Journal of Microbiology

Journal Articles

Crystal structure of the nuclease and capping domain of SbcD from Staphylococcus aureus: Jinwook Lee , Inseong Jo , Jinsook Ahn , Seokho Hong , Soyeon Jeong , Aeran Kwon , Nam-Chul Ha; J. Microbiol. 2021;59(6):584-589. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-1012-0

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The SbcCD complex is an essential component of the DNA double-strand break (DSB) repair system in bacteria. The bacterial SbcCD complex recognizes and cleaves the DNA ends in DSBs by ATP-dependent endo- and exonuclease activities as an early step of the DNA repair process. SbcD consists of nuclease, capping, and helix-loop-helix domains. Here, we present the crystal structure of a SbcD fragment from Staphylococcus aureus, which contained nuclease and capping domains, at a resolution of 2.9 Å. This structure shows a dimeric assembly similar to that of the corresponding domains of SbcD from Escherichia coli. The S. aureus SbcD fragment exhibited endonuclease activities on supercoiled DNA and exonuclease activity on linear and nicked DNA. This study contributes to the understanding of the molecular basis for how bacteria can resist sterilizing treatment, causing DNA damage.

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Staphylococcus aureus SOS response: Activation, impact, and drug targets
Kaiying Cheng, Yukang Sun, Huan Yu, Yingxuan Hu, Yini He, Yuanyuan Shen
mLife.2024; 3(3): 343. CrossRef

Epidemiology and resistance features of Acinetobacter baumannii isolates from the ward environment and patients in the burn ICU of a Chinese hospital: Yali Gong , Xiaodong Shen , Guangtao Huang , Cheng Zhang , Xiaoqiang Luo , Supeng Yin , Jing Wang , Fuquan Hu , Yizhi Peng , Ming Li; J. Microbiol. 2016;54(8):551-558. Published online August 2, 2016; DOI: https://doi.org/10.1007/s12275-016-6146-0

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Abstract

Acinetobacter baumannii is an important opportunistic pathogen that causes severe nosocomial infections, especially in intensive care units (ICUs). Over the past decades, an everincreasing number of hospital outbreaks caused by A. baumannii have been reported worldwide. However, little attention has been directed toward the relationship between A. baumannii isolates from the ward environment and patients in the burn ICU. In this study, 88 A. baumannii isolates (26 from the ward environment and 62 from patients) were collected from the burn ICU of the Southwest Hospital in Chongqing, China, from July through December 2013. Antimicrobial susceptibility testing results showed that drug resistance was more severe in isolates from patients than from the ward environment, with all of the patient isolates being fully resistant to 10 out of 19 antimicrobials tested. Isolations from both the ward environment and patients possessed the β-lactamase genes blaOXA-51, blaOXA-23, blaAmpC, blaVIM, and blaPER. Using pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST), these isolates could be clustered into 4 major PFGE types and 4 main sequence types (ST368, ST369, ST195, and ST191) among which, ST368 was the dominant genotype. Epidemiologic and molecular typing data also revealed that a small-scale outbreak of A. baumannii infection was underway in the burn ICU of our hospital during the sampling period. These results suggest that dissemination of β-lactamase genes in the burn ICU might be closely associated with the high-level resistance of A. baumannii, and the ICU environment places these patients at a high risk for nosocomial infection. Cross-contamination should be an important concern in clinical activities to reduce hospital acquired infections caused by A. baumannii.

