Journal of Microbiology

Research Article

PneusPage: A WEB-BASED TOOL for the analysis of Whole-Genome Sequencing Data of Streptococcus pneumonia: Eunju Hong, Youngjin Shin, Hyunseong Kim, Woo Young Cho, Woo-Hyun Song, Seung-Hyun Jung, Minho Lee; J. Microbiol. 2025;63(1):e.2409020. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2409020

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Abstract PDF Supplementary Material: With the advent of whole-genome sequencing, opportunities to investigate the population structure, transmission patterns, antimicrobial resistance profiles, and virulence determinants of Streptococcus pneumoniae at high resolution have been increasingly expanding. Consequently, a user-friendly bioinformatics tool is needed to automate the analysis of Streptococcus pneumoniae whole-genome sequencing data, summarize clinically relevant genomic features, and further guide treatment options. Here, we developed PneusPage, a web-based tool that integrates functions for species prediction, molecular typing, drug resistance determination, and data visualization of Streptococcus pneumoniae. To evaluate the performance of PneusPage, we analyzed 80 pneumococcal genomes with different serotypes from the Global Pneumococcal Sequencing Project and compared the results with those from another platform, PathogenWatch. We observed a high concordance between the two platforms in terms of serotypes (100% concordance rate), multilocus sequence typing (100% concordance rate), penicillin-binding protein typing (88.8% concordance rate), and the Global Pneumococcal Sequencing Clusters (98.8% concordance rate). In addition, PneusPage offers integrated analysis functions for the detection of virulence and mobile genetic elements that are not provided by previous platforms. By automating the analysis pipeline, PneusPage makes whole-genome sequencing data more accessible to non-specialist users, including microbiologists, epidemiologists, and clinicians, thereby enhancing the utility of whole-genome sequencing in both research and clinical settings. PneusPage is available at https://pneuspage.minholee.net/.

Journal Articles

Hydroxychloroquine an Antimalarial Drug, Exhibits Potent Antifungal Efficacy Against Candida albicans Through Multitargeting: Sargun Tushar Basrani, Tanjila Chandsaheb Gavandi, Shivani Balasaheb Patil, Nandkumar Subhash Kadam, Dhairyasheel Vasantrao Yadav, Sayali Ashok Chougule, Sankunny Mohan Karuppayil, Ashwini Khanderao Jadhav; J. Microbiol. 2024;62(5):381-391. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00111-6

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Abstract: Candida albicans is the primary etiological agent associated with candidiasis in humans. Unrestricted growth of C. albicans can progress to systemic infections in the worst situation. This study investigates the antifungal activity of Hydroxychloroquine (HCQ) and mode of action against C. albicans. HCQ inhibited the planktonic growth and yeast to hyphal form morphogenesis of C. albicans significantly at 0.5 mg/ml concentration. The minimum inhibitory concentrations (MIC(50)) of HCQ for C. albicans adhesion and biofilm formation on the polystyrene surface was at 2 mg/ml and 4 mg/ml respectively. Various methods, such as scanning electron microscopy, exploration of the ergosterol biosynthesis pathway, cell cycle analysis, and assessment of S oxygen species (ROS) generation, were employed to investigate HCQ exerting its antifungal effects. HCQ was observed to reduce ergosterol levels in the cell membranes of C. albicans in a dose-dependent manner. Furthermore, HCQ treatment caused a substantial arrest of the C. albicans cell cycle at the G0/G1 phase, which impeded normal cell growth. Gene expression analysis revealed upregulation of SOD2, SOD1, and CAT1 genes after HCQ treatment, while genes like HWP1, RAS1, TEC1, and CDC 35 were downregulated. The study also assessed the in vivo efficacy of HCQ in a mice model, revealing a reduction in the pathogenicity of C. albicans after HCQ treatment. These results indicate that HCQ holds for the development of novel antifungal therapies.

Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil: Yong-Seok Kim , Eun-Mi Hwang , Chang-Myeong Jeong , Chang-Jun Cha; J. Microbiol. 2023;61(10):891-901. Published online October 18, 2023; DOI: https://doi.org/10.1007/s12275-023-00081-1

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Abstract

Two novel bacterial strains CJ74T and CJ75T belonging to the genus Flavobacterium were isolated from freshwater of Han River and ginseng soil, South Korea, respectively. Strain CJ74T was Gram-stain-negative, aerobic, rod-shaped, non-motile, and non-flagellated, and did not produce flexirubin-type pigments. Strain CJ75T was Gram-stain-negative, aerobic, rodshaped, motile by gliding, and non-flagellated, and produced flexirubin-type pigments. Both strains were shown to grow optimally at 30 °C in the absence of NaCl on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ74T and CJ75T belonged to the genus Flavobacterium and were most closely related to Flavobacterium niveum TAPW14T and Flavobacterium foetidum CJ42T with 96.17% and 97.29% 16S rRNA sequence similarities, respectively. Genomic analyses including the reconstruction of phylogenomic tree, average nucleotide identity, and digital DNA-DNA hybridization suggested that they were novel species of the genus Flavobacterium. Both strains contained menaquinone 6 (MK-6) as the primary respiratory quinone and phosphatidylethanolamine as a major polar lipid. The predominant fatty acids of both strains were iso-C15:0 and summed feature 3 ( C16:1 ω7c and/or C16: 1 ω6c). Based on the polyphasic taxonomic study, strains CJ74T and CJ75T represent novel species of the genus Flavobacterium, for which names Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov. are proposed, respectively. The type strains are CJ74T (=KACC 19819T =JCM 32889T) and CJ75T (=KACC 23149T =JCM 36132T).

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Discovery of two novel Flavobacterium species with potential for complex polysaccharide degradation
Xu-Dong Lian, Yong Guan, Yue Jiang, Dong-Heui Kwak, Mi-Kyung Lee, Zhun Li
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Ammonia-oxidizing activity and microbial structure of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and complete ammonia oxidizers in biofilm systems with different salinities
Haojie Qiu, Weihua Zhao, Yingying Qin, Yanyan Wang, Meng Bai, Shaoqing Su, Chao Wang, Zhisheng Zhao
Bioresource Technology.2025; 423: 132248. CrossRef
mKmer: an unbiased K-mer embedding of microbiomic single-microbe RNA sequencing data
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Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] CrossRef
Validation List no. 218. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
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Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum sp. nov., F. limnophilum sp. nov., F. lacustre: Hyunyoung Jo , Miri S. Park , Yeonjung Lim , Ilnam Kang , Jang-Cheon Cho; J. Microbiol. 2023;61(5):495-510. Published online May 23, 2023; DOI: https://doi.org/10.1007/s12275-023-00054-4

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Abstract

Eleven bacterial strains were isolated from freshwater environments and identified as Flavobacterium based on 16S rRNA gene sequence analyses. Complete genome sequences of the 11 strains ranged from 3.45 to 5.83 Mb with G + C contents of 33.41–37.31%. The average nucleotide identity (ANI) values showed that strains IMCC34515T and IMCC34518 belonged to the same species, while the other nine strains represented each separate species. The ANI values between the strains and their closest Flavobacterium species exhibited ≤ 91.76%, indicating they represent each novel species. All strains had similar characteristics such as being Gram-stain-negative, rod-shaped, and contained iso-C15:0 as the predominant fatty acid, menaquinone-6 as the respiratory quinone, and phosphatidylethanolamine and aminolipids as major polar lipids. Genomic, phylogenetic, and phenotypic characterization confirmed that the 11 strains were distinct from previously recognized Flavobacterium species. Therefore, Flavobacterium praedii sp. nov. (IMCC34515T = KACC 22282T = NBRC 114937T), Flavobacterium marginilacus sp. nov. (IMCC34673T = KACC 22284T = NBRC 114940T), Flavobacterium aestivum sp. nov. (IMCC34774T = KACC 22285T = NBRC 114941T), Flavobacterium flavigenum sp. nov. (IMCC34775T = KACC22286T = NBRC 114942T), Flavobacterium luteolum sp. nov. (IMCC34776T = KACC 22287T = NBRC 114943T), Flavobacterium gelatinilyticum sp. nov. (IMCC34777T = KACC 22288T = NBRC 114944T), Flavobacterium aquiphilum sp.nov. (IMCC34779T = KACC 22289T = NBRC 114945T), Flavobacterium limnophilum sp. nov. (IMCC36791T = KACC22290T = NBRC 114947T), Flavobacterium lacustre sp. nov. (IMCC36792T = KACC 22291T = NBRC 114948T), and Flavobacterium eburneipallidum sp. nov. (IMCC36793T = KACC 22292T = NBRC 114949T) are proposed as novel species.

