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Article ; Online: Development of a Single Locus Sequence Typing (SLST) Scheme for Typing Bacterial Species Directly from Complex Communities.

Scholz, Christian F P / Jensen, Anders

Methods in molecular biology (Clifton, N.J.)

2017 Volume 1535, Page(s) 97–107

Abstract: The protocol describes a computational method to develop a Single Locus Sequence Typing (SLST) scheme for typing bacterial species. The resulting scheme can be used to type bacterial isolates as well as bacterial species directly from complex communities ...

Abstract	The protocol describes a computational method to develop a Single Locus Sequence Typing (SLST) scheme for typing bacterial species. The resulting scheme can be used to type bacterial isolates as well as bacterial species directly from complex communities using next-generation sequencing technologies.
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-6673-8_7
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Article ; Online: The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov.

Scholz, Christian F P / Kilian, Mogens

International journal of systematic and evolutionary microbiology

2016 Volume 66, Issue 11, Page(s) 4422–4432

Abstract: The genus Propionibacterium in the family Propionibacteriaceaeconsists of species of various habitats, including mature cheese, cattle rumen and human skin. Traditionally, these species have been grouped as either classical or cutaneous propionibacteria ... ...

Abstract	The genus Propionibacterium in the family Propionibacteriaceaeconsists of species of various habitats, including mature cheese, cattle rumen and human skin. Traditionally, these species have been grouped as either classical or cutaneous propionibacteria based on characteristic phenotypes and source of isolation. To re-evaluate the taxonomy of the family and to elucidate the interspecies relatedness we compared 162 public whole-genome sequences of strains representing species of the family Propionibacteriaceae. We found substantial discrepancies between the phylogenetic signals of 16S rRNA gene sequence analysis and our high-resolution core-genome analysis. To accommodate these discrepancies, and to address the long-standing issue of the taxonomically problematic Propionibacterium propionicum, we propose three novel genera, Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov., and an amended description of the genus Propionibacterium. Furthermore, our genome-based analyses support the amounting evidence that the subdivision of Propionibacterium freudenreichii into subspecies is not warranted. Our proposals are supported by phylogenetic analyses, DNA G+C content, peptidoglycan composition and patterns of the gene losses and acquisitions in the cutaneous propionibacteria during their adaptation to the human host.
MeSH term(s)	Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Humans ; Peptidoglycan/chemistry ; Phylogeny ; Propionibacteriaceae/classification ; Propionibacteriaceae/genetics ; Propionibacterium/classification ; Propionibacterium/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skin/microbiology
Chemical Substances	DNA, Bacterial ; Peptidoglycan ; RNA, Ribosomal, 16S
Language	English
Publishing date	2016-08-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2002336-4
ISSN	1466-5034 ; 1466-5026
ISSN (online)	1466-5034
ISSN	1466-5026
DOI	10.1099/ijsem.0.001367
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Article ; Online: Re-evaluation of the taxonomy of the Mitis group of the genus Streptococcus based on whole genome phylogenetic analyses, and proposed reclassification of Streptococcus dentisani as Streptococcus oralis subsp. dentisani comb. nov., Streptococcus tigurinus as Streptococcus oralis subsp. tigurinus comb. nov., and Streptococcus oligofermentans as a later synonym of Streptococcus cristatus.

Jensen, Anders / Scholz, Christian F P / Kilian, Mogens

International journal of systematic and evolutionary microbiology

2016 Volume 66, Issue 11, Page(s) 4803–4820

Abstract: The Mitis group of the genus Streptococcus currently comprises 20 species with validly published names, including the pathogen S. pneumoniae. They have been the subject of much taxonomic confusion, due to phenotypic overlap and genetic heterogeneity, ... ...

