Annals of Clinical Microbiology, The official Journal of the Korean Society of Clinical Microbiology

6

Weeks in Review

2

Weeks to Publication
Indexed in KCI, KoreaMed, Synapse, DOAJ
Open Access, Peer Reviewed
pISSN 2288-0585 eISSN 2288-6850

March, 2021. Vol. 24 No. 1.

Original article

Application of 16S rRNA Gene-Targeted Next-Generation Sequencing for Bacterial Pathogen Detection in Continuous Ambulatory Peritoneal Dialysis Peritonitis

Young Ah Kim, Ea Wha Kang, Hye Su Moon, Daewon Kim, Dongeun Yong

Ann Clin Microbiol 2020 March, 23(1): 1-10. Published on 20 March 2020.

Background: 16S rRNA gene-targeted next-generation sequencing (NGS) can detect microorganisms in a comprehensive reference database. To date, NGS has been successfully applied to samples such as urine, blood, and synovial fluid. However, there is no data for continuous ambulatory peritoneal dialysis (CAPD) fluid. The purpose of this study was to evaluate the clinical usefulness of microbiome analysis of CAPD fluids for the diagnosis of CAPD peritonitis.

Methods: We included 21 patients with high suspicion of CAPD peritonitis. Routine CAPD fluid culture was performed using a pellet of 50 mL CAPD fluid onto the chocolate and blood agar for two days, and thioglycollate broth for one week. 16S rRNA gene-targeted NGS of pellets, stored at -70°C was performed with MiSeq (Illumina, USA).

Results: Many colonized or pathogenic bacteria were detected from CAPD fluids using NGS and the microbiomes were composed of 1 to 29 genera with a cut-off 1.0. Compared to the culture results, NGS detected the same pathogens in 6 of 18 valid results (three samples failed with low read count). Additionally, using NGS, anaerobes such as Bacteroides spp. and Prevotella spp. were detected in six patients. In two of five samples in which no bacterial growth was detected, possible pathogens were detected by NGS.

Conclusion: To our knowledge, this is the first report about the application of 16S rRNA gene-targeted NGS for diagnosis of CAPD peritonitis. Etiology of culture-negative CAPD peritonitis can be better defined in NGS. Furthermore, it also helped the detection of anaerobic bacteria.

[in Korean]

Original article

Evaluation of Synergistic Effect of Combined Treatment with Linalool and Colistin on Multidrug-Resistant Acinetobacter baumannii to Expand Candidate for Therapeutic Option

Ung-Jun Kim, Choon-Mee Kim, Sook-Jin Jang, Seul-Bi Lee, Seong-Sik Cho, Seok-Hoon Jeong, Young-Jin Ko, Seong-Ho Kang, Geon Park, Dong-Min Kim, Na-Ra Yoon, Young-Joon Ahn, Donghoon Lim, Joong-Ki Kook

Ann Clin Microbiol 2020 March, 23(1): 11-20. Published on 20 March 2020.

Background: Acinetobacter baumannii infection is a significant health problem worldwide due to increased drug resistance. The limited antimicrobial alternatives for the treatment of severe infections by multidrug-resistant A. baumannii (MDRAB) make the search for other therapeutic options more urgent. Linalool, the major oil compound in Coriandrum sativum, was recently found to have high antibacterial activity against A. baumannii. The purpose of this study was to investigate the synergistic effect of linalool and colistin combinations against MDRAB and extensively drug-resistant A. baumannii (XDRAB).

Methods: A total of 51 strains of A. baumannii clinical isolates, consisting of 10 MDRAB and 41 XDRAB were tested. We determined the minimum inhibitory concentration (MIC) of linalool for the test strains using the broth microdilution method and searched for interactions using the time-kill assay.

Results: The time-kill assay showed that the linalool and colistin combination displayed a high rate of synergy (92.1%) (by synergy criteria 2), low rate of indifference (7.8%), and a high rate of bactericidal activity (74.5%) in the 51 clinical isolates of A. baumannii. The synergy rates for the linalool and colistin combination against MDRAB and XDRAB were 96% and 92.1%, respectively. No antagonism was observed for the linalool and colistin combination.

Conclusions: The combination of linalool and colistin showed a high synergy rate, which may be beneficial for controlling MDRAB infections. Therefore, this combination is a good candidate for in vivo studies to assess its efficacy in the treatment of MDRAB infections.

[in Korean]

Original article

Frequency of Mycobacterium tuberculosis Among M. tuberculosis Complex Strains Isolated from Clinical Specimen

Hyunmi Cho, Jong-Bae Kim, Young Uh

Ann Clin Microbiol 2020 March, 23(1): 21-31. Published on 20 March 2020.

