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

Salmonella Typhimurium ST313 isolated in Brazil revealed to be more invasive and inflammatory in murine colon compared to ST19 strains: Amanda Aparecida Seribelli , Tamara R. Machado Ribeiro , Patrick da Silva† , Isabela Mancini Martins , Felipe Pinheiro Vilela , Marta I. Cazentini Medeiros , Kamila Chagas Peronni , Wilson Araújo da Silva Junior , Cristiano Gallina Moreira , Juliana Pfrimer Falcão; J. Microbiol. 2021;59(9):861-870. Published online August 12, 2021; DOI: https://doi.org/10.1007/s12275-021-1082-z

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Salmonella Typhimurium (ST313) has caused an epidemic of invasive disease in sub-Saharan Africa and has been recently identified in Brazil. As the virulence of this ST is poorly understood, the present study aimed to (i) perform the RNAseq in vitro of S. Typhimurium STm30 (ST313) grown in Luria-Bertani medium at 37°C; (ii) compare it with the RNAseq of the S. Typhimurium SL1344 (ST19) and S. Typhimurium STm11 (ST19) strains under the same growing conditions; and (iii) examine the colonization capacity and expression of virulence genes and cytokines in murine colon. The STm30 (ST313) strain exhibited stronger virulence and was associated with a more inflammatory profile than the strains SL1344 (ST19) and STm11 (ST19), as demonstrated by transcriptome and in vivo assay. The expression levels of the hilA, sopD2, pipB, and ssaS virulence genes, other Salmonella pathogenicity islands SPI-1 and SPI-2 genes or effectors, and genes of the cytokines IL-1β, IFN-γ, TNF-α, IL-6, IL-17, IL-22, and IL-12 were increased during ST313 infection in C57BL/6J mice. In conclusion, S. Typhimurium STm30 (ST313) isolated from human feces in Brazil express higher levels of pathogenesis- related genes at 37°C and has stronger colonization and invasion capacity in murine colon due to its high expression levels of virulence genes, when compared with the S. Typhimurium SL1344 (ST19) and STm11 (ST19) strains. STm30 (ST313) also induces stronger expression of pro-inflammatory cytokines in this organ, suggesting that it causes more extensive tissue damage.

Citations

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Whole-Genome Sequencing Reveals the Population Structure and Genetic Diversity of Salmonella Typhimurium ST34 and ST19 Lineages
Zhen-xu Zhuo, Yu-lian Feng, Xi-wei Zhang, Hao Liu, Fang-yin Zeng, Xiao-yan Li
Journal of Microbiology.2024; 62(10): 859. CrossRef
Incremental increases in physiological fluid shear progressively alter pathogenic phenotypes and gene expression in multidrug resistant Salmonella
Jiseon Yang, Jennifer Barrila, Eric A. Nauman, Seth D. Nydam, Shanshan Yang, Jin Park, Ami D. Gutierrez-Jensen, Christian L. Castro, C. Mark Ott, Kristina Buss, Jason Steel, Anne D. Zakrajsek, Mary M. Schuff, Cheryl A. Nickerson
Gut Microbes.2024;[Epub] CrossRef
Virulence potential of Salmonella 1,4, [5],12:i:- strains isolated during decades from different sources in the Southeast region of Brazil
Giovana do Nascimento Pereira, Amanda Aparecida Seribelli, Carolina Nogueira Gomes, Felipe Pinheiro Vilela, Ludmilla Tonani, Monique Ribeiro Tiba-Casas, Marta Inês Cazentini Medeiros, Dália dos Prazeres Rodrigues, Márcia Regina von Zeska Kress, Juliana Pf
Brazilian Journal of Microbiology.2023; 54(4): 2827. CrossRef
Invasive non-typhoidal Salmonella (iNTS) aminoglycoside-resistant ST313 isolates feature unique pathogenic mechanisms to reach the bloodstream
Isabela Mancini Martins, Amanda Aparecida Seribelli, Tamara R. Machado Ribeiro, Patrick da Silva, Bruna Cardinali Lustri, Rodrigo T. Hernandes, Juliana Pfrimer Falcão, Cristiano Gallina Moreira
Infection, Genetics and Evolution.2023; 116: 105519. CrossRef
Regulator of RNase E activity modulates the pathogenicity of Salmonella Typhimurium
Jaejin Lee, Eunkyoung Shin, Ji-Hyun Yeom, Jaeyoung Park, Sunwoo Kim, Minho Lee, Kangseok Lee
Microbial Pathogenesis.2022; 165: 105460. CrossRef
Antimicrobial resistance and genetic background of non-typhoidal Salmonella enterica strains isolated from human infections in São Paulo, Brazil (2000–2019)
Aline Parolin Calarga, Marco Tulio Pardini Gontijo, Luiz Gonzaga Paula de Almeida, Ana Tereza Ribeiro de Vasconcelos, Leandro Costa Nascimento, Taíse Marongio Cotrim de Moraes Barbosa, Thalita Mara de Carvalho Perri, Silvia Regina dos Santos, Monique Ribe
Brazilian Journal of Microbiology.2022; 53(3): 1249. CrossRef

