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      • Oral intake of Lactobacillus rhamnosus M21 enhances the survival rate of mice lethally infected with influenza virus

        Song, J.A.,Kim, H.J.,Hong, S.K.,Lee, D.H.,Lee, S.W.,Song, C.S.,Kim, K.T.,Choi, I.S.,Lee, J.B.,Park, S.Y. Chinese Society of Microbiology ; Chinese Society 2016 Journal of microbiology, immunology and infection Vol.49 No.1

        <P>Background: Influenza viruses cause acute respiratory disease. Because of the high genetic variability of viruses, effective vaccines and antiviral agents are limited. Considering the fact that the site of influenza virus entry is the mucosa of the upper respiratory tract, probiotics that can enhance mucosal immunity as well as systemic immunity could be an important source of treatment against influenza infection. Methods: Mice were fed with Lactobacillus rhamnosus M21 or skim milk and were challenged with influenza virus. The resulting survival rate, lung inflammation, and changes in the cytokine and secretory immunoglobulin A (sigA) levels were examined. Results: Because of infection (influenza virus), all the mice in the control group and 60% of the mice in the L. rhamnosus M21 group died; however, the remaining 40% of the mice fed with L. rhamnosus M21 survived the infection. Pneumonia was severe in the control group but moderate in the group treated with L. rhamnosus M21. Although there were no significant changes in the proinflammatory cytokines in the lung lysates of mice collected from both groups, levels of interferon-y and interleukin-2, which are representative cytokines of type I helper T cells, were significantly increased in the L. rhamnosus M21-treated group. An increase in sigA as well as the diminution of inflammatory cells in bronchoalveolar lavage fluid was also observed in the L. rhamnosus M21-treated group. Conclusion: These results demonstrate that orally administered L. rhamnosus M21 activates humoral as well as cellular immune responses, conferring increased resistance to the host against influenza virus infection. Copyright (C) 2014, Taiwan Society of Microbiology. Published by Elsevier Taiwan LLC. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/</P>

      • Integrating genomics into the taxonomy and systematics of the <i>Bacteria</i> and <i>Archaea</i>

        Chun, Jongsik,Rainey, Fred A. International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.2

        <P>The polyphasic approach used today in the taxonomy and systematics of the <I>Bacteria</I> and <I>Archaea</I> includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the <I>Bacteria</I> and <I>Archaea</I> coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of <I>International Journal of Systematic and Evolutionary Microbiology</I> contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.</P>

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      • PCR-Reverse Blot Hybridization Assay for Screening and Identification of Pathogens in Sepsis

        Choi, Yeonim,Wang, Hye-Young,Lee, Gyusang,Park, Soon-Deok,Jeon, Bo-Young,Uh, Young,Kim, Jong Bae,Lee, Hyeyoung American Society for Microbiology 2013 Journal of clinical microbiology Vol.51 No.5

        <P>Rapid and accurate identification of the pathogens involved in bloodstream infections is crucial for the prompt initiation of appropriate therapy, as this can decrease morbidity and mortality rates. A PCR-reverse blot hybridization assay for sepsis, the reverse blot hybridization assay (REBA) Sepsis-ID test, was developed; it uses pan-probes to distinguish Gram-positive and -negative bacteria and fungi. In addition, the assay was designed to identify bacteria and fungi using six genus-specific and 13 species-specific probes; it uses additional probes for antibiotic resistance genes, i.e., the <I>mecA</I> gene of methicillin-resistant <I>Staphylococcus aureus</I> (MRSA) and the <I>vanA</I> and <I>vanB</I> genes of vancomycin-resistant enterococci (VRE). The REBA Sepsis-ID test successfully identified clinical isolates and blood culture samples as containing Gram-positive bacteria, Gram-negative bacteria, or fungi. The results matched those obtained with conventional microbiological methods. For the REBA Sepsis-ID test, of the 115 blood culture samples tested, 47 (40.8%) and 49 (42.6%) samples were identified to the species and genus levels, respectively, and the remaining 19 samples (16.5%), which included five Gram-positive rods, were identified as Gram-positive bacteria, Gram-negative bacteria, or fungi. The antibiotic resistances of the MRSA and VRE strains were identified using both conventional microbiological methods and the REBA Sepsis-ID test. In conclusion, the REBA Sepsis-ID test developed for this study is a fast and reliable test for the identification of Gram-positive bacteria, Gram-negative bacteria, fungi, and antibiotic resistance genes (including <I>mecA</I> for MRSA and the <I>vanA</I> and <I>vanB</I> genes for VRE) in bloodstream infections.</P>

