Phylogenetic Analysis Based on Whole Genome Sequences, Antibiotic Resistance, and Virulence of Salmonella enterica Clinical Isolates from South Korea.

Salmonella is a major cause of foodborne disease and frequently causes human salmonellosis in South Korea. In this study, we investigated the genome diversity, antimicrobial resistance, and virulence of clinical isolates of Salmonella enterica from South Korea. We collected 42 S. enterica subsp. enterica isolates from two hospitals in South Korea. Whole genome sequences were determined. Serovars and sequence types (STs) based on multilocus sequence typing (MLST) were identified from whole genome sequences. Phylogenetic trees based on whole genome sequences and a minimum spanning tree based on MLST were constructed. Human serum resistance assays and gentamicin protection assays were performed to assess in vitro virulence. Nineteen serovars were identified among 42 clinical isolates, including nine Salmonella Typhi isolates. There were inconsistencies between serogroups and phylogenetic clusters in the phylogenetic tree and minimum spanning tree, but high clonality of S. Typhi was observed. Salmonella Typhi isolates were divided into two clusters, corresponding to ST1 and ST2. Isolates of serovars Typhimurium and I4,[5],12:i:- clustered into a group, and a hybrid isolate between the two serovars was identified. Four ciprofloxacin-resistant isolates were identified among nine S. Typhi isolates, and all isolates of S. Enteritidis and S. Panama were resistant to colistin. The gentamicin protection assay revealed that serogroup D1 was significantly less virulent than the other serogroups. Our study suggests high diversity of S. enterica clinical isolates from South Korea and non-monophyly of serogroups. In addition, subgroups of S. Typhi isolates and a hybrid isolate between serovars Typhimurium and I4,[5],12:i:- were identified.

Re-identification and Characterization of Multidrug-Resistant Corynebacterium haemomassiliense-Like Organisms from Humans.

Recently, non-diphtheriae Corynebacterium spp. have been increasingly reported in patients. In addition, several novel species of Corynebacterium isolated from humans. Here, we report two cases of human infections caused by Corynebacterium haemomassiliense-like organisms, which had not been identified at the species level by MALDI-TOF MS analysis. They were revealed to be closely related to C. haemomassiliense, a recently described species by three housekeeping genes (16S rRNA, rpoB, and gyrA) and phenotypic features. Both strains were multidrug-resistant but susceptible to vancomycin, meropenem, and linezolid. Our report suggests that human infections by the recently described Corynebacterium species may not be limited to a specific region, in addition to difficulty of classifying the genus Corynebacterium.

Roles of crrAB two-component regulatory system in Klebsiella pneumoniae: growth yield, survival in initial colistin treatment stage, and virulence.

OBJECTIVES: Alternation of the colistin resistance-regulating two-component regulatory system (crrAB) is a colistin-resistance mechanism in Klebsiella pneumoniae (K. pneumoniae), but its role in bacteria is not fully understood. METHODS: Twelve colistin-susceptible K. pneumoniae clinical isolates were included in this study: six crrAB-positive and six crrAB-negative. We deleted the crrAB genes from two crrAB-positive isolates and complemented them. We measured the growth yields by determining growth curves in lysogeny broth and minimal media with or without Fe2+. In vitro selection rates for colistin resistance were determined by exposure to colistin, and survival rates against high concentrations of colistin (20 mg/L) at the early stage of growth (20 min) were investigated. Virulence was determined using a serum bactericidal assay and Galleria mellonella larval infection. RESULTS: The presence of crrAB was not associated with colistin resistance and did not increase the in vitro selection rate of colistin resistance after exposure. The growth yield of crrAB-positive isolates was higher in lysogeny broth media and increased when Fe2+ was added to minimal media. The crrAB-positive isolates showed higher survival rates in the early stages of exposure to high colistin concentrations. Decreased serum resistance was identified in the crrAB-deleted mutants. More G. mellonella larvae survived when infected by crrAB-deleted mutants, and higher survival rates of bacteria were identified within the larvae infected with wild-type than crrAB-deletant isolates. CONCLUSION: Through rapid response to external signals, crrAB would provide advantages for K. pneumoniae survival by increasing the final growth yield and initial survival against colistin treatment. This may partly contribute to the bacterial virulence.

