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Streptococcus bouchesdurhonensis sp. nov. isolated from a bronchoalveolar lavage of a patient with pneumonia. Arch Microbiol 2022; 205:3. [PMID: 36436132 DOI: 10.1007/s00203-022-03348-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/28/2022]
Abstract
Strain Marseille-Q6994 was isolated from a 72-year-old patient with pneumonia from Bouches-du-Rhône department, in France. Cells were Gram positive, non-motile, catalase and oxidase-negative cocci. The major fatty acids were hexadecanoic (47.4%) and tetradecanoic acids (28.3%). 16S rRNA gene sequence comparison suggested that strain Marseille-Q6994 was affiliated to the Streptococcus genus. GroEL phylogenetic analysis separated strain Marseille-Q6994 in a distinct branch from the closely related Streptococcus-type strains with standing in nomenclature. Whole genome sequencing-based methods (OrthoAverage Nucleotide Identity, digital DNA-DNA hybridization and pangenome analysis) supported the classification of the strain into a novel species. Therefore, based on the phenotypic, genomic, and phylogenetic analyses, we propose the name Streptococcus bouchesdurhonensis sp. nov for which strain Marseille-Q6994T (CSUR Marseille-Q6994 = DSMZ 113892) is the type strain.
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2
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Park SY, Muhammad N, Kim SG, Kwon H, Seo S, Kim JH. Streptococcus ruminicola sp. nov., new species of the Streptococcus bovis/Streptococcus equinus complex (SBSEC) isolated from the rumen of Korean domestic ruminants. Arch Microbiol 2022; 204:636. [PMID: 36127476 DOI: 10.1007/s00203-022-03255-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/30/2022] [Accepted: 09/12/2022] [Indexed: 11/28/2022]
Abstract
A total of three Gram-positive, and oxidase and catalase-negative facultative anaerobic non-motile bacteria were isolated from the rumen fluid of cows and goats and these strains were designated CNU_G2T, CNU_77-61, and CNU_G3. They grew at 20-45 °C, pH 6.5-7, and 0-6.5% NaCl (w/v). The G + C contents (%) of the three isolates were 37.9, 37.8 and 37.8, respectively. Phylogenomic analysis indicated that these strains were distinct from other Streptococcus species. The average nucleotide identity between the isolates and the closest strain S. infantarius subsp. infantarius ATCC BAA-102T was 94.0-94.5%, while the digital DNA-DNA hybridization (dDDH) values between the isolates and the aforementioned related strain were 58.2-61.4%, respectively. Fatty acid analysis revealed higher proportions of C16:0 (> 28%) in all three isolates, while the proportion of C18:0 was higher in CNU_G2T (25.8%); however, it was less than 12% in all the representing strains used in the study. The C14:0 composition of strains CNU_77-61 (22.1%) and CNU_G3 (24.1%) was higher than that of type strains of CNU_G2T (8.1%). Based on the morphological, biochemical, and molecular phylogenetic features of the three novel isolates, they represent a novel species of the genus Streptococcus, for which we propose as Streptococcus ruminicola sp. nov. The type strain is CNU_G2T (= KCTC 43308T = GDMCC 1.2785T).
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Affiliation(s)
- Seon Young Park
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Korea
| | - Neak Muhammad
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeonbuk, 56212, Korea.,University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Song-Gun Kim
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeonbuk, 56212, Korea.,University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Hyemin Kwon
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.,Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Korea
| | - Seongwon Seo
- Division of Animal and Dairy Sciences, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, Korea
| | - Ji Hyung Kim
- Department of Food Science and Biotechnology, College of Bio-Nano Technology, Gachon University, Seongnam, 13120, Korea.
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3
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Król J, Nowakiewicz A, Błaszków A, Brodala M, Domagała A, Prassol AN, Sławska D, Wojtynia J. Genetic diversity of oral streptococci in the guinea pig as assessed by sequence analysis of the 16S rRNA and groEL genes. Folia Microbiol (Praha) 2021; 67:311-318. [PMID: 34932210 PMCID: PMC8933309 DOI: 10.1007/s12223-021-00936-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 11/28/2021] [Indexed: 11/29/2022]
Abstract
The aim of the present study was to characterize bacteria of the genus Streptococcus isolated from the oral cavity of the guinea pig as well as to assess the significance of these microorganisms as potential veterinary and human pathogens. Sixty-two streptococcal isolates recovered from 27 clinically healthy guinea pigs were examined genotypically by sequencing the 16S rRNA and groEL genes. Among these isolates, only 13 could be assigned to a species described previously (mainly Streptococcus parasanguinis, S. mitis and S. suis), and the majority of the remaining ones differed considerably from the streptococcal species known to date (16S rRNA and groEL sequence similarities were < 97% and < 87%, respectively). Based on 16S rRNA sequences, these unidentified isolates were divided into seven groups (clades), of which clades I through III comprised most of the isolates examined and had also the widest distribution among guinea pig colonies. Upon groEL gene sequence analysis, however, members of the three clades grouped together without forming such distinct clusters. The remaining clades distinguished by 16S rRNA sequencing could also be discerned by the second gene, and they contained only a few isolates often restricted to one or a few animal colonies. The present work reveals that the guinea pig mouth is inhabited by a vast number of phylogenetically diverse, so far unrecognized populations of streptococci, most of them being apparently host-specific genomospecies. On the contrary, S. parasanguinis and S. mitis are also common human commensals and S. suis is a well-recognized zoonotic pathogen.
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Affiliation(s)
- Jarosław Król
- Department of Pathology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, St. Norwida 31, 50-375, Wrocław, Poland.
| | - Aneta Nowakiewicz
- Sub-Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, St. Akademicka 12, 20-033, Lublin, Poland
| | - Alicja Błaszków
- Student of the Faculty of Veterinary Medicine, University of Environmental and Life Sciences, Wrocław, Poland
| | - Maria Brodala
- Student of the Faculty of Veterinary Medicine, University of Environmental and Life Sciences, Wrocław, Poland
| | - Adrianna Domagała
- Student of the Faculty of Veterinary Medicine, University of Environmental and Life Sciences, Wrocław, Poland
| | - Anna-Nicole Prassol
- Student of the Faculty of Veterinary Medicine, University of Environmental and Life Sciences, Wrocław, Poland
| | - Dominika Sławska
- Student of the Faculty of Veterinary Medicine, University of Environmental and Life Sciences, Wrocław, Poland
| | - Julita Wojtynia
- Student of the Faculty of Veterinary Medicine, University of Environmental and Life Sciences, Wrocław, Poland
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Qi H, Liu D, Zou Y, Wang N, Tian H, Xiao C. Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child's oropharynx. Antonie van Leeuwenhoek 2021; 114:113-127. [PMID: 33387140 PMCID: PMC7878260 DOI: 10.1007/s10482-020-01505-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/25/2020] [Indexed: 01/01/2023]
Abstract
Using the culturomics approach, we isolated a new Streptococcus species, strain C17T, from the oropharynx mucosa sample of a healthy 5-year-old child living in Shenyang, China. We studied the phenotypic, phylogenetic, and genomic characteristics of strain C17T, which was identified as a Gram-positive, coccus-shaped, non-motile, aerobic, catalase-negative bacteria. Its growth temperatures ranged from 20 to 42 °C, with optimal growth at 37 °C. Acid production could be inhibited by two sugars, trehalose and raffinose. In C17T, the reactions for enzyme lipase (C14) were confirmed to be negative, whereas those for alkaline phosphatase, α-glucosidase, and hippuric acid hydrolysis were positive. The C17T genome contained 2,189,419 base pairs (bp), with an average G+C content of 39.95%, encoding 2092 genes in total. The 16S ribosomal RNA sequence showed 99.8% similarity with the newly identified Streptococcus pseudopneumoniae ATCC BAA-960T. The main fatty acid components in C17T were C16:0, C18:1 w7c, C18:0, and C18:1 w9c, all of which can be found in other species of the Streptococcus genus. Strain C17T showed high susceptibility to clindamycin, linezolid, vancomycin, chloramphenicol, and cefepime, and moderate susceptibility to erythromycin. The obtained dDDH value between strain C17T and the closest species was 52.9%. In addition, the whole genome sequence of strain C17T had an 82.21–93.40% average nucleotide identity (ANI) with those strains of closely related Streptococcus species, indicating that the strain C17T was unique among all Streptococcus species. Based on these characteristics, we determine that C17T is a novel species, named Streptococcus symci sp. nov. (= GDMCC 1.1633 = JCM 33582).
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Affiliation(s)
- He Qi
- Liaoning University of Traditional Chinese Medicine, Shenyang, People's Republic of China
- Department of Medical technology, Medical Science Institute of Liaoning, Shenyang, People's Republic of China
| | - Defeng Liu
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Yang Zou
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Nan Wang
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Han Tian
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Chunling Xiao
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China.
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Aulia Rahma A, Somowiyarjo S, Joko T. Induced Disease Resistance and Promotion of Shallot Growth by <i>Bacillus velezensis</i> B-27. Pak J Biol Sci 2020; 23:1113-1121. [PMID: 32981242 DOI: 10.3923/pjbs.2020.1113.1121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVES Shallot is a vegetable crop with high economic value, but its productivity is still relatively low due to various limitations. One of the most hampering factors is moler disease and purple blotch disease caused by Fusarium sp. and Alternaria porri, respectively. Numerous efforts have been made to control these diseases either using chemical fungicides or through improvement of resistant cultivar. This study aimed to determine moler and purple disease suppression and improvement of plant growth by Bacillus as Plant Growth Promoting Rhizobacteria (PGPR) on shallot. MATERIALS AND METHODS Molecular identification of Bacillus was performed by partial gyrB gene sequencing using universal gyrB-F/gyrB-R primers. Field observation and experiments were performed using completely randomized factorial block design single factor with 3 blocks for replication. RESULTS The partial gyrB gene sequences showed high similarity between Bacillus isolate B-27 and Bacillus velezensis. The application of Bacillus isolate B-27 to shallots was shown to reduce the intensity of moler and purple blotch diseases by 67%. On top of that, Bacillus isolate B-27 increased the plant height up to 27.12 cm, the number of leaves up to 23 blades, tillers up to 8 bulbs and the tuber weight during harvest time up to 33.64 kg. CONCLUSION Molecular identification based on partial gyrB gene sequence analysis suggested that Bacillus isolate B-27 has close relationship with Bacillus velezensis. Besides, the application of Bacillus isolate B-27 on shallot could reduce the disease intensity and increase height, number of tillers and plant yield significantly.
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Cheng X, Dou Z, Yang J, Gu Y, Liu D, Xie L, Ren T, Liu Y, Yu Z, Tang Y, Wang M. Highly Sensitive and Rapid Identification of Streptococcus agalactiae Based on Multiple Cross Displacement Amplification Coupled With Lateral Flow Biosensor Assay. Front Microbiol 2020; 11:1926. [PMID: 32983004 PMCID: PMC7485445 DOI: 10.3389/fmicb.2020.01926] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 07/22/2020] [Indexed: 12/30/2022] Open
Abstract
Streptococccus agalactiae (S. agalactiae) is an important neonatal pathogen that is associated with mortality and morbidity. Therefore, we developed a rapid, accurate, and sensitive method based on multiple cross displacement amplification (MCDA) for the detection of the target pathogen. Four sets of MCDA primers were designed for targeting the S. agalactiae-specific groEL gene, and one set of MCDA primers with the optimum amplification efficiency was screened for establishing the S. agalactiae-MCDA assay. As a result, the newly-developed assay could be conducted at a fixed temperature (61°C) for only 30 min, eliminating the use of complex instruments. A portable and user-friendly nanoparticle-based lateral flow biosensor (LFB) assay was employed for reporting MCDA results within 2 min. Our results suggested that the detection limit of the S. agalactiae-MCDA-LFB assay is 300 fg per reaction, and no cross-reaction occurred with non-S. agalactiae strains. For 260 vaginal and rectal swabs, the detection rate of the MCDA-LFB assay was 7.7%, which was in accordance with the reference method of enrichment/qPCR, and higher by 4.6% than the CHROMagar culture. Moreover, the total procedure time of the MCDA-LFB assay was around 50 min, including sample collection, template preparation, MCDA reaction, and result reporting. Therefore, the MCDA-LFB assay is superior to enrichment/qPCR and CHROMagar culture and has great promise for point-of-care testing of S. agalactiae from vaginal and rectal swabs of pregnant women in resource-limited settings.