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Prevalence, Characterization, and Epidemiological Relationships between ESBL and Carbapenemase-Producing Escherichia coli, Klebsiella pneumoniae, and Acinetobacter spp. Isolated from Humans and the Kitchen Environment of Two Greek Hospitals
Anestis Tsitsos, Alexandros Damianos, Maria Boutel, Panagiota Gousia, Nikolaos Soultos, Anna Papa, Ilias Tirodimos, Vangelis Economou
Antibiotics.2024; 13(10): 934. CrossRef
Molecular Typing and Resistance Profile of Acinetobacter baumannii Isolates during the COVID-19 Pandemic: Findings from the “EPIRADIOCLINF” Project
Antonella Agodi, Arturo Montineri, Rosa Manuele, Paola Noto, Giuseppe Carpinteri, Giacomo Castiglione, Patrizia Grassi, Antonio Lazzara, Anna Rita Mattaliano, Giuseppa Granvillano, Claudia La Mastra, Maria Clara La Rosa, Andrea Maugeri, Martina Barchitta
Antibiotics.2023; 12(10): 1551. CrossRef
Dissemination and Genetic Relatedness of Multidrug-Resistant and Extensively Drug-Resistant Acinetobacter baumannii Isolates from a Burn Hospital in Iraq
Aras A. K Shali, Paywast J Jalal, Sehand K Arif, Abdelaziz Ed-dra
Canadian Journal of Infectious Diseases and Medical Microbiology.2022; 2022: 1. CrossRef
Acinetobacter baumannii Isolates from COVID-19 Patients in a Hospital Intensive Care Unit: Molecular Typing and Risk Factors
Mariateresa Ceparano, Valentina Baccolini, Giuseppe Migliara, Claudia Isonne, Erika Renzi, Daniela Tufi, Corrado De Vito, Maria De Giusti, Maria Trancassini, Francesco Alessandri, Giancarlo Ceccarelli, Francesco Pugliese, Paolo Villari, Maria Angiulli, St
Microorganisms.2022; 10(4): 722. CrossRef
The characteristic and potential therapeutic effect of isolated multidrug-resistant Acinetobacter baumannii lytic phage
Behnam Sisakhtpour, Arezoo Mirzaei, Vajihe Karbasizadeh, Nafiseh Hosseini, Mehdi Shabani, Sharareh Moghim
Annals of Clinical Microbiology and Antimicrobials.2022;[Epub] CrossRef
The Relationship between Carbapenem Resistance and Biofilm Formation in Clinical Acinetobacter Baumannii Isolates
Fariba Naeimi Mazraeh, Naser Alizadeh, Roghayeh Nouri, Hossein Samadi Kafil, Shahram Abdoli Oskouie, Mohammad Ahangarzadeh Rezaee
SSRN Electronic Journal .2022;[Epub] CrossRef
The Low-Alkalinity Polymyxin Derivative, AL-6, Shows High Activity Against Multidrug-Resistant Acinetobacter baumannii Clinical Isolates In Vitro and A. baumannii ATCC 19606 In Vivo: Preliminary Analysis of the Antibacterial Mechanism
Dai-Jie Chen, A-Long Cui, Jia-Rong Chen, Ping Yang, Jie Jin, Lei Shao, Zhuo-Rong Li
Microbial Drug Resistance.2021; 27(7): 933. CrossRef
Different Infection Profiles and Antimicrobial Resistance Patterns Between Burn ICU and Common Wards
Yali Gong, Yuan Peng, Xiaoqiang Luo, Cheng Zhang, Yunlong Shi, Yixin Zhang, Jun Deng, Yizhi Peng, Gaoxing Luo, Haisheng Li
Frontiers in Cellular and Infection Microbiology.2021;[Epub] CrossRef
Epidemiological Analysis of Multidrug-Resistant Acinetobacter baumannii Isolates in a Tertiary Hospital Over a 12-Year Period in China
Meijie Jiang, Xia Chen, Shuang Liu, Zhijun Zhang, Ning Li, Chao Dong, Ling Zhang, Haiyan Wu, Shuping Zhao
Frontiers in Public Health.2021;[Epub] CrossRef
Pathogenic Characteristics and Risk Factors for ESKAPE Pathogens Infection in Burn Patients
Zhaoyinqian Li, Jingling Xie, Jiaxin Yang, Siyi Liu, Zixuan Ding, Jingchen Hao, Yinhuan Ding, Zhangrui Zeng, Jinbo Liu
Infection and Drug Resistance.2021; Volume 14: 4727. CrossRef
High frequency of blaPER-1 gene in clinical strains of Acinetobacter baumannii and its association with quorum sensing and virulence factors
