A probability matrix for the identification of campylobacters, helicobacters and allied taxa

On, Stephen L. W.; Holmes, B.; Sackin, M. J.

doi:10.1111/j.1365-2672.1996.tb03529.x

Cited by 96 publications

(158 citation statements)

References 29 publications

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“…Since the studies of On et al (1996) demonstrated that A. nitrofigilis was able to hydrolyse indoxyl acetate, which contradicted previous data (Mills & Gherna, 1987), all species of the genus Arcobacter have been considered to be indoxyl-acetate-hydrolysis-positive. In the present study, using four strains of A. nitrofigilis (CECT 7204 T , LMG 7547, F2173 and F2176), the results of On et al (1996) were corroborated as, despite the reactions being slower and weaker than that observed for the other species, they were clearly positive. The susceptibility to cefoperazone (64 mg l 21 ) differentiated the novel isolates from A. butzleri, A. cibarius, A. cryaerophilus and A. skirrowii.…”

contrasting

confidence: 53%

Arcobacter mytili sp. nov., an indoxyl acetate-hydrolysis-negative bacterium isolated from mussels

Collado

Cleenwerck

Trappen

et al. 2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

118

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Three Arcobacter isolates, recovered from mussels (genus Mytilus), and one isolate from brackish water in Catalonia (north-east Spain) showed a novel pattern using a recently described identification method for members of the genus Arcobacter, 16S rRNA gene RFLP. Enterobacterial repetitive intergenic consensus PCR fingerprinting demonstrated that the three isolates from mussels belonged to two genotypes and that the fourth isolate from water belonged to a third genotype. Analysis of the 16S rRNA and rpoB gene sequences showed that the new isolates formed a separate lineage within the genus Arcobacter. This was also confirmed by the low DNA-DNA relatedness values (16-30%) of the isolates with the type strains of recognized Arcobacter species. Hydrolysis of indoxyl acetate, a characteristic trait for all species of the genus Arcobacter, was negative for the novel isolates. The susceptibility of the novel isolates to cefoperazone, together with the lack of urease production and nitrate reduction, further enabled them to be differentiated from recognized Arcobacter species based on physiological characteristics. Genotypic and phenotypic characteristics indicated that the new isolates represent a novel species of the genus Arcobacter, for which the name Arcobacter mytili sp. nov. is proposed, with the type strain F2075(T) (=CECT 7386(T) =LMG 24559(T)). The DNA G + C content of strain F2075(T) was 26.9 mol%

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contrasting

confidence: 53%

Arcobacter mytili sp. nov., an indoxyl acetate-hydrolysis-negative bacterium isolated from mussels

Collado

Cleenwerck

Trappen

et al. 2009

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLO

118

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“…Certain tests demonstrated notable discriminatory potential, and also proved signi®cant when used to evaluate the results of PCR and PFGE assays (see below). Table 1 summarizes the identi®cations obtained by computer-aided analysis of strain test results using each of the two probability matrices investigated (On 1996b;On et al 1996). In brief, the full matrix analysis identi®ed 28 strains as Camp.…”

Section: Phenotypic Characterization and Probabilistic Identi®cation mentioning

confidence: 99%

Evaluation of numerical analysis of PFGE-DNA profiles for differentiating Campylobacter fetus subspecies by comparison with phenotypic, PCR and 16S rDNA sequencing methods

On¹,

Harrington²

2001

J Appl Microbiol

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Aims: To assess the ef®cacy of numerical analysis of PFGE-DNA pro®les for identi®cation and differentiation of Campylobacter fetus subspecies. Methods and Results: 31 Camp. fetus strains were examined by phenotypic, PCR-and PFGE-based methods, and the 16S rDNA sequences of 18 strains compared. Numerical analysis of PFGE-DNA pro®les divided strains into two clusters at the 86% similarity level. One cluster contained 19 strains clearly identi®ed as Camp. fetus subsp. venerealis. The other cluster comprised 12 strains, of which 10 were unambiguously identi®ed as Camp. fetus subsp. fetus. The remaining two strains were identi®ed as Camp. fetus subsp. venerealis by either phenotypic or PCR methods, but not both. At higher similarity levels, clusters containing isolates from each of two countries were identi®ed, suggesting that certain clones predominate in certain geographical regions. Conclusions: Numerical analysis of PFGE-DNA pro®les is an effective method for differentiating Camp. fetus subspecies. Signi®cance and Impact of the Study: Critical comparison of PFGE, PCR, 16S rDNA sequencing and phenotypic methods for differentiation of Camp. fetus subspecies was attained. Novel phenotypic markers for distinguishing subspecies were identi®ed. Evidence for dominant clones of each subspecies in certain countries was provided.