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Affiliation(s)
- Xueqin Cheng
- Department of Respiratory and Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China.,Hubei Key Laboratory of Embryonic Stem Cell Research, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhiqian Dou
- Department of Gynaecology and Obstetrics, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jing Yang
- Department of Pharmacy, Wuhan General Hospital of the Chinese People's Liberation Army, Wuhan, China
| | - Yulong Gu
- Department of Clinical Laboratory, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Dexi Liu
- Department of Stomatology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Ling Xie
- Department of Dermatology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Tao Ren
- Department of Respiratory and Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yan Liu
- Department of Respiratory and Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhifang Yu
- Department of Respiratory and Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yijun Tang
- Department of Respiratory and Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Meifang Wang
- Department of Respiratory and Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
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Alnakip MEA, Rhouma NR, Abd-Elfatah EN, Quintela-Baluja M, Böhme K, Fernández-No I, Bayoumi MA, Abdelhafez MM, Taboada-Rodríguez A, Calo-Mata P, Barros-Velázquez J. Discrimination of major and minor streptococci incriminated in bovine mastitis by MALDI-TOF MS fingerprinting and 16S rRNA gene sequencing. Res Vet Sci 2020; 132:426-438. [PMID: 32777539 DOI: 10.1016/j.rvsc.2020.07.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/13/2020] [Accepted: 07/30/2020] [Indexed: 02/05/2023]
Abstract
The current work investigated the discriminatory potential of MALDI-TOF MS fingerprinting towards most-relevant major (Streptococcus agalactiae, S. dysgalactiae, S. uberis) and minor (S. canis, S. parauberis, S. salivarius, S. equinus and S. gallolyticus) streptococci involved in bovine mastitis (BM), in comparison to 16S rRNA gene sequencing (GS)-based identification. The MALDI-TOF MS-generated spectral fingerprints were recruited for eliciting a detailed proteomic map that demonstrated clear variability for inter- and intra-species-specific biomarkers. Besides, a phyloproteomic dendrogram was evolved and comparatively analyzed against the phylogenetic one obtained from 16S rRNA GS in order to assess the differentiation of streptococci of bovine origin based on variability of protein fingerprints versus the variation of 16S rRNA gene homology. Results showed that the discrimination of BM-implicated streptococci can be obtained by both approaches; however MALDI-TOF MS was superior, achieving more variability at both intra- and sub-species levels. MALDI-TOF MS spectral analytics revealed that Streptococcus spp. exhibited three genus-specific biomarkers (peaks with m/z values at 2112, 4452 and 5955) and all streptococci exhibited spectral variability at both species and subspecies levels. Remarkably, MALDI-TOF MS fingerprinting was found to be at least as robust as 16S rRNA GS-based identification, allowing much cheaper and faster analysis, and additionally exhibiting high reliability for characterization of BM-implicated streptococci, thus proving to be a powerful tool that can be used independently within dairy diagnostics.
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Affiliation(s)
- Mohamed E A Alnakip
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain; Department of Food Control, Faculty of Veterinary Medicine, Zagazig University, 44519, Egypt
| | - Nasreddin R Rhouma
- Department of Biology, Faculty of Science, Misurata University, Libya; Department of Food science and Technology, Faculty of Agriculture, Misurata University, Libya
| | - Eman N Abd-Elfatah
- Department of Food Control, Faculty of Veterinary Medicine, Zagazig University, 44519, Egypt
| | - Marcos Quintela-Baluja
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - Inmaculada Fernández-No
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - Mohmaed A Bayoumi
- Department of Food Control, Faculty of Veterinary Medicine, Zagazig University, 44519, Egypt
| | - Mostafa M Abdelhafez
- Department of Food science and Technology, Faculty of Agriculture, Misurata University, Libya
| | - Amaury Taboada-Rodríguez
- Food Biotechnology Group, Department of Nutrition and Food Science, Faculty of Veterinary Sciences, Murcia university, Campus Espinardo, 30100 Murcia, Spain
| | - Pillar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - J Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain.
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8
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Foster G, Kirchner M, Muchowski J, Duggett N, Randall L, Knight HI, Whatmore AM. Streptococcus caledonicus sp. nov., isolated from sheep. Int J Syst Evol Microbiol 2020; 70:2611-2615. [PMID: 32160144 DOI: 10.1099/ijsem.0.004081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five strains of an unidentified Gram-positive, catalase-negative, chain-forming coccus-shaped organism recovered from sheep in Scotland were characterized using phenotypic and molecular taxonomic methods. Based on morphological and biochemical criteria, the strains were tentatively identified as streptococci but they did not appear to correspond to any recognised species of the genus. Comparative 16S rRNA gene sequencing showed the strains were highly related to each other and confirmed their placement in the genus Streptococcus, with a maximum nucleotide identity of around 97 % to extant species. Best matches were with Streptococcus hillyeri followed by Streptococcus porci. Average nucleotide identity and in silico DNA-DNA hybridization values determined from whole-genome sequence were also consistent with the group representing a novel species. Best matches, again seen to S. hillyeri, followed by S. porci and S. plurextorum, were below accepted cut-off values for species delineation. Based on biochemical criteria and molecular genetic evidence, it is proposed that the unknown isolates from sheep be assigned to a new species of the genus Streptococcus as Streptococcus caledonicus sp. nov. The type strain of Streptococcus caledonicus is S784/96/1T=CCUG 73951T=NCTC 14363T.
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Affiliation(s)
- Geoffrey Foster
- SRUC Veterinary Services, An Lochran, 10 Inverness Campus, Inverness IV2 5NA, UK
| | - Miranda Kirchner
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, KT15 3NB, UK
| | - Jakub Muchowski
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, KT15 3NB, UK
| | - Nicholas Duggett
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, KT15 3NB, UK
| | - Luke Randall
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, KT15 3NB, UK
| | - Hazel I Knight
- SRUC Veterinary Services, Mill of Craibstone, Bucksburn, Aberdeen AB21 9TB, UK
| | - Adrian M Whatmore
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, KT15 3NB, UK
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Chen Q, Wu G, Chen H, Li H, Li S, Zhang C, Pang X, Wang L, Zhao L, Shen J. Quantification of Human Oral and Fecal Streptococcus parasanguinis by Use of Quantitative Real-Time PCR Targeting the groEL Gene. Front Microbiol 2020; 10:2910. [PMID: 31921079 PMCID: PMC6933288 DOI: 10.3389/fmicb.2019.02910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/03/2019] [Indexed: 11/13/2022] Open
Abstract
Two pairs of species-specific PCR primers targeting the housekeeping groEL gene, Spa146f-Spa525r and Spa93f-Spa525r, were designed to quantify human oral and fecal Streptococcus parasanguinis. Blast analysis against reference sequences of NCBI nucleotide collection database and the Chaperonin Sequence Database showed the forward primers Spa146f and Spa93f 100% matched only with S. parasanguinis, and the in silico Simulated PCR algorithm showed both primer pairs hit only S. parasanguinis groEL gene in Chaperonin Sequence Database. The two primer pairs were respectively used to perform PCR with saliva DNA of each of 6 human subjects, and the amplicons of individual PCR reactions were cloned. The phylogenetic analysis showed cloned sequences were all affiliated to S. parasanguinis, which further validates the specificity of two primer pairs, and that individual subjects harbored multiple genotypes of S. parasanguinis in saliva. By spiking S. parasanguinis into human fecal samples, we found the quantification limit of quantitative real-time PCR (qPCR) assays for both primer pairs was 5-6 log10 groEL copies/g feces. Human fecal S. parasanguinis amounts quantified with qPCR using each of the two primer pairs correlated well with those determined with metagenomic sequencing. qPCR with either primer pair showed periodontitis patients had significantly lower level of saliva S. parasanguinis than healthy people. In both feces and saliva, the S. parasanguinis abundances quantified with two primer pairs exhibited strong and significant correlation. Our results show that the two S. parasanguinis-specific primer pairs can be used to quantify and profile human saliva and fecal S. parasanguinis.
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Affiliation(s)
- Qiurong Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guojun Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyan Pang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Linghua Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Liping Zhao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Shen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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Leigh WJ, Zadoks RN, Costa JZ, Jaglarz A, Thompson KD. Development and evaluation of a quantitative polymerase chain reaction for aquatic Streptococcus agalactiae based on the groEL gene. J Appl Microbiol 2020; 129:63-74. [PMID: 31851413 DOI: 10.1111/jam.14556] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/23/2019] [Accepted: 12/08/2019] [Indexed: 01/19/2023]
Abstract
AIMS The aim of this study was to develop a TaqMan quantitative polymerase chain reaction (qPCR), based on the Streptococcus agalactiae groEL gene, to specifically quantify levels of bacteria within samples derived from aquatic sources, particularly aquaculture. Enumeration of bacteria by qPCR was compared with culture-based methods. METHODS AND RESULTS The qPCR was sensitive to 33 isolates of S. agalactiae, representing 11 clonal complexes from aquatic, bovine and human hosts. The specificity of the assay was 92·5% at a threshold Cq value of 35. No cross-reaction with Streptococcus iniae was noted and of the 22 comparator species screened to test assay specificity, Streptococcus porcinus had a Cq value of 33·7 S, while Streptococcus gallolyticus subsp. macedonicus and Streptococcus ictaluri had one replicate value above the Cq threshold of 35 (34·5 and 34·4 respectively), while only S. agalactiae were detected with a Cq value of 30. The limit of detection of the assay was 1·7 copies per µl at Cq 35. Discrepancies between molecular and culture-based methods of enumeration were noted. CONCLUSIONS The qPCR was able to detect a diverse range of S. agalactiae isolates from different clonal complexes (CCs) and could distinguish between S. agalactiae and closely related species, notably S. iniae. The results suggest that a Cq 30 would be a very meaningful cut-off, allowing the detection of infected fish while ruling out all false positives. SIGNIFICANCE AND IMPACT OF THE STUDY This rapid and sensitive qPCR assay is useful to quantify DNA copy number in the laboratory and could prove useful for detecting low levels of S. agalactiae in aquaculture systems, including Oreochromis niloticus culture.