Fariba Naeimi Mazraeh, Alka Hasani, Javid Sadeghi, Hossein Samadi Kafil, Mohammad Hossein Soroush Barhaghi, Fatemeh Yeganeh Sefidan, Hamideh Rishi Sharabiani, Yalda Hematyar, Mohammad Ahangarzadeh Rezaee
Gene Reports.2021; 24: 101232. CrossRef
Isolation and Characterization of a Novel Myophage Abp9 Against Pandrug Resistant Acinetobacater baumannii
Lingli Jiang, Jingjie Tan, Yi Hao, Qi Wang, Xiaorui Yan, Dali Wang, Li Tuo, Zairong Wei, Guangtao Huang
Frontiers in Microbiology.2020;[Epub] CrossRef
Molecular typing of multi-drug resistant Acinetobacter baumannii isolates from clinical and environmental specimens in three Iranian hospitals by pulsed field gel electrophoresis
Ali Mohammadi Bardbari, Parviz Mohajeri, Mohammad Reza Arabestani, Manoochehr Karami, Fariba Keramat, Saba Asadollahi, Amir Khodavirdipour, Mohammad Yousef Alikhani
BMC Microbiology.2020;[Epub] CrossRef
The impact of serum protein binding on bacterial killing of minocycline
Li-Xia Xie, Jian Zhou, Kimberly R. Ledesma, Paul R. Merlau, Vincent H. Tam
Journal of Global Antimicrobial Resistance.2020; 21: 252. CrossRef
The distribution of mutations and hotspots in transcription regulators of resistance-nodulation-cell division efflux pumps in tigecycline non-susceptible Acinetobacter baumannii in China
Qingye Xu, Xiaoting Hua, Jintao He, Di Zhang, Qiong Chen, Linghong Zhang, Belinda Loh, Sebastian Leptihn, Yurong Wen, Paul G. Higgins, Yunsong Yu, Zhihui Zhou
International Journal of Medical Microbiology.2020; 310(8): 151464. CrossRef
In vitro activities of Eravacycline against 336 isolates collected from 2012 to 2016 from 11 teaching hospitals in China
Chunjiang Zhao, Xiaojuan Wang, Yawei Zhang, Ruobing Wang, Qi Wang, Henan Li, Hui Wang
BMC Infectious Diseases.2019;[Epub] CrossRef
Carbapenem-resistant Acinetobacter baumannii in patients with burn injury: A systematic review and meta-analysis
William Gustavo Lima, Geisa Cristina Silva Alves, Cristina Sanches, Simone Odília Antunes Fernandes, Magna Cristina de Paiva
Burns.2019; 45(7): 1495. CrossRef
Global Transcriptomic Analysis of the Interactions between Phage φAbp1 and Extensively Drug-Resistant Acinetobacter baumannii
Zichen Yang, Supeng Yin, Gang Li, Jing Wang, Guangtao Huang, Bei Jiang, Bo You, Yali Gong, Cheng Zhang, Xiaoqiang Luo, Yizhi Peng, Xia Zhao, Sergio Baranzini
mSystems.2019;[Epub] CrossRef
Environmental contamination by carbapenem-resistant Acinetobacter baumannii: The effects of room type and cleaning methods
Anat Or Lerner, Jalal Abu-Hanna, Yehuda Carmeli, Vered Schechner
Infection Control & Hospital Epidemiology.2019; : 1. CrossRef
Janus N,N-dimethylformamide as a solvent for a gradient porous wound dressing of poly(vinylidene fluoride) and as a reducer for in situ nano-silver production: anti-permeation, antibacterial and antifouling activities against multi-drug-resistant bacteria
Menglong Liu, Ying Wang, Xiaodong Hu, Weifeng He, Yali Gong, Xiaohong Hu, Meixi Liu, Gaoxing Luo, Malcolm Xing, Jun Wu
RSC Advances.2018; 8(47): 26626. CrossRef
Whole-Genome Analysis of an Extensively Drug-Resistant Acinetobacter baumannii Strain XDR-BJ83: Insights into the Mechanisms of Resistance of an ST368 Strain from a Tertiary Care Hospital in China
Yang-Yang Zhang, Zhi-Xin Liang, Chun-Sun Li, Yan Chang, Xiu-Qing Ma, Ling Yu, Liang-An Chen
Microbial Drug Resistance.2018; 24(9): 1259. CrossRef
Multilocus sequence typing and molecular characterization of β-lactamase genes among Acinetobacter baumannii isolates in a burn center
Guangtao Huang, Yuan Peng, Yong Yang, Chengyong Tang, Yuexian Fu
Burns.2017; 43(7): 1473. CrossRef

