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1.
Article in English | WPRIM | ID: wpr-311386

ABSTRACT

<p><b>OBJECTIVE</b>In this study, milk from a cow with mastitis was analyzed to determine the presence of mycobacterial infection. Milk quality and security problems pertaining to the safe consumption of dairy products were also discussed in this study.</p><p><b>METHODS</b>Milk was preprocessed with 4% NaOH. Then, mycobacteria were isolated from the milk sample on L-J medium. The isolate was identified using multiple loci Polymerase Chain Reaction (PCR) and multi-locus sequence analysis with 16S rRNA, sodA, hsp65, and ITS genes. The drug sensitivity of the isolate to 27 antibiotics was tested through alamar blue assay.</p><p><b>RESULTS</b>Smooth, moist, pale yellow colonies appeared on the L-J medium within a week after inoculation. Based on the results of multiple loci PCR analysis, the isolate was preliminarily identified as non-tuberculous mycobacteria. The 16S rRNA, SodA, hsp65, and ITS gene sequences of the isolate exhibited 99%, 99%, 99%, and 100% similarities, respectively, with those of the published reference strains of Mycobacterium elephantis (M. elephantis). The drug sensitivity results showed that the strain is resistant to isoniazid, p-aminosalicylic acid, and trimesulf but is sensitive to ofloxacin, rifampicin, amikacin, capreomycin, moxifloxacin, kanamycin, levofloxacin, cycloserine, ethambutol, streptomycin, tobramycin, rifabutin, ciprofloxacin, linezolid, cefoxitin, clarithromycin, and minocycline.</p><p><b>CONCLUSION</b>To the best of our knowledge, this study is initially to report the isolation of M. elephantis from the milk of a cow with mastitis in China.</p>


Subject(s)
Animals , Anti-Bacterial Agents , Pharmacology , Cattle , China , Drug Resistance, Bacterial , Female , Mastitis, Bovine , Epidemiology , Microbiology , Milk , Microbiology , Mycobacterium , Genetics , Mycobacterium Infections , Epidemiology , Microbiology , Phylogeny , Polymerase Chain Reaction
2.
Chinese Journal of Endemiology ; (6): 476-481, 2012.
Article in Chinese | WPRIM | ID: wpr-642843

ABSTRACT

Objective To study the single nucleotide polymorphisms (SNP) characteristics of Yersinia pestis strains from different natural foci in China.Methods Genome-wide comparison was done to find SNP sites by the Mummer program among 9 Yersinia pestis genome which was downloaded from NCBI.Then 13 genic fragments including 19 SNP sites were amplified by PCR and sequenced in 133 Yersinia pestis strains,and the results were cluster analyzed with the BioNumerics software.Results Three thousand seven hundred and eighty sequence variation sites were found by genome-wide comparison.Using the different combinations of SNP sites,UPGMA cluster analysis revealed obvious geographic regional and eco-aggregation characteristics of Yersinia pestis strains isolated from China.Conclusions As relatively stable genetic markers,SNP can better reflect the genome characteristics of Yersinia pestis in different plague natural foci of China.

