ライフサイエンスコーパス: ribotype

1 er half of the isolates belonged to a single ribotype.

2 e composition and expression of a particular ribotype.

3 inst 16 C. difficile isolates of defined PCR-ribotype.

4 t both the epidemic 027 ribotype and the 012 ribotype.

5 in nor nisin inhibited outgrowth for the 012 ribotype.

6 typing was performed on clusters of the same ribotype.

7 es were found among the 15 strains that were ribotyped.

8 Fifteen selected strains were ribotyped.

9 to three non-toxigenic strains of different ribotypes.

10 nd 078) cause more severe disease than other ribotypes.

11 s contained both multiple REA groups and PCR ribotypes.

12 enes appeared to be associated with specific ribotypes.

13 re similar adjusting for locally circulating ribotypes.

14 tet genes were found among various ribotypes.

15 ctrophoresis types, 4 coagulase types, and 2 ribotypes.

16 57 isolates produced 97 PFGE profiles and 51 ribotypes.

17 ad previously been categorized into 19 PvuII ribotypes.

18 uate stool toxin levels and C. difficile PCR ribotypes.

19 etitive fitness compared to strains of other ribotypes.

20 027 strains outcompeted the strains of other ribotypes.

21 typed using high-throughput, fluorescent PCR ribotyping.

22 analysis (MLVA) compared to typing using PCR ribotyping.

23 test using MLVA and in the control using PCR ribotyping.

24 y rate was 90%, yielding 11,294 isolates for ribotyping.

25 ormed by sequencing of the tcdC gene and PCR ribotyping.

26 All C. difficile strains were typed by PCR-ribotyping.

27 iginating from 26 countries were analyzed by ribotyping.

28 consistent with those of both emm typing and ribotyping.

29 staphylococcal (CoNS) isolates identified by ribotyping.

30 g pulsed-field gel electrophoresis (PFGE) or ribotyping.

31 ce typing (using six housekeeping genes) and ribotyping.

32 tergenic consensus (ERIC)-PCR, and automated ribotyping.

33 nal strain, all 90 isolates were analyzed by ribotyping.

34 the results of the Dienes test and those of ribotyping.

35 racterized by serotyping and automated EcoRI ribotyping.

36 pulsed-field gel electrophoresis (PFGE), and ribotyping.

37 olates was further differentiated with PvuII ribotyping.

38 nth period were typed by the Dienes test and ribotyping.

39 ans strains was evaluated by both AP-PCR and ribotyping.

40 que strains as judged by the Dienes test and ribotyping.

41 cible and could be used as an alternative to ribotyping.

42 hat afforded by plasmid profile analysis and ribotyping.

43 ates were typed by polymerase chain reaction ribotyping.

44 cile by anaerobic culture, and performed PCR ribotyping.

45 . difficile strains, including the J strain (ribotype 001 and PFGE NAP2), the toxin A-negative 017 st

46 isolates and clinical isolates of four other ribotypes (001, 002, 014, and 053).

47 he Xpert C. difficile assay for detection of ribotypes 002, 027, and 106 (P < 0.0001, P < 0.0001, and

48 t the NAPCR1 variant belongs to C. difficile ribotype 012 and sequence type 54, as does the reference

49 Ribotype 014-020 associated with IDSA severity and 30-da

50 s, ribotype 027 fell from 16.5% to 9.3%, and ribotype 014-027 remained stable at 18.9%.

51 ortality was only 4% (3 of 84) in ST 44 (PCR ribotype 015) (adjusted P = .05 vs other clade 1).

52 and PCR ribotyping; sequence type 37 (ST37)/ribotype 017 (RT017) (n = 68, 16.5%) was the dominant ge

53 infection with indistinguishable isolates of ribotype 017, with evidence of spread both within and be

54 One of the 137 unique ribotypes was ribotype 027 (16.2%).

55 ype III, North American PFGE type 1, and PCR-ribotype 027 (NAP1/027).

56 rain of C. difficile designated BI, NAP1, or ribotype 027 (which are synonymous terms).

