scholarly journals Improved Identification of Mycobacteria by Using the Microbial Identification System in Combination with Additional Trimethylsulfonium Hydroxide Pyrolysis

1998 ◽  
Vol 36 (9) ◽  
pp. 2477-2480 ◽  
Author(s):  
K.-Dieter Müller ◽  
Ernst N. Schmid ◽  
Reiner M. Kroppenstedt

The MIDI automated Microbial Identification System (MIS) uses gas chromatography (GC) analysis of whole-cell fatty acid methyl esters (FAMEs) between 9 and 20 carbons in length to characterize a wide range of bacterial genera and species, including mycobacteria. Mycolic acid cleavage products (MACPs) with chain lengths of C22 to C26 are not released by MIDI sample preparation of mycobacteria. Therefore, the MIS library search report often matches several mycobacterial species without any significant difference in the similarity indices. The problem is solved by adding trimethylsulfonium hydroxide (TMSH) instead of sodium sulfate in the last step of sample preparation, thus allowing the identification of MACPs in addition to FAMEs. Only one GC run parameter has to be changed: the temperature program must be extended from 260 to 310°C. The MIS library search report for the identification of bacteria is not disturbed by TMSH. The combination of conventional library search report with the information of typical MACP patterns yields significantly better discrimination of mycobacterial species than the MIDI method allows.

Plant Disease ◽  
2008 ◽  
Vol 92 (7) ◽  
pp. 1135-1135 ◽  
Author(s):  
K. Rungnapha ◽  
S. H. Yu ◽  
G. L. Xie

In December 2006, a rot symptom of unknown etiology was observed on stems of plants (Euphorbia pulcherrima cv. Fu-xing) at a flower nursery in the Zhejiang Province of China where we had previously reported leaf spot of poinsettia caused by Xanthomonas campestris (2). Chlorotic spots anywhere along the stem and purplish black petioles were the first noticeable symptoms. The spots rapidly coalesced, forming large irregular chlorotic areas. Petioles turned black and shriveled and affected leaves wilted. Infected tissues were soft and water soaked. Ten bacterial strains were isolated from the diseased samples and five were selected for identification. They were similar to those of the standard reference strains of Pectobacterium chrysanthemi (Dickeya sp.), LMG 2804 from Belgium and ZUPB20056 from China, in phenotypic tests based on the Biolog Microbial Identification System, version 4.2 (Biolog Inc., Hayward, CA), pathogenicity tests, gas chromatography of fatty acid methyl esters (FAME) using the Microbial Identification System (MIDI Inc, Newark, DE) with aerobic bacterial library (TABA50), and transmission electron microscopy (TEM,KYKY-1000B, Japan). All strains tested were gram-negative facultative anaerobic rods measuring 1.5 to 3.6 × 0.6 to 1.1 μm, with peritrichous flagella. Colonies were gray-white and slightly raised with smooth margins on nutrient agar. They were negative for trehalose and positive for phosphatase production and reducing substances from sucrose. A hypersensitive reaction was observed on tobacco cv. Benshi, 24 h after inoculation. All five isolates, LMG 2804, and ZUPB20056 were identified as P. chrysanthemi (Dickeya sp.) with a Biolog similarity index of 0.58 to 0.83, 0.68, and 0.72 and a FAME similarity index of 0.52 to 0.80, 0.59, and 0.70, respectively. Identification as P. chrysanthemi (Dickeya sp.) was confirmed by PCR with specific primers used by Nassar et al (3). Koch's postulates were completed with the inoculation of 12 4-month-old intact poinsettia plants of cv. Fu-xing with cell suspensions containing 108 CFU/ml by a pinprick at the base of the stem. All five strains induced stem infection similar to those observed in natural infections. No symptoms were noted on the two control plants inoculated with sterilized distilled water by the same method. The bacterium was reisolated from symptomatic stems of poinsettia plants. P. chrysanthemi (Dickeya sp.) was first reported in United States as the cause of bacterial stem rot of poinsettia in 1972 (1). To our knowledge, this is the first report of poinsettia stem rot caused by P. chrysanthemi (Dickeya sp.) in China. The disease cycle and the control strategies of the bacterial stem rot of poinsettia in the regions are being further studied. References: (1) H. A. J. Hoitink et al. Plant Dis. Rep. 56:480, 1972. (2) B. Li et al. Plant Pathol. 55:293, 2006. (3) A. A. Nassar et al. Appl. Environ. Microbiol. 62:2228, 1996.


