Journal of Microbiology

Journal Articles

Infection Dynamics of Dengue Virus in Caco-2 Cells Depending on Its Differentiation Status: Jayoung Nam, Jisu Lee, Geon A Kim, Seung-Min Yoo, Changhoon Park, Myung-Shin Lee; J. Microbiol. 2024;62(9):799-809. Published online August 30, 2024; DOI: https://doi.org/10.1007/s12275-024-00161-w

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Abstract: Dengue virus (DENV), from the Flaviviridae family, is the causative agent of dengue fever and poses a significant global health challenge. The virus primarily affects the vascular system and liver; however, a growing body of evidence suggests its involvement in the gastrointestinal (GI) tract, contributing to clinical symptoms such as abdominal pain, vomiting, and diarrhea. However, the mechanisms underlying DENV infection in the digestive system remain largely unexplored. Prior research has detected viral RNA in the GI tissue of infected animals; however, whether the dengue virus can directly infect human enterocytes remains unclear. In this study, we examine the infectivity of human intestinal cell lines to the dengue virus and their subsequent response. We report that the Caco-2 cell line, a model of human enterocytes, is susceptible to infection and capable of producing viruses. Notably, differentiated Caco-2 cells exhibited a lower infection rate yet a higher level of virus production than their undifferentiated counterparts. These findings suggest that human intestinal cells are a viable target for the dengue virus, potentially elucidating the GI symptoms observed in dengue fever and offering a new perspective on the pathogenetic mechanisms of the virus.

Genetically Engineered CLDN18.2 CAR-T Cells Expressing Synthetic PD1/CD28 Fusion Receptors Produced Using a Lentiviral Vector: Heon Ju Lee, Seo Jin Hwang, Eun Hee Jeong, Mi Hee Chang; J. Microbiol. 2024;62(7):555-568. Published online May 3, 2024; DOI: https://doi.org/10.1007/s12275-024-00133-0

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Abstract: This study aimed to develop synthetic Claudin18.2 (CLDN18.2) chimeric antigen receptor (CAR)-T (CAR-T) cells as a treatment for advanced gastric cancer using lentiviral vector genetic engineering technology that targets the CLDN18.2 antigen and simultaneously overcomes the immunosuppressive environment caused by programmed cell death protein 1 (PD-1). Synthetic CAR T cells are a promising approach in cancer immunotherapy but face many challenges in solid tumors. One of the major problems is immunosuppression caused by PD-1. CLDN18.2, a gastric-specific membrane protein, is considered a potential therapeutic target for gastric and other cancers. In our study, CLDN18.2 CAR was a second-generation CAR with inducible T-cell costimulatory (CD278), and CLDN18.2-PD1/CD28 CAR was a third-generation CAR, wherein the synthetic PD1/CD28 chimeric-switch receptor (CSR) was added to the second-generation CAR. In vitro, we detected the secretion levels of different cytokines and the killing ability of CAR-T cells. We found that the secretion of cytokines such as interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α) secreted by three types of CAR-T cells was increased, and the killing ability against CLDN18.2-positive GC cells was enhanced. In vivo, we established a xenograft GC model and observed the antitumor effects and off-target toxicity of CAR-T cells. These results support that synthetic anti-CLDN18.2 CAR-T cells have antitumor effect and anti-CLDN18.2-PD1/CD28 CAR could provide a promising design strategy to improve the efficacy of CAR-T cells in advanced gastric cancer.

Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica: Joo-Han Gwak , Samuel Imisi Awala , So-Jeong Kim , Sang-Hoon Lee , Eun-Jin Yang , Jisoo Park , Jinyoung Jung , Sung-Keun Rhee; J. Microbiol. 2023;61(11):967-980. Published online December 7, 2023; DOI: https://doi.org/10.1007/s12275-023-00090-0

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Abstract

Antarctic polynyas have the highest Southern Ocean summer primary productivity, and due to anthropogenic climate change, these areas have formed faster recently. Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant microorganisms in the ocean and play a primary role in the global nitrogen cycle. We utilized metagenomics and metatranscriptomics to gain insights into the physiology and metabolism of AOA in polar oceans, which are associated with ecosystem functioning. A polar-specific ecotype of AOA, from the “Candidatus Nitrosomarinus”-like group, was observed to be dominant in the Amundsen Sea Polynya (ASP), West Antarctica, during a succession of summer phytoplankton blooms. AOA had the highest transcriptional activity among prokaryotes during the bloom decline phase (DC). Metatranscriptomic analysis of key genes involved in ammonia oxidation, carbon fixation, transport, and cell division indicated that this polar AOA ecotype was actively involved in nitrification in the bloom DC in the ASP. This study revealed the physiological and metabolic traits of this key polar-type AOA in response to phytoplankton blooms in the ASP and provided insights into AOA functions in polar oceans.