57 The ribotype 027 and 078 strains also have the capacity to p

58 hat elevated stool toxins and infection with ribotype 027 associate with severe disease and adverse o

59 and used it to test competition between four ribotype 027 clinical isolates and clinical isolates of

60 assess the in vitro recovery of C. difficile ribotype 027 contamination ( approximately 10(0), 10(1),

61 ly emerged, accounting for 10.6% of strains, ribotype 027 fell from 16.5% to 9.3%, and ribotype 014-0

62 Infection with ribotype 027 independently predicts severe CDI and morta

63 Clostridium difficile ribotype 027 predominated, but decreased markedly from 5

64 ent work has raised some doubt as to whether ribotype 027 strains are hypervirulent, the strains are

65 n colonic organoids, that TcdB from epidemic ribotype 027 strains does not require Frizzled 1/2/7 bin

66 de that one possible mechanism through which ribotype 027 strains have caused outbreaks worldwide is

67 w that CDT enhances the virulence of two PCR-ribotype 027 strains in mice.

68 We found that ribotype 027 strains outcompeted the strains of other ri

69 Initial reports indicated that ribotype 027 strains were associated with increased morb

70 at could lead to the increased prevalence of ribotype 027 strains would be if these strains had incre

71 rulence factors toxin A and B, epidemic, PCR Ribotype 027 strains, such as R20291, produce a third to

72 Adjusting for covariates, including age, Ribotype 027 was a significant predictor of severe CDI (

73 different subtypes of Clostridium difficile ribotype 027 within the same feces specimen.

74 d-field gel electrophoresis strain type NAP1/ribotype 027) was the most prevalent (32.6%); 43.5% of t

75 Hypervirulent strains (e.g. ribotype 027) with higher morbidity and mortality additi

76 mmunities were inoculated with C. difficile (ribotype 027).

77 sis type NAP1, and polymerase chain reaction ribotype 027, is designated BI/NAP1/027.

78 ne of the other virulence factors, including ribotype 027, were predictive of RCDI.

79 ple factors, including reduced prevalence of ribotype 027.

80 e prevalence of epidemic strains, especially ribotype 027.

81 No children carried hypervirulent PCR ribotype 027.

82 I by Xpert C. difficile, of which three were ribotype 027.

83 hallenged with a strain of the hypervirulent ribotype 027.

84 and patients with polymerase chain reaction ribotype 027.

85 11), then clade 2 (20% [111 of 560]; 99% PCR ribotype 027/ST 1) versus clade 1 (12% [137 of 1168]; ad

86 phylogenetic clade of C. difficile strains (ribotype 027; North American pulsed-field electrophoresi

87 However, the association between ribotypes 027 and 078 and severe CDI was not significant

88 also demonstrated with key disease isolates (ribotypes 027 and 078), which are members of the hypervi

89 gional variations in prevalence occurred for ribotypes 027, 002, 015, and 078.

90 Adjusting for hospital, ribotype-027 had the highest proportion of linked isolat

91 Isolates with the PCR ribotype 078 belong to clade 5, and are often associated

92 of a non-sporulating variant of C. difficile ribotype 078 harbouring mutations leading to premature s

93 Colonisation of animals and humans by ribotype 078 raises questions about possible zoonotic tr

94 on, and also the diversity of reservoirs for ribotype 078 strains within the environment.

95 lates comprised four PCR ribotypes, but one, ribotype 078, predominated (83%).

96 PCR ribotype 078/ST 11 (clade 5) leads to severe CDI; thus o

97 [16 of 63]; polymerase chain reaction (PCR) ribotype 078/ST 11), then clade 2 (20% [111 of 560]; 99%

98 shedding of three L. monocytogenes subtypes (ribotypes 1058A, 1039E and 1042B) using data from one st

99 ws that shed any L. monocytogenes subtype or ribotypes 1058A, 1039E, and 1042B, (ii) the duration of

100 In 2016, compared to 2010-2013, ribotype 106 newly emerged, accounting for 10.6% of stra

101 r, across all pairs of samples sharing a PCR ribotype, 192/283 (68%) differed by >10 STRDs and 217/28

102 Of 350 isolates, 244 (70%) were known PCR ribotypes, 224 (68%) were 1 of 8 common REA groups, and

103 Clostridium difficile PCR ribotype 265 (toxin A negative, B positive) was most pre

104 between three-fourths of pediatric and adult ribotype 265 strains, without a clear epidemiological li

105 elucidate the source and epidemiology of PCR ribotype 265, primarily found in children.