Abstract	The Mitis group of the genus Streptococcus currently comprises 20 species with validly published names, including the pathogen S. pneumoniae. They have been the subject of much taxonomic confusion, due to phenotypic overlap and genetic heterogeneity, which has hampered a full appreciation of their clinical significance. The purpose of this study was to critically re-examine the taxonomy of the Mitis group using 195 publicly available genomes, including designated type strains for phylogenetic analyses based on core genomes, multilocus sequences and 16S rRNA gene sequences, combined with estimates of average nucleotide identity (ANI) and in silico and in vitro analyses of specific phenotypic characteristics. Our core genomic phylogenetic analyses revealed distinct clades that, to some extent, and from the clustering of type strains represent known species. However, many of the genomes have been incorrectly identified adding to the current confusion. Furthermore, our data show that 16S rRNA gene sequences and ANI are unsuitable for identifying and circumscribing new species of the Mitis group of the genus Streptococci. Based on the clustering patterns resulting from core genome phylogenetic analysis, we conclude that S. oligofermentans is a later synonym of S. cristatus. The recently described strains of the species Streptococcus dentisani includes one previously referred to as 'S. mitis biovar 2'. Together with S. oralis, S. dentisani and S. tigurinus form subclusters within a coherent phylogenetic clade. We propose that the species S. oralis consists of three subspecies: S. oralis subsp. oralis subsp. nov., S. oralis subsp. tigurinus comb. nov., and S. oralis subsp. dentisani comb. nov.
MeSH term(s)	Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Multilocus Sequence Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Streptococcus/classification ; Streptococcus oralis/classification
Chemical Substances	DNA, Bacterial ; RNA, Ribosomal, 16S
Language	English
Publishing date	2016-08-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2002336-4
ISSN	1466-5034 ; 1466-5026
ISSN (online)	1466-5034
ISSN	1466-5026
DOI	10.1099/ijsem.0.001433
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Article ; Online: Septicemia with Streptococcus pseudopneumoniae: report of three cases with an apparent hepatic or bile duct association.

Fuursted, Kurt / Littauer, Pia Jeanette / Greve, Thomas / Scholz, Christian F P

Infectious diseases (London, England)

2016 Volume 48, Issue 8, Page(s) 636–639

Abstract: Streptococcus pseudopneumoniae was described in 2004 as a new human pathogen, acknowledged in a range of clinical infections typically associated to the respiratory tract. This report demonstrates that S. pseudopneumoniae has the potential to cause ... ...

Abstract	Streptococcus pseudopneumoniae was described in 2004 as a new human pathogen, acknowledged in a range of clinical infections typically associated to the respiratory tract. This report demonstrates that S. pseudopneumoniae has the potential to cause invasive infection. In blood cultures from three patients, growth of an atypical Streptococcus pneumoniae (non-capsular, non-serotypeable, optochin susceptible under ambient atmosphere and bile-intermediately soluble) was recovered. All three patients had a history of a haematological disease (myelodysplastic syndrome and multiple myeloma) and an apparent origin of infection related to the liver or bile duct. All isolates were genome sequenced and subsequently identified as S. pseudopneumoniae by multi-locus sequence analysis (MLSA). Multi-locus sequence typing (MLST) based on the S. pneumoniae scheme revealed unknown sequence types and the antibiogram and resistome revealed no antibiotic resistance.
MeSH term(s)	Aged ; Aged, 80 and over ; Bile Duct Diseases/complications ; Bile Duct Diseases/microbiology ; Female ; Humans ; Male ; Middle Aged ; Pneumococcal Infections/complications ; Pneumococcal Infections/microbiology ; Sepsis/complications ; Sepsis/microbiology ; Streptococcus pneumoniae/classification ; Streptococcus pneumoniae/genetics
Language	English
Publishing date	2016-08
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	2839775-7
ISSN	2374-4243 ; 2374-4235
ISSN (online)	2374-4243
ISSN	2374-4235
DOI	10.3109/23744235.2016.1157896
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Article: Draft Genome Sequences of Two Propionibacterium acnes Strains Isolated from Progressive Macular Hypomelanosis Lesions of Human Skin.

Petersen, Rolf / Lomholt, Hans B / Scholz, Christian F P / Brüggemann, Holger

Genome announcements

2015 Volume 3, Issue 6

Abstract: Propionibacterium acnes is a Gram-positive bacterium that is prevalent on human skin. It has been associated with skin disorders such as acne vulgaris and progressive macular hypomelanosis (PMH). Here, we report draft genome sequences of two type III P. ... ...