Inverse PCR for subtyping of Acinetobacter baumannii carrying ISAba1: Shukho Kim , Yun-Ju Park , Jungmin Kim; J. Microbiol. 2016;54(5):376-380. Published online April 20, 2016; DOI: https://doi.org/10.1007/s12275-016-6038-3

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Abstract

Acinetobacter baumannii has been prevalent in nosocomial infections, often causing outbreaks in intensive care units. ISAba1 is an insertion sequence that has been identified only in A. baumannii and its copy number varies among strains. It has been reported that ISAba1 provides a promoter for blaOXA-51-like, blaOXA-23-like, and blaampC, which are associated with the resistance of A. baumannii to carbapenems and cephalosporins. The main purpose of this study was to develop a novel inverse PCR method capable of typing A. baumannii strains. The method involves three major steps: cutting of genomic DNA with a restriction enzyme, ligation, and PCR. In the first step, bacterial genomic DNA was digested with DpnI. In the second step, the digested genomic DNAs were ligated to form intramolecular circular DNAs. In the last step, the ligated circular DNAs were amplified by PCR with primers specific for ISAba1 and the amplified PCR products were electrophoresed. Twenty-two clinical isolates of A. baumannii were used for the evaluation of the inverse PCR (iPCR) typing method. Dendrogram analysis revealed two major clusters, similar to pulsed-field gel electrophoresis (PFGE) results. Three ISAba1-associated genes – blaampC, blaOXA-66-like, and csuD – were amplified and detected in the clinical isolates. This novel iPCR typing method is comparable to PFGE in its ability to discriminate A. baumannii strains, and is a promising molecular epidemiological tool for investigating A. baumannii carrying ISAba1.

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DNA sonication inverse PCR for genome scale analysis of uncharacterized flanking sequences
David E. Alquezar‐Planas, Ulrike Löber, Pin Cui, Claudia Quedenau, Wei Chen, Alex D. Greenwood, Susan Johnston
Methods in Ecology and Evolution.2021; 12(1): 182. CrossRef
Update on the Epidemiological Typing Methods for Acinetobacter Baumannii
Rayane Rafei, Marwan Osman, Fouad Dabboussi, Monzer Hamze
Future Microbiology.2019; 14(12): 1065. CrossRef
Identification and characterization of a novel cold-tolerant extracellular protease from Planococcus sp. CGMCC 8088
Kun Chen, Qingshan Mo, Huan Liu, Feiyan Yuan, Haonan Chai, Fuping Lu, Huitu Zhang
Extremophiles.2018; 22(3): 473. CrossRef

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

Enteric Bacteria Isolated from Acute Diarrheal Patients in the Republic of Korea between the Year 2004 and 2006: Seung-Hak Cho , Hyun-Ho Shin , Yeon-Hwa Choi , Mi-Sun Park , Bok-Kwon Lee; J. Microbiol. 2008;46(3):325-330. Published online July 5, 2008; DOI: https://doi.org/10.1007/s12275-008-0015-4

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Abstract: In an epidemiological survey of human enterobacterial infections in the Republic of Korea during three years from 2004 to 2006, we isolated 1,784 (6.2%, isolation rate of enteropathogens from stool samples) in 2004, 2,547 (9.5%) in 2005 and 3,506 bacteria (12.3%) from people who visited clinics. Among the isolated bacteria, pathogenic Escherichia coli, especially, EAEC was the most frequently identified pathogen in both urban and rural regions followed by Staphylococcus aureus, Salmonella species, Bacillus cereus, Vibrio parahaemolyticus, Campylobacter jejuni, Clostridium perfringens, and Shigella species. Distinct seasonality was found in V. parahaemolyticus species, while this pathogen showed no age-specific patterns. However, other bacteria, i.e., pathogenic E. coli, S. aureus, Salmonella spp., and B. cereus showed similar seasonality throughout the year, showing a slight increase in the infection rate during the summer months and high prevalence among children under 10 years of age and elder-age people. The antibiotic susceptibility patterns of pathogenic E. coli, Salmonella spp., and S. aureus showed high resistance to penicillins. However, both pathogenic E. coli and Salmonella spp. were susceptible to several cephems, imipenem, and amikacin. Moreover, S. aureus strains resistant to vancomycin were not found. In conclusion, these surveillances can play an important role for the control and prevention to the diseases originated by enteritis bacteria.

