Molecular characterization and antibiotic resistance of Staphylococcus aureus strains isolated from patients with diarrhea in Korea between the years 2007 and 2022.

To investigate the molecular characteristics and antibiotic resistance of Staphylococcus aureus isolates from patients with diarrhea in Korea, 327 S. aureus strains were collected between 2007 and 2022. The presence of staphylococcal enterotoxin (SE) and toxic shock syndrome toxin-1 (TSST-1) genes in S. aureus isolates was determined by PCR. The highest expression of the TSST-1 gene was found in the GIMNO type (43.1% of GIMNO type). GIMNO type (Type I) refers to each staphylococcal enterotoxin (SE) gene gene (initials of genes): G = seg; I = sei; M = selm; N = seln; O = selo. Moreover, Type I isolates showed a significantly higher resistance to most antibiotics. A total of 195 GIMNO-type S. aureus strains were analyzed using multilocus sequence typing (MLST), and 18 unique sequence types (STs) were identified. The most frequent sequence type was ST72 (36.9%), followed by ST5 (22.1%) and ST30 (16.9%). Interestingly, ST72 strains showed a higher prevalence of MRSA than the other STs. In conclusion, our results were the first reported for S. aureus strains in Korea, which significantly expanded S. aureus genotype information for the surveillance of pathogenic S. aureus and may provide important epidemiological information to resolve several infectious diseases caused by S. aureus. Supplementary Information: The online version contains supplementary material available at 10.1007/s10068-023-01478-9.

Evaluation of Microbiological Contamination of Dummies Used in Cardiopulmonary Resuscitation in Korea.

OBJECTIVES: In order to prevent infections through dummies used during Cardiopulmonary Resuscitation (CPR) training, we analyzed the microbiological contamination on dummies used in CPR institutions. METHODS: A total of 31 dummy samples were collected from 13 different institutions in Korea, and were evaluated for the number of contaminating bacteria and fungi on the surface. PCR and biochemical tests were performed to identify pathogenic bacteria and fungi, including Methicillin-Resistant Staphylococcus aureus (MRSA). Moreover, we further assessed the survival rate of microorganisms on the surface of the dummies. RESULTS: We assessed the total number of microorganisms on the surface to be 77,752CFU/cm2 (±50,047CFU), which is up to 188 times higher than the required surface contamination level. Grampositive cocci such as Micrococcus spp. and Staphylococcus spp. accounted for the highest proportion (55.3%). Especially, we detected three MRSA strains. Considering the isolated fungi and yeast, Aspergillus spp. and Candidia spp. accounted for the highest proportion. Assessing the contamination level simulation and survival rate on the humanoid surface showed that within two weeks of training, the level of contamination on the dummy's surface exceeded the standard, and artificially contaminated pathogenic strains on the surface of the dummy survived for at least 40 days. CONCLUSION: To minimize the possibility of secondary infections during CPR training, there is a requirement for a standardized protocol for proper microbiological management of dummies.

Improving the accuracy of coliform detection in meat products using modified dry rehydratable film method.

This study was undertaken to improve the detection accuracy for coliform bacteria, by analyzing biochemical properties of false positive and false negative colonies isolated from two dry rehydratable film methods, 3 M™ Petrifilm™ E. coli/Coliform count (PCC) and MC-Media Pad coliform count (MCC). The detection accuracy of PCC and MCC was determined to be 99.4% and 97.9%, respectively, with the detection error being 0.6% and 2.1%, respectively. False positive colonies (red colony without gas) on PCC were identified as Hafnia alvei and Enterobacter cloacae. All false positive colonies on MCC were identified as Aeromonas caviae; this organism gives a positive oxidase test, whereas coliform bacteria are oxidase negative. In conclusion, we propose that for improving detection accuracy of coliform bacteria, the incubation time of PCC should be modified and increased from 24 h to 48 h, and the oxidase test of MCC isolates should be included in the Korea Food Code.

Comparative genomic analysis of enterotoxigenic Escherichia coli O159 strains isolated from diarrheal patients in Korea.

BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) is a common cause of bacterial infection that leads to diarrhea. Although some studies have proposed a potential association between the toxic profile and genetic background, association between toxin of ETEC and phylo-group has not been reported yet. The objective of this study was to examine genomic and phylogenetic characteristics of ETEC strain NCCP15731 and NCCP15733 by whole genome sequencing and comparative genomic analysis of two phylo-groups of O159 reference strains. RESULTS: Whole genome sequencing showed that genome size of NCCP15731 strain was 4,663,459 bp, containing 4435 CDS and 19 RNAs. The genome size of NCCP15733 was 4,645,336 bp, containing 4369 CDS and 23 RNAs. Both NCCP15731 and NCCP15733 were classified in the phylo-group A, which is one of major E. coli phylogenetic groups. Their serotype was O159:H34. They possessed the virulence factor such as adherence systems, auto transporter systems, and flagella segments of major driving force for ETEC pathogenicity. They also harbored STh enterotoxin. Hierarchical clustering result based on the presence or absence of a total of 108 major virulence factors of 14 O159 ETEC strains showed that seven strains in phylo-group A and seven strains in phylo-group B1 were clustered each other, respectively. Colonization factors (CFs) of NCCP15731 or NCCP15733 were not detected. CONCLUSIONS: Serotype of NCCP15731 and NCCP15733, representing major types of ETEC in Korea, was O159:H34 and their MLST type was ST218. Comparison with other O159 strains revealed that NCCP15731 was specialized for transporter system and secretion system whereas NCCP15733 had unique genes related to capsular polysaccharide. Compared with E159, the most recent common ancestor, these two strains had different toxin type and virulence factors. These results will improve our understanding of ETEC O159 strains to prevent ETEC disease.

Characterization of Clostridium difficile Strains Isolated from Patients with C. difficile-associated Disease in Korea.

OBJECTIVES: Studies on Clostridium difficile are rare in Korea. We investigated the epidemiological characteristics of C. difficile isolates from patients with C. difficile-associated disease (CDAD) in Korea. METHODS: Multiplex polymerase chain reaction was performed to detect the presence of tcdA and tcdB toxin genes. Antimicrobial susceptibility test was carried out by the disk-dilution method. C. difficile strains were subtyped by automated repetitive-element palindromic PCR (rep-PCR). RESULTS: Among patients with CDAD, 73 (25.8%), 32 (11.3%), 32 (11.3%), and 26 (9.2%) suffered from pneumonia, cancer or neoplasm, diabetes, and colitis, respectively. Of all stool samples, 43 samples (15.2%) were positive for C. difficile strains. We observed two expression patterns of toxin genes: tcdA+/tcdB+ (86% isolates) and tcdA-/tcdB+ (14% isolates), with all isolates expressing tcdB. Furthermore, some isolates were resistant to clindamycin (65%), ampicillin (56%), and cefazolin (40%), but all were susceptible to vancomycin and metronidazole. The tested samples were classified into diverse clusters using automated rep-PCR. CONCLUSION: Our findings revealed the characteristics and antibiotic resistance of C. difficile isolates from patients in Korea. The epidemiological data may provide valuable insight into development of treatment strategies for C. difficile infections in Korea.

Comparative genomic analysis and characteristics of NCCP15740, the major type of enterotoxigenic Escherichia coli in Korea.

BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) cause infectious diarrhea and diarrheal death. However, the genetic properties of pathogenic strains vary spatially and temporally, making prevention and treatment difficult. In this study, the genomic features of the major type of ETEC in Korea from 2003 to 2011 were examined by whole-genome sequencing of strain NCCP15740, and a comparative genomic analysis was performed with O6 reference strains. RESULTS: The assembled genome size of NCCP15740 was 4,795,873 bp with 50.54% G+C content. Using rapid annotation using subsystem technology analysis, we predicted 4492 ORFs and 17 RNA genes. NCCP15740 was investigated for enterotoxin genes, colonization factor (CF) genes, serotype, multilocus sequence typing (MLST) profiles, and classical and nonclassical virulence factors. NCCP15740 belonged to the O6:H16 serotype and possessed enterotoxin genes encoding heat-stable toxin (STh) and heat-labile toxin (LT); 87.5% of the O6 serotype strains possessed both toxin types. NCCP15740 carried the colonization factors CS2 and CS3, whereas most O6 strains carried CS2-CS3-CS21 (79.2%). NCCP15740 harbored fewer virulence factors (59.4%) than the average observed in other O6 strains (62.0%). Interestingly, NCCP15740 did not harbor any nonclassical virulence genes. CONCLUSIONS: The major type of ETEC in Korea had the same MLST sequence type as that of isolates from the USA obtained in 2011 and 2014, but had different colonization factor types and virulence profiles. These results provide important information for the development of an ETEC vaccine candidate.