106 t to least, plasmid profiling [40 types], PS ribotyping [34 types], and PFGE [23 types]).

107 This was also the most common ribotype (94%) among 33 calf isolates but was rarely ide

108 REA, slpAST, MLST, and PCR-ribotyping all included AP-B (toxinotype III, binary tox

109 th the results compared to those obtained by ribotype analysis.

110 Strains were also subjected to PFGE and ribotyping analysis.

111 The isolates had distinct ribotype and pulsed-field gel electorphoresis patterns a

112 ence on the association between C. difficile ribotype and severe disease.

113 were effective against both the epidemic 027 ribotype and the 012 ribotype.

114 Forty isolates represented 40 different ribotypes and Dienes types.

115 pitope sequences across several C. difficile ribotypes and homologous repeat sequences within TcdA su

116 the hypotheses that infection with specific ribotypes and presence of stool toxins independently ass

117 sures favouring multidrug-resistant epidemic ribotypes and was associated with substantial declines i

118 sures favouring multidrug-resistant epidemic ribotypes and was associated with substantial declines i

119 typing, with 85 outbreaks being confirmed by ribotyping and 62 by MLVA.

120 ates were typed by polymerase chain reaction-ribotyping and analyzed for the presence of toxin genes.

121 m a transtracheal swab was compared by using ribotyping and antibiotic susceptibility analyses.

122 Ribotyping and AP-PCR analysis confirmed a previous repo

123 It was recently reported that both PvuII ribotyping and HinfI/DdeI restriction endonuclease analy

124 ence in the mean turnaround time between the ribotyping and MLVA typing (13.6 and 5.3 days, respectiv

125 Routine polymerase chain reaction (PCR) ribotyping and multiple-locus variable-number tandem-rep

126 Fingerprinting of genomic DNA by ribotyping and PFGE produced a significant variation in

127 e finding that differences in the results of ribotyping and plasmid analysis change over time suggest

128 was more discriminatory than EcoRI or PvuII ribotyping and provided subtype data with better epidemi

129 stant isolates was investigated by automated ribotyping and pulsed-field gel electrophoresis (PFGE).

130 The isolates were subtyped by ribotyping and pulsed-field gel electrophoresis.

131 Ribotyping and RAPD clearly demonstrated the household t

132 PFGE and AFLP were less discriminatory than ribotyping and RAPD.

133 kota isolates were indistinguishable by both ribotyping and RAPD.

134 Ribotyping and REA identified numerous, previously unrec

135 A combination of ribotyping and serotyping showed that two bovine isolate

136 ed patients and characterized them using PCR-ribotyping and virulence factor analysis.

137 Both PstI/SphI ribotyping and XbaI-PFGE provided a similar degree of st

138 Isolates were ribotyped, and multiple-locus variable-number tandem-rep

139 olates were grouped into 13 Dienes types, 12 ribotypes, and 14 PFGE types.

140 ciated disease serotypes, virulence factors, ribotypes, and antimicrobial susceptibility phenotypes.

141 EcoRI ribotyping differentiated 17 ribotypes, and DNA sequencing of the housekeeping gene s

142 een Listeria monocytogenes genetic lineages, ribotypes, and serotypes, 235 L. monocytogenes isolates

143 ion was 0.980 for the Dienes test, 0.979 for ribotyping, and 0.992 for PFGE.

144 AT probes was less discriminating than MLST, ribotyping, and enterobacterial repetitive intergenic co

145 Pulsed-field gel electrophoresis (PFGE), ribotyping, and multilocus sequence typing are commonly

146 The methodologies for RAPD typing, ribotyping, and PFGE typing of C. diphtheriae strains we

147 d gel electrophoresis [PFGE], PstI/SphI [PS] ribotyping, and plasmid profiling).

148 g methods, such as serotyping, phage typing, ribotyping, and pulsed-field gel electrophoresis, can yi

149 olates by multilocus enzyme electrophoresis, ribotyping, and random amplified polymorphic DNA showed

150 Pulsed-field gel electrophoresis (PFGE), ribotyping, and repetitive extragenic palindromic sequen

151 rotyping, pulsed-field restriction analysis, ribotyping, and repetitive-sequence (BOX element) PCR.

