Muriicola soli sp. nov., isolated from soil.

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002T was isolated from island soil. The isolate grew at 20-37 °C (optimum, 30 °C), at pH 6.0-9.5 (optimum, pH 7) and in the presence of 0.5-4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8T and Muriicola jejuensis EM44T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C15 : 1 G and iso-C15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, ß-galactosidase and ß-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002T and M. jejuensis and that between the strain and M. marianensis A6B8T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002T should be recognized as a novel species of the genus Muriicola, for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002T (=KCTC 62790T=JCM 32370T).

Prevalence, Characterization, and Antimicrobial Susceptibility of Listeria monocytogenes from Raw Beef and Slaughterhouse Environments in Korea.

The prevalence of Listeria monocytogenes in raw beef and in slaughterhouse environments was investigated from April 2019 to February 2020. Three hundred raw beef samples were purchased from 50 retailers and 10 restaurants (5 samples per source). One hundred and thirty-four samples from slaughterhouse environments were collected by swabbing (10 × 10 cm) the surfaces, gloves, splitting saw, and drains. L. monocytogenes was detected and identified according to the method described in ISO 11290-1, and confirmed by 16S rRNA sequencing. L. monocytogenes was detected in raw beef (2/300, 0.7%), gloves used in carcass splitting (6/21, 28.6%), the splitting saw (1/18, 5.6%), and the drain zone (1/15, 6.7%). All isolates were serotype 1/2a or 1/2c, based on screening using multiplex PCR-based serogrouping assay and serotyping kit for O-H antigens. Pulsed-field gel electrophoresis (PFGE) following ApaI digestion of eight PFGE pulsotypes and four PFGE groups were identified. Biofilm formation analysis using Crystal Violet staining revealed the highest biofilm formation in strain LM-16, followed by D190613. Although L. monocytogenes isolates were susceptible to most antimicrobials, some resistance to penicillin (8/15, 53.3%) and tetracycline (2/15, 13.3%) was observed. Through PFGE, G190426, G190829, and G200210 isolated from the same location in this study were genetically homologous similar to the LM-16 strain, previously isolated from beef carcass in 2006. These results suggest that LM-16 has been continuously present in biofilms in the slaughterhouse environments since 2006. Our study indicates that L. monocytogenes contamination in raw beef could consistently occur during beef processing in slaughterhouse environments through contact with gloves, splitting saws, and drains.

Nocardioides euryhalodurans sp. nov., Nocardioides seonyuensis sp. nov. and Nocardioides eburneiflavus sp. nov., isolated from soil.

Three aerobic, rod-shaped actinobacterial strains, designated MMS17-SY117T, MMS17-SY207-3T and MMS17-SY213T, were isolated from soil and their taxonomic positions were analysed using a polyphasic approach. The isolates showed best growth at 30 °C, pH 7 and 0-1 % (w/v) NaCl. On the basis of 16S rRNA gene sequence similarity, the isolates were affiliated to the genus Nocardioides, and the closest species to MMS17-SY117T, MMS17-SY207-3T and MMS17-SY213T were Nocardioides aestuarii JC2056T (97.76%), Nocardioides currus IB-3T (97.41%) and Nocardioides exalbidus RC825T (98.71%), respectively. Each isolate formed a distinct cluster within the Nocardioides clade in the phylogenetic tree. The orthologous average nucleotide identity and digital DNA-DNA hybridization values were in the range of 74.4-85.7 % and 16.6-39.2 %, respectively, with the type strains of related species. The major polar lipids in all three strains were phosphatidylinositol, phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids were iso-C16 : 0 and C17 : 1 ω8c. MK-8(H4) was the major isoprenoid quinone and ll-DAP was the major diamino acid. Galactose, glucose and rhamnose were present in the whole-cell hydrolysate, and MMS17-SY213T also contained mannose and ribose. The DNA G+C contents of MMS17-SY117T, MMS17-SY207-3T and MMS17-SY213T were 72.2, 70.4 and 71.5 mol%, respectively. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of each strain as representing a new species of Nocardioides, for which the names Nocardioides euryhalodurans sp. nov. (MMS17-SY117T=KCTC 49175T=JCM 32831T), Nocardioides seonyuensis sp. nov. (MMS17-SY207-3T=KCTC 49176T=JCM 32832T) and Nocardioides eburneiflavus sp. nov. (MMS17-SY213T=KCTC 49177T=JCM 32833T) are proposed accordingly.

Prevalence and Antimicrobial Characteristics of Shiga Toxin-Producing Escherichia coli Isolates from Pork in Korea.