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Alleviated photoinhibition on nitrification in the Indian Sector of the Southern Ocean
Lingfang Fan, Min Chen, Zifei Yang, Minfang Zheng, Yusheng Qiu
Acta Oceanologica Sinica.2024; 43(7): 52. CrossRef

Review

[MINIREVIEW]Gain and loss of antibiotic resistant genes in multidrug resistant bacteria: One Health perspective: Misung Kim , Jaeeun Park , Mingyeong Kang , Jihye Yang , Woojun Park; J. Microbiol. 2021;59(6):535-545. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-1085-9

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Abstract

The emergence of multidrug resistance (MDR) has become a global health threat due to the increasing unnecessary use of antibiotics. Multidrug resistant bacteria occur mainly by accumulating resistance genes on mobile genetic elements (MGEs), made possible by horizontal gene transfer (HGT). Humans and animal guts along with natural and engineered environments such as wastewater treatment plants and manured soils have proven to be the major reservoirs and hotspots of spreading antibiotic resistance genes (ARGs). As those environments support the dissemination of MGEs through the complex interactions that take place at the human-animalenvironment interfaces, a growing One Health challenge is for multiple sectors to communicate and work together to prevent the emergence and spread of MDR bacteria. However, maintenance of ARGs in a bacterial chromosome and/or plasmids in the environments might place energy burdens on bacterial fitness in the absence of antibiotics, and those unnecessary ARGs could eventually be lost. This review highlights and summarizes the current investigations into the gain and loss of ARG genes in MDR bacteria among human-animal- environment interfaces. We also suggest alternative treatments such as combinatory therapies or sequential use of different classes of antibiotics/adjuvants, treatment with enzymeinhibitors, and phage therapy with antibiotics to solve the MDR problem from the perspective of One Health issues.

