Increasing Prevalence of Vancomycin-Resistant Enterococcus faecium, Expanded-Spectrum Cephalosporin-Resistant Klebsiella pneumoniae, and Imipenem-Resistant Pseudomonas aeruginosa in Korea: KONSAR Study in 2001

The 5th year KONSAR surveillance in 2001 was based on routine test data at 30 participating hospitals. It was of particular interest to find a trend in the resistances of enterococci to vancomycin, of Enterobacteriaceae to the 3rd generation cephalosporin and fluoroquinolone, and of Pseudomonas aeruginosa and acinetobacters to carbapenem. Resistance rates of Gram-positive cocci were: 70% of Staphylococcus aureus to oxacillin; 88% and 16% of Enterococcus faecium to ampicillin and vancomycin, respectively. Seventy-two percent of pneumococci were nonsusceptible to penicillin. The resistance rates of Enterobacteriaceae were: Escherichia coli, 28% to fluoroquinolone; Klebsiella pneumoniae, 27% to ceftazidime, and 20% to cefoxitin; and Enterobacter cloacae, ≥40% to cefotaxime and ceftazidime. The resistance rates of P. aeruginosa were 21% to ceftazidime, 17% to imipenem, and those of the acinetobacters were ≥61% to ceftazidime, aminoglycosides, fluoroquinolone and cotrimoxazole. Thirty-five percent of non-typhoidal salmonellae were ampicillin resistant, and 66% of Haemophilus influenzae were β-lactamase producers. Notable changes over the 1997-2001 period were: increases in vancomycin-resistant E. faecium, and amikacin- and fluoroquinolone-resistant acinetobacters. With the increasing prevalence of resistant bacteria, nationwide surveillance has become more important for optimal patient management, for the control of nosocomial infection, and for the conservation of the newer antimicrobial agents

Regional TMPRSS2 V197M Allele Frequencies Are Correlated with COVID-19 Case Fatality Rates.

Coronavirus disease, COVID-19 (coronavirus disease 2019), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has a higher case fatality rate in European countries than in others, especially East Asian ones. One potential explanation for this regional difference is the diversity of the viral infection efficiency. Here, we analyzed the allele frequencies of a nonsynonymous variant rs12329760 (V197M) in the TMPRSS2 gene, a key enzyme essential for viral infection and found a significant association between the COVID-19 case fatality rate and the V197M allele frequencies, using over 200,000 present-day and ancient genomic samples. East Asian countries have higher V197M allele frequencies than other regions, including European countries which correlates to their lower case fatality rates. Structural and energy calculation analysis of the V197M amino acid change showed that it destabilizes the TMPRSS2 protein, possibly negatively affecting its ACE2 and viral spike protein processing

Candida haemulonii and Closely Related Species at 5 University Hospitals in Korea: Identification, Antifungal Susceptibility, and Clinical Features

Background. Candida haemulonii, a yeast species that often exhibits antifungal resistance, rarely causes human infection. During 2004-2006, unusual yeast isolates with phenotypic similarity to C. haemulonii were recovered from 23 patients (8 patients with fungemia and 15 patients with chronic otitis media) in 5 hospitals in Korea. Methods. Isolates were characterized using D1/D2 domain and ITS gene sequencing, and the susceptibility of the isolates to 6 antifungal agents was tested in vitro. Results. Gene sequencing of the blood isolates confirmed C. haemulonii group I (in 1 patient) and Candida pseudohaemulonii (in 7 patients), whereas all isolates recovered from the ear were a novel species of which C. haemulonii is its closest relative. The minimum inhibitory concentration (MIC) ranges of amphotericin B, fluconazole, itraconazole, and voriconazole for all isolates were 0.5-32 mu g/mL (MIC(50), 1 mu g/mL), 2-128 mu g/mL (MIC(50), 4 mu g/mL), 0.125-4 mu g/mL (MIC(50), 0.25 mu g/mL), and 0.03-2 mu g/mL (MIC(50), 0.06 mu g/mL), respectively. All isolates were susceptible to caspofungin (MIC, 0.125-0.25 mu g/mL) and micafungin (MIC, 0.03-0.06 mu g/mL). All cases of fungemia occurred in patients with severe underlying diseases who had central venous catheters. Three patients developed breakthrough fungemia while receiving antifungal therapy, and amphotericin B therapeutic failure, which was associated with a high MIC of amphotericin B (32 mu g/mL), was observed in 2 patients. Conclusions. Candida species that are closely related to C. haemulonii are emerging sources of infection in Korea. These species show variable patterns of susceptibility to amphotericin B and azole antifungal agents.Shin JH, 2007, J CLIN MICROBIOL, V45, P2385, DOI 10.1128/JCM.00381-07Khan ZU, 2007, J CLIN MICROBIOL, V45, P2025, DOI 10.1128/JCM.00222-07Lee JS, 2007, J CLIN MICROBIOL, V45, P1005, DOI 10.1128/JCM.02264-06Pfaller MA, 2006, J CLIN MICROBIOL, V44, P819, DOI 10.1128/JCM.44.3.819-826.2006Sugita T, 2006, MICROBIOL IMMUNOL, V50, P469Clancy CJ, 2005, ANTIMICROB AGENTS CH, V49, P3171, DOI 10.1128/AAC.49.8.3171-3177.2005Odds FC, 2004, J CLIN MICROBIOL, V42, P3475, DOI 10.1128/JCM.42.8.3475-3482.2004Rodero L, 2002, J CLIN MICROBIOL, V40, P2266, DOI 10.1128/JCM.40.6.2266-2269.2002*CLSI, 2002, M27A2 CLSISugita T, 1999, J CLIN MICROBIOL, V37, P1985Pfaller MA, 1998, DIAGN MICR INFEC DIS, V32, P223Nguyen MH, 1998, J INFECT DIS, V177, P425Kurtzman CP, 1997, J CLIN MICROBIOL, V35, P1216LEHMANN PF, 1993, J CLIN MICROBIOL, V31, P1683GARGEYA IB, 1991, J MED VET MYCOL, V29, P335