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Affiliation(s)
- W J Leigh
- Moredun Research Institute, Pentlands Science Park, Penicuik, UK.,Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - R N Zadoks
- Moredun Research Institute, Pentlands Science Park, Penicuik, UK.,Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - J Z Costa
- Moredun Research Institute, Pentlands Science Park, Penicuik, UK
| | - A Jaglarz
- Moredun Research Institute, Pentlands Science Park, Penicuik, UK
| | - K D Thompson
- Moredun Research Institute, Pentlands Science Park, Penicuik, UK
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11
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Ercibengoa M, Morales M, Alonso M, Ardanuy C, Marimón JM. Variants of the bile: solubility test to differentiate Streptococcus pneumoniae from other viridans group streptococci. Future Microbiol 2019; 14:949-955. [PMID: 31373220 DOI: 10.2217/fmb-2019-0073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Bile salts promote the specific autolysis of pneumococcal cells, allowing the differentiation between Streptococcus pneumoniae and other viridans group streptococci (VGS). Material & methods: One hundred clinical VGS isolates identified by amplification and sequencing of 16S rRNA, groEL and sodA genes were analyzed with different variants of bile-solubility tests: tube testing read by naked eye; tube testing where the lysis was measured as the decrease of turbidity with a densitometer; and direct testing on blood agar plate. Results: As expected, all S. pneumoniae isolates were fully lysed in the presence of bile salts except for one isolate that partially lysate in tube testing as well as on the blood agar plate. None of the VGS were lysed by bile salts. Conclusion: Bile-solubility testing is an accurate and technically nondemanding method to discriminate between S. pneumoniae and other VGS species.
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Affiliation(s)
- María Ercibengoa
- Biodonostia, Infectious Diseases Area, Respiratory Infection and Antimicrobial Resistance Group; Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation, Microbiology Department, 20014 San Sebastian, Spain
| | - María Morales
- Biodonostia, Infectious Diseases Area, Respiratory Infection and Antimicrobial Resistance Group; Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation, Microbiology Department, 20014 San Sebastian, Spain
| | - Marta Alonso
- Biodonostia, Infectious Diseases Area, Respiratory Infection and Antimicrobial Resistance Group; Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation, Microbiology Department, 20014 San Sebastian, Spain
| | - Carmen Ardanuy
- Network for Respiratory Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Microbiology Department, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), University of Barcelona, Spain
| | - José M Marimón
- Biodonostia, Infectious Diseases Area, Respiratory Infection and Antimicrobial Resistance Group; Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation, Microbiology Department, 20014 San Sebastian, Spain
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12
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Arredondo A, Àlvarez G, Nart J, Mor C, Blanc V, León R. Detection and expression analysis of tet(B) in Streptococcus oralis. J Oral Microbiol 2019; 11:1643204. [PMID: 31448060 PMCID: PMC6691830 DOI: 10.1080/20002297.2019.1643204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/28/2019] [Accepted: 07/03/2019] [Indexed: 11/22/2022] Open
Abstract
Tetracycline resistance can be achieved through tet genes, which code for efflux pumps, ribosomal protection proteins and inactivation enzymes. Some of these genes have only been described in either Gram-positive or Gram-negative bacteria. This is the case of tet(B), which codes for an efflux pump and, so far, had only been found in Gram-negative bacteria. In this study, tet(B) was detected in two clinical Streptococcus oralis strains isolated from the gingival sulci of two subjects. In both cases, the gene was completely sequenced, yielding 100% shared identity and coverage with other previously published sequences of tet(B). Moreover, we studied the expression of tet(B) using RT-qPCR in the isolates grown with and without tetracycline, detecting constitutive expression in only one of the isolates, with no signs of expression in the other one. This is the first time that the presence and expression of the tet(B) gene has been confirmed in Gram-positive bacteria, which highlights the potential of the genus Streptococcus to become a reservoir and a disseminator of antibiotic resistance genes in an environment so prone to horizontal gene transfer as is the oral biofilm.
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Affiliation(s)
- Alexandre Arredondo
- Department of Microbiology, Dentaid Research Center, Cerdanyola del Vallès, Spain.,Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Gerard Àlvarez
- Department of Microbiology, Dentaid Research Center, Cerdanyola del Vallès, Spain
| | - José Nart
- Department of Periodontology, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Carolina Mor
- Department of Periodontology, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Vanessa Blanc
- Department of Microbiology, Dentaid Research Center, Cerdanyola del Vallès, Spain
| | - Rubén León
- Department of Microbiology, Dentaid Research Center, Cerdanyola del Vallès, Spain
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13
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MacFadyen AC, Waller AS, Paterson GK. Streptococcus hillyeri sp. nov., isolated from equine trachea. Int J Syst Evol Microbiol 2019; 69:3009-3013. [PMID: 31287393 DOI: 10.1099/ijsem.0.003489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain 28462T, which had Gram-stain-positive, catalase-negative coccus-shaped cells, was isolated from a routine tracheal sample from a 3 year old thoroughbred horse. 16S rRNA gene sequence analysis revealed it to be most closely related to, but distinct from, Streptococcus henryi (95.7 % identity), Streptococcusplurextorum (95.8 %), Streptococcusporci (96.4 %) and Streptococcus caprae (95.1 %). Similarity values derived from sequences from sodA and rpoB genes were consistent with strain 28462T belonging to a species distinct from these four streptococci. At the whole genome level, strain 28462T had an average nucleotide identity value <95 % and an inferred DNA-DNA hybridization value <70 % when compared to S. henryi, Streptococcus. plurextorum and S. porci with no S. caprae genome sequence being available. Finally, various phenotypic characteristics distinguish strain 28462T from each of these species. Based on the genotypic and phenotypic results, it is proposed that strain 28462T is a novel species, with the name Streptococcus hillyeri sp. nov. The type strain is 28462T (=DSM 107591T=CCUG 72762T).
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Affiliation(s)
- A C MacFadyen
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - A S Waller
- Animal Health Trust, Lanwades Park Kentford, Newmarket, Suffolk, CB8 7UU, UK
| | - G K Paterson
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
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14
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Gonzales-Siles L, Salvà-Serra F, Degerman A, Nordén R, Lindh M, Skovbjerg S, Moore ERB. Identification and capsular serotype sequetyping of Streptococcus pneumoniae strains. J Med Microbiol 2019; 68:1173-1188. [PMID: 31268417 DOI: 10.1099/jmm.0.001022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Correct serotype identification of Streptococcus pneumoniae (pneumococcus) is important for monitoring disease epidemiology and assessing the impacts of pneumococcal vaccines. Furthermore, correct identification and differentiation of the pathogenic S. pneumoniae from closely related commensal species of the mitis group of the genus Streptococcus are essential for correct serotype identification. METHODOLOGY A new protocol for determining the existing 98 serotypes of pneumococcus was developed, applying two PCR amplifications and amplicon sequencing, using newly designed internal primers. The new protocol was validated using S. pneumoniae genome sequences, reference strains with confirmed serotypes and clinical isolates, and comparing the results with those from the traditional Quellung reaction or antiserum panel gel precipitation, in addition to real-time PCR analysis. The taxonomic identifications of 422 publicly available (GenBank) genome sequences of S. pneumoniae, Streptococcus pseudopneumoniae and Streptococcus mitis were assessed by whole-genome sequence average nucleotide identity based on blast (ANIb) analysis. RESULTS The proposed sequetyping protocol generates a 1017 bp whole cpsB region sequence, increasing resolution for serotype identification in pneumococcus isolates. The identifications of all GenBank genome sequences of S. pneumoniae were confirmed, whereas most of the S. pseudopneumoniae and almost all of the S. mitis genome sequences did not fulfil the ANIb thresholds for species-level identification. The housekeeping biomarker gene, groEL, correctly identified S. pneumoniae but often misclassified S. pseudopneumoniae and S. mitis as S. pneumoniae. CONCLUSIONS These studies affirm the importance of applying reliable identification protocols for S. pneumoniae before serotyping; our protocols provide reliable diagnostic tools, as well as an improved workflow, for serotype identification of pneumococcus and differentiation of serogroup 6 types.
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Affiliation(s)
- Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden.,Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Anna Degerman
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Rickard Nordén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Susann Skovbjerg
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Edward R B Moore
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.,Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
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15
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Mühldorfer K, Rau J, Fawzy A, Heydel C, Glaeser SP, van der Linden M, Kutzer P, Knauf-Witzens T, Hanczaruk M, Eckert AS, Eisenberg T. Streptococcus castoreus, an uncommon group A Streptococcus in beavers. Antonie van Leeuwenhoek 2019; 112:1663-1673. [PMID: 31250158 DOI: 10.1007/s10482-019-01293-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/20/2019] [Indexed: 01/21/2023]
Abstract
Streptococcus castoreus is a rarely encountered beta-haemolytic group A Streptococcus with high tropism for the beaver as host. Based on 27 field isolates under study, evidence strongly suggests that S. castoreus behaves as an opportunistic pathogen in beavers. Although it belongs to the resident mucosal microbiota, this Streptococcus species is associated with purulent lesions in diseased animals. With few exceptions, isolates proved to be highly similar in a panel of phenotypic (including biochemistry, resistance pattern, MALDI-TOF mass spectrometry and Fourier transform-infrared spectroscopy) and classic molecular (16S rRNA and sodA gene) analyses, and thus did not show any specific pattern according to host species or spatio-temporal origin. Conversely, S. castoreus isolates were differentiated into a multitude of pulsed-field gel electrophoresis 'pulsotypes' that did not seem to reflect true epidemiologic lineages. In contrast, single reactions of genomic fingerprinting using BOX-, (GTG)5- and RAPD-PCRs revealed at least subclusters with respect to host species, geographic origin or year, and confirmed the co-colonization of individuals with more than one isolate. In addition to isolates from free-ranging Eurasian beavers (Castor fiber), this study includes S. castoreus from captive North American beavers (Castor canadensis) for the first time.
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Affiliation(s)
- Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany.
| | - Jörg Rau
- Chemical and Veterinary Investigations Office Stuttgart, Schaflandstraße 3/2, 70736, Fellbach, Germany
| | - Ahmad Fawzy
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza Square, 12211, Egypt
- Hessian State Laboratory (LHL), Schubertstr. 60, 35392, Giessen, Germany
| | - Carsten Heydel
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Frankfurter Str. 85-89, 35392, Giessen, Germany
| | - Stefanie P Glaeser
- Institute of Applied Microbiology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
| | - Mark van der Linden
- German National Reference Center for Streptococci, Department of Medical Microbiology, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Peter Kutzer
- Landeslabor Berlin-Brandenburg, Gerhard-Neumann-Straße 2, 15236, Frankfurt (Oder), Germany
| | - Tobias Knauf-Witzens
- Wilhelma - Zoological and Botanical Gardens, Wilhelma 13, 70342, Stuttgart, Germany
| | - Matthias Hanczaruk
- Bavarian Health and Food Safety Authority, Veterinärstr. 2, 85764, Oberschleißheim, Germany
| | - Anna Sophie Eckert
- Hessian State Laboratory (LHL), Schubertstr. 60, 35392, Giessen, Germany
| | - Tobias Eisenberg
- Hessian State Laboratory (LHL), Schubertstr. 60, 35392, Giessen, Germany
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Frankfurter Str. 85-89, 35392, Giessen, Germany
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16
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Shewmaker PL, Whitney AM, Gulvik CA, Humrighouse BW, Gartin J, Moura H, Barr JR, Moore ERB, Karlsson R, Pinto TCA, Teixeira LM. Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound. Int J Syst Evol Microbiol 2019; 69:2268-2276. [PMID: 31125302 DOI: 10.1099/ijsem.0.003459] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two unusual catalase-negative, Gram-stain-positive, Vagococcus-like isolates that were referred to the CDC Streptococcus Laboratory for identification are described. Strain SS1994T was isolated from ground beef and strain SS1995T was isolated from a human foot wound. Comparative 16S rRNA gene sequence analysis of isolates SS1994T and SS1995T against Vagococcus type strain sequences supported their inclusion in the genus Vagococcus. Strain SS1994T showed high sequence similarity (>97.0 %) to the two most recently proposed species, Vagococcus martis (99.2 %) and Vagococcus teuberi (99.0 %) followed by Vagococcus penaei (98.8 %), strain SS1995T (98.6 %), Vagococcus carniphilus (98.0 %), Vagococcus acidifermentans (98.0 %) and Vagococcus fluvialis (97.9 %). The 16S rRNA gene sequence of strain SS1995T was most similar to V. penaei (99.1 %), followed by SS1994T (98.6 %), V. martis (98.4 %), V. teuberi (98.1 %), V. acidifermentans (97.8 %), and both V. carniphilus and V. fluvialis (97.5 %). A polyphasic taxonomic study using conventional biochemical and the rapid ID 32 STREP system, MALDI-TOF MS, cell fatty acid analysis, pairwise sequence comparisons of the 16S rRNA, rpoA, rpoB, pheS and groL genes, and comparative core and whole genome sequence analyses revealed that strains SS1994T and SS1995T were two novel Vagococcus species. The novel taxonomic status of the two isolates was confirmed with core genome phylogeny, average nucleotide identity <84 % and in silico DNA-DNA hybridization <28 % to any other Vagococcus species. The names Vagococcusbubulae SS1994T=(CCUG 70831T=LMG 30164T) and Vagococcusvulneris SS1995T=(CCUG 70832T=LMG 30165T) are proposed.