Citations

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Unexpected vulnerability of Enterococcus faecium to polymyxin B under anaerobic condition
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Antimicrobial Resistance in the Context of Animal Production and Meat Products in Poland—A Critical Review and Future Perspective
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Resistome Diversity in Escherichia coli Isolates of Global Wastewaters
Pavithra Anantharaman Sudhakari, Bhaskar Chandra Mohan Ramisetty
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Transfer dynamics of antimicrobial resistance among gram-negative bacteria
Bangjuan Wang, Muhammad Haris Raza Farhan, Linlin Yuan, Yuxin Sui, Jinhua Chu, Xiaohan Yang, Yuxin Li, Lingli Huang, Guyue Cheng
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Pedobacter faecalis sp. nov., isolated from the faeces of eland, Taurotragus oryx
Yerim Park, Jihyeon Min, Bitnara Kim, Woojun Park
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Co-selection mechanism for bacterial resistance to major chemical pollutants in the environment
Meixia Huo, Xiangyue Xu, Kun Mi, Wenjin Ma, Qin Zhou, Xudong Lin, Guyue Cheng, Lingli Huang
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Repeated Exposure of Vancomycin to Vancomycin-Susceptible Staphylococcus aureus (VSSA) Parent Emerged VISA and VRSA Strains with Enhanced Virulence Potentials
An Nguyen, J. Jean Sophy Roy, Ji-Hoon Kim, Kyung-Hee Yun, Wonsik Lee, Kyeong Kyu Kim, Truc Kim, Akhilesh Kumar Chaurasia
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Human Disturbance Increases Health Risks to Golden Snub-Nosed Monkeys and the Transfer Risk of Pathogenic Antibiotic-Resistant Bacteria from Golden Snub-Nosed Monkeys to Humans
Shuzhen Zou, Tingting Yuan, Tan Lu, Jiayu Yan, Di Kang, Dayong Li
Animals.2023; 13(19): 3083. CrossRef
Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome
Mathijs J. P. Theelen, Roosmarijn E. C. Luiken, Jaap A. Wagenaar, Marianne M. Sloet van Oldruitenborgh-Oosterbaan, John W. A. Rossen, Femke J. W. C. Schaafstra, David A. van Doorn, Aldert L. Zomer
Microbiome.2023;[Epub] CrossRef
Genomic evidences of gulls as reservoirs of critical priority CTX-M-producing Escherichia coli in Corcovado Gulf, Patagonia
Danny Fuentes-Castillo, Daniela Castro-Tardón, Fernanda Esposito, Ingrith Neves, Larissa Rodrigues, Herrison Fontana, Bruna Fuga, José L. Catão-Dias, Nilton Lincopan
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Poultry manure-derived microorganisms as a reservoir and source of antibiotic resistance genes transferred to soil autochthonous microorganisms
Magdalena Męcik, Martyna Buta-Hubeny, Łukasz Paukszto, Mateusz Maździarz, Izabela Wolak, Monika Harnisz, Ewa Korzeniewska
Journal of Environmental Management.2023; 348: 119303. CrossRef
Fabrication of Co-Assembly from Berberine and Tannic Acid for Multidrug-Resistant Bacteria Infection Treatment
Tingting Zheng, Huan Chen, Chenyang Wu, Jinrui Wang, Mengyao Cui, Hanyi Ye, Yifan Feng, Ying Li, Zhengqi Dong
Pharmaceutics.2023; 15(7): 1782. CrossRef
Grazing disturbance increased the mobility, pathogenicity and host microbial species of antibiotic resistance genes, and multidrug resistance genes posed the highest risk in the habitats of wild animals
Shuzhen Zou, Tan Lu, Cailiang Huang, Jie Wang, Dayong Li
Frontiers in Environmental Science.2023;[Epub] CrossRef
Application of electrochemical oxidation for the enhancement of antibiotic resistant bacteria removal in stormwater bioretention cells
XiaoJun Zuo, SongHu Zhang, FanXin Kong, QiangQiang Xu
Science of The Total Environment.2023; 861: 160477. CrossRef
Blue Light Sensing BlsA-Mediated Modulation of Meropenem Resistance and Biofilm Formation in Acinetobacter baumannii
Jihye Yang, Sohyeon Yun, Woojun Park, Mark J. Mandel
mSystems.2023;[Epub] CrossRef
AamA-mediated epigenetic control of genome-wide gene expression and phenotypic traits in Acinetobacter baumannii ATCC 17978
Jihye Yang, Yongjun Son, Mingyeong Kang, Woojun Park
Microbial Genomics .2023;[Epub] CrossRef
Response behavior of antibiotic resistance genes and human pathogens to slope gradient and position: An environmental risk analysis in sloping cultivated land
Kailin Xu, Xuna Liu, Lina Pang, Yao Yue, Efthalia Chatzisymeon, Ping Yang
Science of The Total Environment.2023; 905: 166994. CrossRef
The β-Lactamase Activity at the Community Level Confers β-Lactam Resistance to Bloom-Forming Microcystis aeruginosa Cells
Yerim Park, Wonjae Kim, Minkyung Kim, Woojun Park
Journal of Microbiology.2023; 61(9): 807. CrossRef
Bactericidal activity of silver nanoparticles in drug-resistant bacteria
C. Chapa González, L. I. González García, L. G. Burciaga Jurado, A. Carrillo Castillo
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Computational modelling of epithelial cell monolayers during infection with Listeria monocytogenes
Raul Aparicio-Yuste, Francisco Serrano-Alcalde, Marie Muenkel, Jose Manuel Garcia-Aznar, Effie E. Bastounis, Maria Jose Gomez-Benito
Computer Methods in Applied Mechanics and Engineering.2022; 401: 115477. CrossRef
Gold nanoparticle-DNA aptamer-assisted delivery of antimicrobial peptide effectively inhibits Acinetobacter baumannii infection in mice
Jaeyeong Park, Eunkyoung Shin, Ji-Hyun Yeom, Younkyung Choi, Minju Joo, Minho Lee, Je Hyeong Kim, Jeehyeon Bae, Kangseok Lee
Journal of Microbiology.2022; 60(1): 128. CrossRef
Antibiotic resistome in a large urban-lake drinking water source in middle China: Dissemination mechanisms and risk assessment
Maozhen Han, Lu Zhang, Na Zhang, Yujie Mao, Zhangjie Peng, Binbin Huang, Yan Zhang, Zhi Wang
Journal of Hazardous Materials.2022; 424: 127745. CrossRef
Occurrence of antibiotic resistance genes and multidrug-resistant bacteria during wastewater treatment processes
Mingyeong Kang, Jihye Yang, Suhyun Kim, Jaeeun Park, Misung Kim, Woojun Park
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Occurrence and spread of antibiotic-resistant bacteria on animal farms and in their vicinity in Poland and Ukraine—review
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Application of Electrochemical Oxidation for the Enhancement of Antibiotic Resistant Bacteria Removal in Stormwater Bioretention Cells
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Journal Articles

Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish): Dong-Wook Hyun , Yun-Seok Jeong , Jae-Yun Lee , Hojun Sung , So-Yeon Lee , Jee-Won Choi , Hyun Sik Kim , Pil Soo Kim , Jin-Woo Bae; J. Microbiol. 2021;59(6):552-562. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-1036-5