3.
Chinese Journal of Endemiology ; (6): 476-480, 2011.
Article in Chinese | WPRIM | ID: wpr-642946

ABSTRACT

Objective Measurement and analysis of the complete genome sequences of Yersinia Pestis from a new plague natural foci and adjacent foci in China, to know the genetic relationship among the epidemic strain isolated in Yulong (D 106004) and Jianchuan strains (D 182038) and the Tibetan strain ( Z 176003 ). Methods Three complete genome sequences were sequenced using the whole-genome shotgun and Solexa method and comparative genomics analysis was done among the three sequences. Genome comparative analysis among the coding sequences was done by BLAST software, SNPs finding was done by the program, genome rearrangements were analyzed using MAUVE software. Results All of the genomes of Yersinia pestis strains D182038, D106004 and Z176003 consist of a single circular chromosome and three virulence plasmids, pMT1, pCD1 and pPCP1. They had similar characteristics in chromosome and plasmid features, and there were no significant difference in coming sequence (CDS) of the cluster of orthologous groups of proteins (COG) functional classification and the number of insertion sequence in the three strains (x2 =3.03, 0.257, all P > 0.05). The comparative genomics results showed that the three bacteria had 2882 genes with 100% homology, of 3636 genes predicted in D106004, 2994 were identical with D182038's and 3113 with Z176003's, and of which 240 had 90% homology with D182038's and 200 with Z176003 's. Synonymous single nucleotide polymorphisms(sSNPs) were 59 and 68, and non-synonymous SNPs(nsSNPs) were 104 and 203 between strains D106004 and Z176003/D182038. There were 11 segments rearrangements between D106004 and Z176003, which was less than 16 segments rearrangements between D106004 and D182038. ConclusionsThe three strains are highly homologous, the Yulong strain has more similarity with Tibet strain than with Jianchuan strain, the strain from Yulong foci may be evolved from Tibet foci.

4.
Chinese Journal of Epidemiology ; (12): 366-369, 2011.
Article in Chinese | WPRIM | ID: wpr-273184

ABSTRACT

Objective To study the identification characteristics of rRNA genes on Yersinia (Y.)pestis.Methods By means of comparative genomics,we compared the rRNA genome sequences of nine completely sequenced strains of Y. pestis isolated from China and other countries by Clustal W software.we also compared the 2000 bp sequence adjacent to the rRNA genes,rRNA genes and 16S-23S rRNA spacer region respectively to determine the identification features of rRNA genes for Y. pestis.Results There were 6 rRNA gene clusters in the strains of D182038,D106004,Z176003 and CO92 respectively(6 copies strain).There were 7 rRNA gene clusters in the strains of 91001,KIM,Nepa1516,Antiqua and Pestoides F(7 copies strain).According to the 2000 bp sequence,13 types of rRNA gene clusters could classify the strains between the 6 copies and 7 copies.There were 4 types of tRNA gene among the 16S-23S rRNA spacer region that could classify the strains among the 6 copies and 7 copies strains respectively.The number of point mutation among the 23S rRNA gene was statistically different in some copies under ANOVA analysis(F=0.548,P=0.815>0.05 among the strains and F=5.228,P<0.01 among the copies).Conclusion The 2000 bp sequence adjacent to the rRNA genes,tRNA gene and 23S rRNA gene sequence could serve as the identification sign of rRNA genes for classifing the strains of Y. pestis.

5.
Article in Chinese | WPRIM | ID: wpr-242640

ABSTRACT

<p><b>OBJECTIVE</b>To investigate the molecular characteristics of phage-type 6b isolates emerging in 1998-2001 cholera epidemics in Sichuan province.</p><p><b>METHODS</b>Isolates were analyzed by phage-typing, pulsed field gel electrophoresis (PFGE) and ompW gene sequencing.</p><p><b>RESULTS</b>All phage-type 1b and 6b isolates in Sichuan province from 1998 to 2001 were toxigenic. A total of 24 patterns were identified after PFGE analysis, and one predominant pattern consisted of 13 isolates. Several 1b and 6b isolates from Sichuan and isolates of the 1b from other provinces showed the same PFGE pattern. Mutation in ompW gene was found in 6b isolates.</p><p><b>CONCLUSION</b>V.cholerae O1 6b isolates in Sichuan province from 1998 to 2001 have special genetic markers, and might genetically correlate with contemporaneous 1b isolates.</p>


Subject(s)
Bacterial Typing Techniques , Bacteriophage Typing , China , Epidemiology , Cholera , Epidemiology , Microbiology , DNA, Bacterial , Genetics , Electrophoresis, Gel, Pulsed-Field , Genes, Bacterial , Genotype , Vibrio cholerae , Classification , Genetics
6.
Chinese Journal of Endemiology ; (6): 598-601, 2008.
Article in Chinese | WPRIM | ID: wpr-643289

