Application of MLST and Pilus Gene Sequence Comparisons to Investigate the Population Structures of Actinomyces naeslundii and Actinomyces oris

Henssge, Uta; Do, Thuy; Gilbert, Steven C.; Cox, S.T.; Clark, Douglas; Wickström, Claes; Ligtenberg, A.J.M.; Radford, David R.; Beighton, David

doi:10.1371/journal.pone.0021430

Cited by 10 publications

(19 citation statements)

References 41 publications

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“…Our phylogenetic results confirm the species identification by the IDNS database; the majority of species identifications match well to publically available type strain sequences. There are some clusters of mixed species, such as those sharing recent common ancestry with A. oris and A. viscosus, supporting previous reports of heterogeneity within these species (28)(29)(30). Interestingly, our data also illustrate how diverse the oral taxons are, as shown by the dark (9) 47 (41) 15 (13) 43 (37) 115 a Includes the following species according to 16S sequencing: Actinomyces F507T (2), Actinomyces ARUP UnID 100, 97, 68, and 50 (4), Actinomyces 606220/2008 (1), Actinomyces GTC3949 (1), Actinomyces oral taxon 169, 170, 171, 172, 175, 180, and A50 (15), Actinomyces S8 86-2a (1), Actinomyces sp2-iso-aAG2 (3), and Actinomyces TeJ5 (2).…”

Section: Patient Demographicssupporting

confidence: 86%

Species-Level Identification of Actinomyces Isolates Causing Invasive Infections: Multiyear Comparison of Vitek MS (Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry) to Partial Sequencing of the 16S rRNA Gene

2016

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Actinomyces species are uncommon but important causes of invasive infections. The ability of our regional clinical microbiology laboratory to report species-level identification of Actinomyces relied on molecular identification by partial sequencing of the 16S ribosomal gene prior to the implementation of the Vitek MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry [MALDI-TOF MS]) system. We compared the use of the Vitek MS to that of 16S rRNA gene sequencing for reliable species-level identification of invasive infections caused by Actinomyces spp. because limited data had been published for this important genera. A total of 115 cases of Actinomyces spp., either alone or as part of a polymicrobial infection, were diagnosed between 2011 and 2014. Actinomyces spp. were considered the principal pathogen in bloodstream infections (n ‫؍‬ 17, 15%), in skin and soft tissue abscesses (n ‫؍‬ 25, 22%), and in pulmonary (n ‫؍‬ 26, 23%), bone (n ‫؍‬ 27, 23%), intraabdominal (n ‫؍‬ 16, 14%), and central nervous system (n ‫؍‬ 4, 3%) infections. Compared to sequencing and identification from the SmartGene Integrated Database Network System (IDNS), Vitek MS identified 47/115 (41%) isolates to the correct species and 10 (9%) isolates to the correct genus. However, the Vitek MS was unable to provide identification for 43 (37%) isolates while 15 (13%) had discordant results. Phylogenetic analyses of the 16S rRNA sequences demonstrate high diversity in recovered Actinomyces spp. and provide additional information to compare/confirm discordant identifications between MALDI-TOF and 16S rRNA gene sequences. This study highlights the diversity of clinically relevant Actinomyces spp. and provides an important typing comparison. Based on our analysis, 16S rRNA gene sequencing should be used to rapidly identify Actinomyces spp. until MALDI-TOF databases are optimized.A ctinomyces species are uncommon human bacterial pathogens that can cause a wide variety of invasive infections (1). The Actinomyces genus is part of the family Actinomycetaceae, of which there are currently 47 published species, but several novel Actinomyces taxa have recently been described by molecular analyses targeting the ribosomal 16S rRNA gene (2). For example, the Human Oral Microbiome Database (www.homd.org) currently reports many species-level Actinomyces taxa that have not yet been named (3). The pathogenic role of known and novel Actinomyces spp. in contributing alone or as part of polymicrobial flora to human invasive infections is underappreciated because many clinical microbiology laboratories continue to rely on phenotypic methods for identification (4-7). Because Actinomyces spp. grow best under anaerobic conditions and are notoriously fastidious, slow -growing organisms, they may be missed as important pathogens by routine aerobic culture techniques and incubation periods (2,8).Upon microscopic examination, Actinomyces isolates typically appear as Gram-positive bacilli that may be coryneform-like with palisading or branching ...

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Section: Patient Demographicssupporting

confidence: 86%

Species-Level Identification of Actinomyces Isolates Causing Invasive Infections: Multiyear Comparison of Vitek MS (Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry) to Partial Sequencing of the 16S rRNA Gene

2016

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“…The selected house-keeping genes, atpA (ATP synthase F1, alpha subunit, ANA_0169), metG (methionyl-tRNA synthetase, ANA 1898), rpoB (DNA-directed RNA polymerase, beta subunit, ANA_1497), pgi (glucose-6-phosphate isomerase, ANA_0727), gltA (citrate synthase I, ANA_1674), gyrA (DNA gyrase, A subunit, ANA_2224), pheS (phenylalanyl-tRNA synthetase, alpha subunit, ANA_1034) and 2 genes for fimbrial proteins, Type-2 fimbriae fimA (ANA_0024 fimbrial structural subunit) and type-1 fimbriae fimP (ANA_2510 Type-1 fimbrial major subunit precursor) of strain Chiba 101 were compared to those of the Actinomyces denticolens DSM 20671 T . The previously reported Actinomyces oris sequences [ 11 ] were used as the reference sequences [EU603149 ( pgi ), EU620779 ( atpA ), EU620895 ( gltA ), EU621011 ( gyrA ), EU621127 ( metG ) EU621243 ( rpoB ) and GQ354571 ( pheS )].…”

