Capsular polysaccharide (CPS) genes and pilus islands encode important virulence factors for group B
Streptococcus
(GBS) genomes. This study aims to detect phylogenetic inconsistency in CPS genes and ...pilus islands in GBSs and to explore its relationship with invasiveness. A total of 1016 GBS genomes were downloaded from the NCBI public database. The multi-locus sequence typing (MLST) and Bayesian analysis of Population Structure (BAPS) analyses were both conducted for phylogeny construction. Serotyping and pilus typing were determined in silico using the genomic sequences. The CPS and pilus typing results were generally consistent with MLST and BAPS clustering. GBS isolates of serotype II and of the PI-1 + PI-2b and PI-2a types were more prone to phylogenetic inconsistency than the others. Isolates of serotype Ib and of PI-1 + PI-2a were more likely to appear as colonizing strains, whereas PI-2b was more likely to appear in invasive strains. For serotype V, phylogenetic inconsistency occurred more commonly in colonizing isolates, while for serotype III, the opposite occurred. The present study profiles for the first time the phylogenetic inconsistency of CPS genes and pilus islands in global GBS isolates, which is helpful for infection control and the development of new vaccines for the prevention of GBS occurrence.
Group B Streptococcus (GBS) is a leading cause of invasive neonatal infections. This study aimed to investigate the trend of GBS serotype and genotype change and their correlation with antimicrobial ...resistance before and after implementation of intrapartum antibiotic prophylaxis (IAP).
We performed serotyping, whole-genome sequencing, antimicrobial susceptibility testing, and single-nucleotide polymorphism (SNP)-based phylogenetic analysis on 238 invasive GBS isolates collected from October 1998 to February 2020 in Taiwan.
There were 7 serotypes and 6 clonal complexes (CCs) among the 238 GBS isolates, and more than half of the isolates carried multiple antimicrobial resistance genes. The expansion of CC17 strains and the increase in late-onset disease occurred synchronously after the implementation of IAP. Analysis of the carriage isolates from pregnant women showed diverse serotype distribution in the IAP era. The antimicrobial susceptibility testing showed that all 238 strains were susceptible to ampicillin and penicillin, while the number of various resistance genes in GBS genomes was found increased with the expansion of CC17. Compared with reference genomes, 697 nonsynonymous SNPs in 443 protein-coding genes were CC17 specific.
The study revealed the expansion of GBS CC17 and the increase of late-onset disease that occurred simultaneously with the implementation of IAP. Although the susceptibility of CC17 to antimicrobial agents is not different from that of other sequence types at present, GBS with phenotypic resistance to antimicrobials may emerge in the future, given the environmental selection pressure and the continued accumulation of SNP mutations.
Pseudogenes (genes disrupted by frameshift or in-frame stop codons) are ubiquitously present in the bacterial genome and considered as nonfunctional fossil. Here, we used RNA-seq and ...mass-spectrometry technologies to measure the transcriptomes and proteomes of Salmonella enterica serovars Paratyphi A and Typhi. All pseudogenes' mRNA sequences remained disrupted, and were present at comparable levels to their intact homologs. At the protein level, however, 101 out of 161 pseudogenes suggested successful translation, with their low expression regardless of growth conditions, genetic background and pseudogenization causes. The majority of frameshifting detected was compensatory for -1 frameshift mutations. Readthrough of in-frame stop codons primarily involved UAG; and cytosine was the most frequent base adjacent to the codon. Using a fluorescence reporter system, fifteen pseudogenes were confirmed to express successfully in vivo in Escherichia coli. Expression of the intact copy of the fifteen pseudogenes in S. Typhi affected bacterial pathogenesis as revealed in human macrophage and epithelial cell infection models. The above findings suggest the need to revisit the nonstandard translation mechanism as well as the biological role of pseudogenes in the bacterial genome.
•Patients with late viral clearance are associated with poorer outcomes and mortality.•Dexamethasone use and cycle threshold values are risk factors for late viral clearance.•Dexamethasone use is ...associated with late viral clearance in nonsevere COVID-19.
This study explored the outcomes and predictors of early viral clearance among patients with COVID-19.
