Draft Genome Sequence of an Antibiotic-Resistant Propionibacterium acnes Strain, PRP-38, from the Novel Type IC Cluster

McDowell, Andrew; Hunyadkürti, Judit; Horváth, Balázs; Vörös, Andrea; Barnard, Emma; Patrick, Sheila; Nagy, István

doi:10.1128/jb.00479-12

Cited by 21 publications

(18 citation statements)

References 18 publications

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“…Of the 67 P. acnes isolates, 52% were found to belong to the type II lineage, present in 12/24 (50%) patients, 28% were type IA, present in 10/24 (42%) patients, 11% type III, present in 5/24 (21%) patients, and 9% type IB, recovered from 4/24 (17%) patients ( P < 0.001). No isolates were found to belong to the recently described type IC lineage [26]. In 6/24 patients, multiple P. acnes phylogroups were identified from the five tissue samples obtained.…”

Section: Resultsmentioning

confidence: 99%

“…All P. acnes isolates were examined with the mouse mAbs QUBPa1 and QUBPa2, which target dermatan-sulphate-binding adhesins and a carbohydrate/glycolipid-containing antigen on type IA and type II strains, respectively [17, 18]. Strains of type IB or type III do not react with these mAbs, while all type IC isolates analysed to date show dual reaction in keeping with their distinct nature [26]. Slides were viewed using a Leitz Dialux 20 fluorescence microscope.…”

Section: Methodsmentioning

confidence: 99%

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Genotypic and Antimicrobial Characterisation ofPropionibacterium acnesIsolates from Surgically Excised Lumbar Disc Herniations

Rollason

McDowell

Albert

et al. 2013

BioMed Research International

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The anaerobic skin commensal Propionibacterium acnes is an underestimated cause of human infections and clinical conditions. Previous studies have suggested a role for the bacterium in lumbar disc herniation and infection. To further investigate this, five biopsy samples were surgically excised from each of 64 patients with lumbar disc herniation. P. acnes and other bacteria were detected by anaerobic culture, followed by biochemical and PCR-based identification. In total, 24/64 (38%) patients had evidence of P. acnes in their excised herniated disc tissue. Using recA and mAb typing methods, 52% of the isolates were type II (50% of culture-positive patients), while type IA strains accounted for 28% of isolates (42% patients). Type III (11% isolates; 21% patients) and type IB strains (9% isolates; 17% patients) were detected less frequently. The MIC values for all isolates were lowest for amoxicillin, ciprofloxacin, erythromycin, rifampicin, tetracycline, and vancomycin (≤1mg/L). The MIC for fusidic acid was 1-2 mg/L. The MIC for trimethoprim and gentamicin was 2 to ≥4 mg/L. The demonstration that type II and III strains, which are not frequently recovered from skin, predominated within our isolate collection (63%) suggests that the role of P. acnes in lumbar disc herniation should not be readily dismissed.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genotypic and Antimicrobial Characterisation ofPropionibacterium acnesIsolates from Surgically Excised Lumbar Disc Herniations

Rollason

McDowell

Albert

et al. 2013

BioMed Research International

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“…The commensal Gram-positive bacteria P. acnes live in consistent environmental conditions, predominantly on the human skin. Nagy et al (37)(38)(39)(40) have sequenced the genomes of 12 P. acnes isolates and analysed them along with the publicly available genomes. When compared with the metabolically versatile and a cosmopolitan bacterium R. palustris with six publicly available genome projects on isolates from diverse environments (41,42), the P. acnes strains show less variation in CU per orthologous group than do the R. palustris strains (Figure 3).…”

Section: Metagenome-centric Bias In Codon Usage Is Phylogeny-independentmentioning

confidence: 99%

“…Genome sequencing of 12 P. acnes isolates (Supplementary Table S3) was performed on the SOLiD 3 System (Applied Biosystems, now part of Life Technologies) following the manufacturer's instructions. For this, DNA was extracted using the AquaGenomic kit (MultiTarget Pharmaceutical) and the preparation of the libraries and sequencing were performed using cycled ligation sequencing on a SOLiD 3 System; detailed procedure is described elsewhere (38)(39)(40). P. acnes strains were assigned STRING/COG categories and ORFs with the same method as metagenomes.…”

