the pathogenicity of H. haemolyticus is much reduced compared with H. influenzae. While up to 20% of presumptive H. influenzae nasopharyngeal isolates can be identified as H. haemolyticus by molecular characterization (7-9), H. haemolyticus is rarely cultured from middle ear fluid (10, 11), supporting the view that H. haemolyticus, in contrast to NTHi, is a respiratory commensal infrequently associated with otitis media. Reinvestigation of presumptive H. influenzae isolates, cultured from lower respiratory tract samples from cystic fibrosis patients (12) or from unselected clinical samples submitted to the laboratory on suspicion of lower respiratory tract infection (13), detected that Ͻ1% were misidentified strains, further supporting a minor pathogenic role for H. haemolyticus.H. haemolyticus was traditionally identified by its hemolytic action on erythrocytes, but it has become clear that a large proportion of H. haemolyticus strains is nonhemolytic (10,14). Such strains, which are designated as nonhemolytic H. haemolyticus, can only be differentiated from H. influenzae by DNA sequencing or extended phen...

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Intra- and Intergenomic Variation of Ribosomal RNA Operons in Concurrent Alteromonas macleodii Strains

et al. 2012

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Biodiversity estimates based on ribosomal operon sequence diversity rely on the premise that a sequence is characteristic of a single specific taxon or operational taxonomic unit (OTU). Here, we have studied the sequence diversity of 14 ribosomal RNA operons (rrn) contained in the genomes of two isolates (five operons in each genome) and four metagenomic fosmids, all from the same seawater sample. Complete sequencing of the isolate genomes and the fosmids establish that they represent strains of the same species, Alteromonas macleodii, with average nucleotide identity (ANI) values >97 %. Nonetheless, we observed high levels of intragenomic heterogeneity (i.e., variability between operons of a single genome) affecting multiple regions of the 16S and 23S rRNA genes as well as the internally transcribed spacer 1 (ITS-1) region. Furthermore, the ribosomal operons exhibited intergenomic heterogeneity (i.e., variability between operons located in separate genomes) in each of these regions, compounding the variability. Our data reveal the extensive heterogeneity observed in natural populations of A. macleodii at a single point in time and support the idea that distinct lineages of A. macleodii exist in the deep Mediterranean. These findings highlight the potential of rRNA fingerprinting methods to misrepresent species diversity while simultaneously failing to recognize the ecological significance of individual strains.

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Increased level of intragenomic 16S rRNA gene heterogeneity in commensal strains closely related to Haemophilus influenzae

Cited by 9 publications

References 30 publications

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

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

Complete Deletion of the Fucose Operon in Haemophilus influenzae Is Associated with a Cluster in Multilocus Sequence Analysis-Based Phylogenetic Group II Related to Haemophilus haemolyticus: Implications for Identification and Typing

Intra- and Intergenomic Variation of Ribosomal RNA Operons in Concurrent Alteromonas macleodii Strains

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