PubMed · 12375442
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Haruo Watanabe, Jun Terajima, Hidemasa Izumiya, Sunao Iyoda. 2003. Molecular typing methods for STEC.. https://doi.org/10.1385/1-59259-316-x%3A55
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Two novel aerobic bacterial strains, designated SGZ-38T and sgz301269T, were isolated from the root of Pennisetum sp. and paddy soil, respectively. Strain SGZ-38T grew at 10-40 ℃ (optimum 30 °C) and pH 5.0-12.0 (optimum 6.5) and tolerated up to 1.0% NaCl (w/v), whereas strain sgz301269T grew at 15-37 °C (optimum 30 °C), pH 5.0-9.5 (optimum 7.0) and 0-2% NaCl (optimum 0%). Phylogenetic trees based on the 16S rRNA gene and genomes placed both strains into distinct lineages, forming separated clades from their closest relatives. Strain SGZ-381T exhibited the highest 16S rRNA gene similarities to "Neorhizobium deserti" ACCC 61627T (97.4%), and strain sgz301269T had the highest 16S rRNA gene sequence similarity to Neotabrizicola shimadae N10T (97.6%). The respiratory quinone in both strains was ubiquinone-10. The main fatty acids of SGZ-381T were Summed feature 8, Summed feature 2 and C16:0, whereas strain sgz301269T included C10:0 3OH, C18:0 3OH and Summed feature 8. The DNA G+C content of SGZ-381T and sgz301269T was 62.1% and 65.5%, respectively. The average nucleotide identity and digital DNA-DNA hybridization values between each strain and their respective closest species were 74.6% and 20.1%, 75.3% and 17.4% respectively, below the thresholds for species delineation. Based on the comprehensive chemotaxonomic, phylogenetic, and phenotypic evidence, proposed names of the novel strains are Neorhizobium fuzhouense sp. nov. (type strain SGZ-381T=GDMCC1.4207T=JCM 36770T), Neotabrizicola paludis sp. nov. (type strain sgz301269T=MCCC 1K09178T=KCTC 8856T).
To evaluate the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying Staphylococcus aureus and in determining its methicillin resistance, we analyzed 76 S. aureus clinical isolates using a linear MALDI-TOF MS. Spectral profile data obtained were compared with the database provided with the instrument, and 74% of the isolates were identified as S. aureus, as confirmed by a nuc-based PCR test. The determination of the methicillin resistance in S. aureus is based on the fact that the spectral profiles of methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) differ greatly from each other. Replicate spectral profiles obtained from each isolate were combined to be a representative spectrum of it, and representative spectral profiles from all the isolates constitute a user's self-established database. All the spectral profiles in the database were classified into two groups based on clustering analysis, and one is for MSSA and another MRSA. There was a little discrepancy between the results from MALDI-TOF MS and from PCR. Seven isolates that are negative for the mecA gene by PCR were identified as MRSA by MALDI-TOF MS. The discrepancy may be partially explained by the heterogeneous nature of methicillin resistance in S. aureus. Our results suggested that comparison of MALDI-TOF MS spectral profiles of microorganism could serve as a simple and rapid method for bacterial identification and antibiotic susceptibility analysis.
OBJECTIVE: To investigate the presence of Alloiococcus otitidis (A. otitidis) in MEEs from patients with otitis media with effusion (OME) using PCR and to correlate the findings with the clinical picture of children with OME for assessing the clinical role of A. otitidis in OME. METHODS: Bacterial culture and PCR were used to detect A. otitidis, Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis in MEE samples from 123 patients with OME. The culture and PCR results and the clinical picture of the patients were compared. RESULTS: Bacteria were cultured in 55 (45%) of the 123 MEEs, and major pathogens (S. pneumoniae, H. influenzae and M. catarrhalis) were found in 40 (33%); A. otitidis was not found in culture. PCR of the MEEs yielded positive results for one or more of the four tested pathogens in 108 (88%) of the samples and 25 (20%) were positive for A. otitidis. The effusions that persisted 3 months or longer had a higher prevalence of A. otitidis than those with shorter durations (P=0.03). A. otitidis was found to be more often positive in PCR in mucoid MEEs than in mucoserous MEEs (30 vs. 9%; P=0.015). CONCLUSIONS: While A. otitidis is extremely difficult to detect with bacterial culture, PCR provides a sensitive and specific means for detecting it. A. otitidis is associated with a more prolonged course and mucoid MEEs in OME. Thus, its existence seems to be related to a more chronic stage of OME, but its pathogenic potential should be the subject of further investigation.