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Affiliation(s)
- Patricia L Shewmaker
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Anne M Whitney
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Christopher A Gulvik
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Ben W Humrighouse
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jarrett Gartin
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Hercules Moura
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - John R Barr
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Edward R B Moore
- Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-41346 Region Västra Götaland, Sweden.,Culture Collection University of Gothenburg (CCUG), Gothenburg, Sweden.,Department of Infectious Disease, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-41346, Sweden
| | - Roger Karlsson
- Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-41346 Region Västra Götaland, Sweden.,Department of Infectious Disease, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-41346, Sweden.,Nanoxis Consulting AB, SE-40016 Gothenburg, Sweden
| | - Tatiana C A Pinto
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucia M Teixeira
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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17
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Ercibengoa M, Goenaga MA, Ardanuy C, Grau I, García-de-la-Maria C, Almela M, Miro JM, Navas E, Fariñas MC, de Alegría CR, de la Torre J, Fernández F, Marín M, Muñoz P, Orden B, Oteo JA, García-Álvarez L, de Alarcón A, Jiménez JAL, Marimón JM. Epidemiological and clinical characteristics of Streptococcus tigurinus endocarditis. BMC Infect Dis 2019; 19:291. [PMID: 30922322 PMCID: PMC6440093 DOI: 10.1186/s12879-019-3914-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 03/18/2019] [Indexed: 11/23/2022] Open
Abstract
Background Streptococcus tigurinus was recently described as a new streptococcal species within the viridans group streptococci (VGS). The objectives of the present work were to analyse the clinical and microbiological characteristics of S. tigurinus isolated from patients with bacteraemias, to determine the prevalence of S. tigurinus among VGS endocarditis in Spain, and to compare the clinical characteristics and outcomes of endocarditis caused by S. tigurinus and other VGS. Methods Retrospective nationwide study, performed between 2008 and 2016 in 9 Spanish hospitals from 7 different provinces comprising 237 cases of infective endocarditis. Streptococcal isolates were identified by sequencing fragments of their 16S rRNA, sodA and groEL genes. Clinical data of patients with streptococcal endocarditis were prospectively collected according to a pre-established protocol. Results Patients with endocarditis represented 7/9 (77.8%) and 26/86 (30.2%) of the bacteraemias caused by S. tigurinus and other VGS, respectively (p < 0.001), in two of the hospital participants. Among patients with streptococcal endocarditis, 12 different Streptococcus species were recognized being S. oralis, S. tigurinus and S. mitis the three more common. No relevant statistical differences were observed in the clinical characteristics and outcomes of endocarditis caused by the different VGS species. Conclusions In this multicenter study performed in Spain, S. tigurinus showed a higher predilection for the endocardial endothelium as compared to other VGS. However, clinical characteristics and outcomes of endocarditis caused by S. tigurinus did not significantly differ from endocarditis caused by other oral streptococci.
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Affiliation(s)
| | | | - Carmen Ardanuy
- CIBER Enfermedades Respiratorias-CIBERES, Madrid, Spain.,Servicio de Microbiologia, Hospital Universitari de Bellvitge. Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), University of Barcelona, Barcelona, Spain
| | - Immaculada Grau
- CIBER Enfermedades Respiratorias-CIBERES, Madrid, Spain.,Servicio de Enfermedades Infecciosas, Hospital Universitari de Bellvitge. Institut d' Investigació Biomèdica de Bellvitge (IDIBELL), University of Barcelona, Barcelona, Spain
| | - Cristina García-de-la-Maria
- Servicio de Enfermedades Infecciosas, Hospital Clínic de Barcelona, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Manuel Almela
- Servicio de Microbiología, Hospital Clínic de Barcelona, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Jose María Miro
- Servicio de Enfermedades Infecciosas, Hospital Clínic de Barcelona, Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Enrique Navas
- Servicio de Enfermedades Infecciosas, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - María Carmen Fariñas
- Servicio de Enfermedades Infecciosas, Hospital Universitario Marqués de Valdecilla, Universidad de Cantabria, Santander, Spain
| | - Carlos Ruiz de Alegría
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Universidad de Cantabria, Santander, Spain
| | - Javier de la Torre
- Grupo de Enfermedades Infecciosas de la Unidad de Medicina Interna, Hospital Costa del Sol, Marbella, Málaga, Spain
| | - Fernando Fernández
- Servicio de Microbiología, Hospital Costa del Sol, Marbella, Málaga, Spain
| | - Mercedes Marín
- CIBER Enfermedades Respiratorias-CIBERES, Madrid, Spain.,Departamento de Medicina, Servicio de Microbiología y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Facultad de Medicina, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio, Marañón, Madrid, Spain
| | - Patricia Muñoz
- CIBER Enfermedades Respiratorias-CIBERES, Madrid, Spain.,Departamento de Medicina, Servicio de Microbiología y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Facultad de Medicina, Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio, Marañón, Madrid, Spain
| | - Beatriz Orden
- Departamento de Microbiología, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain
| | - José Antonio Oteo
- Departamento de Enfermedades Infecciosas, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
| | - Lara García-Álvarez
- Departamento de Enfermedades Infecciosas, Hospital Universitario San Pedro, Logroño, La Rioja, Spain
| | - Arístides de Alarcón
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine. Infectious Diseases Research Group, Institute of Biomedicine of Seville (IBIS), University of Seville/CSIC/University Virgen del Rocío and Virgen Macarena, Sevilla, Spain
| | - José Antonio Lepe Jiménez
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine. Infectious Diseases Research Group, Institute of Biomedicine of Seville (IBIS), University of Seville/CSIC/University Virgen del Rocío and Virgen Macarena, Sevilla, Spain
| | - Jose María Marimón
- CIBER Enfermedades Respiratorias-CIBERES, Madrid, Spain. .,Servicio de Microbiología, Hospital Universitario Donostia-IIS Biodonostia, Paseo Dr Beguiristain s/n, 20014, San Sebastián, Spain.
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18
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An Overview on Streptococcus bovis/Streptococcus equinus Complex Isolates: Identification to the Species/Subspecies Level and Antibiotic Resistance. Int J Mol Sci 2019; 20:ijms20030480. [PMID: 30678042 PMCID: PMC6386949 DOI: 10.3390/ijms20030480] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/14/2019] [Accepted: 01/20/2019] [Indexed: 01/09/2023] Open
Abstract
Streptococcus bovis/Streptococcus equinus complex (SBSEC), a non-enterococcal group D Streptococcus spp. complex, has been described as commensal bacteria in humans and animals, with a fecal carriage rate in humans varying from 5% to over 60%. Among streptococci, SBSEC isolates represent the most antibiotic-resistant species—with variable resistance rates reported for clindamycin, erythromycin, tetracycline, and levofloxacin—and might act as a reservoir of multiple acquired genes. Moreover, reduced susceptibility to penicillin and vancomycin associated with mobile genetic elements have also been detected, although rarely. Since the association of SBSEC bacteremia and colon lesions, infective endocarditis and hepatobiliary diseases has been established, particularly in elderly individuals, an accurate identification of SBSEC isolates to the species and subspecies level, as well as the evaluation of antibiotic resistance, are needed. In this paper, we reviewed the major methods used to identify SBSEC isolates and the antimicrobial resistance rates reported in the scientific literature among SBSEC species.
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19
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Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures. INFECTION GENETICS AND EVOLUTION 2018; 66:130-151. [DOI: 10.1016/j.meegid.2018.09.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 09/12/2018] [Accepted: 09/19/2018] [Indexed: 11/21/2022]
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20
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Charniauskaya MI, Bukliarevich AA, Delegan YA, Akhremchuk AE, Filonov AE, Titok MA. Biodiversity of Hydrocarbon-Oxidizing Soil Bacteria from Various Climatic Zones. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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21
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Leigh WJ, Zadoks RN, Jaglarz A, Costa JZ, Foster G, Thompson KD. Evaluation of PCR primers targeting the groEL gene for the specific detection of Streptococcus agalactiae in the context of aquaculture. J Appl Microbiol 2018; 125:666-674. [PMID: 29786935 DOI: 10.1111/jam.13925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/01/2018] [Accepted: 05/04/2018] [Indexed: 02/06/2023]
Abstract
AIMS The aim of this study was to design a set of primers for specific detection and identification of Streptococcus agalactiae in polymerase chain reaction (PCR) that can detect a diverse range of S. agalactiae isolates from different hosts and that it is capable of discriminating between S. agalactiae and other species that are closely related or potentially present in aquaculture environments, notably Streptococcus iniae. METHODS AND RESULTS Primers, based on the groEL2 gene of S. agalactiae, were shown to be epidemiologically sensitive to 97 isolates of S. agalactiae, representing 11 clonal complexes derived from piscine, terrestrial and aquatic mammalian host species. The primers were tested with 10 S. iniae isolates and 22 other comparator species with no cross-reaction observed after optimization of reaction conditions. They have a high analytical sensitivity, detecting as few as 10 copies of S. agalactiae genomic DNA per reaction and are capable of detecting the target in DNA extracted from the brains of infected fish. CONCLUSIONS The primers proved suitable for the sensitive and specific detection of S. agalactiae from dairy-, human- and fish-related origins by PCR. SIGNIFICANCE AND IMPACT OF THE STUDY Due to the importance of S. agalactiae as a pathogen, many PCR primers have been published for this bacterium, designed largely for its detection in dairy and human samples, but many cross-reacting with S. iniae. The ability to differentiate between S. agalactiae and S. iniae in aquaculture derived samples is important as both infect fish, causing similar disease symptoms and are phenotypically similar, yet control strategies and zoonotic risk are species specific.