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        Performance of a Novel Fluorogenic Assay for Detection of Carbapenemase-Producing <i>Enterobacteriaceae</i> from Bacterial Colonies and Directly from Positive Blood Cultures

        Kim, Hoon Seok,Kim, Jung Ok,Lee, Ji Eun,Park, Kang Gyun,Lee, Hae Kyung,Kim, Soo-Young,Min, Sun-Joon,Kim, Juhyeon,Park, Yeon-Joon American Society for Microbiology 2019 Journal of clinical microbiology Vol.58 No.1

        <P>Rapid and accurate detection of carbapenemase-producing <I>Enterobacteriaceae</I> (CPE) is critical for appropriate treatment and infection control. We compared a rapid fluorogenic assay using a carbapenem-based fluorogenic probe with other phenotypic assays: modified carbapenem inactivation method (mCIM), Carba NP test (CNP), and carbapenemase inhibition test (CIT).</P><P>Rapid and accurate detection of carbapenemase-producing <I>Enterobacteriaceae</I> (CPE) is critical for appropriate treatment and infection control. We compared a rapid fluorogenic assay using a carbapenem-based fluorogenic probe with other phenotypic assays: modified carbapenem inactivation method (mCIM), Carba NP test (CNP), and carbapenemase inhibition test (CIT). A total of 217 characterized isolates of <I>Enterobacteriaceae</I> were included as follows: 63 CPE; 48 non-carbapenemase-producing carbapenem-resistant <I>Enterobacteriaceae</I> (non-CP-CRE); 53 extended-spectrum β-lactamase producers; and 53 third-generation-cephalosporin-susceptible isolates. The fluorogenic assay using bacterial colonies (Fluore-C) was conducted by lysing the isolates followed by centrifugation and mixing the supernatant with fluorogenic probe. In addition, for the fluorogenic assay using spiked blood culture bottles (Fluore-Direct), pellets were obtained via the saponin preparation method, which can directly identify the pathogens using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). The fluorescence signal was measured over 50 min using a fluorometer. The fluorescent signal of CPE was significantly higher than that of non-CPE in both Fluore-C (median relative fluorescence units [RFU] [range], 5,814 [240 to 32,009] versus 804 [36 to 2,480], respectively; <I>P < </I>0.0001) and Fluore-Direct (median RFU [range], 10,355 [1,689 to 31,463] versus 1,068 [428 to 2,155], respectively; <I>P < </I>0.0001) tests. Overall, positive and negative percent agreements of Fluore-C, mCIM, CNP, CIT, and Fluore-Direct were 100% and 98.7%, 98.3% and 97.5%, 88.1% and 100%, 96.4% and 98.7%, and 98.3% and 98.1%, respectively. The relatively lower positive percent agreement (PPA) of CNP was mainly observed in OXA-type CPE. The fluorogenic assay showed excellent performance with bacterial colonies and also directly from positive blood cultures. We included many non-CP-CRE isolates for strict evaluation. The fluorogenic assay will be a useful tool for clinical microbiology laboratories.</P>

      • Virulence factors of uropathogenic Escherichia coli of urinary tract infections and asymptomatic bacteriuria in children

        Yun, K.W.,Kim, H.Y.,Park, H.K.,Kim, W.,Lim, I.S. Chinese Society of Microbiology ; Chinese Society 2014 Journal of microbiology, immunology and infection Vol.47 No.6