Shiga toxin-producing Escherichia coli (STEC) strains are important food-borne pathogens that can be transmitted through the consumption of food products derived from pigs. Moreover, antimicrobial resistance in STEC has been a matter of increasing concern. The aim of this study was to investigate the prevalence and antimicrobial characteristics of STEC isolates from pork in Korea. We isolated 131 isolates of E. coli from 334 pork samples collected from slaughterhouses and retail markets from 2008 to 2009. Among the 131 isolates, 6 (4.58%) were confirmed to belong to 6 different serotypes of STEC. All six STEC isolates contained stx1 and eaeA virulence genes, and four of them additionally carried the hly gene. The minimum inhibitory concentration (MIC) of 15 antibiotics (amoxicillin/clavulanic acid, ampicillin, cephalothin, cefoxitin, ceftiofur, gentamicin, neomycin, streptomycin, nalidixic acid, ciprofloxacin, colistin, chloramphenicol, florfenicol, tetracycline and sulfamethoxazole/trimethoprim) toward the STEC isolates was determined. As a result, three strains were associated with high MICs for florfenicol and chloramphenicol (64 µg/mL). Furthermore, all three strains were found to contain the florfenicol-resistant gene (floR) but not the chloramphenicol-resistant gene (cat). Sequence alignment and BLAST analysis of the polymerase chain reaction products of the floR gene indicated that they contained sequences with homology to the floR gene of E. coli or Salmonella enterica serovar, Heidelberg. This is the first report on the detection of floR in STEC isolated from pork obtained from retail markets in Korea.

Streptomyces fodineus sp. nov., an actinobacterium with antifungal activity isolated from mine area soil.

A novel actinobacterial strain producing an antifungal substance was isolated from a sample of acidic mine area soil, and its taxonomic position was evaluated. The novel strain, designated TW1S1T, formed white-grey aerial mycelium and yellow substrate mycelium on oatmeal agar. Growth occurred at 10-45 °C (optimum, 30 °C), pH 4-9 (pH 6-7) and in the presence of up to 8 % (w/v) NaCl. Melanin was produced on peptone-yeast extract-iron agar. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that the novel strain should be assigned to the genus Streptomyces, and the closest species was Streptomyces puniciscabiei S77T with 99.1 % sequence similarity, which was followed by Streptomyces durhamensis NRRL B-3309T (99.0 %), Streptomyces filipinensis NBRC 12860T (98.9 %) and Streptomyces yaanensis Z4T (98.7 %). The chemotaxonomic properties were consistent with those of Streptomyces. ll-Diaminopimelic acid was the diagnostic diamino acid, and alanine, glutamic acid and glycine were present in the peptidoglycan. The cell-wall hydrolysate also contained galactose, glucose, mannose and ribose. The predominant isoprenoid quinones were MK-9(H4) and MK-9(H6), the major polar lipids were phosphatidylglycerol and an unidentified phospholipid, and the main fatty acids were iso-C16 : 0 and anteiso-C15 : 0. However, strain TW1S1T could be distinguished from its neighbouring species by its phenotypic properties. In addition, the genome-based comparison with the closest species indicated that strain TW1S1T should be recognized as a separate species. The phylogenetic, phenotypic and chemotaxonomic as well as genomic evidence supported that TW1S1T represents a novel species of Streptomyces, for which the name Streptomycesfodineus sp. nov. is proposed (type strain, TW1S1T = KCTC 49013T = JCM 32404T).

Prevalence and characteristics of foodborne pathogens from slaughtered pig carcasses in Korea.

The introduction of bacteria into slaughterhouses can lead to microbial contamination in carcasses during slaughter, and the initial level of bacteria in carcasses is important because it directly affects spoilage and the shelf life. This study was conducted to investigate the microbiological quality, and the prevalence of foodborne pathogens in 200 carcasses from 20 pig slaughterhouses across Korea. Distribution of microbial counts were significantly higher for aerobic bacteria at 3.01-4.00 log10 CFU/cm2 (42.0%) and 2.01-3.00 log10 CFU/cm2 (28.5%), whereas most of Escherichia coli showed the counts under 1.00 log10 CFU/cm2 (87.0%) (P < 0.05). The most common pathogen isolated from 200 carcasses was Staphylococcus aureus (11.5%), followed by Yersinia enterocolitica (7.0%). In total, 17 S. aureus isolates from four slaughterhouses were divided into six pulsotypes and seven spa types, and showed the same or different types depending on the slaughterhouses. Interestingly, isolates from two slaughterhouses carried only LukED associated with the promotion of bacterial virulence, whereas, isolates from two other slaughterhouses carried one or more toxin genes associated with enterotoxins including sen. In total, 14 Y. enterocolitica isolates from six slaughterhouses were divided into nine pulsotypes, 13 isolates belonging to biotype 1A or 2 carried only ystB, whereas one isolate belonging to bio-serotype 4/O:3 carried both ail and ystA. This is the first study to investigate microbial quality and the prevalence of foodborne pathogens in carcasses from slaughterhouses nationally, and the findings support the need for ongoing slaughterhouse monitoring to improve the microbiological safety of pig carcasses.