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Affiliation(s)
- W J Leigh
- Moredun Research Institute, Pentlands Science Park, Penicuik, UK.,Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - R N Zadoks
- Moredun Research Institute, Pentlands Science Park, Penicuik, UK.,Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - A Jaglarz
- Moredun Research Institute, Pentlands Science Park, Penicuik, UK
| | - J Z Costa
- Moredun Research Institute, Pentlands Science Park, Penicuik, UK
| | - G Foster
- SAC Consulting Veterinary Services, Drummond Hill, Stratherrick Road, Inverness, UK
| | - K D Thompson
- Moredun Research Institute, Pentlands Science Park, Penicuik, UK
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22
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Niu L, Hu S, Lu S, Lai XH, Yang J, Jin D, Rao L, Lu G, Xu J. Isolation and characterization of Streptococcus respiraculi sp. nov. from Marmota himalayana (Himalayan marmot) respiratory tract. Int J Syst Evol Microbiol 2018; 68:2082-2087. [PMID: 29717973 DOI: 10.1099/ijsem.0.002806] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Two bacterial strains were individually isolated from Marmota himalayana respiratory tracts; the animals were from the Tibet-Qinghai Plateau, PR China. The isolates were Gram-stain-positive, catalase-negative, coccus-shaped, chain-forming organisms. Analysis of 16S rRNA gene sequences indicated that the type strain HTS25T shared 98.0, 97.4, 97.2 and 97.1 % similarity with Streptococcus cuniculi, Streptococcus acidominimus, Streptococcus marmotae and Streptococcus himalayensis respectively. Sequence analysis of the sodA and rpoB genes indicated that HTS25T was closely related to S. marmotae (similarities of 94.7 and 91.4 % respectively). Analysis of groEL sequences showed interspecies similarity of 84.8 % between HTS25T and S. himalayensis. A whole-genome phylogenetic tree reconstructed from 81 core genes from the genomes of 17 members of the genus Streptococcus was used to validate that HTS25T forms a distinct subline from other recognized species of the genus Streptococcus. DNA-DNA hybridization of HTS25T showed a maximum estimated DNA reassociation value of 32.1 % to Streptococcus cuniculi CCUG 65085T. On the basis of the results of phenotypic and phylogenetic analyses, we propose that the two isolates be classified as representing a novel species of the genus Streptococcus, named Streptococcus respiraculi sp. nov. The type strain is HTS25T (=DSM 101998T=CGMCC 1.15531T). The genome of Streptococcus respiraculi sp. nov. strain HTS25T (2 067 971 bp) contains 2001 genes with an average DNA G+C content of 42.7 mol%.
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Affiliation(s)
- Lina Niu
- Department of Pathogen Biology, School of Basic Medicine and Life Science, Hainan Medical University; Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University); Hainan Medical University-University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou 571199, PR China.,State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shoukui Hu
- Peking University shougang hospital, Beijing 100144, PR China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- School of Biology and Food Sciences, Shangqiu Normal University, Shangqiu, Henan 476000, PR China.,Central Laboratory of Ganzhou People's Hospital, Ganzhou, Jiangxi Province 341000, PR China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Langyu Rao
- Department of Pathogen Biology, School of Basic Medicine and Life Science, Hainan Medical University; Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University); Hainan Medical University-University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou 571199, PR China
| | - Gang Lu
- Department of Pathogen Biology, School of Basic Medicine and Life Science, Hainan Medical University; Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University); Hainan Medical University-University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou 571199, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
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23
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Zamora L, Pérez-Sancho M, Fernández-Garayzábal JF, Orden JA, Domínguez-Bernal G, de la Fuente R, Domínguez L, Vela AI. Streptococcus ovuberis sp. nov., isolated from a subcutaneous abscess in the udder of a sheep. Int J Syst Evol Microbiol 2017; 67:4340-4344. [DOI: 10.1099/ijsem.0.002213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Leydis Zamora
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
| | - Marta Pérez-Sancho
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
| | - Jose Francisco Fernández-Garayzábal
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - Jose Antonio Orden
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - Gustavo Domínguez-Bernal
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - Ricardo de la Fuente
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - Lucas Domínguez
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - Ana Isabel Vela
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
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24
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Shewmaker PL, Whitney AM, Gulvik CA, Lipman NS. Streptococcus azizii sp. nov., isolated from naïve weanling mice. Int J Syst Evol Microbiol 2017; 67:5032-5037. [PMID: 29022542 DOI: 10.1099/ijsem.0.002407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three isolates of a previously reported novel catalase-negative, Gram-stain-positive, coccoid, alpha-haemolytic, Streptococcus species that were associated with meningoencephalitis in naïve weanling mice were further evaluated to confirm their taxonomic status and to determine additional phenotypic and molecular characteristics. Comparative 16S rRNA gene sequence analysis showed nearly identical intra-species sequence similarity (≥99.9 %), and revealed the closest phylogenetically related species, Streptococcus acidominimus and Streptococcuscuniculi, with 97.0 and 97.5 % sequence similarity, respectively. The rpoB, sodA and recN genes were identical for the three isolates and were 87.6, 85.7 and 82.5 % similar to S. acidominimus and 89.7, 86.2 and 80.7 % similar to S. cuniculi, respectively. In silico DNA-DNA hybridization analyses of mouse isolate 12-5202T against S. acidominimus CCUG 27296T and S. cuniculi CCUG 65085T produced estimated values of 26.4 and 25.7 % relatedness, and the calculated average nucleotide identity values were 81.9 and 81.7, respectively. These data confirm the taxonomic status of 12-5202T as a distinct Streptococcus species, and we formally propose the type strain, Streptococcusazizii 12-5202T (=CCUG 69378T=DSM 103678T). The genome of Streptococcus azizii sp. nov. 12-5202T contains 2062 total genes with a size of 2.34 Mbp, and an average G+C content of 42.76 mol%.
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Affiliation(s)
| | - Anne M Whitney
- Centers for Disease Control and Prevention, Atlanta, Georgia 30329, USA
| | | | - Neil S Lipman
- Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY 10065, USA
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25
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Current challenges in the accurate identification of Streptococcus pneumoniae and its serogroups/serotypes in the vaccine era. J Microbiol Methods 2017; 141:48-54. [DOI: 10.1016/j.mimet.2017.07.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 11/21/2022]
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26
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Lourenço J, Watkins ER, Obolski U, Peacock SJ, Morris C, Maiden MCJ, Gupta S. Lineage structure of Streptococcus pneumoniae may be driven by immune selection on the groEL heat-shock protein. Sci Rep 2017; 7:9023. [PMID: 28831154 PMCID: PMC5567354 DOI: 10.1038/s41598-017-08990-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022] Open
Abstract
Populations of Streptococcus pneumoniae (SP) are typically structured into groups of closely related organisms or lineages, but it is not clear whether they are maintained by selection or neutral processes. Here, we attempt to address this question by applying a machine learning technique to SP whole genomes. Our results indicate that lineages evolved through immune selection on the groEL chaperone protein. The groEL protein is part of the groESL operon and enables a large range of proteins to fold correctly within the physical environment of the nasopharynx, thereby explaining why lineage structure is so stable within SP despite high levels of genetic transfer. SP is also antigenically diverse, exhibiting a variety of distinct capsular serotypes. Associations exist between lineage and capsular serotype but these can be easily perturbed, such as by vaccination. Overall, our analyses indicate that the evolution of SP can be conceptualized as the rearrangement of modular functional units occurring on several different timescales under different pressures: some patterns have locked in early (such as the epistatic interactions between groESL and a constellation of other genes) and preserve the differentiation of lineages, while others (such as the associations between capsular serotype and lineage) remain in continuous flux.
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Affiliation(s)
- José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
| | | | - Uri Obolski
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Samuel J Peacock
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | | | - Sunetra Gupta
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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27
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Conrads G, Barth S, Möckel M, Lenz L, van der Linden M, Henne K. Streptococcus tigurinus is frequent among gtfR-negative Streptococcus oralis isolates and in the human oral cavity, but highly virulent strains are uncommon. J Oral Microbiol 2017; 9:1307079. [PMID: 28473881 PMCID: PMC5405715 DOI: 10.1080/20002297.2017.1307079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 02/10/2017] [Indexed: 11/25/2022] Open
Abstract
Streptococcus tigurinus is a new member of the Mitis group and is associated with infective endocarditis. Low and high virulent variants have been described. A search was made in the national reference collection of endocarditis isolates for S. tigurinus–like strains by sequencing housekeeping genes (16S rRNA-gene, gdh, groEL, sodA). The strains were further profiled by polymerase chain reaction (PCR) targeting a choice of virulence genes (rib-like, cshA-like, gtfR, int, pitA, hylA). To study the prevalence and abundance of S. tigurinus in the saliva and on the mucosal membranes of 35 healthy adults, PCRs detecting two variants of the 16S operon and virulence genes were applied. Among the endocarditis isolates, eight strains (all gtfR-negative and former S. oralis) holding the specific S. tigurinus 16S motif were found, but the pattern of genes related to high virulence found in the S. tigurinus type strain could not be detected in any of these strains. A close phylogenetic proximity between S. tigurinus and S. oralis was observed, with intersectional hybrid strains formed. This was supported by concatenated housekeeping sequences, in silico DNA–DNA hybridization, pathogenomic profiling, and multidimensional scaling. In the oral samples, S. tigurinus could be detected frequently, especially in the most common operon variant, but none of the type strain–related virulence factors were found. Low virulent S. tigurinus–like strains can be found frequently and in high prevalence (66%) and abundance (12.5%) in the oral cavity of healthy adults. In strain collections, they are among the formerly known gtfR-negative S. oralis. Highly virulent strains seem to be uncommon. Though closely related, S. oralis and S. tigurinus can be separated by the presence or absence of gtfR and dextran production. Hybrids of both species can be found. The variable arsenal of virulence genes found in this study emphasizes the genetic plasticity of Mitis group streptococci.
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Affiliation(s)
- Georg Conrads
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH Aachen University Hospital, Aachen, Germany
| | - Svenja Barth
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH Aachen University Hospital, Aachen, Germany
| | - Maureen Möckel
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH Aachen University Hospital, Aachen, Germany
| | - Lucas Lenz
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH Aachen University Hospital, Aachen, Germany
| | - Mark van der Linden
- Institute of Medical Microbiology and National Reference Center for Streptococci, RWTH Aachen University Hospital, Aachen, Germany
| | - Karsten Henne
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH Aachen University Hospital, Aachen, Germany
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28
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Niu L, Lu S, Lai XH, Hu S, Chen C, Zhang G, Yang J, Jin D, Wang Y, Lan R, Lu G, Xie Y, Ye C, Xu J. Streptococcus himalayensis sp. nov., isolated from the respiratory tract of Marmota himalayana. Int J Syst Evol Microbiol 2017; 67:256-261. [PMID: 27902227 DOI: 10.1099/ijsem.0.001609] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Five strains of Gram-positive-staining, catalase-negative, coccus-shaped, chain-forming organisms isolated separately from the respiratory tracts of five Marmota himalayana animals in the Qinghai-Tibet Plateau of China were subjected to phenotypic and molecular taxonomic analyses. Comparative analysis of the 16S rRNA gene indicated that these singular organisms represent a new member of the genus Streptococcus, being phylogenetically closest to Streptococcus marmotae DSM 101995T (98.4 % similarity). The groEL, sodA and rpoB sequence analysis showed interspecies similarity values between HTS2T and Streptococcus. marmotae DSM 101995T, its closest phylogenetic relative based on 16S rRNA gene sequences, of 98.2, 78.8 and 93.7 %, respectively. A whole-genome phylogenetic tree built from 82 core genes of genomes from 16 species of the genus Streptococcus validated that HTS2T forms a distinct subline and exhibits specific phylogenetic affinity with S. marmotae. In silico DNA-DNA hybridization of HTS2T showed an estimated DNA reassociation value of 40.5 % with Streptococcus. marmotae DSM 101995T. On the basis of their phenotypic characteristics and phylogenetic findings, it is proposed that the five isolates be classified as representatives of a novel species of the genus Streptococcus, Streptococcus himalayensis sp. nov. The type strain is HTS2T (=DSM 101997T=CGMCC 1.15533T). The genome of Streptococcus himalayensis sp. nov. strain HTS2T contains 2195 genes with a size of 2 275 471 bp and a mean DNA G+C content of 41.3 mol%.