Background: Rapid and accurate detection of Mycobacterium tuberculosis (MTB) is of primary importance for infection control and selection of anti-tuberculosis drugs. However, most clinical laboratories report MTB complex (MTC) without reporting MTB because MTC comprising MTB, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium microti, Mycobacterium caprae and Mycobacterium pinnipedii have 99.9% similarity at the nucleotide level and identical 16S rRNA sequences. This study was conducted to analyze the species frequency of MTC isolates obtained from clinical specimen.

Methods: Of 310 MTC isolates obtained from clinical samples in a tertiary care hospital from February 2017 to August 2018, MolecuTech Real TB-Taq (YD Diagnostics, Korea) real-time PCR was performed, specifically to detect MTB. For DNA showing MTB negative results by MTBspecific real-time PCR or pyrazinamide-resistant strains, PCR-based MTC typing, spoligotyping, and exact tandem repeat D gene sequencing were performed.

Results: All the 310 MTC isolates were identified to be MTB. Two MTB strains of East-AfricanIndian 4-Vietnam genotype, which have not been reported in Korea, were also found.

Conclusion: There was no zoonotic tuberculosis in this study. Since we investigated only 310 MTC isolates detected in only one medical institution, multi-center study is needed to accurately know the prevalence of zoonotic tuberculosis in Korea.

[in Korean]

Original article

Season and Temperature Effects on Bloodstream Infection Incidence in a Korean Tertiary Referral Hospital

Young Suk Sohn, Jung-Hyun Byun, Young Ah Kim, Dong Chun Shin, Kyungwon Lee

Ann Clin Microbiol 2020 March, 23(1): 33-43. Published on 20 March 2020.

Background: The weather has well-documented effects on infectious disease and reports suggest that summer peaks in the incidences of gram-negative bacterial infections among hospitalized patients. We evaluated how season and temperature changes affect bloodstream infection (BSI) incidences of major pathogens to understand BSI trends with an emphasis on acquisition sites.

Methods: Incidence rates of BSIs by Staphylococcus aureus, Enterococcus spp., Escherichia coli, Klebsiella pneumoniae, Acinetobacter spp., and Pseudomonas aeruginosa were retrospectively analyzed from blood cultures during 2008–2016 at a university hospital in Seoul, Korea according to the acquisition sites. Warm months (June–September) had an average temperature of ≥20 °C and cold months (December–February) had an average temperature of ≤5 °C.

Results: We analyzed 18,047 cases, where 43% were with community-onset BSI. E. coli (N = 5,365) was the most common pathogen, followed by Enterococcus spp. (N = 3,980), S. aureus (N = 3,075), K. pneumoniae (N = 3,043), Acinetobacter spp. (N = 1,657), and P. aeruginosa (N = 927). The incidence of hospital-acquired BSI by Enterococcus spp. was weakly correlated with temperature, and the median incidence was higher during cold months. The incidence of community-onset BSI by E. coli was higher in warm months and was weakly correlated with temperature.

Conclusion: We found seasonal or temperature-associated variation in some speciesassociated BSIs. This could be a useful information for enhancing infection control and public health policies by taking season or climate into consideration.

Original article

Role of Efflux Pump Gene adeIJK to Multidrug Resistance in Acinetobacter baumannii Clinical Isolates

Ji Ae Choi, Choon-Mee Kim, Sook-Jin Jang, Seong-Sik Cho, Chul Ho Jang, Young-Jin Ko, SeongHo Kang, Geon Park

Ann Clin Microbiol 2020 March, 23(1): 33-43. Published on 20 March 2020.

Background: The emergence of multidrug-resistant Acinetobacter baumannii as a nosocomial pathogen is one of the major public health problems. The aim of this study was to evaluate the role of an efflux pump gene adeJ for the multidrug resistance of A. baumannii clinical isolates.

Methods: Two groups (MDRAB and SAB) of A. baumannii clinical isolates were studied. The SAB group consisted of strains that did not meet the criteria of MDRAB and were susceptible to more categories of antibiotics than MDRAB. Antimicrobial susceptibility results obtained by VITEKⅡ system were used in data analysis and bacterial group allocation. We performed realtime reverse transcription PCR to determine relative expression of adeJ. We compared relative expression of adeJ in comparison groups by considering two viewpoints: i) MDRAB and SAB groups and ii) susceptible and non-susceptible groups for each antibiotic used in this study.

Results: The mean value of relative expression of adeJ of MDRAB and SAB groups was 1.4 and 0.92, respectively, and showed significant difference (P=0.002). The mean values of relative expression of adeJ of susceptible and non-susceptible groups to the antibiotics cefepime, ceftazidime, ciprofloxacin, imipenem, meropenem, tigecycline, piperacillin/ tazobactam, ticarcillin/clavulanic acid, trimethoprim/sulfamethoxazole, piperacillin, and gentamicin showed statistically significant differences.

Conclusion: The overexpression of adeIJK might contribute to the multi-drug resistance in A. baumannii clinical isolates. Further, the overexpression of adeIJK might be one of the factors contributing to the resistance to numerous antibiotics.

[in Korean]