scholarly journals Campylobacter fetus subsp. testudinum subsp. nov., isolated from humans and reptiles

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 2944-2948 ◽  
Author(s):  
Collette Fitzgerald ◽  
Zheng chao Tu ◽  
Mary Patrick ◽  
Tracy Stiles ◽  
Andy J. Lawson ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Campylobacter Fetus ◽  
Phenotypic Tests ◽  
Tof Ms

A polyphasic study was undertaken to determine the taxonomic position of 13 Campylobacter fetus -like strains from humans (n = 8) and reptiles (n = 5). The results of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS and genomic data from sap analysis, 16S rRNA gene and hsp60 sequence comparison, pulsed-field gel electrophoresis, amplified fragment length polymorphism analysis, DNA–DNA hybridization and whole genome sequencing demonstrated that these strains are closely related to C. fetus but clearly differentiated from recognized subspecies of C. fetus . Therefore, this unique cluster of 13 strains represents a novel subspecies within the species C. fetus , for which the name Campylobacter fetus subsp. testudinum subsp. nov. is proposed, with strain 03-427T ( = ATCC BAA-2539T = LMG 27499T) as the type strain. Although this novel taxon could not be differentiated from C. fetus subsp. fetus and C. fetus subsp. venerealis using conventional phenotypic tests, MALDI-TOF MS revealed the presence of multiple phenotypic biomarkers which distinguish Campylobacter fetus subsp. testudinum subsp. nov. from recognized subspecies of C. fetus .

scholarly journals Acinetobacter gandensis sp. nov. isolated from horse and cattle

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4007-4015 ◽  
Author(s):  
Annemieke Smet ◽  
Piet Cools ◽  
Lenka Krizova ◽  
Martina Maixnerova ◽  
Ondrej Sedo ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Tof Ms

We previously reported the presence of an OXA-23 carbapenemase in an undescribed species of the genus Acinetobacter isolated from horse dung at the Faculty of Veterinary Medicine, Ghent University, Belgium. Here we include six strains to corroborate the delineation of this taxon by phenotypic characterization, DNA–DNA hybridization, 16S rRNA gene and rpoB sequence analysis, % G+C determination, MALDI-TOF MS and fatty acid analysis. The nearly complete 16S rRNA gene sequence of strain UG 60467T showed the highest similarities with those of the type strains of Acinetobacter bouvetii (98.4 %), Acinetobacter haemolyticus (97.7 %), and Acinetobacter schindleri (97.2 %). The partial rpoB sequence of strain UG 60467T showed the highest similarities with ‘Acinetobacter bohemicus’ ANC 3994 (88.6 %), A. bouvetii NIPH 2281 (88.6 %) and A. schindleri CIP 107287T (87.3 %). Whole-cell MALDI-TOF MS analyses supported the distinctness of the group at the protein level. The predominant fatty acids of strain UG 60467T were C12 : 0 3-OH, C12 : 0, C16 : 0, C18 : 1ω9c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). Strains UG 60467T and UG 60716 showed a DNA–DNA relatedness of 84 % with each other and a DNA–DNA relatedness with A. schindleri LMG 19576T of 17 % and 20 %, respectively. The DNA G+C content of strain UG 60467T was 39.6 mol%. The name Acinetobacter gandensis sp. nov. is proposed for the novel taxon. The type strain is UG 60467T ( = ANC 4275T = LMG 27960T = DSM 28097T).

scholarly journals Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae

2020 ◽  
Vol 70 (6) ◽  
pp. 3755-3762 ◽  
Author(s):  
Chien-Hsun Huang ◽  
Chih-Chieh Chen ◽  
Jong-Shian Liou ◽  
Ai-Yun Lee ◽  
Jochen Blom ◽  
...  
Keyword(s):  
Lactobacillus Casei ◽  
Type Species ◽  
Nucleotide Identity ◽  
Phenotypic Characterization ◽  
Species Definition ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Tof Ms