ABSTRACT

Objective To study the genotyping distribution of the Yersinia pestis(Y.pestis)strains by characterizing the diversity of the insertion sequence IS100 within the Y.pestis genome.Methods Derived fromthe known sequence of oriental strain CO92,5 pairs of locus-specific primers originating from both sides of the adjacent region of IS100 copies were designed,and two other complementary primers inside the IS100 sequence were designed to correspond with the outer primers.Then,91 Y.pestis strains and l pseudotubebculosis strain were tested by the specific PCR method using the primers described above and the PCR products were conformed by the sequence analysis,then further analysis WaS performed after the IS100 status was marked on the map of the plague focus type of china.Results The 91 Y.pestis strains had different IS100 status in their genome on tested loci.some possessed IS100 insertion,some didn't,and others changed their genome constitution.The IS100 possession on the 5 loci also suggested a distribution of regionality.Conclusion The analysis of some IS100 insertion element loci reveals that the IS100 genotyping distribution is consistent with the plague focus of type of China.And IS100genotyping pattern of the Y.pestis stains well reflects its genome constitution and the high flowability in its natural evolution.

7.
Chinese Journal of Endemiology ; (6): 326-328, 2008.
Article in Chinese | WPRIM | ID: wpr-642669

ABSTRACT

Objective To develop a rapid test for the detection of F1 antigen of Yersinia Pestis based on gold-immunochromatography.Methods F1 antibodies were coupled with colloidal gold to prepare collidal gold reagent,which was used to detect F1 antibodies based on double antigen sandwich.The collidal gold reagent was estimated for its sensitivity specificity and stablity in labs and 1798 samples were detected in 17 surveillance spots.Results The reagent was sensitive to 0.0010 g/L F1 antigens.The reagens kept stable when it had been placed at 4℃ or room-temperature for 12 months and did not react to Yersinia pseudotuberculosis and Yersinia enterolitica.In 17 surveillance labs the reagent was used to test 1798 viscera samples from animal.resulting an accordance rate of 97.11%(1746/1798)to bacterial culture and 96.83%(1741/1798)accordance to reverse indirect hemagglutination assay(RIHA),showing a higher detection rate[9.23%(166/1798)]compared with RIHA[6.79%(122/1798)]and bacterial culture[6.28%(113/1798)].Conclusions The collidal gold reagent,sensitive and specific in diagnosing Yersinia pestis infection of both human and animals,is a rapid method in surveillance spot.

8.
Chinese Journal of Epidemiology ; (12): 712-715, 2006.
Article in Chinese | WPRIM | ID: wpr-233888

ABSTRACT

<p><b>OBJECTIVE</b>To study the genotyping of Bacillus anthracis based on multiple-locus variable-number tandem repeats(VNTR) in the B. anthracis genome.</p><p><b>METHODS</b>We selected 13 VNTR loci (which cited from published articles) to study 88 strains of B. anthracis isolated from China. The methods used were: (1) Selecting the primers which were at both ends of the tandem repeat locus; (2) Amplifying the sequence of the locus by PCR; (3)cDetecting the PCR products by agarose gel and polyacrylamide electrophoresis; (4)Analyzing the PCR products and computing the molecular weight by analysis software of gel images;(5) Double-checking with sequencing results; (6)Reckoning the repeat numbers and study the VNTRs loci characters.</p><p><b>RESULTS</b>(1) We used multiple-locus variable-number tandem repeat analysis (MLVA) to characterize 88 B. anthracis isolates from diverse geographic locations which were divided into 45 MLVA genotypes and 3 groups through cluster analysis. The genotypes was relative to restricted geographical region. It seemed clear that the multiple isolates from the same anthrax outbreak frequently having identical genotypes. (2)Results from VNTR analysis showed that A16R vaccine strain isolated from China was having the nature of representativeness in the country.</p><p><b>CONCLUSION</b>Analysis showed that the VNTR patterns was an appropriate study method for B. anthracis genetic diversity from different geographical areas and different time. Isolates from the same anthrax outbreak had identical</p>


Subject(s)
Anthrax , Epidemiology , Genetics , Bacillus anthracis , Genetics , China , Epidemiology , Genetic Variation , Genotype , Geography , Polymerase Chain Reaction , Sequence Analysis, DNA , Tandem Repeat Sequences
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