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Indoor pollution of funeral homes and potential health risk of workers: A case study in central China
Jinjun Ye, Zhengtao Ai, Lup Wai Chew
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Leonor Matos, Lorrie Maccarrio, Ana Paula Chung, Diogo N. Proença, Søren Sørensen, Paula V. Morais, Romeu Francisco
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov
Izzet Burcin Saticioglu, Hilal Ay, Soner Altun, Nihed Ajmi, Enes Said Gunduz, Huban Gocmen, Muhammed Duman
Systematic and Applied Microbiology.2024; 47(4): 126518. CrossRef
Leuconostoc aquikimchii sp. nov., a Lactic Acid Bacterium Isolated from Cabbage Watery Kimchi
Subin Kim, Se Hee Lee, Ki Hyun Kim, Misun Yun
Journal of Microbiology.2024; 62(12): 1089. CrossRef
Overproduction of Xanthophyll Pigment in Flavobacterium sp. JSWR-1 under Optimized Culture Conditions
Jegadeesh Raman, Young-Joon Ko, Jeong-Seon Kim, Da-Hye Kim, Soo-Jin Kim
Journal of Microbiology and Biotechnology.2024; 34(3): 710. CrossRef
Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream
Sumin Kim, Miri S. Park, Ilnam Kang, Jang-Cheon Cho
Current Microbiology.2024;[Epub] CrossRef
Congregibacter variabilis sp. nov. and Congregibacter brevis sp. nov. Within the OM60/NOR5 Clade, Isolated from Seawater, and Emended Description of the Genus Congregibacter
Hyeonsu Tak, Miri S. Park, Hyerim Cho, Yeonjung Lim, Jang-Cheon Cho
Journal of Microbiology.2024; 62(9): 739. CrossRef
Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef

Transcriptome‑based Mining of the Constitutive Promoters for Tuning Gene Expression in Aspergillus oryzae: Kobkul Laoteng , Jutamas Anantayanon , Chanikul Chutrakul , Sarocha Panchanawaporn , Sukanya Jeennor; J. Microbiol. 2023;61(2):199-210. Published online February 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00020-0

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Abstract

Transcriptional regulation has been adopted for developing metabolic engineering tools. The regulatory promoter is a crucial genetic element for strain optimization. In this study, a gene set of Aspergillus oryzae with highly constitutive expression across different growth stages was identified through transcriptome data analysis. The candidate promoters were functionally characterized in A. oryzae by transcriptional control of β-glucuronidase (GUS) as a reporter. The results showed that the glyceraldehyde triphosphate dehydrogenase promoter (PgpdA1) of A. oryzae with a unique structure displayed the most robust strength in constitutively controlling the expression compared to the PgpdA2 and other putative promoters tested. In addition, the ubiquitin promoter (Pubi) of A. oryzae exhibited a moderate expression strength. The deletion analysis revealed that the 5' untranslated regions of gpdA1 and ubi with the length of 1028 and 811 nucleotides, counted from the putative translation start site (ATG), respectively, could efficiently drive the GUS expression. Interestingly, both promoters could function on various carbon sources for cell growth. Glucose was the best fermentable carbon source for allocating high constitutive expressions during cell growth, and the high concentrations (6–8% glucose, w/v) did not repress their functions. It was also demonstrated that the secondary metabolite gene coding for indigoidine could express under the control of PgpdA1 or Pubi promoter. These strong and moderate promoters of A. oryzae provided beneficial options in tuning the transcriptional expression for leveraging the metabolic control towards the targeted products.