Comparative analysis of IR-Biotyper, MLST, cgMLST, and WGS for clustering of vancomycin-resistant Enterococcus faecium in a neonatal intensive care unit

ABSTRACTHealthcare-associated infections caused by vancomycin-resistant Enterococcus faecium (VREFM) pose a significant threat to healthcare. Confirming the relatedness of the bacterial isolates from different patients is challenging. We aimed to assess the efficacy of IR-Biotyper, multilocus sequencing typing (MLST), and core-genome MLST (cgMLST) in comparison with whole-genome sequencing (WGS) for outbreak confirmation in the neonatal intensive care unit (NICU). Twenty VREFM isolates from four neonates and ten control isolates from unrelated patients were analyzed. Genomic DNA extraction, MLST, cgMLST, and WGS were performed. An IR-Biotyper was used with colonies obtained after 24 h of incubation on tryptic soy agar supplemented with 5% sheep blood. The optimal clustering cutoff for the IR-Biotyper was determined by comparing the results with WGS. Clustering concordance was assessed using the adjusted Rand and Wallace indices. MLST and cgMLST identified sequence types (ST) and complex types (CT), revealing suspected outbreak isolates with a predominance of ST17 and CT6553, were confirmed by WGS. For the IR-Biotyper, the proposed optimal clustering cut-off range was 0.106–0.111. Despite lower within-run precision, of the IR-Biotyper, the clustering concordance with WGS was favorable, meeting the criteria for real-time screening. This study confirmed a nosocomial outbreak of VREFM in the NICU using an IR-Biotyper, showing promising results compared to MLST. Although within-run precision requires improvement, the IR-Biotyper demonstrated high discriminatory power and clustering concordance with WGS. These findings suggest its potential as a real-time screening tool for the detection of VREFM-related nosocomial outbreaks.IMPORTANCEIn this study, we evaluated the performance of the IR-Biotyper in detecting nosocomial outbreaks caused by vancomycin-resistant Enterococcus faecium, comparing it with MLST, cgMLST, and WGS. We proposed a cutoff that showed the highest concordance compared to WGS and assessed the within-run precision of the IR-Biotyper by evaluating the consistency in genetically identical strain when repeated in the same run

False Positive Cases in Automated Blood Culture Systems Due to Hyperleukocytosis

Automated blood culture systems are widely used in clinical microbiology laboratories to minimize the workload of laboratory personnel and permit fast turnaround times. However, sometimes false positive signals occur due to leukocytosis, presence of fastidious bacteria, or unexplained causes. We experienced false positive signal in a patient with hyperleukocytosis for the first time since the automated blood culture system was introduced in our hospital over 20 years ago. We present two case reports with literature review and describe the procedure for dealing with false-positive cases in our hospital

Performance of MALDI-TOF Mass Spectrometry (VITEK MS) in the Identification of <i>Salmonella</i> Species

Salmonella is a major pathogen causing foodborne infections in humans. Salmonella isolates are identified using biochemical and serological tests, including automated systems such as the VITEK2 system. However, there are few reports on Salmonella identification using VITEK MS. Therefore, we aimed to evaluate the usefulness of MALDI-TOF VITEK MS for Salmonella identification. A total of 1389 Salmonella isolates were identified using VITEK MS ver3.0 or ver3.2. All Salmonella isolates were confirmed by serotyping using the Kauffmann-White scheme, and the results were compared with the VITEK MS results. A total of 1389 Salmonella isolates, including 66 serotypes, were correctly identified at the genus level by VITEK MS. However, these systems failed to correctly identify typhoidal Salmonella. Among the five Salmonella enterica ssp. diarizonae isolates, only one was correctly identified, whereas one and three isolates were partially identified and misidentified, respectively. On the other hand, the VITEK2 system successfully identified all typhoidal Salmonella (Typhi and Paratyphi A) and Salmonella enterica ssp. diarizonae isolates. VITEK MS was useful for identifying Salmonella species isolated from clinical specimens; however, additional biochemical tests, such as the VITEK2 System, should be considered to accurately identify Salmonella ser. Typhi, and Salmonella ser. Paratyphi A