Prevalence and Virulence Characteristics of Enterococcus faecalis and Enterococcus faecium in Bovine Mastitis Milk Compared to Bovine Normal Raw Milk in South Korea.

Enterococcus spp. are pathogens that cause environmental mastitis and are difficult to eliminate owing to their resistance to antibiotics. To compare the virulence characteristics of isolates from bovine mastitis milk (BMM) and bovine normal raw milk (NRM), we isolated Enterococcus spp. from 39 dairy farms in South Korea from 2015−2020. A total of 122 Enterococcus spp. were identified, with Enterococcus faecalis (73.8%) accounting for the majority, followed by Enterococcus faecium (26.2%). E. faecalis isolated from BMM harbored gelE, asa1, esp, and cylA genes with a prevalence of 85.7, 71.4, 54.3, and 30.0%, respectively. These genes were significantly more abundant in BMM than in NRM, except for asa1 (p < 0.0001). Interestingly, strong biofilm and gelatinase formation was predominately observed for BMM isolates and this was significantly correlated to the presence of esp and gelE genes (p < 0.05). BMM isolates demonstrated higher resistance to tetracycline (59.3%), followed by chloramphenicol (21.0%), rifampicin (18.5%), doxycycline (4.9%), ciprofloxacin (1.2%), and nitrofurantoin (1.2%), than those from NRM. E. faecalis harboring esp, gelE, and cylA may be causative agents for bovine mastitis and act as a reservoir for the transmission of virulence factors to humans.

Distribution and Characterization of Antimicrobial Resistant Pathogens in a Pig Farm, Slaughterhouse, Meat Processing Plant, and in Retail Stores.

The emergence of antibiotic resistance in foodborne pathogens isolated from meat pro-ducts and their producing environment has been an increasing and leading threat to public health. The aim of the study was to identify pathogens and their antimicrobial resistance isolated from pig production to pork meat distribution phases. Through this study, food spoilage and foodborne or clinical pathogenic bacteria were isolated and identified from pork (belly and neck) meat product and its related environmental samples that include pig swabs, diets, feces, liquid manure, workers' gloves, dust fan swabs, carcass swabs, floor swabs, and drain water in the affiliated farm, slaughterhouse, meat processing plant, and in retail stores. All carcasses at the slaughterhouse and meat products at the meat processing plant were tracked from pigs at a targeted farm. Nine different selective media agars were used to effectively isolate various pathogenic bacteria. A total of 283 presumptive pathogenic bacteria isolated from 126 samples were selected and identified using MALDI-ToF MS. Twenty-three important foodborne pathogens were identified, and some of them, Shiga-toxin-producing E. coli (STEC), Listeria monocytogenes, Staphylococcus aureus, and Yersinia enterocolitica, were further confirmed using PCR. The PFGE patterns of 12 STEC isolates were grouped by sample source or site. All the foodborne pathogens used in the study were not resistant to amoxicillin/clavulanate, ciprofloxacin, and gentamicin, whereas some of the STEC, L. monocytogenes, and S. aureus isolates were resistant to various antibiotics, including ampicillin, erythromycin, tetracycline, and vancomycin. The most common antimicrobial resistance pattern in the pathogenic STEC isolates was AMP-KAN-STR-SXT-TET. Consequently, this study provides valuable information for the distribution of antimicrobial-resistant pathogens along the pork meat production chain and can assist farmers and stakeholders to develop a systematic strategy for reducing the current emergence and spread of antimicrobial resistance in the different phases of pig production and distribution.

Surveillance of the infection prevention and control practices of healthcare workers by an infection control surveillance-working group and a team of infection control coordinators during the COVID-19 pandemic.