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Abstract

A polyphasic taxonomic approach was used to characterize three novel bacterial strains, designated as HDW12AT, HDW- 15BT, and HDW15CT, isolated from the intestine of fish species Odontobutis interrupta or Siniperca scherzeri. All isolates were obligate aerobic, non-motile bacteria, and grew optimally at 30°C. Phylogenetic analysis based on 16S rRNA sequences revealed that strain HDW12AT was a member of the genus Nocardioides, and closely related to Nocardioides allogilvus CFH 30205T (98.9% sequence identities). Furthermore, strains HDW15BT and HDW15CT were members of the genus Sphingomonas, and closely related to Sphingomonas lutea JS5T and Sphingomonas sediminicola Dae 20T (97.1% and 97.9% sequence identities), respectively. Strain HDW12AT contained MK-8 (H4), and strains HDW15BT and HDW15CT contained Q-10 as the respiratory quinone. Major polar lipid components of strain HDW12AT were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol, and those of strains HDW15BT and HDW15CT were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The G + C content of strains HDW12AT, HDW15BT, and HDW15CT were 69.7, 63.3, and 65.5%, respectively. The results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses suggest that strain HDW12AT represents a novel species within the genus Nocardioides, and strains HDW15BT and HDW15CT represent two novel species within the genus Sphingomonas. We propose the names Nocardioides piscis for strain HDW12AT (= KACC 21336T = KCTC 49321T = JCM 33670T), Sphingomonas piscis for strain HDW15BT (= KACC 21341T = KCTC 72588T = JCM 33738T), and Sphingomonas sinipercae for strain HDW15CT (= KACC 21342T = KCTC 72589T = JCM 33739T).

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Description of Streptococcus dentalis sp. nov., Streptococcus gingivalis sp. nov., and Streptococcus lingualis sp. nov., Isolated from Human Oral Cavities
Beom-Jin Goo, Young-Sik Choi, Do-Hun Gim, Su-Won Jeong, Jee-Won Choi, Hojun Sung, Jae-Yun Lee, Jin-Woo Bae
Journal of Microbiology.2024; 62(11): 973. CrossRef
Sphingomonas flavescens sp. nov., isolated from soil
Hyosun Lee, Dhiraj Kumar Chaudhary, Dong-Uk Kim
Archives of Microbiology.2024;[Epub] CrossRef
Nocardioides limicola sp. nov., an alkaliphilic alkane degrading bacterium isolated from oilfield alkali-saline soil
Lin Zhu, Biyue Yang, Wenjun Guo, Xinyu Hu, Shenkui Liu, Xiang Xiao, Wei Wei
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
The probiotic roles of Lactiplantibacillus plantarum E2 as a dietary supplement in growth promotion and disease resistance of juvenile large yellow croaker (Larimichthys crocea)
Ruizhe Liu, Shan Wang, Dongliang Huang, Yulu Huang, Tianliang He, Xinhua Chen
Aquaculture.2024; 578: 740082. CrossRef
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Vahid Keshavarz-Tohid, Somayeh Ebrahimi
Physiological and Molecular Plant Pathology.2023; 127: 102124. CrossRef
Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza
Xiaohui Chen, Zhouqing Zheng, Feina Li, Xiao Ma, Feng Chen, Mingsheng Chen, Li Tuo
Systematic and Applied Microbiology.2023; 46(2): 126391. CrossRef
Parasphingorhabdus cellanae sp. nov., isolated from the gut of a Korean limpet, Cellana toreuma
Ji-Ho Yoo, Jeong Eun Han, June-Young Lee, Su-Won Jeong, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Hojun Sung, Euon Jung Tak, Hyun Sik Kim, Pil Soo Kim, Jee-Won Choi, Do-Yeon Kim, In Chul Jeong, Do-Hun Gim, Seo Min Kang, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn
Do-Yeon Kim, In-Chul Jeong, So-Yeon Lee, Yun-Seok Jeong, Jeong Eun Han, Euon Jung Tak, June-Young Lee, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
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Intergenerational Transfer of Persistent Bacterial Communities in Female Nile Tilapia
Yousri Abdelhafiz, Jorge M. O. Fernandes, Claudio Donati, Massimo Pindo, Viswanath Kiron
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Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203
Aharon Oren, George M. Garrity
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Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn's disease
Jae-Yun Lee, Woorim Kang, Na-Ri Shin, Dong-Wook Hyun, Pil Soo Kim, Hyun Sik Kim, June-Young Lee, Euon Jung Tak, Hojun Sung, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Pathogenomics of Streptococcus ilei sp. nov., a newly identified pathogen ubiquitous in human microbiome
Dong-Wook Hyun, Jae-Yun Lee, Min-Soo Kim, Na-Ri Shin, Tae Woong Whon, Kyung Hyun Kim, Pil Soo Kim, Euon Jung Tak, Mi-Ja Jung, June Young Lee, Hyun Sik Kim, Woorim Kang, Hojun Sung, Che Ok Jeon, Jin-Woo Bae
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Intestinibaculum porci gen. nov., sp. nov., a new member of the family Erysipelotrichaceae isolated from the small intestine of a swine: Ji-Sun Kim , Hanna Choe , Yu-Ri Lee , Kyung Mo Kim , Doo-Sang Park; J. Microbiol. 2019;57(5):381-387. Published online February 22, 2019; DOI: https://doi.org/10.1007/s12275-019-8631-8