Taxonomic relationships between Lactobacillus casei , Lactobacillus paracasei and Lactobacillus zeae have long been debated. Results of previous analyses have shown that overall genome relatedness indices (such as average nucleotide identity and core nucleotide identity) between the type strains L. casei ATCC 393T and L. zeae ATCC 15820T were 94.6 and 95.3 %, respectively, which are borderline for species definition. However, the digital DNA‒DNA hybridization value was 57.3 %, which was clearly lower than the species delineation threshold of 70 %, and hence raised the possibility that L. casei could be reclassified into two species. To re-evaluate the taxonomic relationship of these taxa, multilocus sequence analysis (MLSA) based on the concatenated five housekeeping gene (dnaJ, dnaK, mutL, pheS and yycH) sequences, phylogenomic and core genome multilocus sequence typing analyses, gene presence and absence profiles using pan-genome analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling analysis, cellular fatty acid compositions, and phenotype analysis were carried out. The results of phenotypic characterization, MLSA, whole-genome sequence-based analyses and MALDI-TOF MS profiling justified an independent species designation for the L. zeae strains, and supported an emended the description of the name of Lactobacillus zeae (ex Kuznetsov 1956) Dicks et al. 1996, with ATCC 15820T (=DSM 20178T=BCRC 17942T) as the type strain.

scholarly journals Clostridium ramosum rapidly identified by MALDI-TOF MS. A rare gram-variable agent of bacteraemia.

2020 ◽  
Vol 2 (8) ◽  
Author(s):  
M.C. Legaria ◽  
S.D. García ◽  
V. Tudanca ◽  
C. Barberis ◽  
L. Cipolla ◽  
...  
Keyword(s):  
Type Species ◽  
Clinical Symptoms ◽  
Gc Content ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Clostridium ramosum is an enteric anaerobic, endospore-forming, gram-positive rod with a low GC content that is rarely associated with disease in humans. We present a case of C. ramosum bacteraemia. To the best of our knowledge, this is the second case of C. ramosum bacteraemia in an elderly patient presenting with fever, abdominal pain and bilious emesis. We highlight the Gram stain variability, the lack of visualization of spores and the atypical morphology of the colonies that showed C. ramosum in a polymicrobial presentation that initially appeared to show monomicrobial bacteraemia. The microorganism was rapidly identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We present a comprehensive literature review of 32 cases of clinical infections by C. ramosum in which we describe, if available, sex, age, clinical symptoms, predisposing conditions, other organisms present in the blood culture, other samples with C. ramosum , identification methodology, treatment and outcome.

scholarly journals Description of Lysinibacillus sinduriensis sp. nov., and transfer of Bacillus massiliensis and Bacillus odysseyi to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov. with emended description of the genus Lysinibacillus

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2347-2355 ◽  
Author(s):  
Min Young Jung ◽  
Joong-Su Kim ◽  
Woon Kee Paek ◽  
Igor Styrak ◽  
In-Soon Park ◽  
...  
Keyword(s):  
Cell Wall ◽  
Related Species ◽  
Type Species ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Group 2 ◽  
Phenotypic Tests

A Gram-positive, rod-shaped, endospore-forming bacterium, designated strain BLB-1T, was isolated from samples of tidal flat sediment from the Yellow Sea. 16S rRNA gene sequence analysis demonstrated that the isolate belonged to the Bacillus rRNA group 2 and was closely related to Bacillus massiliensis CIP 108446T (97.4 %), Bacillus odysseyi ATCC PTA-4993T (96.7 %), Lysinibacillus fusiformis DSM 2898T (96.2 %) and Lysinibacillus boronitolerans DSM 17140T (95.9 %). Sequence similarities with related species in other genera, including Caryophanon , Sporosarcina and Solibacillus , were <96.1 %. Chemotaxonomic data supported the affiliation of strain BLB-1T with the genus Lysinibacillus . The major menaquinone was MK-7, the cell-wall sugars were glucose and xylose, the cell-wall peptidoglycan type was A4α (l-Lys–d-Asp), the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown phospholipids, and the major fatty acids were anteiso-C15 : 0 (35.6 %), iso-C15 : 0 (25.6 %) and anteiso-C17 : 0 (16.5 %). The most closely related species, Bacillus massiliensis and Bacillus odysseyi , were also assigned to this genus based on phylogenetic analysis and phenotypic data. The results of DNA–DNA hybridizations and phenotypic tests supported the differentiation of all three taxa from species of the genus Lysinibacillus with validly published names. Thus, strain BLB-1T ( = KCTC 13296T  = JCM 15800T) represents a novel species, for which the name Lysinibacillus sinduriensis sp. nov. is proposed. It is also proposed that Bacillus massiliensis CIP 108446T ( = 4400831T = CCUG49529T  = KCTC 13178T) and Bacillus odysseyi NBRC 100172T ( = 34hs-1T  = ATCC PTA-4993T  = NRRL B-30641T  = DSM 18869T  = CIP 108263T  = KCTC 3961T) be transferred to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov., respectively.