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Construction of an Aspergillus oryzae △nptB△pyrG Host for Homologous Expression of Lipase and Catalytic Property Characterization of Recombinant Lipase
Yueting Zhang, Hongmei Nie, Fei Zhang, Mengmeng Jin, Zhao Wang, Jianyong Zheng
Applied Biochemistry and Biotechnology.2025; 197(2): 873. CrossRef
Transcriptome-Based Mining of the Strong Promoters for Hyperproduction of Gibberellin GA3 in Fusarium fujikuroi
Qi Guo, Yue-Feng Zhong, Xin-Yu Chen, Ya-Wen Li, Yu-Xin Yang, Zhi-Kui Nie, Tian-Qiong Shi
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Ying Zhang, Yunyang Ma, Bing Hu, H.M. Zabed, A.K. Singh, M.A. Ibrahim, N. Chen
BIO Web of Conferences.2024; 142: 03018. CrossRef
Development of Aspergillus oryzae BCC7051 as a Robust Cell Factory Towards the Transcriptional Regulation of Protease-Encoding Genes for Industrial Applications
Sarocha Panchanawaporn, Chanikul Chutrakul, Sukanya Jeennor, Jutamas Anantayanon, Kobkul Laoteng
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Exploring and Engineering Novel Strong Promoters for High-Level Protein Expression in Bacillus subtilis DB104 through Transcriptome Analysis
Ji-Su Jun, Hyang-Eun Jeong, Kwang-Won Hong
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Sukanya Jeennor, Jutamas Anantayanon, Sarocha Panchanawaporn, Chanikul Chutrakul, Wanwipa Vongsangnak, Kobkul Laoteng
Microbial Cell Factories.2023;[Epub] CrossRef

Two novel synthetic peptides inhibit quorum sensing-dependent biofilm formation and some virulence factors in Pseudomonas aeruginosa PAO1: Mostafa N. Taha , Amal E. Saafan , A. Ahmedy , Eman El Gebaly , Ahmed S. Khairalla; J. Microbiol. 2019;57(7):618-625. Published online June 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8548-2

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Abstract

Quorum sensing (QS) regulates virulence factor expression in Pseudomonas aeruginosa. Inhibiting the QS-controlled virulence factors without inhibiting the growth of P. aeruginosa is a promising approach for overcoming the widespread resistance of P. aeruginosa. This study was proposed to investigate the effects of two novel synthetic peptides on the biofilm development and virulence factor production of P. aeruginosa. The tested strain was P. aeruginosa PAO1. The results indicated that both of the synthetic peptides (LIVRHK and LIVRRK) inhibited (P < 0.05) the formation of biofilms and the production of virulence factors, including pyocyanin, protease, and rhamnolipids, without inhibiting the growth of PAO1. Additionally, we detected transcriptional changes related to QS and found a significant reduction in the levels of gene expression of lasI, lasR, rhlI, and rhlR. This study demonstrates that LIVRRK and LIVRHK are novel synthetic peptides that can act as potent inhibitors of QS-regulated virulence factors in P. aeruginosa. Moreover, these synthetic peptides have potential applications in the treatment of biofilmrelated diseases. Both peptides may be able to control chronic infections and biofilm-associated problems of P. aeruginosa.

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Li Li, Jiaxin Li, Xiaodan Yu, Ruipin Cao, Meiling Hong, Zuxian Xu, Jian Ren Lu, Yinglu Wang, Hu Zhu
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The Role of Quorum Sensing Molecules in Bacterial–Plant Interactions
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Role of putative virulence traits of Campylobacter jejuni in regulating differential host immune responses: Ankita Singh , Amirul Islam Mallick; J. Microbiol. 2019;57(4):298-309. Published online February 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8165-0

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Abstract

Among the major enteric pathogens, Campylobacter jejuni is considered an important source of diarrheal illness in humans. In contrast to the acute gastroenteritis in humans, C. jejuni exhibits prolonged cecal colonization at a high level with little or no pathology in chickens. Although several known virulence determinants of C. jejuni have been found to be associated with a higher degree of pathogenesis in humans, to date, little is known about their functions in the persistent colonization of chickens. The present study was undertaken to assess the role of C. jejuni in imparting differential host immune responses in human and chicken cells. Based on the abundance of major genes encoding virulence factors (GEVFs), we used a particular isolate that harbors the cadF, flaA, peb1, racR, ciaB, cdtB, and hcp genes. This study showed that hypervirulent C. jejuni isolate that encodes a functional type VI secretion system (T6SS) has a greater ability to invade and create characteristic “attaching and effacing” lesions in human INT407 compared to primary chicken embryo intestinal cells (CEICs). Furthermore, we demonstrated that the higher bacterial invasion in human INT407 triggered higher levels of expression of major proinflammatory cytokines, such as IL- 1β and IL-6, and significant downregulation of IL-17A gene expression (P ≤ 0.05). The findings of the present study suggest that the enhanced ability of C. jejuni to invade human cells is tightly regulated by proinflammatory cytokines in the gut and possibly holds the keys to the observed differences in pathogenesis between human and chicken cells.

