Journal of Microbiology

Article

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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Article

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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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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Article

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 PDF

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
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Research Support, Non-U.S. Gov't

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 PDF

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.

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Rene S. Hendriksen, Aroon Bangtrakulnonth, Chaiwat Pulsrikarn, Srirat Pornruangwong, Gorrawan Noppornphan, Hanne-Dorthe Emborg, Frank M. Aarestrup
Foodborne Pathogens and Disease.2009; 6(8): 1009. CrossRef

Research Support, Non-U.S. Gov't

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 PDF: 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.

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 PDF: 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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