152 Restriction endonuclease analysis (REA), PCR ribotyping, and serogrouping differentiated 11, 4, and 3

153 popular C. difficile-typing technique is PCR ribotyping, and we previously developed methods using fl

154 tinct from those seen elsewhere, and certain ribotypes appeared to be unique to particular countries.

155 Successful ribotypes are determined by natural selection, and can b

156 avium and B. hinzii, although the results of ribotyping are more easily interpreted.

157 Both the Dienes test and ribotyping are useful methods for identifying individual

158 sed in vitro by all 77 Clostridium difficile ribotypes assayed.

159 s strains and isolates of a single ribotype, ribotype B, recovered between 1939 and 1998 from patient

160 lved macrochromosomal RFLPs were analyzed, a ribotype-based phylogenic tree was constructed, and case

161 Porcine isolates comprised four PCR ribotypes, but one, ribotype 078, predominated (83%).

162 t length polymorphism, and identification of ribotype by PCR.

163 eld gel electrophoresis (PFGE) and automated ribotyping by using HindIII and PvuII.

164 Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse

165 Rates of 9 of the 10 most common ribotypes changed significantly (P < .05) during 2007-20

166 tion through dysbiosis, epidemic C difficile ribotypes characterised by multidrug resistance might de

167 four other molecular subtyping methods: MEE, ribotyping (ClaI), random amplified polymorphic DNA assa

168 and healthy tissues was the dominance of one ribotype, closely related to the plant pathogen, Rhytism

169 deep-sea leech species (80-94% of recovered ribotypes) collected over 19 months from two different l

170 erior discriminatory performance of the PFGE-ribotyping combination was proven in two ways: (i) by de

171 Our data show that (i) EcoRI ribotyping, combined with hylB and sodA sequencing, prov

172 Five PCR ribotypes contained multiple REA groups, and three North

173 Some EcoRI ribotypes contained multiple serotypes; a subset of thes

174 HindIII ribotypes correlated well with PFGE.

175 ertain whether the Eastern European epidemic ribotype could be further discriminated, 10 strains of r

176 (intergenic transcribed spacer PCR [ITS-PCR] ribotyping) could distinguish among type strains of the

177 iscrimination [D] = 0.995) than either EcoRI ribotyping (D = 0.950) or AscI or ApaI single-enzyme PFG

178 ould be further discriminated, 10 strains of ribotype D1 (the epidemic ribotype) from different geogr

179 inct electrophoretic type complex and are of ribotypes D1 and D4.

180 -style sequencer to generate fluorescent PCR ribotyping data.

181 cost-effective generation of fluorescent PCR ribotyping data.

182 2 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton c

183 pulsed-field gel electrophoresis (PFGE), PCR ribotyping, detection of a binary toxin gene, and detect

184 y C. difficile strains representing multiple ribotypes develop two colony morphotypes, termed rough a

185 NAP1V) belongs to the NAP1 genotype but to a ribotype different from the epidemic NAP1/RT027 strain.

186 EcoRI ribotyping differentiated 17 ribotypes, and DNA sequenci

187 d Corethron We found only a few cosmopolitan ribotypes displaying an even distribution across station

188 e for identifying polymorphism was PstI-SphI ribotyping, distinguishing a total of 22 patterns, 10 of

189 e the molecular epidemiology with respect to ribotype distribution and cross-infection.

190 problem, with cross-infection and a distinct ribotype distribution, in a large Chinese hospital.

191 gh antibiotic stewardship should account for ribotype distributions and non-linear effects.

192 ical burdens from C difficile infections and ribotype distributions in a health board serving 11% of

193 The EcoRI ribotype diversity among bovine isolates (Simpson's nume

194 ose proximity did not necessarily share more ribotype diversity than institutions that were farther a

195 m difficile outbreaks suggested that certain ribotypes (eg, 027 and 078) cause more severe disease th

196 Age, comorbidities, severe CDI, and ribotypes F027, F001, and F053-163 were associated with

197 More than 50% of the ribotypes fall into discrete clusters containing less th

198 le serotypes, demonstrating the potential of ribotyping for serotype prediction.

199 lative abundance of 98 Clostridium difficile ribotypes from clinical cases of disease at health care

200 ted, 10 strains of ribotype D1 (the epidemic ribotype) from different geographical regions were rando

201 8 different plasmid profiles and three PvuII ribotypes generated by the same strains.