2003 ◽  
Vol 31 (2) ◽  
pp. 133-140 ◽  
Author(s):  
A Ozbek ◽  
O Aktas

The cellular fatty acid profiles of 67 strains belonging to three different species of the genus Mycobacterium were determined by gas chromatography of the fatty acid methyl esters, using the MIDI Sherlock® Microbial Identification System (MIS). The species M. tuberculosis, M. xenopi and M. avium complex were clearly distinguishable and could be identified based on the presence and concentrations of 12 fatty acids: 14:0, 15:0, 16:1ω7c, 16:1ω6c, 16:0, 17:0, 18:2ω6,9c, 18:1ω9c, 18:0, 10Me-18:0 tuberculostearic acid, alcohol and cyclopropane. Fatty acid analysis showed that there is great homogeneity within and heterogeneity between Mycobacterium species. Thus the MIS is an accurate, efficient and relatively rapid method for the identification of mycobacteria.


Plant Disease ◽  
1998 ◽  
Vol 82 (7) ◽  
pp. 831-831 ◽  
Author(s):  
D. O. Chellemi ◽  
H. A. Dankers ◽  
K. Hill ◽  
R. E. Cullen ◽  
G. W. Simone ◽  
...  

In September 1997, wilted 4-week-old tomato (Lycopersicon esculentum Mill.) plants were observed in a commercial production field in St. Lucie County, FL. Closer inspection of affected plants revealed hollow stems and petioles with dark, water-soaked lesions. Diseased tissue was macerated and streaked onto nutrient agar (NA) and crystal violet pectate (CVP) agar. After incubation for 2 days at 30°C, isolates produced pits on the CVP agar. Isolates were transferred onto NA and the incubation and transfer procedure was performed two additional times to obtain pure cultures. Suspensions of bacterial cells were injected into tomato and tobacco leaves to test for a hypersensitive or pathogenic reaction. Isolates produced collapsed necrotic tissue on tomato while no reaction was observed on tobacco. Tests for differentiating species and subspecies in the ‘carotovora’ group of Erwinia were conducted following the protocol of Dickey and Kelman (1). With known cultures of E. carotovora subsp. carotovora and E. chrysanthemi as controls, the isolate from tomato was determined to function as a facultative anaerobe, utilize asparagine as a sole source of carbon and nitrogen, and give positive reactions for pectate degradation, phosphatase, and growth at 37°C. Known cultures of E. carotovora subsp. carotovora, E. chrysanthemi, and the tomato isolate were grown on trypticase soy broth agar for 24 h at 28°C and their cellular fatty acids derivatized to fatty acid methyl esters (FAMEs). Statistical analyses of FAME profile data (MIDI Microbial Identification System, Newark, DE, version 3.60) identified the tomato isolate as Erwinia chrysanthemi. Pathogenicity was determined by inoculating 50-day-old tomato plants (cv. SunPride) with a suspension of E. chrysanthemi obtained from nutrient broth plates incubated at 24°C for 60 h. Three plants each were inoculated with the E. chrysanthemi identified from tomato, sterile water, and known cultures of E. chrysanthemi and E. carotovora subsp. carotovora by placing a drop at the junction of the petiole and stem and passing a sterile needle through the drop into the stem. Plants were maintained in a greenhouse. Dark, water-soaked cankers were observed on the stems of plants inoculated with E. chrysanthemi, including the tomato isolate and E. carotovora subsp. carotovora, after 7 days. No symptoms were observed on plants inoculated with sterile water. Reisolation of the pathogen and identification was performed with tissue from one of the symptomatic inoculated plants. Analyses of FAMEs confirmed E. chrysanthemi as the causal agent. This is the first report of E. chrysanthemi causing a vascular disease of field-grown tomato in Florida. Reference: (1) R. S. Dickey and A. Kelman. 1988. Pages 44–59 in: Laboratory Guide for Identification of Plant Pathogenic Bacteria. N. W. Schaad, ed. American Phytopathological Society, St. Paul, MN.