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Abstract

A strictly anaerobic, Gram-stain-positive, catalase-negative, non-motile, rod-shaped bacterium, designated SG0102T, was isolated from the small intestine of a swine. Optimal growth occurred at 37°C and pH 7.0. Furthermore, growth was observed in the presence of up to 3% (w/v) NaCl but not at salinity levels higher than 4%. The comparative analysis of 16S rRNA gene sequences showed that strain SG0102T was most closely related to Kandleria vitulina DSM 20405T (93.3%), followed by Catenibacterium mitsuokai KCTC 5053T (91.1%), Sharpea azabuensis KCTC 15217T (91.0%), and Eggerthia catenaformis DSM 5348T (89.6%). The average nucleotide identity values between strain SG0102T and related species, K. vitulina DSM 20405T, C. mitsuokai KCTC 5053T, S. azabuensis KCTC 15217T, and E. catenaformis DSM 5348T, were 71.0, 69.3, 70.0, and 69.2%, respectively. The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SG0102T belonged to the family Erysipelotrichaceae in the class Erysipelotrichia. The DNA G+C content of the strain SG0102T was 39.5 mol%. The major cellular fatty acids (> 10%) of strain SG0102T were C16:0, C16:0 dimethyl acetal, and C18:2 ω9/12c. The cell wall peptidoglycan of strain SG0102T contained the meso-diaminopimelic acid. The strain SG0102T produced lactic acid as a major end product of fermentation. These distinct phenotypic and phylogenetic properties suggest that strain SG0102T represents a novel species in a novel genus of the family Erysipelotrichaceae, for which the name Intestinibaculum porci gen. nov. sp. nov. is proposed. The type strain is SG0102T (= KCTC 15725T = NBRC 113396T).

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An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021
Erik Munson, Sara D. Lawhon, Claire R. Burbick, Amanda Zapp, Maia Villaflor, Elizabeth Thelen, Romney M. Humphries
Journal of Clinical Microbiology.2023;[Epub] CrossRef
Rumen microbial composition associated with the non‐glucogenic to glucogenic short‐chain fatty acids ratio in Holstein cows
Shuhei Takizawa, Takumi Shinkai, Yosuke Kobayashi, Masahiro Masuda, Kenji Hashiba, Kota Uchisawa, Fuminori Terada
Animal Science Journal.2023;[Epub] CrossRef
The gut microbiome and resistome of conventionally vs. pasture-raised pigs
Devin B. Holman, Katherine E. Gzyl, Arun Kommadath
Microbial Genomics .2023;[Epub] CrossRef
Copranaerobaculum intestinale gen. nov., sp. nov., a novel anaerobic bacterium isolated from human faeces
Jun-Hui Feng, Yu-Xiao Chang, Liang-Hui Li, Meng-Meng Li, Zong-Yu Huang, Ni Han, Wen-Jun Li, Rui-Fu Yang, Ping-Hua Qu, Yu-Jing Bi
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Differences in the Composition of the Rumen Microbiota of Finishing Beef Cattle Divergently Ranked for Residual Methane Emissions
Paul E. Smith, Alan K. Kelly, David A. Kenny, Sinéad M. Waters
Frontiers in Microbiology.2022;[Epub] CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(3): 1443. CrossRef

Comparison of virulence between matt and mucoid colonies of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 isolated from a single patient: Haejeong Lee , Jin Yang Baek , So Yeon Kim , HyunJi Jo , KyeongJin Kang , Jae-Hoon Ko , Sun Young Cho , Doo Ryeon Chung , Kyong Ran Peck , Jae-Hoon Song , Kwan Soo Ko; J. Microbiol. 2018;56(9):665-672. Published online August 23, 2018; DOI: https://doi.org/10.1007/s12275-018-8130-3

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Abstract

Nine Klebsiella pneumoniae isolates coproducing NDM-1 and OXA-232 carbapenemases were successively isolated from a single patient. Although they were isolated simultaneously and were isogenic, they presented different colony phenotypes (matt and mucoid). All nine isolates were resistant to most antibiotics except colistin and fosfomycin. In addition, matt-type isolates were resistant to tigecycline. No differences were detected in the cps cluster sequences, except for the insertion of IS5 in the wzb gene of two matt-type isolates. In vitro virulence assays based on production of capsular polysaccharide, biofilm formation, and resistance to human serum indicated that the mucoid-type isolates were significantly more virulent than the matt-type. In addition, mucoid-type isolates showed higher survival rates than the matt-type ones in infection experiments in the fruit fly, suggesting a higher virulence of K. pneumoniae isolates with a mucoid phenotype. To our knowledge, this is the first report of K. pneumoniae colonies with different phenotypes being isolated from the same sample. In addition, we show that virulence varies with colony phenotype. Dissemination of K. pneumoniae isolates expressing both antibiotic resistance and high virulence would constitute a great threat.