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Targeted Bioimaging of Microencapsulated Recombinant LAB Vector Expressing Fluorescent Reporter Protein: A Non-invasive Approach for Microbial Tracking
Prakash Biswas, Afruja Khan, Amirul Islam Mallick
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Identification and functional characterization of putative ligand binding domain(s) of JlpA protein of Campylobacter jejuni
Chandan Gorain, Subhadeep Gupta, S.S. Mahafujul Alam, Mehboob Hoque, Andrey V. Karlyshev, Amirul Islam Mallick
International Journal of Biological Macromolecules.2024; 264: 130388. CrossRef
Heterogeneity and Compositional Diversities of Campylobacter jejuni Outer Membrane Vesicles (OMVs) Drive Multiple Cellular Uptake Processes
Afruja Khan, Avijit Sardar, Pradip K. Tarafdar, Amirul I. Mallick
ACS Infectious Diseases.2023; 9(11): 2325. CrossRef
Multimodal Biofilm Inactivation Using a Photocatalytic Bismuth Perovskite–TiO2–Ru(II)polypyridyl-Based Multisite Heterojunction
Noufal Kandoth, Sonu Pratap Chaudhary, Subhadeep Gupta, Kumari Raksha, Atin Chatterjee, Shresth Gupta, Safakath Karuthedath, Catherine S. P. De Castro, Frédéric Laquai, Sumit Kumar Pramanik, Sayan Bhattacharyya, Amirul Islam Mallick, Amitava Das
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In Silico and In Vitro Analysis of Helicobacter pullorum Type Six Secretory Protein Hcp and Its Role in Bacterial Invasion and Pathogenesis
Kashaf Javed, Farzana Gul, Rashda Abbasi, Sidra Batool, Zobia Noreen, Habib Bokhari, Sundus Javed
Current Microbiology.2022;[Epub] CrossRef
Gut Microbe-Derived Outer Membrane Vesicles: A Potential Platform to Control Cecal Load of Campylobacter jejuni
Ankita Singh, Afruja Khan, Tamal Ghosh, Samiran Mondal, Amirul I. Mallick
ACS Infectious Diseases.2021; 7(5): 1186. CrossRef
Mucosal delivery of live Lactococcus lactis expressing functionally active JlpA antigen induces potent local immune response and prevent enteric colonization of Campylobacter jejuni in chickens
Chandan Gorain, Ankita Singh, Sudipta Bhattacharyya, Anirban Kundu, Aritraa Lahiri, Subhadeep Gupta, Amirul I. Mallick
Vaccine.2020; 38(7): 1630. CrossRef
Immunopathological properties of the Campylobacter jejuni flagellins and the adhesin CadF as assessed in a clinical murine infection model
Anna-Maria Schmidt, Ulrike Escher, Soraya Mousavi, Nicole Tegtmeyer, Manja Boehm, Steffen Backert, Stefan Bereswill, Markus M. Heimesaat
Gut Pathogens.2019;[Epub] CrossRef
A One Health approach to prevention, treatment, and control of campylobacteriosis
Francesca Schiaffino, James Platts-Mills, Margaret N. Kosek
Current Opinion in Infectious Diseases.2019; 32(5): 453. CrossRef
Immunogenicity and protective efficacy of mucosal delivery of recombinant hcp of Campylobacter jejuni Type VI secretion system (T6SS) in chickens
Ankita Singh, Khairun Nisaa, Sudipta Bhattacharyya, Amirul Islam Mallick
Molecular Immunology.2019; 111: 182. CrossRef

Potential for colonization of O111:H25 atypical enteropathogenic E. coli: Marta O. Domingos , Keyde C.M. Melo , Irys Viana Neves , Cristiane M. Mota , Rita C. Ruiz , Bruna S. Melo , Raphael C. Lima , Denise S.P.Q. Horton , Monamaris M. Borges , Marcia R. Franzolin; J. Microbiol. 2016;54(11):745-752. Published online October 29, 2016; DOI: https://doi.org/10.1007/s12275-016-6015-x