Plant Disease ◽  
2002 ◽  
Vol 86 (3) ◽  
pp. 326-326
Author(s):  
R. Gitaitis ◽  
J. Wilson ◽  
R. Walcott ◽  
H. Sanders ◽  
W. Hanna

Bacterial stripe, caused by Acidovorax avenae subsp. avenae, was observed on breeding lines of pearl millet (Pennisetum glaucum (L.) R. Br.) in Georgia in 1999 and 2001. A gram-negative, oxidase-positive, rod-shaped bacterium that produced circular, cream-colored, nonfluorescent, butyrous colonies with entire margins on King's medium B was consistently isolated from leaf lesions. The bacterium was identified as A. avenae subsp. avenae by gas-chromatography of extracted, whole-cell, fatty acid methyl esters using the Sherlock Microbial Identification System (MIDI, Newark, DE) and by substrate utilization patterns using the Biolog Identification System (Biolog Inc., Hayward, CA). Isolates from pearl millet produced amplicons of expected size (360 bp) from 16S rDNA after conducting polymerase chain reaction (PCR) with primers WFB1 and WFB2, which are specific for A. avenae. When bacterial suspensions of 1 × 108 CFU/ml were infiltrated into the intercellular spaces of leaves of pearl millet seedlings in the greenhouse, typical water-soaked, reddish-brown stripes developed and were identical to those observed in the field. In contrast to previous reports (1), the pearl millet strains produced atypical symptoms on sweet corn (cvs. Merit and Primetime). Necroses were restricted, lacked customary water-soaking, and were similar to symptoms produced by the watermelon pathogen, A. avenae subsp. citrulli, which was used as a negative control. In contrast, three strains of A. avenae subsp. avenae previously isolated from corn in Georgia produced typical water-soaked stripes in both millet and the sweet corn ‘Merit’. However, like the millet strains, A. avenae subsp. avenae strains from corn produced atypical symptoms on the sweet corn ‘Primetime’. Using immunomagnetic separation and PCR (2), A. avenae subsp. avenae was detected in remaining samples of pearl millet seed planted in Georgia in 2001, as well as in remnant samples of seed sent to Puerto Rico for increase in 2000. The A. avenae subsp. avenae strain recovered from seed was identified by the methods listed above, and in the greenhouse it was identified by the production of typical water-soaked stripes after inoculation of pearl millet. This is the first report of A. avenae subsp. avenae infecting pearl millet in the United States. The detection and distribution of seedborne inoculum in breeding lines is significant since the program at Tifton represents a major effort by the U.S. Department of Agriculture to develop higher-yielding, disease-resistant pearl millet hybrids. Furthermore, the strains from pearl millet appear to be different from previous A. avenae subsp. avenae strains isolated from corn in Georgia, because they did not produce typical disease symptoms when infiltrated in corn leaves. References: (1) L. E. Claflin et al. Plant Dis. 73:1010, 1989. (2) R. R. Walcott and R. D. Gitaitis. Plant Dis. 84:470, 2000.


Plant Disease ◽  
2000 ◽  
Vol 84 (7) ◽  
pp. 785-788 ◽  
Author(s):  
R. E. Baird ◽  
R. D. Gitaitis ◽  
D. E. Carling ◽  
S. M. Baird ◽  
P. J. Alt ◽  
...  

Fatty acid methyl esters (FAMEs) of isolates of Rhizoctonia solani AG-4 and AG-7 were characterized by gas chromatography and analyzed with Microbial Identification System software. Palmitic, stearic, and oleic acids were common in all isolates from both anastomosis groups (AGs) and accounted for 95% of the C14 to C18 fatty acids present. Oleic acid, most common in both R. solani AG-4 and AG-7 isolates, accounted for the greatest percentages of total FAMEs. The presence, quantities, or absence of individual fatty acids could not be used for distinguishing AG-4 and AG-7 isolates. Anteisopentadecanoic and 9-heptadecanoic acids, however, were specific to all three AG-7 isolates from Japan but absent in other AG-7 isolates and all AG-4 isolates. Pentadecanoic acid occurred in only two of the R. solani AG-4 isolates, but was not found in any of the AG-7 isolates. The AG-4 isolates could be distinguished from AG-7 isolates when quantities of FAMEs and key FAME ratios were analyzed with cluster analysis and principle components were plotted. Isolates of AG-7 from Arkansas, Indiana, and Georgia appeared to be more closely related to each other than to AG-7 isolates from Japan and Mexico. These differences in FAMEs were sufficiently distinct that isolate geographical variability could be determined. A dendrogram analysis cluster constructed from the FAMEs data showed results similar to that of the principal component analysis. Euclidean distances of total AG-4 isolates were distinct from total AG-7 isolates. The Arkansas and Indiana AG-7 isolates had a similar Euclidean distance to each another but the percentages were different for the AG-7 isolates from Japan and Mexico. In conclusion, variability of the FAMEs identified in this study would not be suitable as the main diagnostic tool for distinguishing individual isolates of R. solaniAG-4 from AG-7.