This study recruited consecutive patients from March 1, 2020 to July 31, 2021. Early viral clearance was defined as having a duration from symptom onset to successive detection of SARS-CoV-2 polymerase chain reaction cycle threshold (Ct) value of ≥30 within 10 days.
Among the 239 enrolled patients, 54.4% (130 patients) had early viral clearance. A multivariate logistic regression analysis identified that dexamethasone use and day 1 Ct values were independent factors associated with late viral clearance. Patients with mild-moderate severity and who received dexamethasone therapy had a longer time to viral clearance than those who did not receive dexamethasone (17.2 ± 1.8 days vs 12.3 ± 1.1 days, P = 0.018). Patients with severe-critical severity had a similar duration from symptom onset to Ct value ≥30, regardless of dexamethasone therapy (18.3 ± 0.9 days vs 16.7 ± 4.7 days, P = 0.626).
The study revealed that dexamethasone therapy and Ct values are independent predictors of late viral clearance. Patients with severe disease course due to older age, increased number of comorbidities, and worse clinical outcomes experienced delayed viral clearance.
•Clostridium innocuum infection may lead to a poorer clinical remission in ulcerative colitis patients.•The incidence of C. innocuum is higher than Clostridioides difficile in inpatients with ...inflammatory bowel disease, and some patients had coinfection.•We should take C. innocuum into consideration in patients with inflammatory bowel disease with active inflammation and in those with refractory diarrhea with or without C. difficile infection.
Clostridium innocuum (CI) infection can lead to creeping fat in Crohn's disease and is associated with intestinal strictures. At present, no clinical study ever has evaluated the role of CI infection in inflammatory bowel disease (IBD).
In this retrospective cohort study, we enrolled hospitalized IBD patients with culture results for both CI and Clostridioides difficile (CD) in a medical center between October 2019 and April 2021. They were divided into the CI (CI+/CD−), control (CI−/CD−), coinfection (CI+/CD+), and CD (CI−/CD+) groups. We analyzed the risk factors, clinical presentations, and outcomes by comparing the CI and control groups.
We enrolled a total of 90 patients, including 22, 39, 13, and 16 patients in the CI, control, coinfection, and CD groups. The incidence rates of CI (CI+) and CD (CD+) were 39% (35/90) and 32% (29/90), respectively. We analyzed the differences between CI and control groups. We identified the use of steroid (77.3% vs. 46.2%, P = 0.018) and 5-aminosalicylic acid (90.9% vs. 64.1%, P = 0.022) as risk factors of CI infection. Clinical analysis showed that more patients in CI group presented with bloody stool (77.3% vs. 51.3%, P = 0.046). Although CI group had significantly lower overall occurrence of intraabdominal abscess (0% vs. 17.9%, P = 0.042), it showed a lower clinical remission rate (50% vs. 87.5%, P = 0.044) and higher Mayo score at the end of follow-up (10 points vs. 3 points, P = 0.008) in ulcerative colitis.
CI infection may lead to a poorer clinical remission in ulcerative colitis. We should take it into consideration in IBD patents with active inflamamtion or refractory diarrhea with or without CD infection. Precise identification of CI is imperative to guide approproate antimicrobial therapy because of its intrinsic vancomycin resistance nature.
Millions of people throughout the world suffer from parasite infections. Traditionally, technicians use manual eye inspection of microscopic specimens to perform a parasite examination. However, ...manual operations have limitations that hinder the ability to obtain precise egg counts and cause inefficient identification of infected parasites on co-infections. The technician requirements for handling a large number of microscopic examinations in countries that have limited medical resources are substantial. We developed the helminth egg analysis platform (HEAP) as a user-friendly microscopic helminth eggs identification and quantification platform to assist medical technicians during parasite infection examination.
Multiple deep learning strategies including SSD (Single Shot MultiBox Detector), U-net, and Faster R-CNN (Faster Region-based Convolutional Neural Network) are integrated to identify the same specimen allowing users to choose the best predictions. An image binning and egg-in-edge algorithm based on pixel density detection was developed to increase the performance. Computers with different operation systems can be gathered to lower the computation time using our easy-to-deploy software architecture.
A user-friendly interface is provided to substantially increase the efficiency of manual validation. To adapt to low-cost computers, we architected a distributed computing structure with high flexibilities.