Surveillance of Bacterial Pathogens Associated with Acute Diarrheal Disease in the Republic of Korea During One Year, 2003: Seung-Hak Cho , Jong-Hyun Kim , Jong-Chul Kim , Hyun-Ho Shin , Yeon-Ho Kang , Bok-Kwon Lee; J. Microbiol. 2006;44(3):327-335.; DOI: https://doi.org/2379 [pii]

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Abstract: An epidemiological survey of human enterobacterial infections was conducted to determine the prevalence of enteropathogens in the Republic of Korea during one year, 2003. We tested for infectious diseases in 26,992 stool samples obtained from people who visited clinics located in six big cities and six rural provinces. From these samples, we isolated 1,291 cases of enteritis bacterial infection (4.8%). In the urban areas, 821 cases of bacterial infection (6.4%) were identified and, in the rural areas, 479 bacterial strains (3.3%) were isolated. Seasonal patterns were seen for diarrhea associated with S. aureus, E. coli and V. parahaemolyticus, while Salmonella and Shigella infections showed slight seasonal variation. We found that S. aureus and Salmonella were more frequently isolated from children and the elderly; however, the prevalence of E. coli, V. parahaemolyticus, and Shigella were similar in different age groups. Routine monitoring of these infections is considered a worthwhile means by which to elucidate their epidemiology and modes of transmission and ultimately to control them more effectively. Continuous laboratory-based surveillance for findings of enteritis bacterial infection should be emphasized in the prevention of these infections.

Journal Article

Genetic Diversity of Multi-resistant Salmonella enterica Serotype Typhimurium Isolates from Animals and Humans: Yong-Ku Woo , Su-Hwa Lee; J. Microbiol. 2006;44(1):106-112.; DOI: https://doi.org/2329 [pii]

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Abstract: In this study, the genetic diversities of multi-resistant Salmonella typhimurium (ST) isolates were analyzed via the application of both pulsed field gel electrophoresis (PFGE) and Polymerase chain reaction (PCR) analysis methods, using 6 kinds of primers (REP, ERIC, SERE, BOX, P-1254 and OPB-17). And their discriminative abilities (DA) were also compared in order to determine the most effective and reliable analysis method. 118 S. typhimurium isolates, cultured from diverse animals and human patients in Korea beginning in 1993, were analyzed and subjected to a comparison of Simpson’s index of diversity (SID), using both PFGE and PCR methods. PFGE by XbaI enzyme digestion allowed for discrimination into 9 pulsotypes, with high SID values (0.991) on the genomic DNA level. This shows that PFGE is a very discriminative genotypic tool, and also that multiple clones of S. typhimurium isolates had existed in domestic animals and humans in Korea since 1993. However, we could ultimately not to trace the definitive sources or animal reservoirs of specific S. typhimurium isolates examined in this study. Depending on the SID values, the combined
method
(7 kinds of method) was found to be the most discriminative method, followed by (in order) SERE-PCR, REP-PCR, ERIC-PCR, PFGE & OPB-17 (RAPD), P-1254 (RAPD), and BOX-PCR at the 80% clone cut-off value. This finding suggests that the REP-PCR method (which utilizes 4 primer types) may be an alternative tool to PFGE for the genotyping of S. typhimurium isolates, with comparable cost, time, and labor requirement. The establishment of a highly reliable and discriminatory method for epidemiologic analysis is considered necessary in order for researchers to trace the sources of specific pathogens and, consequently, to control and prevent the spread of epidemic S. typhimurium isolates to humans.

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