BACKGROUND: During the ongoing coronavirus disease (COVID-19) pandemic, hospitals have strengthened their guidelines on infection prevention and control (IPC), and a rigorous adherence to these guidelines is crucial. An infection control surveillance-working group (ICS-WG) and infection control coordinators (ICCs) team were created to monitor the IPC practices of the healthcare workers (HCWs) in a regional hospital in Korea. This study analyzed the surveillance results and aimed to identify what IPC practices needed improvement. METHODS: During phase 1 (March to April 2020), the ICS-WG performed random audits, recorded incidences of improper IPC practices, and provided advice to the violators. During phase 2 (April to July), the ICCs inspected the hospital units and proposed practical ideas about IPC. The surveillance and proposals targeted the following practices: patient screening, usage of personal protective equipment (PPE), hand and respiratory hygiene, equipment reprocessing, environmental cleaning, management of medical waste, and social distancing. RESULTS: In phase 1, of the 127 violations observed, most (32.3%) corresponded to hand and respiratory hygiene. In phase 2, the highest proportion of violation per category was observed in the management of medical waste (37.8%); among these, a higher proportion of violation (71.4%) was observed in the collection of medical waste. Of the 106 proposals made by the ICCs, the most addressed practice was patient screening (28.3%). No case of nosocomial infection was reported during the study period. CONCLUSION: Adherence to proper hand and respiratory hygiene was inadequate at the early stage of the COVID-19 pandemic. The results indicate that more attention and further training are needed for the management of medical waste, particularly medical waste collection, and that continuous upgrading of the strategies for patient screening is essential. These results will be useful in helping other healthcare facilities to establish their IPC strategies.

Modulation of hydrolysis and transglycosylation activity of Thermus maltogenic amylase by combinatorial saturation mutagenesis.

The roles of conserved amino acid residues (Val329-Ala330- Asn331-Glu332), constituting an extra sugar-binding space (ESBS) of Thermus maltogenic amylase (ThMA), were investigated by combinatorial saturation mutagenesis. Various ThMA mutants were firstly screened on the basis of starch hydrolyzing activity and their enzymatic properties were characterized in detail. Most of the ThMA variants showed remarkable decreases in their hydrolyzing activity, but their specificity against various substrates could be altered by mutagenesis. Unexpectedly, mutant H-16 (Gly-Leu-Val-Tyr) showed almost identical hydrolyzing and transglycosylation activities to wild type, whereas K-33 (Ser-Gly-Asp-Glu) showed an extremely low transglycosylation activity. Interestingly, K-33 produced glucose, maltose, and acarviosine from acarbose, whereas ThMA hydrolyzed acarbose to only glucose and acarviosine-glucose, which proposes that the substrate specificity, or hydrolysis or transglycosylation activity of ThMA can be modulated by combinatorial mutations near the ESBS.

Safety and efficacy of fimasartan with essential hypertension patients in real world clinical practice: data from a post marketing surveillance in Korea.

The safety and efficacy of fimasartan have been evaluated through post-marketing surveillance in real world clinical practice. The multi-center, prospective, open-label and non-interventional study. A total of 3,945 patients (3,729 patients for safety assessment and 3,473 patients for efficacy assessment) were screened in patients with essential hypertension in 89 study centers from 9 September 2010 through 8 September 2016. Among the total patients, 2,893 patients (77.6%) were administered fimasartan for 24 weeks or longer and were classified as 'patients with long-term follow-up', and the additional safety and efficacy analysis were performed. The improvement was defined as systolic blood pressure (SBP) controlled to ≤ 140 mmHg or decreased SBP differences ≥ 20 mmHg after treatment or diastolic blood pressure (DBP) controlled to ≤ 90 mmHg or decreased DBP differences ≥ 10 mmHg after treatment. Adverse drug reactions (ADRs) were reported in 3.8% patients; dizziness, and hypotension were the most frequently reported ADRs in total patients. The results of patients with long-term follow-up were comparable with total patients. The overall improvement rate in all efficacy assessment at the last visit was 87.1% (3,025/3,473 patients). The overall improvement rate of the patients with long-term follow-up was 88.9%. Fimasartan was well tolerated, with no new safety concerns identified and an effective treatment in the real world clinical practice for Korean patients with hypertension.

Functional expression and enzymatic characterization of Lactobacillus plantarum cyclomaltodextrinase catalyzing novel acarbose hydrolysis.

Cyclomaltodextrinases (CDases) belong to Glycoside Hydrolases (GH) family 13, which show versatile hydrolyzing and/or transglycosylation activity against cyclodextrin (CD), starch, and pullulan. Especially, some CDases have been reported to hydrolyze acarbose, a potent α-glucosidase inhibitor, and transfer the resulting acarviosine-glucose to various acceptors. In this study, a novel CDase (LPCD) gene was cloned from Lactobacillus plantarum WCFS1, which encodes 574 amino acids (64.6 kDa) and shares less than 44% of identities with the known CDase-family enzymes. Recombinant LPCD with C-terminal six-histidines was produced and purified from Escherichia coli. It showed the highest activity on ß-CD at 45°C and pH 5.0, respectively. Gel permeation chromatography analysis revealed that LPCD exists as a dodecameric form (~826 kDa). Its hydrolyzing activity on ß- CD is almost same as that on starch, whereas it can hardly attack pullulan. Most interestingly, LPCD catalyzed the unique modes of action in acarbose hydrolysis to produce maltose and acarviosine, as well as to glucose and acarviosineglucose.