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[PROTOCOL] Drosophila melanogaster as a polymicrobial infection model for Pseudomonas aeruginosa and Staphylococcus aureus: Young-Joon Lee , Hye-Jeong Jang , In-Young Chung , You-Hee Cho; J. Microbiol. 2018;56(8):534-541. Published online July 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8331-9

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Abstract

Non-mammalian infection models have been developed over the last two decades, which is a historic milestone to understand the molecular basis of bacterial pathogenesis. They also provide small-scale research platforms for identification of virulence factors, screening for antibacterial hits, and evaluation of antibacterial efficacy. The fruit fly, Drosophila melanogaster is one of the model hosts for a variety of bacterial pathogens, in that the innate immunity pathways and tissue physiology are highly similar to those in mammals. We here present a relatively simple protocol to assess the key aspects of the polymicrobial interaction in vivo between the human opportunistic pathogens, Pseudomonas aeruginosa and Staphylococcus aureus, which is based on the systemic infection by needle pricking at the dorsal thorax of the flies. After infection, fly survival and bacteremia over time for both P. aeruginosa and S. aureus within the infected flies can be monitored as a measure of polymicrobial virulence potential. The infection takes ~24 h including bacterial cultivation. Fly survival and bacteremia are assessed using the infected flies that are monitored up to ~60 h post-infection. These methods can be used to identify presumable as well as unexpected phenotypes during polymicrobial interaction between P. aeruginosa and S. aureus mutants, regarding bacterial pathogenesis and host immunity.

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Biosynthesis of 2-amino-3-hydroxycyclopent-2-enone moiety of bafilomycin in Kitasatospora cheerisanensis KCTC2395: Nguyen Phan Kieu Hanh , Jae Yoon Hwang , Hye Ryeung Oh , Geum Jin Kim , Hyukjae Choi , Doo Hyun Nam; J. Microbiol. 2018;56(8):571-578. Published online July 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8267-0

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Abstract

Bafilomycins produced by Kitasatospora cheerisanensis KCTC- 2395 belong to the 16-membered macrolactone family plecomacrolide antibiotics. Bafilomycin B1 contains 2-amino- 3-hydroxycyclopent-2-enone (C5N), a five membered ring, which gets condensed via an amide linkage to bafilomycin polyketide. To study the biosynthetic pathway of C5N during bafilomycin biosynthesis in K. cheerisanensis KCTC2395, we attempted the functional analysis of two putative genes, encoding 5-aminolevulinic acid synthase (ALAS) and acyl- CoA ligase (ACL). The amplified putative genes for ALAS and ACL were cloned into the E. coli expression vector pET- 32a(+) plasmid, following which the soluble recombinant ALAS and ACL proteins were purified through nickel-affinity column chromatography. Through HPLC analysis of the enzyme reaction mixture, we confirmed the products of putative ALAS and ACL reaction as 5-aminolevulinic acid (5- ALA) and 5-ALA-CoA, respectively. The optimal pH for the putative ALAS reaction was 7.5, and for putative ACL reaction was 7.0, as confirmed by the colorimetric assay. Furthermore, pyridoxal 5􍿁-phosphate (PLP) was found to be an essential cofactor in the putative ALAS reaction, and ATP was a cofactor for the putative ACL catalysis. Finally, we also confirmed that the simultaneous treatment of putative ACL and putative ALAS enzymes resulted in the production of C5N compound from 5-ALA.

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N-acetylcysteine prevents the development of gastritis induced by Helicobacter pylori infection: Sungil Jang , Eun-Jung Bak , Jeong-Heon Cha; J. Microbiol. 2017;55(5):396-402. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7089-9

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Abstract

Helicobacter pylori (H. pylori) is a human gastric pathogen, causing various gastric diseases ranging from gastritis to gas-tric adenocarcinoma. It has been reported that combining N-acetylcysteine (NAC) with conventional antibiotic therapy increases the success rate of H. pylori eradication. We evalu-ated the effect of NAC itself on the growth and coloniza-tion of H. pylori, and development of gastritis, using in vitro liquid culture system and in vivo animal models. H. pylori growth was evaluated in broth culture containing NAC. The H. pylori load and histopathological scores of stomachs were measured in Mongolian gerbils infected with H. pylori strain 7.13, and fed with NAC-containing diet. In liquid culture, NAC inhibited H. pylori growth in a concentration-depen-dent manner. In the animal model, 3-day administration of NAC after 1 week from infection reduced the H. pylori load; 6-week administration of NAC after 1 week from infection prevented the development of gastritis and reduced H. pylori colonization. However, no reduction in the bacterial load or degree of gastritis was observed with a 6-week administ-ration of NAC following 6-week infection period. Our results indicate that NAC may exert a beneficial effect on reduction of bacterial colonization, and prevents the development of severe inflammation, in people with initial asymptomatic or mild H. pylori infection.