202 ntibiotic susceptibility, biochemical tests, ribotyping, genome restriction mapping, and multilocus s

203 hey were syntenic, overlapping a- and b-type ribotype genomes harbored significant variability.

204 the RNA pool, which we refer to here as the 'ribotype', has a different information content from the

205 Ribotyping identified 18 different strains among the 39

206 al extrapolation, at least 1,633 co-existing ribotypes in the sampled population.

207 fficile typing platform that is based on PCR-ribotyping in conjunction with a semiautomated molecular

208 emperature sediments, ANMEs allied to ANME-1 ribotypes, including a putative ANME-1c group, were foun

209 All ribotypes, including ARL 002, ARL 027, and ARL 106, were

210 Whole-genome sequencing and ribotyping indicated that the NAPCR1 variant belongs to

211 Ribotype is not a significant predictor of severe CDI wh

212 The results revealed that ribotyping is highly discriminatory and reproducible and

213 o were examined by biotyping, PvuII and SmaI ribotyping, IS200 fingerprinting, and pulsed-field gel e

214 th three well-established molecular methods (ribotyping, macrorestriction analysis of genomic DNA, an

215 ferences among isolates, and unlike PFGE and ribotyping, microarrays can be used to identify specific

216 ollowing order: MLVA, REA, PFGE, slpAST, PCR-ribotyping, MLST, and AFLP.

217 Four molecular subtyping methods-ribotyping, multilocus enzyme electrophoresis (MEE), ran

218 The Clostridium difficile Ribotyping Network (CDRN) was established in 2007 as par

219 c cats were found to exhibit the predominant ribotypes observed among human clinical isolates, sugges

220 ., by discriminating isolates with identical ribotypes obtained from different farms.

221 y were challenged with pure cultures, all 10 ribotypes of C. difficile generated higher colony counts

222 rized by ribotyping to determine whether the ribotypes of the cat isolates were genotypically related

223 Ribotyping of IgA-coated cecal microbiota showed Proteob

224 tified a total of 237 quantifiable bacterial ribotypes, of which an average of 73 community members w

225 olates were not randomly distributed between ribotypes or hylB and sodA clusters.

226 ept for patients infected with hypervirulent ribotypes or with stool incontinence, to determine the r

227 of discrimination among isolates than either ribotyping or PFGE, although strain clustering was simil

228 ), and the sensitivity of GDH algorithms for ribotypes other than 027 was lower than that for Xpert C

229 competitive advantage was observed when two ribotype pairs were competed in a mouse model of C. diff

230 olate of anesthesiologist A had an identical ribotype pattern (strain 1); the remaining case-patient'

231 siologist A's hands and home had a different ribotype pattern (strain 2).

232 UMCR1 also had biochemical reactions and a ribotype pattern typical of S. aureus.

233 ocus enzyme electrophoresis but had a unique ribotype pattern.

234 Strains with ribotype patterns D1, D4, and D12 could not be distingui

235 ver, the technique discriminated isolates of ribotype patterns D3, D6, and D7 further.

236 ical, antimicrobial susceptibility, and BglI ribotype patterns that differed from the second patient'

237 s from New Orleans and Jackson had different ribotype patterns, suggesting that the two outbreaks wer

238 accharomyces were shown to share the ITS-PCR ribotyping patterns of both parental species.

239 Ribotyping patterns using the restriction enzymes MaeI a

240 By use of ribotyping, plasmid content, and antibiotic susceptibili

241 C. difficile infection (CDI) to test whether ribotype predicted clinical severity when adjusted for t

242 Of the six P. haemolytica ribotypes, two ribotypes predominated.

243 C. difficile isolates revealed multiple PCR ribotypes present and the emergence of rifamycin resista

244 man infection) and either particular PFGE or ribotype profiles or clusters.

245 of the clinical M1 isolates shared a single ribotype, pulsed-field gel electrophoresis macrorestrict

246 Typing was performed by PCR-ribotyping, pulsed-field gel electrophoresis (PFGE), and

247 comparison of four molecular typing methods (ribotyping, pulsed-field gel electrophoresis [PFGE], ran

248 dicted rapid declines in multidrug-resistant ribotypes R001 and R027.

