Journal of Microbiology

Reviews

Coordinated regulation of interferon and inflammasome signaling pathways by SARS-CoV-2 proteins: Na-Eun Kim , Yoon-Jae Song; J. Microbiol. 2022;60(3):300-307. Published online January 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1502-8

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Type I and III interferons (IFNs) and the nucleotide-binding domain (NBD) leucine-rich repeat (LRR)-containing receptor (NLR) family pyrin domain containing 3 (NLRP3) inflammasome play pivotal roles in the pathogenesis of SARS-CoV-2. While optimal IFN and inflammasome responses are essential for limiting SARS-CoV-2 infection, aberrant activation of these innate immune responses is associated with COVID-19 pathogenesis. In this review, we focus our discussion on recent findings on SARS-CoV-2-induced type I and III IFNs and NLRP3 inflammasome responses and the viral proteins regulating these mechanisms.

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The impact of polymorphic variants of interferon receptor genes on COVID-19 severity and antibiotic resistance
E. A. Krieger, O. V. Samodova, O. A. Svitich, R. V. Samoilikov, E. A. Meremianina, L. V. Ivanova, N. A. Bebyakova, E. N. Ilina, A. V. Pavlenko, Yu. I. Esin, A. L. Arkhipova, S. N. Kovalchuk, A. V. Kudryavtsev
Russian Journal of Infection and Immunity.2024; 13(6): 1027. CrossRef
SARS-CoV-2 ORF8 as a Modulator of Cytokine Induction: Evidence and Search for Molecular Mechanisms
Marília Inês Móvio, Giovana Waner Carneiro de Almeida, Isabella das Graças Lopes Martines, Gilmara Barros de Lima, Sergio Daishi Sasaki, Alexandre Hiroaki Kihara, Emma Poole, Michael Nevels, Maria Cristina Carlan da Silva
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Sensing of viral lung infections by cGAS-STING
Lei Fang, Michael Roth
Exploration of Immunology.2022; : 303. CrossRef
Two years of COVID-19 pandemic: where are we now?
Jinjong Myoung
Journal of Microbiology.2022; 60(3): 235. CrossRef
The Potential of Purinergic Signaling to Thwart Viruses Including SARS-CoV-2
Davide Ferrari, Michele Rubini, Jorge S. Burns
Frontiers in Immunology.2022;[Epub] CrossRef

[MINIREIVEW] Anti-MRSA agent discovery using Caenorhabditis elegans-based high-throughput screening: Soo Min Kim , Iliana Escorbar , Kiho Lee , Beth Burgwyn Fuchs , Eleftherios Mylonakis , Wooseong Kim; J. Microbiol. 2020;58(6):431-444. Published online May 27, 2020; DOI: https://doi.org/10.1007/s12275-020-0163-8

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Staphylococcus aureus is a leading cause of hospital- and community- acquired infections. Despite current advances in antimicrobial chemotherapy, the infections caused by S. aureus remain challenging due to their ability to readily develop resistance. Indeed, antibiotic resistance, exemplified by methicillin- resistant S. aureus (MRSA) is a top threat to global health security. Furthermore, the current rate of antibiotic discovery is much slower than the rate of antibiotic-resistance development. It seems evident that the conventional in vitro bacterial growth-based screening strategies can no longer effectively supply new antibiotics at the rate needed to combat bacterial antibiotic-resistance. To overcome this antibiotic resistance crisis, screening assays based on host–pathogen interactions have been developed. In particular, the free-living nematode Caenorhabditis elegans has been used for drug screening against MRSA. In this review, we will discuss the general principles of the C. elegans-based screening platform and will highlight its unique strengths by comparing it with conventional antibiotic screening platforms. We will outline major hits from high-throughput screens of more than 100,000 small molecules using the C. elegans–MRSA infection assay and will review the mode-of-action of the identified hit compounds. Lastly, we will discuss the potential of a C. elegansbased screening strategy as a paradigm shift screening platform.