Abstract	Propionibacterium acnes is a Gram-positive bacterium that is prevalent on human skin. It has been associated with skin disorders such as acne vulgaris and progressive macular hypomelanosis (PMH). Here, we report draft genome sequences of two type III P. acnes strains, PMH5 and PMH7, isolated from PMH skin lesions.
Language	English
Publishing date	2015-11-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2704277-7
ISSN	2169-8287
ISSN	2169-8287
DOI	10.1128/genomeA.01250-15
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Article: Propionibacterium Acnes

Petersen, Rolf L W / Scholz, Christian F P / Jensen, Anders / Brüggemann, Holger / Lomholt, Hans B

European journal of microbiology & immunology

2017 Volume 7, Issue 1, Page(s) 37–45

Abstract: Progressive macular hypomelanosis (PMH) is a skin disorder that is characterized by hypopigmented macules and usually seen in young adults. The skin microbiota, in particular the ... ...

Abstract	Progressive macular hypomelanosis (PMH) is a skin disorder that is characterized by hypopigmented macules and usually seen in young adults. The skin microbiota, in particular the bacterium
Language	English
Publishing date	2017-02-27
Publishing country	Hungary
Document type	Journal Article
ZDB-ID	2652327-9
ISSN	2062-8633 ; 2062-509X
ISSN (online)	2062-8633
ISSN	2062-509X
DOI	10.1556/1886.2016.00040
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Article ; Online: Multilocus sequence typing and phylogenetic analysis of Propionibacterium acnes.

Kilian, Mogens / Scholz, Christian F P / Lomholt, Hans B

Journal of clinical microbiology

2012 Volume 50, Issue 4, Page(s) 1158–1165

Abstract: Propionibacterium acnes is a commensal of human skin but is also implicated in the pathogenesis of acne vulgaris, in biofilm-associated infections of medical devices and endophthalmitis, and in infections of bone and dental root canals. Recent studies ... ...

Abstract	Propionibacterium acnes is a commensal of human skin but is also implicated in the pathogenesis of acne vulgaris, in biofilm-associated infections of medical devices and endophthalmitis, and in infections of bone and dental root canals. Recent studies associate P. acnes with prostate cancer. As the species includes evolutionary lineages with distinct association with health and disease, there is a need for a high-resolution typing scheme. Recently, two multilocus sequence typing (MLST) schemes were reported, one based on nine and one based on seven housekeeping genes. In the present study, the two schemes were compared with reference to a phylogenetic tree based on 78 P. acnes genomes and their gene contents. Further support for a basically clonal population structure of P. acnes and a scenario of the global spread of epidemic clones of P. acnes was obtained. Compared to the Belfast scheme, the Aarhus MLST scheme (http://pacnes.mlst.net/), which is based on nine genes, offers significantly enhanced resolution and phylogenetic inferences more concordant with analyses based on a comprehensive sampling of the entire genomes, their gene contents, and their putative pathogenic potential.
MeSH term(s)	Algorithms ; Bacterial Typing Techniques/methods ; Genes, Bacterial ; Genes, Essential ; Humans ; Models, Genetic ; Multilocus Sequence Typing/methods ; Phenotype ; Phylogeny ; Propionibacterium acnes/classification ; Propionibacterium acnes/genetics
Language	English
Publishing date	2012-01-18
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.r06129-11
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Article ; Online: Novel molecular method for identification of Streptococcus pneumoniae applicable to clinical microbiology and 16S rRNA sequence-based microbiome studies.

Scholz, Christian F P / Poulsen, Knud / Kilian, Mogens

Journal of clinical microbiology

2012 Volume 50, Issue 6, Page(s) 1968–1973

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Bacteriological Techniques/methods ; Cluster Analysis ; Computational Biology/methods ; Genes, rRNA ; Genetic Variation ; Humans ; Molecular Diagnostic Techniques/methods ; Phylogeny ; Pneumococcal Infections/diagnosis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology ; Streptococcus pneumoniae/classification ; Streptococcus pneumoniae/genetics ; Streptococcus pneumoniae/isolation & purification
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2012-03-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.00365-12
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Article ; Online: Propionibacterium avidum as an Etiological Agent of Prosthetic Hip Joint Infection.