Whole-genome sequencing and comparative genomic analysis of Escherichia coli O91 strains isolated from symptomatic and asymptomatic human carriers.

BACKGROUND: The Shiga toxin-producing Escherichia coli (STEC) O91:H21 strains NCCP15736 and NCCP15737 were isolated during a single outbreak in Korea, NCCP15736 from a symptomatic carrier and NCCP15737 from an asymptomatic carrier. To investigate genomic differences between the two strains, we performed whole-genome sequencing of both strains and conducted a comparative genomic analysis. RESULTS: Using the Illumina HiSeq 2000 platform and Rapid Annotation using the Subsystem Technology (RAST) server, whole-genome sequences of NCCP15736 and NCCP15737 were obtained and annotated. Phylogenetic analysis of ten E. coli strains showed that NCCP15736 and NCCP15737 are evolutionarily close. The two strains were found to be most close to E. coli O91:NM str. 2009C-3745. The genomic comparison showed that the fimD gene of NCCP15737 is truncated and that the truncation could underlie the defects in infection and pathogenicity of NCCP15737. The two strains showed the same virulence factor profiles, and we identified 25 virulence factors from NCCP15736 and NCCP15737, respectively. We identified ten and nine phage-associated regions in the NCCP15736 and NCCP15737 genomes, respectively; the two strains share five of these. CONCLUSIONS: NCCP15736 and NCCP15737 differ at the genomic level, even though they share features such as virulence-related genes. NCCP15737 has a deletion in fimD, which may underlie its asymptomatic character. We conclude that complete genome sequencing and integration of other types of omics data are needed to fully reveal the mechanism underlying the asymptomatic character of NCCP15737.

Draft genome sequence of non-shiga toxin-producing Escherichia coli O157 NCCP15738.

BACKGROUND: The non-shiga toxin-producing Escherichia coli (non-STEC) O157 is a pathogenic strain that cause diarrhea but does not cause hemolytic-uremic syndrome, or hemorrhagic colitis. Here, we present the 5-Mb draft genome sequence of non-STEC O157 NCCP15738, which was isolated from the feces of a Korean patient with diarrhea, and describe its features and the structural basis for its genome evolution. RESULTS: A total of 565-Mbp paired-end reads were generated using the Illumina-HiSeq 2000 platform. The reads were assembled into 135 scaffolds throughout the de novo assembly. The assembled genome size of NCCP15738 was 5,005,278 bp with an N50 value of 142,450 bp and 50.65 % G+C content. Using Rapid Annotation using Subsystem Technology analysis, we predicted 4780 ORFs and 31 RNA genes. The evolutionary tree was inferred from multiple sequence alignment of 45 E. coli species. The most closely related neighbor of NCCP15738 indicated by whole-genome phylogeny was E. coli UMNK88, but that indicated by multilocus sequence analysis was E. coli DH1(ME8569). CONCLUSIONS: A comparison between the NCCP15738 genome and those of reference strains, E. coli K-12 substr. MG1655 and EHEC O157:H7 EDL933 by bioinformatics analyses revealed unique genes in NCCP15738 associated with lysis protein S, two-component signal transduction system, conjugation, the flagellum, nucleotide-binding proteins, and metal-ion binding proteins. Notably, NCCP15738 has a dual flagella system like that in Vibrio parahaemolyticus, Aeromonas spp., and Rhodospirillum centenum. The draft genome sequence and the results of bioinformatics analysis of NCCP15738 provide the basis for understanding the genomic evolution of this strain.