Molecular genomic characterization of severe fever with thrombocytopenia syndrome virus isolates from South Korea: Yu Jung Won , Lae Hyung Kang , Sung Geun Lee , Seung Won Park , Jae Ik Han , Soon Young Paik; J. Microbiol. 2019;57(10):927-937. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-9174-8

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Abstract

Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne emerging infectious disease caused by the SFTS virus (SFTSV) and is a threat to public health due to its high fatality rate. However, details on tick-to-human transmission of SFTSV are limited. In this study, we determined the wholegenome sequence of a South Korean SFTSV strain (CUKJJ01), compared it to those of other recent human SFTSV isolates, and identified the genetic variations and relationships among the SFTSV strains. The genome of CUK-JJ01 was consistent with the genome of other members of the genus Phlebovirus, including the large (L), medium (M), and small (S) segments of 6368, 3378, and 1744 nucleotides, respectively. Based on amino acid sequences of the M and S segments, which are used to distinguish the six SFTSV genotypes, CUK-JJ01 was classified as genotype B. Segment analysis revealed that the L, M, and S segments were 97.49%, 97.18%, and 97.94% similar to those of KAJNH2/2013/ Korea, ZJZHSH-FDE/2012/China, and KADGH/2013/Korea, respectively. Currently, only few studies on SFTSV have been conducted in Korean population and most were limited to serological analysis. Although the present study has limitations in terms of number of sample analyzed, the findings may serve as basis to understand the transmission and spread of SFTSV, as well as for the development of diagnostic and detection methods for viral recombinants by comparing the whole genome sequence of SFTSV isolates from South Korea and that of foreign isolates.

Citations

Citations to this article as recorded by

Circulation of tick-borne pathogens in wildlife of the Republic of Korea
Hye-ryung Byun, Seong-Ryeong Ji, Jun-Gu Kang, Chang-Yong Choi, Ki-Jeong Na, Jong-Taek Kim, Joon-Seok Chae
One Health.2024; 19: 100913. CrossRef
Molecular characterization of the genome of a new bunyavirus isolated in 2023 in Huzhou, China
Shili Song, Zhang Shen, Deshun Xu
Journal of Clinical Virology Plus.2024; 4(3): 100188. CrossRef
Multiple Genotypes and Reassortants of Severe Fever With Thrombocytopenia Syndrome Virus Co‐Circulating in Hangzhou in Southeastern China, 2013–2023
Yanping Wen, Zhimin Ni, Yan Hu, Jun Wu, Yezhen Fang, Guozhong Zhang, Renjie Huang, Shi Cheng, Feifei Cao, Qihao Xu, Yue Yu, Min Liu, Hongnv Yu, Liangliang Huo, Jun Li
Journal of Medical Virology.2024;[Epub] CrossRef
Genetic Diversity, Regional Distribution, and Clinical Characteristics of Severe Fever with Thrombocytopenia Syndrome Virus in Gangwon Province, Korea, a Highly Prevalent Region, 2019–2021
Mi-Young Moon, Hyeon Kyu Kim, Se-Jin Chung, Jae Hwan Byun, Ha-Na Kim, Woan Lee, Soon-Won Lee, Sezim Monoldorova, Sungkyeong Lee, Bo-Young Jeon, Eun-Joo Lim
Microorganisms.2023; 11(9): 2288. CrossRef
Identification of severe fever with thrombocytopenia syndrome virus genotypes in patients and ticks in Liaoning Province, China
Xiao-Hu Han, Yue Ma, Hong-Yan Liu, Dan Li, Yan Wang, Feng-Hua Jiang, Qing-Tian Gao, Feng Jiang, Bao-Shan Liu, Guo-Shun Shen, Ze-Liang Chen
Parasites & Vectors.2022;[Epub] CrossRef
Analysis of cross neutralizing activity of antibodies from sera of severe fever with thrombocytopenia syndrome patients to deal with different genotype strains
Jiaxin Xu, Yuanni Liu, Fan Zhang, Xin Wang, Weijin Huang, Yulong Wu, Boqing Li, Jiapeng Zhuang, Yixing Bing, Youchun Wang, Yuanyuan Qiao
Frontiers in Microbiology.2022;[Epub] CrossRef
Development of a real-time loop-mediated isothermal amplification method for the detection of severe fever with thrombocytopenia syndrome virus
Jae Woong Lee, Yu-Jung Won, Lae Hyung Kang, Sung-Geun Lee, Seung-Won Park, Soon-Young Paik
Journal of Microbiology.2020; 58(8): 711. CrossRef

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