Background: Carbapenem-resistant Pseudomonas aeruginosa (CrPA) is a leading cause of healthcare-associated urinary tract infections (UTIs). Carbapenemase production is an important mechanism that significantly alters the efficacy of frequently used anti-pseudomonal agents. Reporting the current genotypic distribution of carbapenemase-producing P.aeruginosa (CPPA) isolates in relation to antimicrobial susceptibility, UTI risk factors, and mortality is necessary to increase the awareness and control of these strains. Methods: In total, 1,652 non-duplicated P. aeruginosa strains were isolated from hospitalized patients between 2015 and 2020. Antimicrobial susceptibility, carbapenemase genotypes, risk factors for UTI, and associated mortality were analyzed. Results: The prevalence of carbapenem-non-susceptible P. aeruginosa isolates showed a decreasing trend from 2015 to 2018 and then increased in the background of the emergence of New Delhi metallo-β-lactamase (NDM)-type isolates since 2019. The CPPA strains showed 100.0% non-susceptibility to all tested antibiotics, except aztreonam (94.5%) and colistin (5.9%). Carbapenems were identified as a risk and common predisposing factor for UTI (odds ratio [OR] = 1.943) and mortality (OR = 2.766). Intensive care unit (ICU) stay (OR = 2.677) and white blood cell (WBC) count (OR = 1.070) were independently associated with mortality. Conclusions The changing trend and genetic distribution of CPPA isolates emphasize the need for relentless monitoring to control further dissemination. The use of carbapenems, ICU stay, and WBC count should be considered risk factors, and aggressive antibiotic stewardship programs and monitoring may serve to prevent worse outcomes.

Background: Staphylococcal cassette chromosome mec type V (SCCmec V) methicillin-resistant Staphylococcus aureus (MRSA) has been recovered from patients and livestock.Using comparative genomic analyses, we evaluated the phylogenetic emergence of SCCmec V after transmission from overseas donor strains to Korean recipient strains. Methods: Sixty-three complete MRSA SCCmec V genomes (including six Korean clinical isolates) were used to construct a phylogenetic tree. Single-nucleotide polymorphisms were identified using Snippy, and a maximum-likelihood-based phylogenetic tree was constructed using RAxML. The possible emergence of the most common ancestor was estimated using BactDating. To estimate mecA horizontal gene transfer (HGT) events, Rangerdtl was applied to 818 SCCmec V strains using publicly available whole-genome data. Results: The phylogenetic tree showed five major clades. German strains formed a major clade; their possible origin was traced to the 1980s. The emergence of Korean SCCmec V clinical isolates was traced to 2000–2010. mecA HGT events in Staphylococcus spp. were identified in seven strains. P7 (Hong Kong outbreak strain) served as the donor strain for two Korean sequence type (ST) 59 strains, whereas the other five recipient strains emerged from different SCCmec V donors. Conclusions Most Korean SCCmec V strains may have emerged during 2000–2010. A unique MRSA SCCmec V strain, ST72 (a Korean common type of community-associated MRSA), was also identified. The genomic dynamics of this clone with a zoonotic background should be monitored to accurately understand MRSA evolution.

Background: Clinical management of patients infected with hepatitis B virus (HBV) or hepatitis C virus (HCV) relies on the viral load (VL). The Cobas 5800 system (Roche Diagnostics) can determine VLs in 200 and 500 µL samples, but the performance of each protocol has not been compared. We evaluated the performance of both protocols for the HBV and HCV tests. Methods: Precision and linearity were verified using commercial panels. Probit analyses were used to determine limits of detection (LoDs). The results obtained with 336 samples were compared using the 200 and 500 µL protocols. Data from 6,737 retrospective HBV and 768 HCV samples were compared to estimate the effects of the different LoDs on the diagnostic results of the protocols. Correlations between protocols were tested with Spearman’s rank correlation coefficients (rho). Results: The precision and linearity of both protocols were verified. The LoDs for the 200and 500 μL protocols were 6.5 and 2.7 IU/mL for HBV and 29.7 and 8.2 IU/mL for HCV,respectively. The agreement between the protocols ranged from 0.8 to 1.0. The results obtained with the HBV and HCV tests showed a strong correlation (rho = 0.994). Only 0.4% ofHBV and 0.4% of HCV test results were affected by the LoDs of the 200 μL protocol. Conclusions The Cobas 5800 200 and 500 µL protocols for the HBV DNA and HCV RNA tests demonstrated excellent performance. These findings establish the 200 µL protocol as a new option for low-volume samples, especially for pediatric and difficult-to-bleed patients.

Background: Catheter-associated urinary tract infections (CAUTIs) account for a large proportion of healthcare-associated infections and have a significant impact on morbidity, length of hospital stay, and mortality. Adherence to the recommended infection prevention practices can effectively reduce the incidence of CAUTIs. This study aimed to assess the characteristics of CAUTIs and the efficacy of prevention programs across hospitals of various sizes. Methods: Intervention programs, including training, surveillance, and monitoring, were implemented. Data on the microorganisms responsible for CAUTIs, urinary catheter utilization ratio, rate of CAUTIs per 1,000 device days, and factors associated with the use of indwelling catheters were collected from 2017 to 2019. The incidence of CAUTIs and associated data were compared between university hospitals and small- and medium-sized hospitals. Results: Thirty-two hospitals participated in the study, including 21 university hospitals and 11 small- and medium-sized hospitals. The microorganisms responsible for CAUTIs and their resistance rates did not differ between the two groups. In the first quarter of 2018, the incidence rate was 2.05 infections/1,000 device-days in university hospitals and 1.44 infections/1,000 device-days in small- and medium-sized hospitals. After implementing interventions, the rate gradually decreased in the first quarter of 2019, with 1.18 infections/1,000 device-days in university hospitals and 0.79 infections/1,000 device-days in small- and medium-sized hospitals. However, by the end of the study, the infection rate increased to 1.74 infections/1,000 device-days in university hospitals and 1.80 infections/1,000 device-days in small- and medium-sized hospitals. Conclusion We implemented interventions to prevent CAUTIs and evaluated their outcomes. The incidence of these infections decreased in the initial phases of the intervention when adequate support and personnel were present. The rate of these infections may be reduced by implementing active interventions such as consistent monitoring and adherence to guidelines for preventing infections.

Objectives: Despite the introduction of vaccines, treatments, and massive diagnostic testing, the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to overcome barriers that had slowed its previous spread. As the virus evolves towards increasing fitness, it is critical to continue monitoring the occurrence of new mutations that could evade human efforts to control them. Methods: We performed whole-genome sequencing using Oxford Nanopore MinION sequencing on 58 SARS-CoV-2 isolates collected during the ongoing coronavirus disease 2019 pandemic at a tertiary hospital in South Korea and tracked the emergence of mutations responsible for massive spikes in South Korea. Results: The differences among lineages were more pronounced in the spike gene, especiallyin the receptor-binding domain (RBD), than in other genes. Those RBD mutations could compromise neutralization by antibodies elicited by vaccination or previous infections. We also reported multiple incidences of Omicron variants carrying mutations that could impair the diagnostic sensitivity of reverse transcription-polymerase chain reaction-based testing. Conclusion These results provide an understanding of the temporal changes of variants and mutations that have been circulating in South Korea and their potential impacts on antigenicity, therapeutics, and diagnostic escape of the virus. We also showed that the utilization of the nanopore sequencing platform and the ARTIC workf low can provide convenient and accurate SARS-CoV-2 genomic surveillance even at a single hospital.

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, aserine 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: 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, aserine 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.

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: 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 5 µg/ 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.