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

December, 2021. Vol. 24 No. 4.

Mini review

Challenges of Scaling Up SARS-CoV-2 Rapid Antigen Tests

Mi-Kyung Lee

Ann Clin Microbiol 2021 December, 24(4): 111-114. Published on 20 December 2021.

The current reference standard for the diagnosis of coronavirus disease 2019 (COVID-19) is the molecular detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Several rapid antigen tests (RATs) have been developed for the rapid and inexpensive detection of SARS-CoV-2, which can be used at the point-of-care. Although RATs have lower SARS-CoV-2 detection sensitivity than molecular tests, the development of a more cost-effective highthroughput test system that offers a rapid turnaround time is vital for curtailing the spread of SARS-CoV-2. However, because of the growing concern over the substantial risk of false negative results, RATs should be used in conjunction with molecular tests and therefore, an appropriate test algorithm should be developed to achieve this purpose.

[in Korean]

Original article

Trends in Isolation and Antimicrobial Susceptibility of Enteropathogenic Bacteria in 2011-2019 at a Korean Tertiary Care Hospital Compared with Data in the Preceding Reports

Vandarith Nov, Le Phuong Nguyen, Kennedy Mensah Osei, Hyukmin Lee, Dongeun Yong, Kyungwon Lee

Ann Clin Microbiol 2021 December, 24(4): 115-126. Published on 20 December 2021.

Background: Environmental sanitation plays a significant role on the prevalence of enteropathogenic bacteria. This study aimed to determine the trends in the prevalence and antimicrobial resistance profiles of enteropathogenic bacteria from 2011 to 2019.

Methods: A retrospective analysis was performed using data from stool cultures of Salmonella spp., Shigella spp., Plesiomonas shigelloides, Yersinia spp., Vibrio spp., and Campylobacter spp. Samples were obtained between 2011 and 2019 from Severance Hospital. Antimicrobial susceptibility profile was determined using the disk diffusion method for nontyphoidal Salmonella (NTS) and Campylobacter spp., following the Clinical and Laboratory Standards Institute (CLSI) guidelines.

Results: The number of specimens obtained for stool culture increased significantly from 13,412 during the period of 1969–1978, to 48,476 over the past nine years (2011–2019), whereas the ratio of positive specimens decreased significantly from 1,732 (12.9%) to 449 (0.9%). The proportion of samples positive for Salmonella Typhi decreased from 472 (93.6%, 1969–1978) to 4 (1.5%, 2011–2019), whereas the proportion of NTS increased from 14 (2.8%, 1969–1978) to 261 (96.7%, 2011–2019). Among all the enteropathogenic bacteria isolated, Shigella spp. accounted for 60.0% (1,039) isolates from 1969 to 1978, but only 1.6% (7) from 2011 to 2019. Campylobacter was the second most prevalent enteropathogenic bacteria, accounting for 29.4% isolates (132). Among the NTS strains isolated from 2016 to 2019, their susceptibility rates to ampicillin and sulfamethoxazole-trimethoprim were 51.1% and 85.2%, respectively. Additionally, the susceptibility rate of Campylobacter to ciprofloxacin was 15.8%.

Conclusion: The prevalence of Salmonella Typhi and Shigella spp. significantly decreased, whereas those of NTS and Campylobacter spp. increased. Therefore, continuous monitoring of ciprofloxacin-resistant Campylobacter spp. is of vital importance.

Original article

emm Types and Clusters of Group A Streptococcus Causing Acute Pharyngitis in Changwon Korea, 2018–2019

Seon A Jo, Seungjun Lee, Sunjoo Kim

Ann Clin Microbiol 2021 December, 24(4): 127-134. Published on 20 December 2021.

Background: Group A streptococcus (GAS) is the most common cause of bacterial pharyngitis. This study aimed to characterize the molecular epidemiology of GAS infection using an emm-typing and emm-clustering approach.

Methods: A total of 372 patients from Changwon who showed pharyngitis symptoms were recruited during the sampling period of 2018–2019 and throat cultures were obtained from them. emm typing was performed using polymerase chain reaction (PCR) and direct sequencing. emm genotypes and GAS clusters were classified based on a web-based database.

Results: Of the 372 throat swab specimens, 101 (27.2%) were positive for GAS. emm typing analysis was performed on 59 GAS isolates. The most prevalent emm type was emm89 (20.3%), followed by emm12 (16.9%). Seven emm clusters were identified: E4 (emm89/ emm28, 32.2%), A-C4 (emm12, 16.9%), E1 (emm4, 13.6%), A-C5 (emm3, 10.2%), E6 (emm75, 8.5%), M6 (emm6, 8.5%), and A-C3 (emm1, 6.8%).

Conclusion: Diverse and temporal changes were observed in the distribution of emm types and clusters of GAS. Continuous surveillance based on emm genotyping is needed to monitor the epidemiological characteristics of GAS pharyngitis.

Case report

A Case of Whole Genome Analysis of SARSCoV-2 Using Oxford Nanopore MinION System

Jae-Seok Kim, Sung Hee Chung, Jung-Min Kim, Hyun Soo Kim, Han-Sung Kim, Wonkeun Song

Ann Clin Microbiol 2021 December, 24(4): 135-140. Published on 20 December 2021.

The application of whole genome sequencing on SARS-CoV-2 viral genome is essential for our understanding of the molecular epidemiology and spread of viruses in the community. The portable whole genome sequencer MinION (Oxford Nanopore Technologies, ONT, UK) could be feasibly used in a clinical microbiology laboratory without the need of vast resources or stringent operating conditions. We used the MinION sequencer to analyze the viral genome sequence of one SARS-CoV-2 strain. In June 2020, nasopharyngeal specimen from one patient was subjected to whole-genome analysis using the nCoV-2019 sequencing protocol v2 of ARTIC using the MinION sequencer. The ONT MinKNOW software, RAMPART tool, and Genome Workbench were used. We identified 11 nucleotide variants using the Wuhan-Hu-1 isolate (NC_045512.2) as the reference sequence. There were six nucleotide variants (T265I, F924, Y3884L, P4715L, L5462, and Q6804L) in the ORF1ab region, one variant (D614G) in the S gene, one variant (Q57H) in ORF3a, one variant (P302) in the N gene, and two variants in each the 5′UTR and 3′-UTR. In this prolonged coronavirus disease 2019 (COVID-19) pandemic season, the MinION system that operates an amplicon-based whole-genome sequencing protocol could be a rapid and reliable sequencer without the need of cumbersome viral cultivation.

[in Korean]