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Journal Article

Molecular Characteristics and Resistant Mechanisms of Imipenem-Resistant Acinetobacter baumannii Isolates in Shenyang, China: Jing Ping Zhang , Wan Zhu , Su Fei Tian , Yun Zhuo Chu , Bai Yi Chen; J. Microbiol. 2010;48(5):689-694. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0137-3

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The investigation was carried out to elucidate the molecular characteristics and resistant mechanisms of imipenem-resistant Acinetobacter baumannii. Thirty-seven isolates were collected from January 2007 to December 2007. The homology of the isolates was analyzed by both pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The genes of β-lactamases, adeB, and class 1 integron were polymerase chain reaction amplified. Genotype analysis of the 37 A. baumannii isolates by PFGE revealed the circulation of four PFGE types (A-D) ; the A- and B-type accounted for 48.6% and 40.5%, respectively. MLST showed the existence of three allelic profiles. The agar dilution method was carried out to determine the MIC of imipenem, in the absence or presence of carbonyl cyanide m-chlorophenylhydrazone (CCCP, 10 μg/ml). The MICs of the strains to imipenem were between 16 μg/ml and 128 μg/ml. When CCCP was added, a MIC decrease of at least four-fold was observed in 20 isolates, which belonged to the A- or C-type. AdeB and blaPER-1 genes were each detected in 35 isolates, blaOXA-23 gene in 34 isolates and blaOXA-58-like gene in 24 isolates. All isolates harbored blaOXA-51-like genes. No isolates carried the blaIMP-1 gene. Integron was detected in 25 isolates, which mediated the resistance to aminoglycosides and rifampin. The epidemiologic data suggested that the increasing infection of A. baumannii in our hospital was mainly caused by the inter-hospital spread of two epidemic clones. The AdeABC efflux system may be the important factor that leads to the high level of imipenem-resistance in PFGE A-type.

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Resistant mechanisms and molecular epidemiology of imipenem-resistant Acinetobacter baumannii
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Molecular Epidemiology and Mechanisms of Carbapenem Resistance ofAcinetobacterspp. in Asia and Oceania
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Distribution and molecular profiling of class 1 integrons in MDR Acinetobacter baumannii isolates and whole genome-based analysis of antibiotic resistance mechanisms in a representative strain
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Characterization of a Novel Plasmid Type and Various Genetic Contexts of blaOXA-58 in Acinetobacter spp. from Multiple Cities in China
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Research Support, Non-U.S. Gov'ts

Genetic Diversity of Chromosomal Metallo-β-Lactamase Genes in Clinical Isolates of Elizabethkingia meningoseptica from Korea: Jong Hwa Yum , Eun Young Lee , Sung-Ho Hur , Seok Hoon Jeong , Hyukmin Lee , Dongeun Yong , Yunsop Chong , Eun-Woo Lee , Patrice Nordmann , Kyungwon Lee; J. Microbiol. 2010;48(3):358-364. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-9308-5

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This study was performed to characterize the chromosomal metallo-β-lactamases (MBLs) of Elizabethkingia meningoseptica isolated from Korea and to propose a clustering method of BlaB and GOB MBLs based on their amino acid similarities. Chromosomal MBL genes were amplified by PCR from 31 clinical isolates of E. meningoseptica. These PCR products were then cloned into a vector and electrotransformed into E. coli DH5α. Nucleotide sequencing was performed by the dideoxy chain termination method using PCR products or cloned DNA fragments. Antimicrobial susceptibilities were determined by the agar dilution method. PCR experiments showed that all 31 E. meningoseptica isolates contained both the blaB and the blaGOB genes. DNA sequence analysis revealed that E. meningoseptica isolates possessed seven types of blaB gene, including five novel variants (blaB-9 to blaB-13) and 11 types of blaGOB gene, including 10 novel variants (blaGOB-8 to blaGOB-17). The most common combination of MBL was BlaB-12 plus GOB-17 (n=19). Minimum inhibitory concentrations of imipenem and meropenem for the electrotransformants harboring novel BlaB and GOB MBLs were two- or four-fold higher than those for the recipient E. coli DH5α. BlaB and GOB MBLs were grouped in three and six clusters including fifteen novel variants, respectively, based on amino acid similarities.