Leptospira ainlahdjerensis sp. nov., Leptospira ainazelensis sp. nov., Leptospira abararensis sp. nov. and Leptospira chreensis sp. nov., four new species isolated from water sources in Algeria

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Anissa Amara Korba ◽  
Hakim Lounici ◽  
Malia Kainiu ◽  
Antony T. Vincent ◽  
Jean-François Mariet ◽  
...  
Keyword(s):  
Novel Species ◽  
Laser Desorption ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Leptospira strains were isolated from freshwater sampled at four sites in Algeria and characterized by whole-genome sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The cells were spiral-shaped and motile. Phylogenetic and MALDI-TOF MS analyses showed that the strains can be clearly distinguished from the other described species in the genus Leptospir a, therefore representing two novel species of the pathogen subclade P1 and two novel species of the saprophyte subclade S1. The names Leptospira ainlahdjerensis sp. nov. (type strain 201903070T=KIT0297T=CIP111912T), Leptospira ainazelensis sp. nov. (201903071T=KIT0298T=CIP111913T), Leptospira abararensis sp. nov. (201903074T=KIT0299T=CIP111914T) and Leptospira chreensis (201903075T=KIT0300T=CIP111915T) are proposed.

scholarly journals Acinetobacter variabilis sp. nov. (formerly DNA group 15 sensu Tjernberg & Ursing), isolated from humans and animals

2015 ◽  
Vol 65 (Pt_3) ◽  
pp. 857-863 ◽  
Author(s):  
Lenka Krizova ◽  
Jana McGinnis ◽  
Martina Maixnerova ◽  
Matej Nemec ◽  
Laurent Poirel ◽  
...  
Keyword(s):  
Carbon Sources ◽  
Taxonomic Status ◽  
Comparative Sequence Analysis ◽  
Whole Genome ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Group 15 ◽  
Tof Ms

We aimed to define the taxonomic status of 16 strains which were phenetically congruent with Acinetobacter DNA group 15 described by Tjernberg & Ursing in 1989. The strains were isolated from a variety of human and animal specimens in geographically distant places over the last three decades. Taxonomic analysis was based on an Acinetobacter -targeted, genus-wide approach that included the comparative sequence analysis of housekeeping, protein-coding genes, whole-cell profiling based on matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), an array of in-house physiological and metabolic tests, and whole-genome comparative analysis. Based on analyses of the rpoB and gyrB genes, the 16 strains formed respective, strongly supported clusters clearly separated from the other species of the genus Acinetobacter . The distinctness of the group at the species level was indicated by average nucleotide identity values of ≤82 % between the whole genome sequences of two of the 16 strains (NIPH 2171T and NIPH 899) and those of the known species. In addition, the coherence of the group was also supported by MALDI-TOF MS. All 16 strains were non-haemolytic and non-gelatinase-producing, grown at 41 °C and utilized a rather limited number of carbon sources. Virtually every strain displayed a unique combination of metabolic and physiological features. We conclude that the 16 strains represent a distinct species of the genus Acinetobacter , for which the name Acinetobacter variabilis sp. nov. is proposed to reflect its marked phenotypic heterogeneity. The type strain is NIPH 2171T ( = CIP 110486T = CCUG 26390T = CCM 8555T).

scholarly journals First Report of Wohlfahrtiimonas chitiniclastica Isolation from a Patient with Cellulitis in the United States

2015 ◽  
Vol 53 (12) ◽  
pp. 3942-3944 ◽  
Author(s):  
Angel de Dios ◽  
Seby Jacob ◽  
Amit Tayal ◽  
Mark A. Fisher ◽  
Tanis C. Dingle ◽  
...  
Keyword(s):  
United States ◽  
16S Rrna Gene Sequencing ◽  
The United States ◽  
Superior Performance ◽  
Rrna Gene ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

We report the first documented isolation ofWohlfahrtiimonaschitiniclasticafrom a human in the United States. Initially misidentified asAcinetobacter lwoffiiby Vitek-2, the isolate was subsequently identified asW.chitiniclasticaby matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing. While the clinical significance of the isolate in this case is unclear, it highlights the superior performance of MALDI-TOF MS for bacterial identification.

scholarly journals Identification of Photorhabdus symbionts by MALDI-TOF MS

Microbiology ◽  
2020 ◽  
Vol 166 (6) ◽  
pp. 522-530
Author(s):  
Virginia Hill ◽  
Peter Kuhnert ◽  
Matthias Erb ◽  
Ricardo A. R. Machado
Keyword(s):  
Related Species ◽  
Species Level ◽  
Reference Database ◽  
Agricultural Pests ◽  
Closely Related Species ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Tof Ms