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Affiliation(s)
- Lina Niu
- School of Life Science, Shanxi University, Taiyuan 030006, PR China.,Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University), Ministry of Education, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikoux, PR China.,State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- Department of Pediatrics, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China.,Institute of Translational Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Shoukui Hu
- Peking University Shougang Hospital, Beijing 100144, PR China
| | - Cuixia Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Gui Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yi Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Gang Lu
- Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University), Ministry of Education, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikoux, PR China
| | - Yingping Xie
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
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29
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Ricaboni D, Mailhe M, Lagier JC, Michelle C, Armstrong N, Bittar F, Vitton V, Benezech A, Raoult D, Million M. Noncontiguous finished genome sequence and description of Streptococcus timonensis sp. nov. isolated from the human stomach. New Microbes New Infect 2017; 15:77-88. [PMID: 28050252 PMCID: PMC5192475 DOI: 10.1016/j.nmni.2016.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/26/2016] [Accepted: 11/04/2016] [Indexed: 12/31/2022] Open
Abstract
Strain Marseille-P2915T, a Gram-positive, facultative anaerobic and nonmotile coccus, was isolated from the gastric lavage of a patient with severe anaemia. The 16S rRNA and rpoB gene comparison exhibited a sequence identity of 98.7 and 92.6% with Streptococcus infantis strain JCM 10157T, respectively, collocating it within the 'Streptococcus mitis' group. On the basis of phenotypic and genomic analysis, we propose the validation of the type strain Streptococcus timonensis sp. nov. Marseille-P2915T (= DSM 103349 = CSUR P2915).
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Affiliation(s)
- D. Ricaboni
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
- Department of Biomedical and Clinical Sciences, 3rd Division of Clinical Infectious Disease, University of Milan, Luigi Sacco Hospital, Milan, Italy
| | - M. Mailhe
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - J.-C. Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - C. Michelle
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - N. Armstrong
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - F. Bittar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - V. Vitton
- Service de Gastroentérologie, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - A. Benezech
- Service de Gastroentérologie, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - D. Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - M. Million
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
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30
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Mohkam M, Nezafat N, Berenjian A, Mobasher MA, Ghasemi Y. Identification of Bacillus Probiotics Isolated from Soil Rhizosphere Using 16S rRNA, recA, rpoB Gene Sequencing and RAPD-PCR. Probiotics Antimicrob Proteins 2016; 8:8-18. [PMID: 26898909 DOI: 10.1007/s12602-016-9208-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Some Bacillus species, especially Bacillus subtilis and Bacillus pumilus groups, have highly similar 16S rRNA gene sequences, which are hard to identify based on 16S rDNA sequence analysis. To conquer this drawback, rpoB, recA sequence analysis along with randomly amplified polymorphic (RAPD) fingerprinting was examined as an alternative method for differentiating Bacillus species. The 16S rRNA, rpoB and recA genes were amplified via a polymerase chain reaction using their specific primers. The resulted PCR amplicons were sequenced, and phylogenetic analysis was employed by MEGA 6 software. Identification based on 16S rRNA gene sequencing was underpinned by rpoB and recA gene sequencing as well as RAPD-PCR technique. Subsequently, concatenation and phylogenetic analysis showed that extent of diversity and similarity were better obtained by rpoB and recA primers, which are also reinforced by RAPD-PCR methods. However, in one case, these approaches failed to identify one isolate, which in combination with the phenotypical method offsets this issue. Overall, RAPD fingerprinting, rpoB and recA along with concatenated genes sequence analysis discriminated closely related Bacillus species, which highlights the significance of the multigenic method in more precisely distinguishing Bacillus strains. This research emphasizes the benefit of RAPD fingerprinting, rpoB and recA sequence analysis superior to 16S rRNA gene sequence analysis for suitable and effective identification of Bacillus species as recommended for probiotic products.
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Affiliation(s)
- Milad Mohkam
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran
| | - Aydin Berenjian
- Faculty of Science and Engineering, School of Engineering, University of Waikato, Private Bag 3105, Hamilton, 3240, New Zealand
| | - Mohammad Ali Mobasher
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran.,Department of Medical Biotechnology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran. .,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran. .,Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
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Streptococcus dentiloxodontae sp. nov., isolated from the oral cavity of elephants. Int J Syst Evol Microbiol 2016; 66:3878-3883. [DOI: 10.1099/ijsem.0.001280] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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32
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Gherardi G, Palmieri C, Marini E, Pompilio A, Crocetta V, Di Bonaventura G, Creti R, Facinelli B. Identification, antimicrobial resistance and molecular characterization of the human emerging pathogen Streptococcus gallolyticus subsp. pasteurianus. Diagn Microbiol Infect Dis 2016; 86:329-335. [PMID: 27720207 DOI: 10.1016/j.diagmicrobio.2016.09.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/18/2016] [Accepted: 09/20/2016] [Indexed: 11/15/2022]
Abstract
This study aimed to retrospectively identify 22Streptococcus bovis clinical strains based on the new taxonomy, as well as to investigate their antibiotic-resistance and clonality. Strains were identified by Phoenix100 system, 16S rRNA sequencing, and two MALDI-TOF MS platforms (Bruker Biotyper, Vitek MS). Antibiotic resistance was determined both phenotypically and genotypically, and clonality was assessed by PFGE. Most of strains (63.6%) were isolated from urine, and diabetes was the most common underlying disease (31.8%). Phoenix100 system revealed all strains belonged to biotype II, and 16S rRNA sequencing identified all strains as S. gallolyticus subsp pasteurianus (SGSP). Although both MALDI-TOF MS systems correctly identified isolates to the species level, only Bruker Biotyper accurately identified to the subspecies level. Erythromycin-resistant strains (31.8%) were also clindamycin-resistant and positive for erm(B). Strains resistant to tetracycline (68.2%) were also resistant to erythromycin. PFGE showed high genetic variability identifying 17 different pulsotypes, most of which single.
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Affiliation(s)
- Giovanni Gherardi
- Department of Medicine, Campus Biomedico University, Via Alvaro del Portillo 200, 00128 Rome, Italy.
| | - Claudio Palmieri
- Department of Biomedical Sciences and Public Health, Unit of Microbiology, Polytechnic University of Marche, Via Tronto 10/A, 60123 Ancona, Italy
| | - Emanuela Marini
- Department of Biomedical Sciences and Public Health, Unit of Microbiology, Polytechnic University of Marche, Via Tronto 10/A, 60123 Ancona, Italy
| | - Arianna Pompilio
- Department of Medical, Oral and Biotechnological Sciences; and Center of Excellence on Aging and Translational Medicine (CeSI-MeT); "G. d'Annunzio" University of Chieti, Via Vestini 31, 66100 Chieti, Italy
| | - Valentina Crocetta
- Department of Medical, Oral and Biotechnological Sciences; and Center of Excellence on Aging and Translational Medicine (CeSI-MeT); "G. d'Annunzio" University of Chieti, Via Vestini 31, 66100 Chieti, Italy
| | - Giovanni Di Bonaventura
- Department of Medical, Oral and Biotechnological Sciences; and Center of Excellence on Aging and Translational Medicine (CeSI-MeT); "G. d'Annunzio" University of Chieti, Via Vestini 31, 66100 Chieti, Italy
| | - Roberta Creti
- Department of Infectious, Parasitic, and Immunomediated Diseases, Istituto Superiore di Sanità, Viale Regina Margherita 299, 00161 Rome, Italy
| | - Bruna Facinelli
- Department of Biomedical Sciences and Public Health, Unit of Microbiology, Polytechnic University of Marche, Via Tronto 10/A, 60123 Ancona, Italy
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33
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Niu L, Lu S, Hu S, Jin D, Lai X, Yang J, Chen C, Wang Y, Bai X, Lan R, Lv G, Xie Y, Ye C, Xu J. Streptococcus halotolerans sp. nov. isolated from the respiratory tract of Marmota himalayana in Qinghai-Tibet Plateau of China. Int J Syst Evol Microbiol 2016; 66:4211-4217. [PMID: 27469933 DOI: 10.1099/ijsem.0.001337] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Two Gramstaining-positive, catalase-negative, α-hemolytic, coccus-shaped organisms were isolated separately from the respiratory tracts of two Marmota himalayana animals from the Qinghai-Tibet Plateau, PR China. Morphological, biological, biochemical, and molecular genetic studies were performed on these two isolates (HTS9T and HTS12). Their biochemical characteristics, such as acid production from different sugars and enzymatic activities, indicated that they represented a member of the genus Streptococcus. They are most closely related to Streptococcus thoraltensis CIP 105518T based on sequence analysis of their 16S rRNA, groEL, sodA and rpoB genes, with similarities of 97.6, 89.9, 92.6 and 91.1 % the four genes respectively. The whole genome phylogenetic tree reconstructed using 372 core genes from 65 genomes of members of the genus Streptococcus validates that HTS9T forms a distinct subline and exhibits specific phylogenetic affinity with S. thoraltensis. In silico DNA-DNA hybridization of HTS9T showed a DNA reassociation value of 32.1 %, closest to that of S. thoraltensis CIP 105518T. Based on their phenotypic characteristics and in particular the phylogenetic findings (DNA-DNA hybridization, three phylogenetic trees built from the partial 16S rRNA/housekeeping genes, and from 372 core genes of 65 genomes of members of the genus Streptococcus), we propose with confidence that strains HTS9T and HTS12 should be classified as representing a novel species of the genus Streptococcus, Streptococcus halotolerans sp. nov. The type strain is HTS9T (=DSM 101996T=CGMCC1.15532T). Genome analysis of Streptococcus halotolerans sp. nov. shows that its genome is 1 823 556 bp long with a DNA G+C content of 39.9 mol% and contains 2068 genes.
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Affiliation(s)
- Lina Niu
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
- School of Tropical and Laboratory Medicine, Hainan Medical University, Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University), Ministry of Education, Haikou, PR China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shoukui Hu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xinhe Lai
- Institute of Inflammation and Diseases, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
- Institute of Translational Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Cuixia Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yiting Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiangning Bai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Gang Lv
- School of Tropical and Laboratory Medicine, Hainan Medical University, Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University), Ministry of Education, Haikou, PR China
| | - Yingping Xie
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
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Okura M, Osaki M, Nomoto R, Arai S, Osawa R, Sekizaki T, Takamatsu D. Current Taxonomical Situation of Streptococcus suis. Pathogens 2016; 5:pathogens5030045. [PMID: 27348006 PMCID: PMC5039425 DOI: 10.3390/pathogens5030045] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/09/2016] [Accepted: 06/20/2016] [Indexed: 12/31/2022] Open
Abstract
Streptococcus suis, a major porcine pathogen and an important zoonotic agent, is considered to be composed of phenotypically and genetically diverse strains. However, recent studies reported several “S. suis-like strains” that were identified as S. suis by commonly used methods for the identification of this bacterium, but were regarded as distinct species from S. suis according to the standards of several taxonomic analyses. Furthermore, it has been suggested that some S. suis-like strains can be assigned to several novel species. In this review, we discuss the current taxonomical situation of S. suis with a focus on (1) the classification history of the taxon of S. suis; (2) S. suis-like strains revealed by taxonomic analyses; (3) methods for detecting and identifying this species, including a novel method that can distinguish S. suis isolates from S. suis-like strains; and (4) current topics on the reclassification of S. suis-like strains.
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Affiliation(s)
- Masatoshi Okura
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.
| | - Makoto Osaki
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.
| | - Ryohei Nomoto
- Department of Infectious Diseases, Kobe Institute of Health, 4-6-5 Minatojima-Nakamachi, Chuo-ku, Kobe, Hyogo 650-0045, Japan.
| | - Sakura Arai
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Ro Osawa
- Organization for Advanced Science and Technology, Kobe University, 1-1 Rokko-dai, Nada-ku, Kobe, Hyogo 657-8501, Japan.
| | - Tsutomu Sekizaki
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Daisuke Takamatsu
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.
- The United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu, Gifu 501-1193, Japan.