2013 ◽  
Vol 634-638 ◽  
pp. 1179-1183 ◽  
Author(s):  
Jing Deng ◽  
Hua Chang Wu ◽  
Xing Xiu Zhao ◽  
Jiao Jiao Shi

Sufu is a traditional Chinese fermented food. The safety of spontaneous fermentation products has been concerned by more and more people. A total of four isolates with big clear halos on the casein medium plate were isolated from spontaneous fermented Sufu in southern Sichuan. A1 and A3 most likely belong to Bacillus cereus B according to their phenotype and Biolog Microbial Identification System. B2 was classified in group as Bacillus amyloliquefaciens B with the same methods. A2 was identified as Bacillus subtilis according to their phenotype and 16SrRNA. The safety of the strains are also discussed.


1992 ◽  
Vol 58 (6) ◽  
pp. 2089-2092 ◽  
Author(s):  
J M Klingler ◽  
R P Stowe ◽  
D C Obenhuber ◽  
T O Groves ◽  
S K Mishra ◽  
...  

Plant Disease ◽  
2008 ◽  
Vol 92 (3) ◽  
pp. 483-483 ◽  
Author(s):  
G. F. Wang ◽  
K. Praphat ◽  
G. L. Xie ◽  
B. Zhu ◽  
B. Li ◽  
...  

In August of 2006, a new bacterial disease was noted in Hangzhou mulberry orchards of Zhejiang Province, China where bacterial wilt of mulberry caused by Ralstonia solanacearum was previously reported (3). In the summer, the disease caused severe wilt, especially on 1- or 2-year-old mulberry plants, that resulted in premature plant death. Leaf wilt symptoms generally started on older leaves at the bottom of the plant and spread to the younger leaves. The leaves of infected plants became withered and dry, turned dark brown, and eventually the plants became defoliated. The root xylem of infected plants was moist and discolored with brown stripes. The phloem was asymptomatic, however, in severe infections, the phloem was decayed. The observation of wilting proceeding from the bottom of the plant to the top distinguishes this disease from bacterial wilt caused by R. solanacearum. Five bacterial strains isolated from infected mulberry plants showed characteristics similar to those of the standard reference strain of Enterobacter cloacae subsp. cloacae IBJ0611from China, but differed from R. solanacearum IBJ35, E. cancerogenus LMG2693T, and E. cloacae subsp. dissolvens LMG2683T from the University of Gent, Belgium in phenotypic tests, including the Biolog Identification System version 4.2 (Biolog Inc., Hayward CA), pathogenicity tests, transmission electron microscopy (TEM,KYKY-1000B, Japan) observation, and gas chromatographic analysis of fatty acid methyl esters (FAMEs) using the Microbial Identification System (MIDI Company, Newark, DE) with the aerobic bacterial library (TABA50). Isolates were gram negative, facultative anaerobic, rod shaped, 0.3 to 1.0 × 1.0 to 3.0 μm with peritrichous flagella. Colonies on nutrient agar were light yellow, smooth, circular, entire, and convex with no green fluorescent diffusible pigment on King's medium B (3). Weak hypersensitive reaction was observed on tobacco 3 days after inoculation. All five strains were identified as E. cloacae with Biolog similarity of 0.662 to 0.863 and FAMEs similarity of 0.632 to 0.701. Inoculation of 10 6-month-old intact mulberry plants of cv Husang with cell suspensions containing 109 CFU/ml by pinprick at the base of the stem reproduced symptoms observed in natural infections. No symptoms were noted on the two control plants inoculated by the same method but with sterilized distilled water. The bacterium was reisolated from the symptomatic mulberry plants. E. cloacae has been reported from the United States as the cause of internal yellowing of papaya fruits (1) and rhizome rot of edible ginger (2). To our knowledge, this is the first report of mulberry wilt caused by E. cloacae in China. References: (1) K. Nishijima et al. Plant Dis. 71:1029, 1987. (2) K. Nishijima et al. Plant Dis. 88:1318, 2004. (3) L. Xu et al. Acta Phytophylacica. Sin. 34:141, 2007.


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