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Mortality Risk and Antibiotic Therapy for Patients with Infections Caused by Elizabethkingia Species—A Meta-Analysis
Chienhsiu Huang, Sufang Kuo, Lichen Lin
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Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup—emerging targets to combat antibiotic resistance
Stefan Krco, Samuel J. Davis, Pallav Joshi, Liam A. Wilson, Marcelo Monteiro Pedroso, Andrew Douw, Christopher J. Schofield, Philip Hugenholtz, Gerhard Schenk, Marc T. Morris
Frontiers in Chemistry.2023;[Epub] CrossRef
Epidemiology and Characteristics of Elizabethkingia spp. Infections in Southeast Asia
Asdren Zajmi, Jeanette Teo, Chew Chieng Yeo
Microorganisms.2022; 10(5): 882. CrossRef
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Izzet Burcin Saticioglu, Muhammed Duman, Soner Altun
Aquaculture.2021; 535: 736364. CrossRef
Core-Proteomics-Based Annotation of Antigenic Targets and Reverse-Vaccinology-Assisted Design of Ensemble Immunogen against the Emerging Nosocomial Infection-Causing Bacterium Elizabethkingia meningoseptica
Muhammad Idrees, Muhammad Yasir Noorani, Kalim Ullah Altaf, Eid A. Alatawi, Faris F. Aba Alkhayl, Khaled S. Allemailem, Ahmad Almatroudi, Murad Ali Khan, Muhammad Hamayun, Taimoor Khan, Syed Shujait Ali, Abbas Khan, Dong-Qing Wei
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Risk Factors for Elizabethkingia Acquisition and Clinical Characteristics of Patients, South Korea
Min Hyuk Choi, Myungsook Kim, Su Jin Jeong, Jun Yong Choi, In-Yong Lee, Tai-Soon Yong, Dongeun Yong, Seok Hoon Jeong, Kyungwon Lee
Emerging Infectious Diseases.2019; 25(1): 42. CrossRef
In vitro activities of imipenem, vancomycin, and rifampicin against clinical Elizabethkingia species producing BlaB and GOB metallo-beta-lactamases
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European Journal of Clinical Microbiology & Infectious Diseases.2019; 38(11): 2045. CrossRef
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Mi-Soon Han, Hyunsoo Kim, Yangsoon Lee, Myungsook Kim, Nam Su Ku, Jun Yong Choi, Dongeun Yong, Seok Hoon Jeong, Kyungwon Lee, Yunsop Chong, Karen C. Carroll
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Wei-Hua Zhao, Zhi-Qing Hu
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Insights from the Genome Annotation of Elizabethkingia anophelis from the Malaria Vector Anopheles gambiae
Phanidhar Kukutla, Bo G. Lindberg, Dong Pei, Melanie Rayl, Wanqin Yu, Matthew Steritz, Ingrid Faye, Jiannong Xu, Zhijian Tu
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Stephanie A. Matyi, Peter R. Hoyt, Akira Hosoyama, Atsushi Yamazoe, Nobuyuki Fujita, John E. Gustafson
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Serotype Distribution and β-Lactam Resistance in Haemophilus influenzae Isolated from Patients with Respiratory Infections in Korea: Songmee Bae , Jaehoon Lee , Eunah Kim , Jaehwa Lee , Jaeyon Yu , Yeonho Kang; J. Microbiol. 2010;48(1):84-88. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0212-9

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Haemophilus influenzae is a frequent causative bacterial pathogen of respiratory tract infections. Resistance to β-lactam antibiotics has been a significant clinical problem in treatment for H. influenzae respiratory infections. This study describes the serotype, antibiotic resistance and distribution of TEM-1 or ROB-1 β-lactamase in H. influenzae isolates from local private hospitals from 2002 to 2004. Among the 100 H. influenzae respiratory isolates, only 7% were identified as serotypes a, b, e, and f, with the remaining 93% being nontypeable. Resistance to ampicillin, cefaclor, and tetracycline was 57%, 46%, and 16%, respectively. All strains were susceptible to azithromycin and ciprofloxacin, whereas amoxicillin/clavulanate, cefotaxime, and imipenem exhibited reduced susceptibilities of 99%, 99%, and 91%, respectively. All 57 ampicillinresistant strains (minimum inhibitory concentration, MIC≥4 µg/ml) were β-lactamase-positive and possessed the TEM-1 type β-lactamase. One β-lactamase-positive amoxicillin/clavulanate-resistant isolate that was resistant to ampicillin (MIC>128 µg/ml) had the TEM-1 type β-lactamase and not susceptible to cefaclor and cefotaxime. Analysis of penicillin binding protein 3 revealed six residues (Asp-350, Met-377, Ala-502, Asn-526, Val-547, and Asn-569)that were substituted by Asn, Ile, Val, Lys, Ile, and Ser, respectively.