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Review

MINIREVIEW] Clinical relevance of infections with zoonotic and human oral species of Campylobacter: Soomin Lee , Jeeyeon Lee , Jimyeong Ha , Yukyung Choi , Sejeong Kim , Heeyoung Lee , Yohan Yoon , Kyoung-Hee Choi; J. Microbiol. 2016;54(7):459-467. Published online June 28, 2016; DOI: https://doi.org/10.1007/s12275-016-6254-x

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Abstract

Genus Campylobacter has been recognized as a causative bacterial agent of animal and human diseases. Human Campylobacter infections have caused more concern. Campylobacters can be classified into two groups in terms of their original host: zoonotic and human oral species. The major zoonotic species are Campylobacter jejuni and Campylobacter coli, which mostly reside in the intestines of avian species and are transmitted to humans via consumption of contaminated poultry products, thus causing human gastroenteritis and other diseases as sequelae. The other campylobacters, human oral species, include C. concisus, C. showae, C. gracilis, C. ureolyticus, C. curvus, and C. rectus. These species are isolated from the oral cavity, natural colonization site, but have potential clinical relevance in the periodontal region to varying extent. Two species, C. jejuni and C. coli, are believed to be mainly associated with intestinal diseases, but recent studies suggested that oral Campylobacter species also play a significant role in intestinal diseases. This review offers an outline of the two Campylobacter groups (zoonotic and human oral), their virulence traits, and the associated illnesses including gastroenteritis.

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

The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding: Kim-Hung Huynh , Myoung-ki Hong , Clarice Lee , Huyen-Thi Tran , Sang Hee Lee , Yeh-Jin Ahn , Sun-Shin Cha , Lin-Woo Kang; J. Microbiol. 2015;53(11):776-782. Published online October 28, 2015; DOI: https://doi.org/10.1007/s12275-015-5475-8

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Abstract

Acinetobacter baumannii, which is emerging as a multidrugresistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 Å. The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays.

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In Silico Design and In Vitro Assessment of Bicyclic Trifluoromethylated Pyrroles as New Antibacterial and Antifungal Agents
Diana Hodyna, Anton Klipkov, Maryna Kachaeva, Yurii Shulha, Igor Gerus, Larysa Metelytsia, Vasyl Kovalishyn
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Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant Acinetobacter baumannii in a Murine Bloodstream Infection Model
Jinxin Zhao, Yan Zhu, Jiru Han, Yu-Wei Lin, Michael Aichem, Jiping Wang, Ke Chen, Tony Velkov, Falk Schreiber, Jian Li
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Identification of natural inhibitors against Acinetobacter baumannii d-alanine-d-alanine ligase enzyme: A multi-spectrum in silico approach
Sajjad Ahmad, Saad Raza, Sumra Wajid Abbasi, Syed Sikander Azam
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Hypermethylation of the interferon regulatory factor 5 promoter in Epstein-Barr virus-associated gastric carcinoma: Seung Myung Dong , Hyun Gyu Lee , Sung-Gyu Cho , Seung-Hyun Kwon , Heejei Yoon , Hyun-Jin Kwon , Ji Hae Lee , Hyemi Kim , Pil-Gu Park , Hoguen Kim , S. Diane Hayward , Jeon Han Park , Jae Myun Lee; J. Microbiol. 2015;53(1):70-76. Published online January 4, 2015; DOI: https://doi.org/10.1007/s12275-014-4654-3