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35
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Shanahan ER, Zhong L, Talley NJ, Morrison M, Holtmann G. Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures. Aliment Pharmacol Ther 2016; 43:1186-96. [PMID: 27086880 DOI: 10.1111/apt.13622] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 03/09/2016] [Accepted: 03/22/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND The mucosa-associated microbiota appears to be highly relevant to host-microbe interactions in the gastrointestinal (GI) tract. Thus, precise characterisation of the mucosa-associated microbiota may provide important insights for diagnostic and therapeutic development. However, for technical reasons, mucosal biopsies taken during standard endoscopic procedures are potentially contaminated by GI luminal contents. AIM To develop and validate a biopsy device that minimises contamination during sampling of the mucosa-associated microbiota. METHODS A new, encased biopsy forceps was developed, the Brisbane Aseptic Biopsy Device (BABD). This comprises sterile forceps encased by a sheath with a plug at the tip, allowing targeted, aseptic sampling of the mucosa. Matched duodenal biopsies were obtained using the BABD, standard biopsy forceps, and a sterile brush, from patients undergoing upper GI endoscopy for iron deficiency (n = 6). Total genomic deoxyribonucleic acid (gDNA) was extracted from samples and bacterial 16S rRNA gene libraries sequenced to investigate the mucosa-associated microbiota. RESULTS Microbial DNA was recovered from biopsies obtained by the BABD, confirming the presence of a duodenal mucosa-associated microbiota. This microbiota was dominated by the genus Streptococcus, with lower levels of Prevotella, Veillonella and Neisseria. At the individual patient level, substantial differences were observed between matched samples obtained using the different devices. A greater degree of bacterial diversity was observed in samples collected using the standard forceps, indicating the BABD affords collection of samples more representative of the mucosa-associated microbiota, by precluding luminal cross-contamination. CONCLUSIONS Cross-contamination can occur when mucosal biopsies are taken during standard endoscopic procedures. Utilising the novel Brisbane Aseptic Biopsy Device can reduce cross-contamination, and it offers improved opportunities to more precisely examine host-mucosa-associated microbiota interactions.
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Affiliation(s)
- E R Shanahan
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Qld, Australia.,Faculty of Medicine and Biomedical Sciences, and Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia.,Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
| | - L Zhong
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Qld, Australia.,Faculty of Medicine and Biomedical Sciences, and Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
| | - N J Talley
- Faculty of Health, The University of Newcastle, Callaghan, NSW, Australia
| | - M Morrison
- Microbial Biology and Metagenomics, The University of Queensland Diamantina Institute, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
| | - G Holtmann
- Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, Qld, Australia.,Faculty of Medicine and Biomedical Sciences, and Faculty of Health and Behavioral Sciences, The University of Queensland, Brisbane, Qld, Australia.,Translational Research Institute (TRI), Brisbane, Qld, Australia
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36
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Bai X, Xiong Y, Lu S, Jin D, Lai X, Yang J, Niu L, Hu S, Meng X, Pu J, Ye C, Xu J. Streptococcuspantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii). Int J Syst Evol Microbiol 2016; 66:3281-3286. [PMID: 27226124 DOI: 10.1099/ijsem.0.001189] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Two bacterial strains were isolated from faecal samples of Tibetan antelopes. The isolates were Gram-stain-positive, catalase-negative, coccus-shaped organisms that were tentatively identified as representing a novel streptococcal species based on their morphological features, biochemical test results and phylogenomic findings. Comparative 16S rRNA gene sequencing studies confirmed that the organisms were members of the genus Streptococcus, but they did not correspond to any recognized species of the genus. The nearest phylogenetic relative of the unknown coccus was Streptococcus ursoris NUM 1615T (93.4 % 16S rRNA gene sequence similarity). Analysis of groEL and rpoB gene sequences of the novel isolates showed interspecies divergence of 27.0 and 22.2 %, respectively, from the type strain of its closest 16S rRNA gene phylogenetic relative, S. ursoris. The complete genome of strain TA 26T has been sequenced. Digital DNA-DNA hybridization studies between strain TA 26T and other species of the genus Streptococcus deposited in the GenBank database showed less than 70 % DNA-DNA relatedness, supporting a novel species status of the strain. On the basis of their genotypic and phenotypic differences from recognized Streptococcus species, the two isolates represent a novel species of the genus Streptococcus, for which the nameStreptococcus pantholopis sp. nov. (type strain TA 26T=CGMCC 1.15667T=DSM 102135T) is proposed.
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Affiliation(s)
- Xiangning Bai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Yanwen Xiong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Xinhe Lai
- Institute of Translational Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China.,Institute of Inflammation and Diseases, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Lina Niu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China.,School of Tropical and Laboratory Medicine, Hainan Medical University, Haikou, PR China
| | - Shoukui Hu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Xiangli Meng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Ji Pu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
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Clinical features and outcome of bone and joint infections with streptococcal involvement: 5-year experience of interregional reference centres in the south of France. New Microbes New Infect 2016; 12:8-17. [PMID: 27222712 PMCID: PMC4872313 DOI: 10.1016/j.nmni.2016.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/24/2016] [Accepted: 03/25/2016] [Indexed: 01/10/2023] Open
Abstract
Streptococcal bone and joint infections are less common than staphylococcal cases. Few studies have reported the cases with well-identified Streptococcus species. Their clinical features and prognosis are not clearly known to date. Moreover, no treatment regimen has yet been clarified. We reviewed the streptococcal bone and joint infection cases managed in our centres from January 2009 to December 2013. We described the epidemiology, clinical and microbiologic characteristics, treatment approach and outcome. Among the 93 cases, 83% of patients were men with a median age of 60 years, and 90% of patients had comorbidities or risk factors. Bacteraemia occurred in 14% of cases. Serious complications occurred in six patients, including severe sepsis (two cases) and infective endocarditis (two cases). Orthopaedic device infections were observed in 35% of cases, including 17 patients with internal osteosynthesis device infection, 14 with prosthetic joint infection and three with vertebral osteosynthesis device infection. The median time between orthopaedic device implantation and onset of infection was 447 days. Fourteen species of Streptococcus were identified, including 97 isolates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and three isolates using molecular identification. The five most represented species included S. agalactiae (37%), S. dysgalactiae (12%), S. anginosus (11%), S. constellatus (10%) and S. pneumoniae (9%). Streptococci isolates were susceptible to amoxicillin, with the exception of one S. mitis isolate. Remission 1 year after the end of treatment was recorded in 83%. One patient died of infection; eight patients had infections that failed to respond to treatment; and seven patients experienced relapse. Twenty patients (22%) had an unfavourable functional outcome, including 19 amputations and one arthrodesis. Five significant prognostic factors associated with an unfavourable clinical outcome were identified, including peripheral neuropathy (p 0.009), peripheral arterial disease (p 0.019), diabetes mellitus (p 0.031), location in the femur (p 0.0036), location in the foot (p 0.0475), osteitis without an orthopaedic device (p 0.041) and infection caused by S. dysgalactiae (p 0.020). The rate of poor outcomes remains high despite the low number of Streptococcus isolates resistant to antibiotics. Some prognostic factors, such as the presence of S. dysgalactiae, are associated with an unfavourable clinical outcome. Antibiotic regimens of streptococcal bone and joint infections are not standardized and need to be further investigated.
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An Update on the Streptococcus bovis Group: Classification, Identification, and Disease Associations. J Clin Microbiol 2016; 54:1694-1699. [PMID: 26912760 DOI: 10.1128/jcm.02977-15] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Streptococcus bovis group has undergone significant taxonomic changes over the past 2 decades with the advent of new identification methods with higher discriminatory power. Although the current classification system is not yet embraced by all researchers in the field and debate remains over the performance of molecular techniques for identification to the species level within the group, important disease associations for several members of the group have been clarified. Here, we provide a brief overview of the history of the S. bovis group, an outline of the currently accepted classification scheme, a review of associated clinical syndromes, and a summary of the performance and diagnostic accuracy of currently available identification methods.
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Streptococcus oricebi sp. nov., isolated from the oral cavity of tufted capuchin. Int J Syst Evol Microbiol 2016; 66:1063-1067. [DOI: 10.1099/ijsem.0.000834] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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40
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Phenotypic, Genotypic, and Antimicrobial Characteristics of Streptococcus halichoeri Isolates from Humans, Proposal To Rename Streptococcus halichoeri as Streptococcus halichoeri subsp. halichoeri, and Description of Streptococcus halichoeri subsp. hominis subsp. nov., a Bacterium Associated with Human Clinical Infections. J Clin Microbiol 2016; 54:739-44. [PMID: 26763962 DOI: 10.1128/jcm.03214-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/05/2016] [Indexed: 11/20/2022] Open
Abstract
Phenotypic, genotypic, and antimicrobial characteristics of six phenotypically distinct human clinical isolates that most closely resembled the type strain of Streptococcus halichoeri isolated from a seal are presented. Sequencing of the 16S rRNA, rpoB, sodA, and recN genes; comparative whole-genome analysis; conventional biochemical and Rapid ID 32 Strep identification methods; and antimicrobial susceptibility testing were performed on the human isolates, the type strain of S. halichoeri, and type strains of closely related species. The six human clinical isolates were biochemically indistinguishable from each other and showed 100% 16S rRNA, rpoB, sodA, and recN gene sequence similarity. Comparative 16S rRNA gene sequencing analysis revealed 98.6% similarity to S. halichoeri CCUG 48324(T), 97.9% similarity to S. canis ATCC 43496(T), and 97.8% similarity to S. ictaluri ATCC BAA-1300(T). A 3,530-bp fragment of the rpoB gene was 98.8% similar to the S. halichoeri type strain, 84.6% to the S. canis type strain, and 83.8% to the S. ictaluri type strain. The S. halichoeri type strain and the human clinical isolates were susceptible to the antimicrobials tested based on CLSI guidelines for Streptococcus species viridans group with the exception of tetracycline and erythromycin. The human isolates were phenotypically distinct from the type strain isolated from a seal; comparative whole-genome sequence analysis confirmed that the human isolates were S. halichoeri. On the basis of these results, a novel subspecies, Streptococcus halichoeri subsp. hominis, is proposed for the human isolates and Streptococcus halichoeri subsp. halichoeri is proposed for the gray seal isolates. The type strain of the novel subspecies is SS1844(T) = CCUG 67100(T) = LMG 28801(T).
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41
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Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR, Wang J, Holden MTG, Parkhill J, Langford PR, Rycroft AN, Wren BW, Tucker AW, Maskell DJ. Whole genome investigation of a divergent clade of the pathogen Streptococcus suis. Front Microbiol 2015; 6:1191. [PMID: 26583006 PMCID: PMC4631834 DOI: 10.3389/fmicb.2015.01191] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/12/2015] [Indexed: 11/23/2022] Open
Abstract
Streptococcus suis is a major porcine and zoonotic pathogen responsible for significant economic losses in the pig industry and an increasing number of human cases. Multiple isolates of S. suis show marked genomic diversity. Here, we report the analysis of whole genome sequences of nine pig isolates that caused disease typical of S. suis and had phenotypic characteristics of S. suis, but their genomes were divergent from those of many other S. suis isolates. Comparison of protein sequences predicted from divergent genomes with those from normal S. suis reduced the size of core genome from 793 to only 397 genes. Divergence was clear if phylogenetic analysis was performed on reduced core genes and MLST alleles. Phylogenies based on certain other genes (16S rRNA, sodA, recN, and cpn60) did not show divergence for all isolates, suggesting recombination between some divergent isolates with normal S. suis for these genes. Indeed, there is evidence of recent recombination between the divergent and normal S. suis genomes for 249 of 397 core genes. In addition, phylogenetic analysis based on the 16S rRNA gene and 132 genes that were conserved between the divergent isolates and representatives of the broader Streptococcus genus showed that divergent isolates were more closely related to S. suis. Six out of nine divergent isolates possessed a S. suis-like capsule region with variation in capsular gene sequences but the remaining three did not have a discrete capsule locus. The majority (40/70), of virulence-associated genes in normal S. suis were present in the divergent genomes. Overall, the divergent isolates extend the current diversity of S. suis species but the phenotypic similarities and the large amount of gene exchange with normal S. suis gives insufficient evidence to assign these isolates to a new species or subspecies. Further, sampling and whole genome analysis of more isolates is warranted to understand the diversity of the species.