Epidemiological Characterization of Opportunistic Mycoses between the Years 2006 and 2010 in Korea.

In order to perform an epidemiological characterization of opportunistic mycosis infections, we collected health insurance data between the years 2006 and 2010 from the Health Insurance Corporation and analyzed the data to determine the prevalence of opportunistic mycoses and treatment management of opportunistic mycoses. The prevalence within the study increased consecutively by 0.02% to 0.12% every year. The annual prevalence of opportunistic mycoses increased from 2.437% in 2006 to 2.709% in 2010. The average annual prevalence was 2.605%. Candidiasis occurred the most frequently, followed by aspergillosis, zygomycosis, and cryptococcosis. The regions with the highest incidences were the capital areas, Gyeonggi and Seoul. By sex, the prevalence in females (4.851%) was 14 times higher than that in males (0.352%). Interestingly, the adults from the 20- to 49-year-old age group showed higher prevalence than children and the elderly. The average duration of hospitalized treatment was 17.31 days and of outpatient treatment was 2.21 days; 3,577 hundred million won was used in total for medical expenses. This study provides useful data to study trends of opportunistic mycoses.

Epidemiological Characterization of Skin Fungal Infections Between the Years 2006 and 2010 in Korea.

OBJECTIVES: The purpose of this study was to build and provide a basic database of skin fungal infections for the effective management of skin fungal infections in the future. METHODS: We collected health insurance data between the years 2006 and 2010 from the Health Insurance Corporation (Seoul, Korea) and analyzed the data to determine the prevalence and treatment management of skin fungal infections. RESULTS: Skin fungal infections were divided into two groups: namely dermatophytosis and other superficial mycoses. Dermatophytosis showed a higher prevalence (16,035,399 cases) than the other superficial mycoses (794,847 cases) within the study period. The prevalence rate decreased consecutively by 0.01% to 0.19% every year. The prevalence according to region showed that Jeolla-do had a high prevalence distribution. The prevalences in men and women were similar (7.01% vs. 6.26%). It is interesting to note that adults from the 50-79-year age group showed a higher prevalence than children and young adults. The average convalescence time (days) of dermatophytosis was longer than that of other superficial mycoses. The total medical expenses were also much higher in dermatophytosis than in the other superficial mycoses. CONCLUSION: This study provides useful data for study trends of skin fungal infections.

Usefulness of the compression-adjusted ventilation for adequate ventilation rate during cardiopulmonary resuscitation.

BACKGROUND: To perform high-quality cardiopulmonary resuscitation (CPR), high-quality chest compression and ventilation support should be performed. However, many providers still have not maintained an adequate ventilation rate but hyperventilated during CPR. Thus, this study was conducted to verify that the compression-adjusted ventilation (CAV) would be a more accurate ventilation method compared with the conventional ventilation (CV). METHODS: Volunteer medical students and emergency medical services personnel were recruited. They were randomly divided into either the CV group or the CAV group. In the CV group, participants performed ventilation with estimation of the rate of 8 to 10 per minute (1 ventilation/6-8 seconds). In the CAV group, the ventilation rate was adjusted in line with the compression rate (compression:ventilation, 12:1). In each group, 2-rescuer adult CPR was performed on a manikin, which was intubated with an endotracheal tube, during a period of 8 minutes. The compression rate and the ventilation rate were recorded during CPR. RESULTS: Data on 56 medical students and 41 emergency medical services personnel were analyzed. No significant difference was observed in compression rate (P =.817); however, median (interquartile range) ventilation rate differed significantly between the CV and CAV groups (8.79 [2.19] per minute vs 9.25 [1.07] per minute, P = .016). In addition, compared with the CV group, adequacy of ventilation rate was better in the CAV group (47.9% vs 85.7%, P < .001). CONCLUSION: In comparison with the CV, the CAV is a more accurate method for maintenance of an adequate ventilation rate.