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Abstract

Interferon regulatory factor-5 (IRF-5), a member of the mammalian IRF transcription factor family, is regulated by p53, type I interferon and virus infection. IRF-5 participates in virus-induced TLR-mediated innate immune responses and may play a role as a tumor suppressor. It was suppressed in various EBV-infected transformed cells, thus it is valuable to identify the suppression mechanism. We focused on a promoter CpG islands methylation, a kind of epigenetic regulation in EBV-associated Burkitt’s lymphomas (BLs) and gastric carcinomas. IRF-5 is not detected in most of EBV-infected BL cell lines due to hypermethylation of IRF-5 distal promoter (promoter-A), which was restored by a demethylating agent, 5-aza-2􍿁-deoxycytidine. Hypomethylation of CpG islands in promoter-A was observed only in EBV type III latent infected BL cell lines (LCL and Mutu III). Similarly, during EBV infection to Akata-4E3 cells, IRF-5 was observed at early time periods (2 days to 8 weeks), concomitant unmethylation of promoter-A, but suppressed in later infection periods as observed in latency I BL cell lines. Moreover, hypermethylation in IRF-5 promoter-A region was also observed in EBV-associated gastric carcinoma (EBVaGC) cell lines or primary gastric carcinoma tissues, which show type I latent infection. In summary, IRF-5 is suppressed by hypermethylation of its promoter-A in most of EBV-infected transformed cells, especially BLs and EBVaGC. EBV-induced carcinogenesis takes an advantage of proliferative effects of TLR signaling, while limiting IRF-5 mediated negative effects in the establishment of EBVaGCs.

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Journal Article

Use of Selected Lactic Acid Bacteria in the Eradication of Helicobacter pylori Infection: Jin-Eung Kim , Min-Soo Kim , Yeo-Sang Yoon , Myung-Jun Chung , Do-Young Yum; J. Microbiol. 2014;52(11):955-962. Published online October 3, 2014; DOI: https://doi.org/10.1007/s12275-014-4355-y

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Abstract

Helicobacter pylori is among the major pathogenic bacteria that cause chronic gastritis and peptic ulcer disease and is related to the development of gastric cancer. Several chemicals, including antibiotics, have been used to eradicate H. pylori; however, they do not always curb the infection. Ten representative type strains of lactic acid bacteria (LAB) were screened for antagonism toward H. pylori via inhibition of urease activity. Strains inhibiting the binding of H. pylori to human gastric cell line cells and suppressing H. pylori-induced interleukin-8 (IL-8) production were also screened. Of these, Pediococcus pentosaseus (SL4), which inhibited the adhesion of H. pylori to MKN-45 gastric cancer cells, Bifidobacterium longum (BG7), with urease inhibiting activity, and Lactococcus lactis (SL3), and Enterococcus faecalis (SL5), which suppressed H. pylori-induced IL-8 production within MKN-45 and AGS cells, were selected. In mouse model, these LAB stains in combination significantly suppressed IL-8 levels in serum. Gastric pH also recovered to normal values after the administration of these LAB. These stains effectively suppressed H. pylori viability, although not to the extent of antibiotic treatment. When used as probiotics, LAB may help decrease the occurrence of gastritis and reduce the risk of H. pylori infection without, inducing side effects.

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FERMENTE GIDALARIN İNSAN SAĞLIĞI ÜZERİNDEKİ ETKİLERİ
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Mehdi Tourani, Maryam Habibzadeh, Ahmad Karkhah, Javad Shokri-Shirvani, Ladan Barari, Hamid Reza Nouri
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Fan Wang, Juerong Feng, Pengfei Chen, Xiaoping Liu, Minxing Ma, Rui Zhou, Ying Chang, Jing Liu, Jin Li, Qiu Zhao
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Research Support, Non-U.S. Gov't

Simultaneous Detection of Waterborne Viruses by Multiplex Real-Time PCR: Lae-Hyung Kang , Se-hwan Oh , Jeong-Woong Park , Yu-Jung Won , Sangryeol Ryu , Soon-Young Paik; J. Microbiol. 2013;51(5):671-675. Published online September 14, 2013; DOI: https://doi.org/10.1007/s12275-013-3199-1

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Abstract

Norovirus, Rotavirus group A, the Hepatitis A virus, and Coxsackievirus are all common causes of gastroenteritis. Conventional diagnoses of these causative agents are based on antigen detection and electron microscopy. To improve the diagnostic potential for viral gastroenteritis, internally controlled multiplex real-time polymerase chain reaction (PCR) methods have been recently developed. In this study, individual real-time PCRs were developed and optimized for specific detections of Norovirus genogroup I, Norovirus genogroup II, Rotavirus group A, the Hepatitis A virus, and Coxsackievirus group B1. Subsequently, individual PCRs were combined with multiplex PCR reactions. In general, multiplex real-time PCR assays showed comparable sensitivities and specificities with individual assays. A retrospective clinical evaluation showed increased pathogen detection in 29% of samples using conventional PCR methods. Prospective clinical evaluations were detected in 123 of the 227 (54%) total samples used in the multiplex realtime PCR analysis. The Norovirus genogroup II was found most frequently (23%), followed by Rotavirus (20%), the Hepatitis A virus (4.5%), Coxsackievirus (3.5%), and Norovirus genogroup I (2.6%). Internally controlled multiplex real-time PCR assays for the simultaneous detection of Rotavirus, Coxsackievirus group B, the Hepatitis A virus, and Norovirus genogroups I and II showed significant improvement in the diagnosis of viral gastroenteritis.

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