        Background/Purpose: The clinical aspects of virulence genes of uropathogenic Escherichia coli (UPEC) are not fully understood. This study compared the presence of virulence genes in UPEC isolated from urinary tract infections (UTIs) and asymptomatic bacteriuria (ABU) in children. Methods: The study included children with UTI (n = 15) or ABU (n = 49) treated at Chung-Ang University Yongsan Hospital between 2010 and 2011. The strains were acquired from each urine sample collected, and 18 major virulence genes were detected by polymerase chain reaction. Antimicrobial susceptibility of all UPEC isolates was determined. Results: Sixty-four E. coli strains were isolated from the urine samples. The most commonly identified virulence gene in both groups was fimH (100.0% in the UTI group and 95.9% in the ABU group). The UTI isolates showed a higher prevalence of papEF and fyuA, and a lower prevalence of feoB than ABU isolates (p < 0.01 for all). The profile of virulence gene, fimH<SUP>+</SUP>kpsMTII<SUP>+</SUP>feoB<SUP>+</SUP> also showed a significant difference between the two groups (p < 0.01). Isolates from ABU were more resistant to most antimicrobials tested. The presence of papEF, feoB, and fyuA also correlated with the antimicrobial susceptibility of UPEC. Conclusion: The virulence gene repertoire was different in the UPEC of UTI and ABU. The papEF, feoB, and fyuA genes showed meaningful differences between the two groups and may have an important role in the pathogenesis of overt UTI.

      • Mapping of the proinflammatory domains of MspTL of Treponema lecithinolyticum

        Jun, Hye-Kyoung,Lee, Hae-Ri,Lee, Sung-Hoon,Choi, Bong-Kyu Microbiology Society 2007 Microbiology Vol.153 No.8

        <P>The major surface protein (MspTL) of Treponema lecithinolyticum, associated with periodontitis and endodontic infections, has been reported to induce proinflammatory mediators such as intercellular adhesion molecule (ICAM)-1, and interleukin (IL)-1beta, IL-6 and IL-8. The purpose of this study was to examine the role of MspTL in cell adhesion/migration and to identify its proinflammatory domains. Using the human monocytic cell line THP-1 and human dermal microvascular endothelial cells (HMEC-1), it was demonstrated that MspTL increased adhesion of monocytes to endothelial cells and transendothelial migration. To analyse the proinflammatory domains of the protein, four gene constructs covering different regions of MspTL were designed and expressed in Escherichia coli using the expression vector pQE-30. Histidine-tagged recombinant proteins were purified using Ni-NTA agarose and polymyxin B agarose to remove LPS contamination. Recombinant truncated polypeptides were assessed for the ability to induce ICAM-1 and proinflammatory factors in THP-1 cells by real-time RT-PCR and ELISA. Of the four polypeptides, the one spanning the N-terminal 86 amino acids significantly induced ICAM-1, IL-1beta, IL-6, IL-8, tumour necrosis factor-alpha (TNF-alpha), cyclooxygenase (COX)-2, and prostaglandin E2 (PGE2). The results indicate that MspTL may induce cell adhesion and inflammation via its N-terminal region.</P>

      • Sphingobacterium daejeonense sp. nov., isolated from a compost sample.

        Kim, Kyoung-Ho,Ten, Leonid N,Liu, Qing-Mei,Im, Wan-Taek,Lee, Sung-Taik Society for General Microbiology 2006 International journal of systematic and evolutiona Vol.56 No.9

        <P>A Gram-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-04(T), was isolated from compost and characterized taxonomically by using a polyphasic approach. The organism grew optimally at 30 degrees Celsius and at pH 6.5-7.0. The isolate was positive for catalase and oxidase tests but negative for gelatinase, indole and H(2)S production. Comparative 16S rRNA gene sequence analysis showed that strain TR6-04(T) fell within the radiation of the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii ATCC 33299(T) (96.7 % sequence similarity); the similarity to sequences of other species within the family Sphingobacteriaceae was less than 92.0 %. The G+C content of the genomic DNA was 38.7 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH and summed feature 4 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c). These chemotaxonomic data supported the affiliation of strain TR6-04(T) to the genus Sphingobacterium. However, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain TR6-04(T) (=KCTC 12579(T)=LMG 23402(T)=CCUG 52468(T)) should be classified as the type strain of a novel species, for which the name Sphingobacterium daejeonense sp. nov. is proposed.</P>

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