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“…+, Positive; 2, negative; V, variable; W, weakly positive. (Atabay et al, 1998); for the anaerobic growth test, a temperature of 25 uC was used for taxon 4 (Atabay et al, 1998) and, for taxon 7, the result was from On et al (1996). DTemperature for the tests was not available.…”

Section: Description Of Arcobacter Marinus Sp Novmentioning

confidence: 99%

Arcobacter marinus sp. nov.

Kim

Hwang

Cho

2010

International Journal of Systematic and Evolutionary Microbiology

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A slightly curved, rod-shaped marine bacterium, designated strain CL-S1 T , was isolated from near Dokdo, an island in the East Sea, Korea. Cells were Gram-negative and grew well under either aerobic or microaerobic conditions. Analyses of the 16S rRNA and gyrA gene sequences of strain CL-S1 T revealed an affiliation with the genus Arcobacter within the class Epsilonproteobacteria. Phylogenetic analyses based on 16S rRNA and gyrA gene sequences showed that strain CL-S1 T formed a robust clade with Arcobacter halophilus LA31B T , with sequence similarities of 96.1 and 88.2 %, respectively. DNA-DNA relatedness between strain CL-S1 T and A. halophilus DSM 18005 T was 44 %, indicating that they represent genomically distinct species. Strain CL-S1 T grew optimally at 30-37 6C, at pH 7 and in the presence of 3-5 % NaCl. The dominant cellular fatty acids were iso-C 15 : 0 2-OH and/or C 16 : 1 v7c (28.4 %), C 16 : 0 (26.2 %) and C 18 : 1 v7c (22.3 %). The DNA G+C content of strain CL-S1 T was 28 mol%. Strain CL-S1 T differed phenotypically from A. halophilus LA31B T based on its ability to grow aerobically at 10 6C and inability to grow under anaerobic conditions. Based on the data presented, strain CL-S1 T is considered to represent a novel species of the genus Arcobacter, for which the name Arcobacter marinus sp. nov. is proposed. The type strain is CL-S1 T (5KCCM 90072 T 5JCM 15502 T ).The genus Arcobacter belongs to the family Campylobacteraceae, which also contains the genera Campylobacter and Sulfurospirillum ( (Neill et al., 1985;Kiehlbauch et al., 1991;Vandamme et al., 1992) and are recognized as potential emerging human pathogens (Mansfield & Forsythe, 2000). A. nitrofigilis was isolated from Spartina alterniflora roots in a salt marsh (McClung et al., 1983). A. halophilus and A. cibarius were isolated from a hypersaline lagoon (Donachie et al., 2005) and the skin of a broiler carcass (Houf et al., 2005), respectively. In the present study, a novel strain affiliated with the genus Arcobacter was isolated and subjected to a polyphasic taxonomic analysis.Seaweeds and a starfish were collected and added to a surface seawater sample (50 ml) taken from the vicinity of Dokdo, an island in the East Sea, Korea. The mixture was maintained at 4 u C for 15 days. The mixture was then homogenized by using a blender and an aliquot (50 ml) was spread onto MY medium (Bouchotroch et al., 2001). The culture was incubated aerobically at 30 u C for 2 weeks. Strain CL-S1 T was isolated and subsequently purified on fresh marine agar 2216 (MA; Difco). Strain CL-S1 T grew well on MA or on saline blood agar [SBA; per litre distilled water: 40 g blood agar base (BBL), 50 ml sheep blood, 30 g NaCl] at 37 u C under either aerobic or microaerobic conditions. The novel strain was preserved in marine broth 2216 (MB; Difco) supplemented with 30 % (v/v) glycerol at 280 u C.For 16S rRNA gene amplification by PCR, DNA was extracted from a single colony by a boiling method (Englen & Kelley, 2000). The crude extracts served as the DNA template for...

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A probability matrix for the identification of campylobacters, helicobacters and allied taxa

Cited by 96 publications

References 29 publications

Arcobacter mytili sp. nov., an indoxyl acetate-hydrolysis-negative bacterium isolated from mussels

Arcobacter mytili sp. nov., an indoxyl acetate-hydrolysis-negative bacterium isolated from mussels

Evaluation of numerical analysis of PFGE-DNA profiles for differentiating Campylobacter fetus subspecies by comparison with phenotypic, PCR and 16S rDNA sequencing methods

Arcobacter marinus sp. nov.

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