Colistin heteroresistance in Citrobacter freundii clinical isolates from Republic of Korea.

We investigated colistin heteroresistance in Citrobacter freundii isolates from Korean hospitals. Using population analysis profiling (PAP), we detected colistin heteroresistance in 31.3% of isolates. Among these, ST217 was the most prevalent clone (58.5%), particularly within colistin-heteroresistant isolates (80.0%). Interestingly, the second most common clone, ST248, was not found in heteroresistant isolates. We identified amino acid changes in PhoQ, PmrA, and PmrB, along with mRNA overexpression in pmrB and arnD. Colistin monotherapy showed no efficacy, but a combination of colistin and ciprofloxacin successfully eradicated all five isolates, even at 0.5 × minimum inhibitory concentrations. This study underscores the high prevalence of colistin heteroresistance in C. freundii isolates, limiting the effectiveness of colistin monotherapy. Combining colistin with ciprofloxacin may offer a viable treatment option for C. freundii infections.

Machine Learning Using Template-Based-Predicted Structure of Haemagglutinin Predicts Pathogenicity of Avian Influenza.

Deep learning presents a promising approach to complex biological classifications, contingent upon the availability of well-curated datasets. This study addresses the challenge of analyzing three-dimensional protein structures by introducing a novel pipeline that utilizes open-source tools to convert protein structures into a format amenable to computational analysis. Applying a two-dimensional convolutional neural network (CNN) to a dataset of 12,143 avian influenza virus genomes from 64 countries, encompassing 119 hemagglutinin (HA) and neuraminidase (NA) types, we achieved significant classification accuracy. The pathogenicity was determined based on the presence of H5 or H7 subtypes, and our models, ranging from zero to six mid-layers, indicated that a four-layer model most effectively identified highly pathogenic strains, with accuracies over 0.9. To enhance our approach, we incorporated Principal Component Analysis (PCA) for dimensionality reduction and one-class SVM for abnormality detection, improving model robustness through bootstrapping. Furthermore, the K-nearest neighbor (K-NN) algorithm was fine-tuned via hyperparameter optimization to corroborate the findings. The PCA identified distinct clustering for pathogenic HA, yielding an AUC of up to 0.85. The optimized K-NN model demonstrated an impressive accuracy between 0.96 and 0.97. These combined methodologies underscore our deep learning framework's capacity for rapid and precise identification of pathogenic avian influenza strains, thus providing a critical tool for managing global avian influenza threats.

Indoor air quality assessment in child care and medical facilities in Korea.

In order to characterize the status of indoor air pollution in some important facilities, a list of key criteria pollutants [particulate matter (PM(10)), carbon dioxide (CO(2)), carbon monoxide (CO), formaldehyde (HCHO), and bioaerosol] was measured from a total of 91 randomly selected sites in 18 different cities, Korea (February 2006 to December 2009). The target facilities include 43 child care facilities, 38 medical facilities, 6 elementary schools, and 4 postnatal care centers. The results showed that some air pollutants (e.g., CO and HCHO) did not exceed the recommended guideline [e.g., the Korean indoor air standard (KIAS) values of 10 ppm and 100 ppb, respectively]. However, concentration of PM(10), CO(2), and bioaerosol occasionally exceeded their respective guidelines (e.g., seven, three, and two cases). Discrete seasonalities were observed from indoor pollutants because of varying ventilation practice (e.g., summer time dominance of PM(10), HCHO, and bioaerosol or winter dominance of CO(2) and CO). However, as the concentrations of the indoor pollutants were scarcely above the recommended guideline level, more diversified approaches are desirable to diagnose the status of indoor pollution and to provide a realistic strategy for the improvement of IAQ.

Prediction of maxillary canine impaction using eruption pathway and angular measurement on panoramic radiographs.