Section: Methodsmentioning

confidence: 99%

<i>Actinomyces denticolens</i> as a causative agent of actinomycosis in animals

Murakami

Kobayashi

Sekigawa

et al. 2018

The Journal of Veterinary Medical Science

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The name “Actinomyces suis” was applied to each actinomycete isolate from swine actinomycosis by Grässer in 1962 and Franke in 1973. Nevertheless, this specific species was not included in the “Approved List of Bacterial Name” due to absence of the type cultures. Therefore, “Actinomyces suis” based on the description of Franke 1973 has been considered as “species incertae sedis”. We isolated a number of Actinomyces strains from swine. The representative strains of them was designated as Chiba 101 that was closely similar to the description in “Actinomyces suis” reported by Franke in 1973. Interestingly, it was found that the biological characteristics of these strains were also very similar to those of Actinomyces denticolens. Furthermore, the average nucleotide identity (ANI) value between strain Chiba 101 and the type-strain of Actinomyces denticolens (=DSM 20671T) was found to be 99.95%. Sequences of the housekeeping genes and 16S rRNA gene showed 100% homology. These results strongly suggested that “Actinomyces suis” Franke 1973 is the same species as Actinomyces denticolens. Since actinomycosis caused by Actinomyces denticolens have been demonstrated in horses recently, it is necessary to recognize that Actinomyces denticolens is the pathogenic actinomycetes in broader range of animals.

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“…The whole genome of selected clinical Actinomyces strains from King’s College London Microbiology Laboratory were sequenced for the first time in this study. However, these strains have been used in various studies since 1990 [ 14 , 15 , 16 , 17 ]. A. oris (previously known as A. naeslundii ) was the most common member of the genus found in dental plaque [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic Diversity among Actinomyces naeslundii Strains and Closely Related Species

Mughal

Niazi²,

Do³

et al. 2023

Microorganisms

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The aim of this study was to investigate and clarify the ambiguous taxonomy of Actinomyces naeslundii and its closely related species using state-of-the-art high-throughput sequencing techniques, and, furthermore, to determine whether sub-clusters identified within Actinomyces oris and Actinomyces naeslundii in a previous study by multi locus sequence typing (MLST) using concatenation of seven housekeeping genes should either be classified as subspecies or distinct species. The strains in this study were broadly classified under Actinomyces naeslundii group as A. naeslundii genospecies I and genospecies II. Based on MLST data analysis, these were further classified as A. oris and A. naeslundii. The whole genome sequencing of selected strains of A. oris (n = 17) and A. naeslundii (n = 19) was carried out using Illumina Genome Analyzer IIxe and Roche 454 allowing paired-end and single-reads sequencing, respectively. The sequences obtained were aligned using CLC Genomic workbench version 5.1 and annotated using RAST (Rapid Annotation using Subsystem Technology) release version 59 accessible online. Additionally, genomes of seven publicly available strains of Actinomyces (k20, MG1, c505, OT175, OT171, OT170, and A. johnsonii) were also included. Comparative genomic analysis (CGA) using Mauve, Progressive Mauve, gene-by-gene, Core, and Pan Genome, and finally Digital DNA-DNA homology (DDH) analysis was carried out. DDH values were obtained using in silico genome–genome comparison. Evolutionary analysis using ClonalFrame was also undertaken. The mutation and recombination events were compared using chi-square test among A. oris and A. naeslundii isolates (analysis methods are not included in the study). CGA results were consistent with previous traditional classification using MLST. It was found that strains of Actinomyces k20, MG1, c505, and OT175 clustered in A. oris group of isolates, while OT171, OT170, and A. johnsonii appeared as separate branches. Similar clustering to MLST was observed for other isolates. The mutation and recombination events were significantly higher in A. oris than A. naeslundii, highlighting the diversity of A. oris strains in the oral cavity. These findings suggest that A. oris forms six distinct groups, whereas A. naeslundii forms three. The correct designation of isolates will help in the identification of clinical Actinomyces isolates found in dental plaque. Easily accessible online genomic sequence data will also accelerate the investigation of the biochemical characterisation and pathogenesis of this important group of micro-organisms.

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Application of MLST and Pilus Gene Sequence Comparisons to Investigate the Population Structures of Actinomyces naeslundii and Actinomyces oris

Cited by 10 publications

References 41 publications

Species-Level Identification of Actinomyces Isolates Causing Invasive Infections: Multiyear Comparison of Vitek MS (Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry) to Partial Sequencing of the 16S rRNA Gene

Species-Level Identification of Actinomyces Isolates Causing Invasive Infections: Multiyear Comparison of Vitek MS (Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry) to Partial Sequencing of the 16S rRNA Gene

<i>Actinomyces denticolens</i> as a causative agent of actinomycosis in animals

Genomic Diversity among Actinomyces naeslundii Strains and Closely Related Species

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