HEAP serves not only as a prediction service provider but also as a parasitic egg database of microscopic helminth egg image collection, labeling data and pretrained models. All images and labeling resources are free and accessible at http://heap.cgu.edu.tw. HEAP can also be an ideal education and training resource for helminth egg examination.
A low-cost capacitive sensing device for liquid-level measurement is presented in this letter. We proposed a novel comb, such as pattern of electrode. An equivalent capacitor can be formed by the ...electrode and the liquid within the container, and the equivalent capacitance will be proportional to the area of the electrode. Therefore, when the liquid-level position reaches a larger area of the comb electrode, the equivalent capacitance will have significant gradient changes. The measurement results show a variation error of about 6%. The comb-electrode offers simple, effective, and accurate advantages without any additional calibration. This comb-electrode is easily to be applied to a non-intrusive monitoring system which can be found in various places around biomedical applications.
Macrolide-resistant Mycoplasma pneumoniae (MRMP) infection is increasing worldwide. However, its clinical significance is still uncertain.
The data of the Laboratory Medicine Department of Chang Gung ...Memorial Hospital in northern Taiwan was searched for children with molecular confirmed macrolide-susceptible Mycoplasma pneumoniae (MSMP) and MRMP infections between January 2011 and December 2018. The clinical features, laboratory data, and chest image presentations were compared between patients with MRMP and MSMP infections and between patients with good and poor macrolide response, respectively.
Records from 158 patients were recovered. Of the enrolled patients 34 (22%) suffered MRMP infection, 27 (17%) had pleural effusions, and 47 (32%) had poor macrolide response. The macrolide resistance rate was 12% in 2011, 20% between 2015 and 2016, and 50% between 2017 and 2018, respectively. Other than a poor macrolide response, the MRMP and MSMP infections are clinically indistinguishable. The presence of pleural effusion and MRMP infections were found to be independently associated with a poor macrolide response, with odds ratios (95% confidence interval) of 14.3 (4.9–42.0) and 14.6 (5.4–40), respectively. The macrolide resistance rate of the patients with a poor macrolide response was 49% and 18% among all the patients enrolled and the patients with a pleural effusion, respectively.
The macrolide resistance rate had possibly increased in recent years in Taiwan and should be continuously monitored. In addition, the macrolide response could be misleading in predicting a macrolide resistance especially for the patients with a pleural effusion.
Iron is an essential element for cellular functions, such as energy metabolism. Trichomonas vaginalis, a human urogenital tract pathogen, is capable of surviving in the environment without sufficient ...iron supplementation. Pseudocysts (cyst-like structures) are an environmentally tolerated stage of this parasite while encountering undesired conditions, including iron deficiency. We previously demonstrated that iron deficiency induces more active glycolysis but a drastic downregulation of hydrogenosomal energy metabolic enzymes. Therefore, the metabolic direction of the end product of glycolysis is still controversial.
In the present work, we conducted an LC‒MS-based metabolomics analysis to obtain accurate insights into the enzymatic events of T. vaginalis under iron-depleted (ID) conditions.
First, we showed the possible digestion of glycogen, cellulose polymerization, and accumulation of raffinose family oligosaccharides (RFOs). Second, a medium-chain fatty acid (MCFA), capric acid, was elevated, whereas most detected C18 fatty acids were reduced significantly. Third, amino acids were mostly reduced, especially alanine, glutamate, and serine. Thirty-three dipeptides showed significant accumulation in ID cells, which was probably associated with the decrease in amino acids. Our results indicated that glycogen was metabolized as the carbon source, and the structural component cellulose was synthesized at same time. The decrease in C18 fatty acids implied possible incorporation in the membranous compartment for pseudocyst formation. The decrease in amino acids accompanied by an increase in dipeptides implied incomplete proteolysis. These enzymatic reactions (alanine dehydrogenase, glutamate dehydrogenase, and threonine dehydratase) were likely involved in ammonia release.
These findings highlighted the possible glycogen utilization, cellulose biosynthesis, and fatty acid incorporation in pseudocyst formation as well as NO precursor ammonia production induced by iron-depleted stress.
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