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Abstract

Using clonal phylogenetic methods, it has been demonstrated that O111:H25 atypical enteropathogenic E. coli (aEPEC) strains belong to distinct clones, suggesting the possibility that their ability to interact with different hosts and abiotic surfaces can vary from one clone to another. Accordingly, the ability of O111:H25 aEPEC strains derived from human, cat and dogs to adhere to epithelial cells has been investigated, along with their ability to interact with macrophages and to form biofilms on polystyrene, a polymer used to make biomedical devices. The results demonstrated that all the strains analyzed were able to adhere to, and to form pedestals on, epithelial cells, mechanisms used by E. coli to become strongly attached to the host. The strains also show a Localized-Adherence- Like (LAL) pattern of adhesion on HEp-2 cells, a behavior associated with acute infantile diarrhea. In addition, the O111:H25 aEPEC strains derived either from human or domestic animals were able to form long filaments, a phenomenon used by some bacteria to avoid phagocytosis. O111:H25 aEPEC strains were also encountered inside vacuoles, a characteristic described for several bacterial strains as a way of protecting themselves against the environment. They were also able to induce TNF-α release via two routes, one dependent on TLR-4 and the other dependent on binding of Type I fimbriae. These O111:H25 strains were also able to form biofilms on polystyrene. In summary the results suggest that, regardless of their source (i.e. linked to human origin or otherwise), O111:H25 aEPEC strains carry the potential to cause human disease.

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Research Support, Non-U.S. Gov'ts

NOTE] Identification of Secreted Virulence Factors of Chromobacterium violaceum: Thiago Castro-Gomes , Mariana S. Cardoso , Wanderson D. DaRocha , Letícia A. Laibida , Andréa M. A. Nascimento , Luciana W. Zuccherato , Maria Fátima Horta , Marcelo P. Bemquerer , Santuza M. R. Teixeira; J. Microbiol. 2014;52(4):350-353. Published online February 17, 2014; DOI: https://doi.org/10.1007/s12275-014-3202-5

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Abstract

Chromobacterium violaceum, a component of tropical soil microbiota, is an opportunistic pathogenic bacterium that can infect humans and other animals. In addition to identifying a large number of genes that demonstrate the vast biotechnological potential of this bacterium, genome sequencing revealed several virulence factors, including different cytolysins, which can be related to its pathogenicity. Here we confirmed these predictions from genomic analyses by identifying, through mass spectrometry, proteins present in the culture supernatant of C. violaceum that may constitute secreted virulence factors. Among them, we identified a secreted collagenase and the product of a gene with sequence similarity to previously characterized bacterial porins.

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2-tert-Butyl-1,4-benzoquinone, a food additive oxidant, reduces virulence factors of Chromobacterium violaceum
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Global Transcriptional Response to Organic Hydroperoxide and the Role of OhrR in the Control of Virulence Traits in Chromobacterium violaceum
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Advances in Chromobacterium violaceum and properties of violacein-Its main secondary metabolite: A review
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Exposure to an extremely low-frequency electromagnetic field only slightly modifies the proteome of Chromobacterium violaceum ATCC 12472
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Guava Leaf Extract Inhibits Quorum-Sensing and Chromobacterium violaceum Induced Lysis of Human Hepatoma Cells: Whole Transcriptome Analysis Reveals Differential Gene Expression
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A New Quorum-Sensing Inhibitor Attenuates Virulence and Decreases Antibiotic Resistance in Pseudomonas aeruginosa: Yu-Xiang Yang , Zhen-Hua Xu , Yu-Qian Zhang , Jing Tian , Li-Xing Weng , Lian-Hui Wang; J. Microbiol. 2012;50(6):987-993. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2149-7

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Abstract

Quorum sensing (QS) has been a novel target for the treatment of infectious diseases. Here structural analogs of Pseudomonas aeruginosa autoinducer N-acyl homoserine lactone (AHL) were investigated for QS inhibitor (QSI) activity and a novel QSI was discovered, N-decanoyl-L-homoserine benzyl ester (C2). Virulence assays showed that C2 downregulated total protease and elastase activities, as well as the production of rhamnolipid, that are controlled by QS in P. aeruginosa wild-type strain PAO1 without affecting growth. C2 was also shown to inhibit swarming motility of PAO1. Using a microdilution checkerboard method, we identified synergistic interactions between C2 and several antibiotics, tobramycin, gentamycin, cefepime, and meropenem. Data from real-time RT-PCR suggested that C2 inhibited the expression of lasR (29.67%), lasI (21.57%), rhlR (28.20%), and rhlI (29.03%).