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Affiliation(s)
- Abiyad Baig
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Sarah E Peters
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Kate J Howell
- Department of Paediatrics, University of Cambridge Cambridge, UK
| | - Roy R Chaudhuri
- Department of Molecular Biology and Biotechnology, University of Sheffield Sheffield, UK
| | - Jinhong Wang
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | | | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Cambridge, UK
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London London, UK
| | | | - Brendan W Wren
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine London, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
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42
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Okamoto M, Imai S, Miyanohara M, Saito W, Momoi Y, Nomura Y, Ikawa T, Ogawa T, Miyabe-Nishiwaki T, Kaneko A, Watanabe A, Watanabe S, Hayashi M, Tomonaga M, Hanada N. Streptococcus panodentissp. nov. from the oral cavities of chimpanzees. Microbiol Immunol 2015; 59:526-32. [DOI: 10.1111/1348-0421.12290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 07/15/2015] [Accepted: 07/29/2015] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | | | | | - Tomoko Ikawa
- Department of Fixed Prosthodontics; Tsurumi University School of Dental Medicine, 2-1-3, Tsurumi; Tsurumi-ku Yokohama 230-8501
| | - Takumi Ogawa
- Department of Fixed Prosthodontics; Tsurumi University School of Dental Medicine, 2-1-3, Tsurumi; Tsurumi-ku Yokohama 230-8501
| | | | | | | | | | - Misato Hayashi
- Language and Intelligence Section; Primate Research Institute, Kyoto University; Inuyama Aichi 484-8506, Japan
| | - Masaki Tomonaga
- Language and Intelligence Section; Primate Research Institute, Kyoto University; Inuyama Aichi 484-8506, Japan
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43
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Comparing Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Phenotypic and Molecular Methods for Identification of Species within the Streptococcus anginosus Group. J Clin Microbiol 2015; 53:3580-8. [PMID: 26354817 DOI: 10.1128/jcm.01892-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 09/01/2015] [Indexed: 11/20/2022] Open
Abstract
The heterogeneity of members of the Streptococcus anginosus group (SAG) has traditionally hampered their correct identification. Recently, the group was subdivided into 6 taxa whose prevalence among human infections is poorly described. We evaluated the accuracy of the Rapid ID32 Strep test, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and a PCR multiplex method to identify 212 SAG isolates recovered from human infections to the species and subspecies level by using multilocus sequence analysis (MLSA) as the gold standard. We also determined the antimicrobial susceptibilities of the isolates. Representatives of all SAG taxa were found among our collection. MALDI-TOF MS and the Rapid ID32 Strep test correctly identified 92% and 68% of the isolates to the species level, respectively, but showed poor performance at the subspecies level, and the latter was responsible for major identification errors. The multiplex PCR method results were in complete agreement with the MLSA identifications but failed to distinguish the subspecies Streptococcus constellatus subsp. pharyngis and S. constellatus subsp. viborgensis. A total of 145 MLSA sequence types were present in our collection, indicating that within each taxon a number of different lineages are capable of causing infection. Significant antibiotic resistance was observed only to tetracycline, erythromycin, and clindamycin and was present in most taxa. MALDI-TOF MS is a reliable method for routine SAG species identification, while the need for identification to the subspecies level is not clearly established.
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44
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Vela AI, Casas-Díaz E, Lavín S, Domínguez L, Fernández-Garayzábal JF. Streptococcus pharyngis sp. nov., a novel streptococcal species isolated from the respiratory tract of wild rabbits. Int J Syst Evol Microbiol 2015; 65:2903-2907. [DOI: 10.1099/ijs.0.000351] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four isolates of an unknown Gram-stain-positive, catalase-negative coccus-shaped organism, isolated from the pharynx of four wild rabbits, were characterized by phenotypic and molecular genetic methods. The micro-organisms were tentatively assigned to the genus Streptococcus based on cellular morphological and biochemical criteria, although the organisms did not appear to correspond to any species with a validly published name. Comparative 16S rRNA gene sequencing confirmed their identification as members of the genus Streptococcus, being most closely related phylogenetically to Streptococcus porcorum 682-03T (96.9 % 16S rRNA gene sequence similarity). Analysis of rpoB and sodA gene sequences showed divergence values between the novel species and S. porcorum 682-03T (the closest phylogenetic relative determined from 16S rRNA gene sequences) of 18.1 and 23.9 %, respectively. The novel bacterial isolate could be distinguished from the type strain of S. porcorum by several biochemical characteristics, such as the production of glycyl-tryptophan arylamidase and α-chymotrypsin, and the non-acidification of different sugars. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be assigned to a novel species of the genus Streptococcus, and named Streptococcus pharyngis sp. nov. The type strain is DICM10-00796BT ( = CECT 8754T = CCUG 66496T).
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Affiliation(s)
- Ana I. Vela
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - Encarna Casas-Díaz
- Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Santiago Lavín
- Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Lucas Domínguez
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
| | - Jose F. Fernández-Garayzábal
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
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45
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Singh NP, Tiwari A, Bansal A, Thakur S, Sharma G, Gabrani R. Genome level analysis of bacteriocins of lactic acid bacteria. Comput Biol Chem 2015; 56:1-6. [DOI: 10.1016/j.compbiolchem.2015.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 02/09/2015] [Accepted: 02/21/2015] [Indexed: 10/23/2022]
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46
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Isaksson J, Rasmussen M, Nilson B, Stadler LS, Kurland S, Olaison L, Ek E, Herrmann B. Comparison of species identification of endocarditis associated viridans streptococci using rnpB genotyping and 2 MALDI-TOF systems. Diagn Microbiol Infect Dis 2014; 81:240-5. [PMID: 25616316 DOI: 10.1016/j.diagmicrobio.2014.12.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/28/2014] [Accepted: 12/20/2014] [Indexed: 11/17/2022]
Abstract
Streptococcus spp. are important causes of infective endocarditis but challenging in species identification. This study compared identification based on sequence determination of the rnpB gene with 2 systems of matrix-assisted laser desorption ionization-time of flight mass spectrometry, MALDI Biotyper (Bruker) and VITEK MS IVD (bioMérieux). Blood culture isolates of viridans streptococci from 63 patients with infective endocarditis were tested. The 3 methods showed full agreement for all 36 isolates identified in the Anginosus, Bovis, and Mutans groups or identified as Streptococcus cristatus, Streptococcus gordonii, or Streptococcus sanguinis. None of the methods could reliably identify the 23 isolates to the species level when designated as Streptococcus mitis, Streptococcus oralis, or Streptococcus tigurinus. In 7 isolates classified to the Mitis group, the rnpB sequences deviated strikingly from all reference sequences, and additional analysis of sodA and groEL genes indicated the occurrence of yet unidentified Streptococcus spp.
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Affiliation(s)
- Jenny Isaksson
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Magnus Rasmussen
- Division for Infection Medicine, Department of Clinical Sciences, Lund University, BMC B14, SE-22184 Lund, Sweden
| | - Bo Nilson
- Clinical Microbiology, Labmedicin, Region Skåne, SE-221 85 Lund, Sweden; Department of Laboratory Medicine Lund, Section of Medical Microbiology, Lund University, SE-22362 Lund, Sweden
| | - Liselott Svensson Stadler
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Siri Kurland
- Section of Infectious Diseases, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Lars Olaison
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, SE-416 85 Gothenburg, Sweden
| | - Elisabeth Ek
- Section of Infectious Diseases, Department of Medical Sciences, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Björn Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden.
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47
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Zbinden A, Bostanci N, Belibasakis GN. The novel species Streptococcus tigurinus and its association with oral infection. Virulence 2014; 6:177-82. [PMID: 25483862 PMCID: PMC4601397 DOI: 10.4161/21505594.2014.970472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Streptococcus tigurinus is a novel species of viridans streptococci, shown to cause severe invasive infections such as infective endocarditis, spondylodiscitis and meningitis. S. tigurinus belongs to the Streptococcus mitis group and is most closely related to Streptococcus mitis, Streptococcus oralis, Streptococcus pneumoniae, Streptococcus pseudopneumoniae and Streptococcus infantis. The presence of S. tigurinus in the human oral cavity has been documented, including in patients with periodontal disease. This review addresses the available scientific knowledge on S. tigurinus and its association with closely related streptococci, and discusses its putative involvement in common oral infections. While there is as yet no strong evidence on the involvement of S. tigurinus with oral infections, its presence in the oral cavity and its association with endocarditis warrants special attention for a link between oral and systemic infection.
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Affiliation(s)
- Andrea Zbinden
- a Institute of Medical Virology; University of Zurich ; Zurich , Switzerland
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48
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Shinozaki-Kuwahara N, Saito M, Hirasawa M, Takada K. Streptococcus
oriloxodontae sp. nov., isolated from the oral cavities of elephants. Int J Syst Evol Microbiol 2014; 64:3755-3759. [DOI: 10.1099/ijs.0.064048-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains were isolated from oral cavity samples of healthy elephants. The isolates were Gram-positive, catalase-negative, coccus-shaped organisms that were tentatively identified as a streptococcal species based on the results of biochemical tests. Comparative 16S rRNA gene sequence analysis suggested classification of these organisms in the genus
Streptococcus
with
Streptococcus criceti
ATCC 19642T and
Streptococcus orisuis
NUM 1001T as their closest phylogenetic neighbours with 98.2 and 96.9 % gene sequence similarity, respectively. When multi-locus sequence analysis using four housekeeping genes, groEL, rpoB, gyrB and sodA, was carried out, similarity of concatenated sequences of the four housekeeping genes from the new isolates and
Streptococcus mutans
was 89.7 %. DNA–DNA hybridization experiments suggested that the new isolates were distinct from
S. criceti
and other species of the genus
Streptococcus
. On the basis of genotypic and phenotypic differences, it is proposed that the novel isolates are classified in the genus
Streptococcus
as representatives of Streptococcus oriloxodontae sp. nov. The type strain of S. oriloxodontae is NUM 2101T ( = JCM 19285T = DSM 27377T).
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Affiliation(s)
- Noriko Shinozaki-Kuwahara
- Department of Oral Microbiology, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba 271-8587, Japan
| | - Masanori Saito
- Department of Oral Microbiology, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba 271-8587, Japan
| | - Masatomo Hirasawa
- Department of Oral Microbiology, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba 271-8587, Japan
| | - Kazuko Takada
- Department of Oral Microbiology, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba 271-8587, Japan
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49
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Pitiwittayakul N, Yukphan P, Sintuprapa W, Yamada Y, Theeragool G. Identification of acetic acid bacteria isolated in Thailand and assigned to the genus Acetobacter by groEL gene sequence analysis. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0994-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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50
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STREPTOCOCCAL ENDOCARDITIS IN A CAPTIVE SOUTHERN WHITE RHINOCEROS (CERATOTHERIUM SIMUM SIMUM). J Zoo Wildl Med 2014; 45:635-7. [DOI: 10.1638/2012-0213r5.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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