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Results from the Survey of Antibiotic Resistance (SOAR) 2012–14 in Thailand, India, South Korea and Singapore
D. Torumkuney, R. Chaiwarith, W. Reechaipichitkul, K. Malatham, V. Chareonphaibul, C. Rodrigues, D. S. Chitins, M. Dias, S. Anandan, S. Kanakapura, Y. J. Park, K. Lee, H. Lee, J. Y. Kim, Y. Lee, H. K. Lee, J. H. Kim, T. Y. Tan, Y. X. Heng, P. Mukherjee, I
Journal of Antimicrobial Chemotherapy.2016; 71(suppl 1): i3. CrossRef
Haemophilus influenzae serotype a as a cause of serious invasive infections
Marina Ulanova, Raymond S W Tsang
The Lancet Infectious Diseases.2014; 14(1): 70. CrossRef
Global Epidemiology of Invasive Haemophilus influenzae Type a Disease: Do We Need a New Vaccine?
Marina Ulanova
Journal of Vaccines.2013; 2013: 1. CrossRef

A Circularly Permuted β-Lactamase as a Novel Reporter for Evaluation of Protein Cyclization Efficiency: Jeong Seon Kwon , Jyotiranjan Bal , Hai Min Hwang , Jeong-Yoon Kim; J. Microbiol. 2008;46(4):456-461. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0106-2

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Split inteins have been used as a versatile tool in protein engineering to mediate efficient in vivo and in vitro trans-splicing of a protein. The trans-splicing ability of split inteins was also applied to the in vivo cyclization of a protein. However, cyclization efficiency is dependent upon the type of split inteins employed and the conditions under which cyclization occur. In this study, a novel reporter system that easily measures the cyclization efficiency of split inteins was developed. For this purpose TEM-1 β-lactamase was divided into two fragments (24~215 and 216~286 amino acids) and circularly permuted. The circularly permuted β-lactamase expressed in Escherichia coli showed little β-lactamase activity, most likely due to the structural modification of the protein. However, when the circularly permuted β-lactamase was cyclized by the Synechocystis sp. PCC6803 DnaB split mini-intein, β-lactamase activity both in vitro and in vivo was recovered. These results suggest that the novel reporter system can be exploited to develop new inteins with high efficiency of in vivo protein cyclization.

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Backbone cyclization of Salmonella typhimurium diaminopropionate ammonia-lyase to enhance the activity and stability
Xiaomei He, Tingting Lin, Yuying Xie, Jinjing Li, Yuanyuan Ge, Shuncheng Zhang, Jun Fan
Protein Expression and Purification.2024; 218: 106447. CrossRef
Off‐Pathway‐Sensitive Protein‐Splicing Screening Based on a Toxin/Antitoxin System
Hannes M. Beyer, Hideo Iwaï
ChemBioChem.2019; 20(15): 1933. CrossRef
Circular Permutation of Bacillus circulans Xylanase: A Kinetic and Structural Study
Stephan Reitinger, Ying Yu, Jacqueline Wicki, Martin Ludwiczek, Igor D’Angelo, Simon Baturin, Mark Okon, Natalie C. J. Strynadka, Stefan Lutz, Stephen G. Withers, Lawrence P. McIntosh
Biochemistry.2010; 49(11): 2464. CrossRef