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Comparative Proteome Analysis of Bacillus anthracis with pXO1 Plasmid Content: Sudipto Shahid , Ji Hyun Park , Hyung Tae Lee , Seong-Joo Kim , Ji Cheon Kim , Sang Hoon Kim , Dal Mu Ri Han , Dong In Jeon , Kyoung Hwa Jung , Young Gyu Chai; J. Microbiol. 2010;48(6):771-777. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0136-4

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Abstract: Bacillus anthracis the causative agent of anthrax, is an important pathogen among the Bacillus cereus group of species because of its physiological characteristics and its importance as a biological warfare agent. Tripartite anthrax toxin proteins and a poly-D-glutamic acid capsule are produced by B. anthracis vegetative cells during mammalian hosts infection and when cultured in conditions that are thought to mimic the host environment. To identify the factors regulating virulence in B. anthracis the whole cell proteins were extracted from two B. anthracis strains and separated by narrow range immobilized pH gradient (IPG) strips (pH 4-7), followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Proteins that were differentially expressed were identified by the peptide fingerprinting using matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS). A total of 23 proteins were identified as being either upregulated or downregulated in the presence or absence of the virulence plasmid pXO1. Two plasmid encoded proteins and 12 cellular proteins were identified and documented as potential virulence factors.

Virulence Determinants in Vancomycin-Resistant Enterococcus faecium vanA Isolated from Different Sources at University Hospital of Londrina, Paraná, Brazil: Flávia Imanishi Ruzon , Suelen Balero de Paula , Renata Lumi Kanoshiki , Jussevania Pereira-Santos , Gilselena Kerbauy , Renata Katsuko Takayama Kobayashi , Lucy Megumi Yamauchi , Márcia Regina Eches Perugini , Sueli Fumie Yamada-Ogatta; J. Microbiol. 2010;48(6):814-821. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0099-5

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Abstract

Enterococcus faecium, especially those showing multidrug resistance, has emerged as a significant cause of healthcare-associated infections worldwide. However, relatively little is known about the virulence and pathogenesis of this species. The aim of this study was to determine the occurrence of four putative virulence determinants of E. faecium and to correlate them with phenotypic traits. Using forty E. faecium vanA-type isolates from hospitalized patients and their environmental vicinity, we determined the following: the antimicrobial susceptibility profile, occurrence of the genes cylA, efaA, esp, and gelE, hemolytic and gelatinase activities, capacity to form biofilm and in vitro adhesion to epithelial cells. All isolates were shown to be resistant to vancomycin and teicoplanin, as well as to two or more other antimicrobials. All isolates harbored at least one putative virulence marker, and the prevalence was as follows: esp, 87.5%; efaA, 82.5%; gelE, 70%; and cylA, 65%. The presence of 4 genes was observed in 32.5% isolates. The presence of the efaA was associated with the presence of esp, regardless of the source of the isolates. A positive association with the presence of cylA and hemolytic activity in the sheep blood agar assay was observed. No association was found for gelE and gelatinase production in the agar plate assay, for efaA and LLC-MK2 cell adhesion, and for esp and biofilm formation on polystyrene surface. These results show the presence of putative virulence genes in multiple antimicrobial resistant E. faecium isolates from different sources in a hospital setting.

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Scandinavian Journal of Infectious Diseases.2014; 46(8): 547. CrossRef
Commensal and environmental vancomycin-resistant Enterococcus faecium isolated in hospital settings: Genotypic diversity, antimicrobial resistance and virulence traits
LVP Gomes, AT Morey, JP Santos, JD Cardoso, CF Oliveira, MRE Perugini, LM Yamauchi, SFY Ogatta
Indian Journal of Medical Microbiology.2014; 32(3): 345. CrossRef
Presence of virulence factors in Enterococcus faecalis and Enterococcus faecium susceptible and resistant to vancomycin
Carolina Baldisserotto Comerlato, Mariah Costa Carvalho de Resende, Juliana Caierão, Pedro Alves d'Azevedo
Memórias do Instituto Oswaldo Cruz.2013; 108(5): 590. CrossRef
Molecular epidemiology of Enterococcus sp. isolated in a university hospital in Algeria
Nassima Djahmi, Adeline Boutet-Dubois, Sabrina Nedjai, Mazouz Dekhil, Albert Sotto, Jean-Philippe Lavigne
Scandinavian Journal of Infectious Diseases.2012; 44(9): 656. CrossRef
Vancomycin-dependent Enterococcus faecium vanA: characterization of the first case isolated in a university hospital in Brazil
G. Kerbauy, M.R.E. Perugini, L.M. Yamauchi, S.F. Yamada-Ogatta
Brazilian Journal of Medical and Biological Research.2011; 44(3): 253. CrossRef

