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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.

Background: Staphylococcus aureus is a common colonizer of the nasal vestibule and is found in approximately 20%–30% of healthy adults, while Staphylococcus epidermidis appears to be the most frequent colonizer in all regions of the upper respiratory tract. Esp, a serine protease of S. epidermidis, was reported to inhibit S. aureus colonization. This study was performed to examine the nasal colonization of S. aureus and S. epidermidis and the presence of esp determinants. Methods: Nasal swab specimens from 54 patients were cultured on blood agar plates (BAP) and selective media for S. aureus (S. aureus ID, bioMerieux, France) for the isolation of S. aureus and S. epidermidis. After 48 hours of incubation of with BAP, three or four colonies suspected of being coagulase-negative staphylococci (CNS) were identified by MALDI-TOF MS (Bruker, Germany). Polymerase chain reaction (PCR) for esp was performed on all CNS isolates identified as S. epidermidis. Results: Forty-three S. epidermidis strains were isolated from 18 (33.3%) of the 54 patients. Nine (50.0%) of the 18 patients carried S. aureus, while the other nine did not. Of the 36 S.epidermidis non-carriers, 13 (36.1%) were colonized by S. aureus. All S. epidermidis strains were confirmed by PCR to have esp determinants. Conclusion: S. epidermidis colonization did not affect S. aureus colonization in the nasal cavity. All S. epidermidis strains harbored the esp gene. We could not find any differences in the nasal colonization rates of S. aureus according to the presence of esp-positive S. epidermidis. Further research on the characterization of S. epidermidis in Korea is needed to understand the association between S. epidermidis and S. aureus colonization.

Background: Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as an important nosocomial pathogen.The purpose of this study was to determine the effective methods for performing surveillance cultures of CRAB. Methods: Nasal and rectal swabs were obtained concurrently from hospitalized intensive care unit patients colonized with CRAB. All the samples were inoculated in CHROMagar Acinetobacter medium with CR102 (CHROMagar), MacConkey agar medium supplemented with 5 μg/mL imipenem (MCA-IPM),, and triptic soy broth medium supplemented with 5μg/mL imipenem (TSB-IPM). CRAB detection rates for each sample were compared. Results: The CRAB detection rate in either one of the nasal or rectal swabs from the 37 patients tested were 89.2% (33/37) with the use of CHROMagar, 78.4% (29/37) with the use of MCA-IMP, and 86.5% (32/37) with the use of TSB-IMP. Conclusion: We determined that concurrent use of both nasal and rectal swabs and CHROMagar could be an effective method for CRAB surveillance cultures.

IIF was higher in NPA (23.4%) than NPFS (5.4%). According to the consensus positive, the positive rates of NPFS were higher than those of NPA when using IIF (45.7% and 30.6%, P=0.048) and culture (38.7% and 27.9%, P=0.004). However, the false-positive rates of NPFS were higher than those of NPA when using IIF (12.4% and 1.2%, P=0.004). The positive rates of NPFS and those of NPA were not different in multiplex RT-PCR (67.6% and 55.9%, P=0.055). Conclusion: The higher sensitivity of IIF for NPFS spe- cimens and of culture for respiratory viruses and the similar sensitivities in multiplex PCR could make them an alternative to NPA samples, especially in physician clinics or emergency rooms. (Ann Clin Microbiol 2015; 18:119-125)