249 clonal group of C. diphtheriae (PFGE type A, ribotype R1), which was identical to the predominant epi

250 PCR-ribotyping, REA, and PFGE provide different but overlapp

251 These included ribotypes related to Corynebacterium (KC190237), Acineto

252 elated isolates, the predominant RiboPrinter ribotype represented 50% of the strains, while the large

253 sity [D] = 0.98 and 0.94 for PFGE typing and ribotyping, respectively).

254 Ribotype restriction fragment length polymorphism (RFLP)

255 protein A gene sequence typing (slpAST), PCR-ribotyping, restriction endonuclease analysis (REA), mul

256 . Y. pestis strains and isolates of a single ribotype, ribotype B, recovered between 1939 and 1998 fr

257 However, PCR ribotype (RT) 017, one of five clonal lineages of human

258 hich are characteristic of the hypervirulent ribotype (RT) 027 strain.

259 rly characterised clade 3, predominantly PCR ribotype (RT)023, of C. difficile revealed distinctive s

260 inct genetic clades encompassing several PCR ribotypes (RT).

261 The ribotypes seen in Europe appeared to be distinct from th

262 ined by multilocus sequence analysis and PCR ribotyping; sequence type 37 (ST37)/ribotype 017 (RT017)

263 The correlation between PCR-ribotyping, sequencing, and Xpert PCR for detection of N

264 presented herein, the combination of REA and ribotyping should provide valuable information in unders

265 As a result, ribotype-specific forms of TcdB exhibit different toxici

266 ntly provided more discriminatory power than ribotyping, there were examples where the use of ribotyp

267 and seven cat isolates were characterized by ribotyping to determine whether the ribotypes of the cat

268 Of the six P. haemolytica ribotypes, two ribotypes predominated.

269 the restriction endonuclease XbaI, while for ribotyping, two restriction endonucleases (PstI and SphI

270 At least 516 ribotypes (unique rRNA sequences) were detected in the s

271 standardized suspensions of 10 C. difficile ribotypes (untreated and alcohol treated) that were also

272 ctors by polymerase chain reaction (PCR) and ribotyped using high-throughput, fluorescent PCR ribotyp

273 The ribotype was identified in 922 patients, of whom 52% wer

274 e if the identical polymerase chain reaction ribotype was identified in index-contact pairs, and as c

275 the P. haemolytica isolates, while only one ribotype was observed for the limited number of P. multo

276 One strain of each ribotype was then randomly chosen and characterized by P

277 One of the 137 unique ribotypes was ribotype 027 (16.2%).

278 Access to C. difficile ribotyping was associated with significant changes in th

279 Ribotyping was less sensitive than PFGE when applied to

280 typing, there were examples where the use of ribotyping was more discriminatory than REA.

281 Ribotyping was performed using the fully automated RiboP

282 Ribotyping was used to identify cultures and indicated d

283 Capillary-based PCR ribotyping was used to quantify the presence/absence and

284 Multiple ribotypes were encountered, but none possessed typical v

285 Four and 21 different ribotypes were found among human and bovine isolates, re

286 dentified among all strains examined, and 12 ribotypes were found among the 15 strains that were ribo

287 Identical ribotypes were identified in 6 index-contact pairs, acco

288 Regionally important ribotypes were identified, and institutions in close pro

289 ifficile were recovered, and seven different ribotypes were identified, the dominant types being 017

290 Six different ribotypes were observed for the P. haemolytica isolates,

291 Four bacterial and nine ciliate ribotypes were observed in both diseases, but absent in

292 PCR ribotypes were obtained for 144 Clostridium difficile is

293 r biotype differentiation; however, PFGE and ribotyping were better (and equal to each other) at disc

294 indistinguishable by the Dienes test and/or ribotyping were characterized further by pulsed-field ge

295 Eleven covariates, including C. difficile ribotype, were significant predictors of severe CDI in u

296 pulsed-field gel electrophoresis (PFGE) and ribotyping, were used to characterize 207 Escherichia co

297 PCR ribotyping, whole-genome sequencing, and phenotypic assa

298 Automated ribotyping with HindIII is an accurate method for geneti

299 criminatory ability of MLVA was greater than ribotyping, with 85 outbreaks being confirmed by ribotyp

300 ified that share a substantial percentage of ribotypes within them.