Modulation of Secreted Virulence Factor Genes by Subinhibitory Concentrations of Antibiotics in Pseudomonas aeruginosa: Lixin Shen , Ying Shi , Dan Zhang , Jinhua Wei , Michael G. Surette , Kangmin Duan; J. Microbiol. 2008;46(4):441-447. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0054-x

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Abstract: Recent studies have shown that subinhibitory antibiotics play important roles in regulating bacterial genes including virulence factor genes. In this study, the expression of 13 secreted virulence related gene clusters of Pseudomonas aeruginosa, an important opportunistic pathogen, was examined in the presence of subinhibitory concentrations of 4 antibiotics: vancomycin, tetracycline, ampicilin and azithromycin. Activation of gene expression was observed with phzA1, rhlAB, phzA2, lasB, exoY, and exoS. Subinhibitory concentrations of vancomycin resulted in more than 10-fold increase of rhlAB and phzA2 transcription. Both rhamnolipid production and pyocyanin production were significantly elevated, correlating phenotypes with the increased transcription. P. aeruginosa swarming and swimming motility also increased. Similar results were observed with subinhibitory tetracycline, azithromycin and ampicillin. These results indicate that the antibiotics at low concentrations can up-regulate virulence factors and therefore influence bacterial pathogenesis.

Rapid Detection of Virulence Factors of Aeromonas Isolated from a Trout Farm by Hexaplex-PCR: In-Young Nam , Kiseong Joh; J. Microbiol. 2007;45(4):297-304.; DOI: https://doi.org/2569 [pii]

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Abstract: The detection of virulence factors of Aeromonas is a key component in determining potential pathogenicity because these factors act multifunctionally and multifactorially. In this study water samples were collected from a trout farm on a seasonal basis, and diseased fish and Aeromonas species were isolated and identified. For rapid detection of six virulence factors of isolated Aeromonas, a hexaplex-polymerase chain reaction (hexaplex-PCR) assay was used. The detected virulence factors include aerolysin (aer), GCAT (gcat), serine protease (ser), nuclease (nuc) lipase (lip) and lateral flagella (laf). The dominant strain found in our isolates was Aeromonas sobria, and the dominant virulence factors were aer and nuc for all seasons. We confirmed that A. sobria and two of the virulence genes (aer and nuc) are related. We proposed a method by which one can identify the major strains of Aeromonas: A. hydrophila, A. sobria, A. caviae, and A. veronii, using hexaplex-PCR.

Characterization of Aeromonas hydrophila Isolated from Rainbow Trouts in Korea: Soondeuk Lee , Sookyung Kim , Yoojung Oh , Yeonhee Lee; J. Microbiol. 2000;38(1):1-7.

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Abstract: Eight strains of Aeromonas hydrophila isolated from diseased trout in Korea were characterized and compared with an American type strain by various methods including biochemical and physiological tests, PCR, randomly amplified polymorphic DNA (RAPD), plasmid profiling, and gel electrophoresis of total, membrane, and extracellular proteins. Virulence factors such as surface array proteins, cytotoxin, hemolysin, haemagglutinin, and protease were also investigated. The Korean strains showed het-erogeneity in lysine decarboxylase production, utilization of various carbon sources, and production of acetoin. Five strains had the same profiles of total and membrane proteins. Six strains haemag-glutinated with trout red blood cells (RBCs) which was inhibited by fucose, galactose, and mannose, except for No. 1 where haemagglutination was inhibited by only galactose and mannose, but not by fucose. Four isolates haemagglutinated with human RBCs which was inhibited by fucose and mannose yet not by galactose. The type strain haemagglutinated only with trout RBCs which was inhibited by fucose, galactose, and mannose. Every isolate secreted protease, hemolysin, cytotoxin, and siderophore, but no enterotoxin. Results showed that the Korean isolates, except for No. 7, had very different biochemical and molecular characteristics from those of the American type strain.

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