Species of the bacterial genus Photorhabus live in a symbiotic relationship with Heterorhabditis entomopathogenic nematodes. Besides their use as biological control agents against agricultural pests, some Photorhabdus species are also a source of natural products and are of medical interest due to their ability to cause tissue infections and subcutaneous lesions in humans. Given the diversity of Photorhabdus species, rapid and reliable methods to resolve this genus to the species level are needed. In this study, we evaluated the potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Photorhabdus species. To this end, we established a collection of 54 isolates consisting of type strains and multiple field strains that belong to each of the validly described species and subspecies of this genus. Reference spectra for the strains were generated and used to complement a currently available database. The extended reference database was then used for identification based on the direct transfer sample preparation method and the protein fingerprint of single colonies. High-level discrimination of distantly related species was observed. However, lower discrimination was observed with some of the most closely related species and subspecies. Our results therefore suggest that MALDI-TOF MS can be used to correctly identify Photorhabdus strains at the genus and species level, but has limited resolution power for closely related species and subspecies. Our study demonstrates the suitability and limitations of MALDI-TOF-based identification methods for assessment of the taxonomic position and identification of Photorhabdus isolates.

scholarly journals Epidemiology of Nontuberculous Mycobacteria in French Polynesia

2015 ◽  
Vol 53 (12) ◽  
pp. 3798-3804 ◽  
Author(s):  
Michael Phelippeau ◽  
Djaltou Aboubaker Osman ◽  
Didier Musso ◽  
Michel Drancourt
Keyword(s):  
Nontuberculous Mycobacteria ◽  
Sequence Similarity ◽  
Gene Sequencing ◽  
French Polynesia ◽  
Rrna Gene ◽  
Mycobacterium Fortuitum ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

As few data are available in the Pacific countries and territories of the Oceania region regarding nontuberculous mycobacteria, we retrospectively identified 87 such isolates from French Polynesia from 2008 to 2013 by hybridization using DNA-strip, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and partialrpoBgene sequencing. PartialrpoBgene sequencing classified 42/87 (48.3%) isolates in theMycobacterium fortuitumcomplex, 28 (32.2%) in theMycobacterium abscessuscomplex, 8 (9.2%) in theMycobacterium mucogenicumcomplex, and 5 (5.7%) in theMycobacterium aviumcomplex. Two isolates were identified asMycobacterium acapulcensisandMycobacteriumcosmeticumby partial 16S rRNA gene sequencing. One isolate, unidentified by MALDI-TOF MS and yielding less than 92% and 96% sequence similarity withrpoBandhsp65reference sequences, respectively, was regarded as a potentially new species. Samples from three patients exhibiting ≥2Mycobacterium porcinumisolates and from one patient with emphysema and a lung abscess exhibiting 2Mycobacterium senegalenseisolates fulfilled the American Thoracic Society microbiological criteria for nontuberculous mycobacterial lung infection. Remote geographic areas, such as French Polynesia, are potential sources for the discovery of new mycobacterial species.

Cohnella terricola sp. nov., isolated from soil

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Jiyoun Kim ◽  
Geeta Chhetri ◽  
Inhyup Kim ◽  
Minchung Kang ◽  
Taegun Seo
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Phenotypic Tests ◽  
A New Species

A Gram-positive, aerobic, flagellated, endospore-forming, rod-shaped strain, designated as G13T, was isolated from soil. The results of 16S rRNA gene sequence analysis led to the conclusion that strain G13T was phylogenetically related to Cohnella boryungensis BR29T (97.5 %) and Cohnella phaseoli CECT 7287T (96.9 %) with digital DNA–DNA hybridization values of 21.0 and 21.4 %, and distantly related to Cohnella thermotolerans CCUG 47242T (94.8 %), type species of the genus Cohnella , at 19.0 %. The genome size of strain G13T was 5 387 258 bp, with 51.3 mol% G+C content. The predominant fatty acids were summed feature 9 (iso-C17 : 1  ω9c and/or C16 : 0 10-methyl), anteiso-C17 : 0, iso-C17 : 0 and iso-C15 : 0. The predominant quinone was menaquinone-7 and the major polar lipids were diphosphatidyglycerol, phosphatidylethanolamine, phosphatidylglycerol, lysylphosphatidylglycerol, three aminophospholipids, two phosphoglycolipids, three aminolipids and two unidentified lipids. Based on the data from phenotypic tests and the genotypic differences between strain G13T and its close phylogenetic relatives, strain G13T represents a new species belonging to the genus Cohnella , for which the name Cohnella terricola sp. nov. (=KACC 19905T=NBRC 113748T) is proposed.

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