Wildeman, Peter / Brüggemann, Holger / Scholz, Christian F P / Leimbach, Andreas / Söderquist, Bo

PloS one

2016 Volume 11, Issue 6, Page(s) e0158164

Abstract: Propionibacterium acnes is well-established as a possible etiologic agent of prosthetic joint infections (PJIs). Other Propionibacterium spp. have occasionally been described as a cause of PJIs, but this has not previously been the case for P. avidum ... ...

Abstract	Propionibacterium acnes is well-established as a possible etiologic agent of prosthetic joint infections (PJIs). Other Propionibacterium spp. have occasionally been described as a cause of PJIs, but this has not previously been the case for P. avidum despite its capacity to form biofilm. We describe two patients with prosthetic hip joint infections caused by P. avidum. Both patients were primarily operated with an anteriorly curved skin incision close to the skin crease of the groin, and both were obese. Initial treatment was performed according to the DAIR procedure (debridement, antibiotics, and implant retention). In case 1, the outcome was successful, but in case 2, a loosening of the cup was present 18 months post debridement. The P. avidum isolate from case 1 and two isolates from case 2 (obtained 18 months apart) were selected for whole genome sequencing. The genome of P. avidum obtained from case 1 was approximately 60 kb larger than the genomes of the two isolates of case 2. These latter isolates were clonal with the exception of SNPs in the genome. All three strains possessed the gene cluster encoding exopolysaccharide synthesis. P. avidum has a pathogenic potential and the ability to cause clinically relevant infections, including abscess formation, in the presence of foreign bodies such as prosthetic joint components. Skin incision in close proximity to the groin or deep skin crease, such as the anteriorly curved skin incision approach, might pose a risk of PJIs by P. avidum, especially in obese patients.
MeSH term(s)	Aged ; Aged, 80 and over ; Arthroplasty, Replacement, Hip/adverse effects ; Female ; Genome, Bacterial ; Hip Prosthesis ; Humans ; Male ; Multigene Family ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide ; Polysaccharides/chemistry ; Postoperative Complications ; Propionibacterium/isolation & purification ; Prosthesis-Related Infections/microbiology ; Skin/pathology
Chemical Substances	Polysaccharides
Language	English
Publishing date	2016
Publishing country	United States
Document type	Case Reports ; Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0158164
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Article ; Online: Genome stability of Propionibacterium acnes: a comprehensive study of indels and homopolymeric tracts.

Scholz, Christian F P / Brüggemann, Holger / Lomholt, Hans B / Tettelin, Hervé / Kilian, Mogens

Scientific reports

2016 Volume 6, Page(s) 20662

Abstract: We present a species-wide comparative analysis of 90 genomes of Propionibacterium acnes that represent the known diversity of the species. Our results are augmented by six high-quality genomes and a manual investigation of all gene-sized indels found in ... ...

Abstract	We present a species-wide comparative analysis of 90 genomes of Propionibacterium acnes that represent the known diversity of the species. Our results are augmented by six high-quality genomes and a manual investigation of all gene-sized indels found in the strains. Overall, the order of genes is conserved throughout the species. A public sybil database for easy comparative analysis of the 90 genomes was established. The analysis of indels revealed a total of 66 loci of non-core genes that correlate with phylogenetic clades. No gene was strain-specific in agreement with our conclusion that the P. acnes pan-genome is closed. An exhaustive search for homopolymeric tracts (HPTs) identified a total of 54 variable-length HPTs almost exclusively of guanine/cytosines located between genes or affecting the reading frame of genes. The repeat variation was consistent with phylogenetic clades suggesting slow accumulation over time rather than active modification. By transcriptome analysis we demonstrate how an HPT variation can affect the gene expression levels. Selected cases of both indels and HPTs are described. The catalogued data and the public P. acnes Sybil database provide a solid foundation for generating hypotheses and facilitate comparative genetic analyses in future P. acnes research.
MeSH term(s)	Databases, Nucleic Acid ; Genome, Bacterial ; Genomic Instability ; INDEL Mutation ; Propionibacterium acnes/genetics
Language	English
Publishing date	2016-02-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep20662
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