Journal of Microbiology

Journal Articles

Sequence Analysis of the Gene Encoding H Antigen in Escherichia coli Isolated from Food in Morocco: Samira Badri , Aziz Fassouane , Ingrid Filliol , Mohammed Hassar , Nozha Cohen; J. Microbiol. 2010;48(2):184-187. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-9182-1

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Abstract: In order to develop other molecular method useful for typing of motile and non motile Escherichia coli strains, a total of 207 strains of E. coli (133 reference strains, 74 food strains) were characterized by analysis of sequences of their amplified flagellin-encoding (fliC) gene products. The collection of reference strains was used for database building of fliC gene sequences. Application of this identification system to 74 E. coli food isolates revealed a reproducible and clear cut classification with very good correlation to results obtained by HhaI restriction of the amplified flagellin gene. The proposed determination of fliC sequences variations should be helpful for epidemiological studies.

Targeting the rpoB Gene Using Nested PCR-Restriction Fragment Length Polymorphism for Identification of Nontuberculous Mycobacteria in Hospital Tap Water: Ji-Hyun Shin , Hae-Kyung Lee , Eun-Jin Cho , Jae-Yon Yu , Yeon-Ho Kang; J. Microbiol. 2008;46(6):608-614. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0102-6

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Abstract: Nontuberculous mycobacteria (NTM) are ubiquitous in the environment and can cause nosocomial infections in immunocompromised patients. Recently the presence of NTM in public drinking water and hospital water distribution systems has been reported. Their ability to form biofilms and their resistance to chlorine both contribute to their survival and colonization in water distribution systems. Here we analyzed thirty-two hospital tap water samples that were collected from different locations in three hospitals so as to evaluate the prevalence of NTM species. The water samples were concentrated by membrane filtration and then eluted with sterilized water following sonication. Two-step direct PCR targeting the rpoB gene, restriction fragment length polymorphism (RFLP) using the MspI restriction enzyme, and sequence analysis were performed for identification of NTM to the species level. The sequences of each PCR product were analyzed using BLASTN. Seven samples (7/32, 21.9%) were positive for NTM as determined by nested-PCR. The PCR-RFLP results indicated five different patterns among the seven positive PCR samples. The waterborn NTM were identified, including M. peregrinum, M. chelonae (2 cases), M. abscessus, M. gordonae (2 cases), and Mycobacterium sp. JLS. The direct two-step PCR-RFLP method targeting the rpoB gene was effective for the detection and the differentiation of NTM species from hospital tap water.

Variation of the Intergenic Spacer (IGS) Region of Ribosomal DNA among Fusarium oxysporum formae speciales: Hyun-Jung Kim , Yong-Keel Choi , Byung-Re Min; J. Microbiol. 2001;39(4):265-272.

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Abstract: Variation within the intergenic spacer (IGS) of the ribosomal DNA gene for twenty-two strains of F. oxysporum and its formae speciales was examined by PCR, coupled with RFLP analysis. The length of the amplified IGS region was about 2.6 kb in all strains except F. oxysporum f. sp. cucumerinum from Korea and F. oxysporum f. sp. niveum. Those two strains were 2.5 kb long. Restriction digestion of IGS-RFLP regions by EcoRI, NruI, HincII, SalI, SmaI, BglII, HindIII, XhoI, and KpnI gave rise to nine IGS haplotypes among all strains. Cluster analysis based on the presence or absence of comigrating restriction fragments show the two groups based on 44% genetic similarity. These results demonstrated that analysis of IGS showed some difference within and between F. oxysporum formae speciales.

PCR-Based RFLP Analysis of ureC Gene for Typing of Indian Helicobacter pylori Strains from Gastric Biopsy Specimens and Culture: Kanchan Kumar Mishra , Shashikant Srivastava , Prabhat P. Dwivedi , Kashi Nath Prasad , Archana Ayyagari; J. Microbiol. 2002;40(4):282-288.

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Abstract: Since culture of Helicobacter pylori is relatively insensitive and cumbersome, molecular detection and typing of H. pylori isolates are gaining importance for strain differentiation. In the present study genomic DNA of 42 gastric biopsies and H. pylori isolates from corresponding patients were analyzed and compared by PCR-based RFLP assay. The 1,132-bp product representing an internal portion of ureC gene of H. pylori was amplified by PCR and digested with restriction enzymes HindIII, AluI and PvuI. The HindIII, AluI and PvuI digestion produced 4, 7, and 2 distinguishable RFLP patterns respectively from 42-H. pylori isolates. By combining all three restriction enzyme digestions, 15 RFLP patterns were observed. However, when PCR products from 42 gastric biopsy specimens were digested by restriction enzymes HindIII, AluI and PvuI, we observed 5, 8 and 2 RFLP patterns, respectively. Patterns from 34 of 42 gastric biopsy specimens matched those of corresponding H. pylori isolates from respective patients. Patterns from the remaining eight biopsy specimens differed and appeared to represent infection with two H. pylori strains. The patterns of one strain from each of these biopsies was identical to that of the isolate from corresponding patients and the second pattern presumably represented the co-infecting strain. From the study, it appears that PCR-based RFLP analysis is a useful primary tool to detect and is distinguish H. pylori strains from gastric biopsy specimens and is superior to culture techniques in the diagnosis of infection with multiple strains of H. pylori.

PCR-DGGE and PCR-RFLP Analyses of the Internal Transcribed Spacer (ITS) of Ribosomal DNA in the Genus Rhizopus: You-Jung Park , Yong-Keel Choi , Byung-Re Min; J. Microbiol. 2003;41(2):157-160.

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Abstract: To estimate genetic relationships within the genus Rhizopus, genetic variations in 20 strains were investigated by DGGE and PCR-RFLP of rDNA ITS region (ITS1, ITS2, 5.8S). The size of the amplified products showed the interspecific polymorphisms, 650 bp, 700 bp, and 900 bp. The DGGE approach allowed the separation of PCR amplicons of the same length according to their sequence variations. When the rDNA ITS region was digested with six restriction enzymes, 20 strains were classified into five RFLP haplotypes. The range of similarity between the 20 strains by PCR-RFLP was 42.3-100%. Based on the results of DGGE and PCR-RFLP, the 20 strains were divided into four groups, R. oryzae, R. stolonifer, R. microsporus and R. homothallicus. Further study of R. homothallicus is required.

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