OBJECTIVES: To compare the normal eruption pattern and angulation in impacted maxillary canines using panoramic radiographs to predict maxillary canine impaction. MATERIALS AND METHODS: Patients aged 6 to 15 years were classified into the normal eruption group (n = 229) and the impaction group (n = 191). At least two panoramic radiographs were taken in the normal eruption group during the eruption process of the maxillary canine. The growth pattern of the maxillary canine was analyzed using an XY coordinate system, with the tip of the maxillary lateral incisor as the origin and the tooth's long axis as the Y-axis and measurement of the relative position of the crown tip and angulation of the maxillary canine. RESULTS: The crown tips of normally erupted maxillary canines were intensively distributed along the distal surface of the maxillary lateral incisor, while those of impacted canines were widely distributed. The angulations of the normally erupted canines increased as eruption increased along the lateral incisor and then decreased at the cervical point of the lateral incisor. The angulations of the impacted canines were scattered, with no uniform pattern. CONCLUSIONS: While using the normal eruption path of the maxillary canine and the pattern of change in angulation based on the distal surface of the maxillary lateral incisor, early intervention or regular follow-up is needed to prevent maxillary canine impaction.

Targeted percutaneous transforaminal endoscopic diskectomy in 295 patients: comparison with results of microscopic diskectomy.

BACKGROUND: The aim of this study is to compare the clinical outcomes and complications after targeted PTED and conventional microscopic diskectomy for removing 1-level unilateral LDH and to evaluate the efficacy of PTED for the treatment of LDH. METHODS: The authors retrospectively examined 915 consecutive patients who underwent PTED (group A, 301 patients) and microscopic diskectomy (group B, 614 patients) for 1-level unilateral LDH. Patients who were treated with a diskectomy in the period from July 2003 to December 2004 were evaluated by telephone interview and institute visit. This assessment was performed at least 18 months (range, 18-36 months) after their operation. The follow-up rate in groups A and B was 97.5% (295 patients) and 96.5% (607 patients), respectively. RESULTS: Good or excellent results were obtained in 84.7% and 85.0% of groups A and B (P = .92). The rates of recurrence were 6.44% and 6.75% in groups A and B (P > .05). Twenty-eight patients (14 cases of recurrence, 5 cases of incomplete removal, 5 cases of stenosis, 2 cases of diskogenic back pain, and 2 cases of diskitis) in group A and 38 patients (26 cases of recurrence, 6 cases of incomplete removal, 2 cases of stenosis, 2 cases of diskogenic back pain, 1 case of hematoma, and 1 case of diskitis) in group B underwent reoperation. CONCLUSIONS: Based on our results, the PTED can be a reasonable alternative to a conventional microscopic diskectomy for the treatment of patients with LDH, except for those in downward far-migrating cases beneath the pedicle of the lower vertebra or in cases involving L5-S1 with a high pelvis.

In Vitro Investigation of Wear of CAD/CAM Polymeric Materials Against Primary Teeth.

The aim of the study was to evaluate the effects of polymeric computer-aided design/computer-aided manufacturing CAD/CAM materials on antagonistic primary tooth wear. Five CAD/CAM polymeric materials were examined: Vipi Block Monocolor (VBM), Yamahachi polymethylmethacrylate (PMMA) (YAP), Mazic Duro (MZD), Vita Enamic (ENA), and Pekkton (PEK). All of the specimens were tested in a thermomechanical loading machine with the primary canine as the antagonist (50 N, 1.2 × 105 cycles, 1.7 Hz, 5/55 °C). The wear losses of the antagonist tooth and the restorative materials were calculated using reverse modelling software and an electronic scale. VBM and ENA showed significantly higher antagonist tooth wear than PEK (p < 0.05), but there was no significant difference observed among VBM, YAP, MZD, and ENA (p > 0.05). PEK showed the largest value in both material volumetric and weight losses. In terms of material volumetric losses, there was no significant difference between all of the groups (p > 0.05). In terms of material weight losses, PEK was significantly larger than ENA (p < 0.05), but there was no significant difference between VBM, YAP, MZD, and ENA (p > 0.05). Volumetric and weight losses of materials showed similar wear behaviour. However, the wear patterns of antagonists and materials were different, especially in PEK.