Section: Single Bacterial Species' Genomes and Annotationmentioning

confidence: 99%

Environmental Shaping of Codon Usage and Functional Adaptation Across Microbial Communities

Lucić¹,

Roller²,

Nágy³

et al. 2015

Encyclopedia of Metagenomics

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Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species' boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a 'functional metagenomics' platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community.

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“…Within the last 10 years, phylogenetic studies based on single and multilocus gene sequencing (18)(19)(20)(21), as well as whole-genome analyses of isolates from the Human Microbiome Project (HMP) and other studies (22)(23)(24)(25)(26)(27)(28), have provided valuable insights into the genetic population structure of P. acnes, particularly in the context of health and disease. The bacterium has an overall clonal structure, and its isolates can be classified into a number of statistically significant clades or phylogroups designated types IA 1 , IA 2 , IB, IC, II, and III; these types appear to display differences in their associations with specific types of infections (20,21) and vary in their production of putative virulence determinants (19,20,(29)(30)(31)(32), inflammatory potential (33)(34)(35)(36), antibiotic resistances (21,37), aggregative properties (16), and morphological characteristics (19).…”

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confidence: 99%

Multiplex Touchdown PCR for Rapid Typing of the Opportunistic Pathogen Propionibacterium acnes

et al. 2015

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bThe opportunistic human pathogen Propionibacterium acnes is composed of a number of distinct phylogroups, designated types IA 1 , IA 2 , IB, IC, II, and III, which vary in their production of putative virulence factors, their inflammatory potential, and their biochemical, aggregative, and morphological characteristics. Although multilocus sequence typing (MLST) currently represents the gold standard for unambiguous phylogroup classification and individual strain identification, it is a labor-intensive and time-consuming technique. As a consequence, we developed a multiplex touchdown PCR assay that in a single reaction can confirm the species identity and phylogeny of an isolate based on its pattern of reaction with six primer sets that target the 16S rRNA gene (all isolates), ATPase (types IA 1 , IA 2 , and IC), sodA (types IA 2 and IB), atpD (type II), and recA (type III) housekeeping genes, as well as a Fic family toxin gene (type IC). When applied to 312 P. acnes isolates previously characterized by MLST and representing types IA 1 (n ‫؍‬ 145), IA 2 (n ‫؍‬ 20), IB (n ‫؍‬ 65), IC (n ‫؍‬ 7), II (n ‫؍‬ 45), and III (n ‫؍‬ 30), the multiplex displayed 100% sensitivity and 100% specificity for detecting isolates within each targeted phylogroup. No cross-reactivity with isolates from other bacterial species was observed. This multiplex assay will provide researchers with a rapid, high-throughput, and technically undemanding typing method for epidemiological and phylogenetic investigations. It will facilitate studies investigating the association of lineages with various infections and clinical conditions, and it will serve as a prescreening tool to maximize the number of genetically diverse isolates selected for downstream higher-resolution sequence-based analyses.

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Draft Genome Sequence of an Antibiotic-Resistant Propionibacterium acnes Strain, PRP-38, from the Novel Type IC Cluster

Cited by 21 publications

References 18 publications

Genotypic and Antimicrobial Characterisation ofPropionibacterium acnesIsolates from Surgically Excised Lumbar Disc Herniations

Genotypic and Antimicrobial Characterisation ofPropionibacterium acnesIsolates from Surgically Excised Lumbar Disc Herniations

Environmental Shaping of Codon Usage and Functional Adaptation Across Microbial Communities

Multiplex Touchdown PCR for Rapid Typing of the Opportunistic Pathogen Propionibacterium acnes

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