Molecular Characterization of Pseudomonas aeruginosa Isolates Resistant to All Antimicrobial Agents, but Susceptible to Colistin, in Daegu, Korea: Yoo Chul Lee , Byung Jun Ahn , Jong Sook Jin , Jung Uk Kim , Sang Hwa Lee , Do Young Song , Won Kil Lee , Je Chul Lee; J. Microbiol. 2007;45(4):358-363.; DOI: https://doi.org/2560 [pii]

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Abstract PDF: Multi-drug resistant Pseudomonas aeruginosa has been implicated in a variety of serious therapeutic problems in clinical environments. Among the 968 P. aeruginosa isolates obtained from two hospitals in Daegu, Korea, we acquired 17 isolates that were resistant to all available tested antimicrobial agents, with the exception of colistin (colistin-only sensitive). We characterized the antimicrobial susceptibilities, metallo-β-lactamases, and epidemiological relatedness among the colistin-only sensitive P. aeruginosa isolates. All colistin-only sensitive isolates were positive in the modified Hodge test and imipenem-EDTA synergy test, thereby indicating the production of metallo-β-lactamases. 11 isolates from the secondary hospital and six isolates from the tertiary teaching hospital harbored blaVIM-2 and blaIMP-1, respectively. The pulsed-field gel electrophoretic analysis of the SpeI-digested DNA from P. aeruginosa isolates indicated that two different clones of colistin-only sensitive P. aeruginosa originated from each hospital, and had spread within the hospital environment. Overall, colistin-only sensitive P. aeruginosa was detected in Korea for the first time, but no pan-drug resistant bacteria were identified. Nationwide surveillance is required in order to monitor the emergence of colistin-only sensitive or pan-drug resistant bacteria.

Multidrug-Resistant Providencia Isolates Carrying blaPER-1, blaVIM-2, and armA: Hee-Woo Lee , Hee-Young Kang , Kyeong-Seob Shin , Jungmin Kim; J. Microbiol. 2007;45(3):272-274.; DOI: https://doi.org/2531 [pii]

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Abstract PDF: During May to July 2004, three strains of Providencia spp. with multidrug-resistance (MDR) were isolated from urinary specimen of three patients hospitalized with a same hospital room. By PCR analysis, all three strains have been found to carry both VIM-2 type metallo-β-lactamase gene and PER-1 type extendedspectrum β-lactamase gene. One out of three strains carried additional resistance gene, armA, 16S rRNA methylase gene responsible for high level resistance to aminoglycosides. To our knowledge, this is the first report on the identification of Providencia spp. simultaneously carrying blaVIM-2, blaPER-1, and armA genes.

Removal of Contaminating TEM-la β-Lactamase Gene from Removal of Contaminating TEM-la β-Lactamase Gene from: Jae Seok Song , Jung Hun Lee , Jung-Hyun Lee , Byeong Chul Jeong , Won-Keun Lee , Sang Hee Lee; J. Microbiol. 2006;44(1):126-128.; DOI: https://doi.org/2326 [pii]

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Abstract PDF: This study confirms that Taq DNA polymerase could be contaminated with the blaTEM-1a gene. It also proposes two different methods that could be used to overcome DNA contamination: (i) DNase I treatment prior to PCR amplification; and (ii) the use of a highly purified Taq DNA polymerase which was devoid of detectable contamination.

Construction of secretion vectors using the α-amylase signal sequence of bacillus subtilis NA64: Kim, Sung Il , Lee, Se Yong; J. Microbiol. 1996;34(1):74-81.

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Abstract PDF: Two secretion vectors, pUBA240 and pUB340 were constructed by using the promoter and secretory signal region of the α-amylase gene from an α-amylase hyperproducing strain, Bacillus subtilis NA64. In this secretion vector system, various restriction enzyme sites are located immediately after the proregion of the α-amylase gene for easy replacement of various foreign structural genes. To evaluate this secretion vectors, the β-lactamase gene of pBR322 was used as a reporter gene. The expressed and biologically active β-lactamase was secreted into the culture broth from B. subtilis LKS86 transformants harboring each β-lactamase secreting plasmid, pUBAbla and pUBSble. In both cases, more than 92% of expressed β- lactamases were located idn the culture medium. The amount of the secreted β-lactamase was about 80% of the total secreted proteins in the culture medium.

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