Rapid inference of antibiotic resistance and susceptibility for Klebsiella pneumoniae by clinical shotgun metagenomic sequencing.

OBJECTIVES: The study aimed to develop a genotypic antimicrobial resistance testing method for Klebsiella pneumoniae using metagenomic sequencing data. METHODS: We utilized Lasso regression on assembled genomes to identify genetic resistance determinants for six antibiotics (Gentamicin, Tobramycin, Imipenem, Meropenem, Ceftazidime, Trimethoprim/Sulfamethoxazole). The genetic features were weighted, grouped into clusters to establish classifier models. Origin species of detected antibiotic resistant gene (ARG) was determined by novel strategy integrating "possible species", "gene copy number calculation" and "species-specific kmers". The performance of the method was evaluated on retrospective case studies. RESULTS: Our study employed machine learning on 3928 K. pneumoniae isolates, yielding stable models with AUCs > 0.9 for various antibiotics. GenseqAMR, a read-based software, exhibited high accuracy (AUC 0.926-0.956) for short-read datasets. The integration of a species-specific kmer strategy significantly improved ARG-species attribution to an average accuracy of 96.67%. In a retrospective study of 191 K. pneumoniae-positive clinical specimens (0.68%-93.39% genome coverage), GenseqAMR predicted 84.23% of AST results on average. It demonstrated 88.76%-96.26% accuracy for resistance prediction, offering genotypic AST results with a shorter turnaround time (mean ± SD: 18.34 ± 0.87 hours) than traditional culture-based AST (60.15 ± 21.58 hours). Furthermore, a retrospective clinical case study involving 63 cases showed that GenseqAMR could lead to changes in clinical treatment for 24 (38.10%) cases, with 95.83% (23/24) of these changes deemed beneficial. CONCLUSIONS: In conclusion, GenseqAMR is a promising tool for quick and accurate AMR prediction in Klebsiella pneumoniae, with the potential to improve patient outcomes through timely adjustments in antibiotic treatment.

Systematic profiling of SARS-CoV-2-specific IgG responses elicited by an inactivated virus vaccine identifies peptides and proteins for predicting vaccination efficacy.

One of the best ways to control COVID-19 is vaccination. Among the various SARS-CoV-2 vaccines, inactivated virus vaccines have been widely applied in China and many other countries. To understand the underlying protective mechanism of these vaccines, it is necessary to systematically analyze the humoral responses that are triggered. By utilizing a SARS-CoV-2 microarray with 21 proteins and 197 peptides that fully cover the spike protein, antibody response profiles of 59 serum samples collected from 32 volunteers immunized with the inactivated virus vaccine BBIBP-CorV were generated. For this set of samples, the microarray results correlated with the neutralization titers of the authentic virus, and two peptides (S1-5 and S2-22) were identified as potential biomarkers for assessing the effectiveness of vaccination. Moreover, by comparing immunized volunteers to convalescent and hospitalized COVID-19 patients, the N protein, NSP7, and S2-78 were identified as potential biomarkers for differentiating COVID-19 patients from individuals vaccinated with the inactivated SARS-CoV-2 vaccine. The comprehensive profile of humoral responses against the inactivated SARS-CoV-2 vaccine will facilitate a deeper understanding of the vaccine and provide potential biomarkers for inactivated virus vaccine-related applications.

[Comparison between recombinant virus assay and live virus assay on evaluating anti-HIV-1 drugs].

OBJECTIVE: To compaire results of recombinant virus assay and live virus assay on evaluateing anti-HIV-1 drugs. METHODS: The pseudoviruse was generated by cotransfection of the plasmid B01 containing gp160 genes and pSG3 delta env plasmid. After co-incubation of pseudovirus with serially diluted drug, the EC50 and ED50 were calculated according to RLU(relative light unit) for each drug. After co-incubation of live virus with serially diluted drug, the EC50 was calculated according to cytopathic effect. RESULTS: EC50 of IDV measured by the recombinant virus assay and live virus assay was 88.9 nmol/L, 89.5 nmol/L, respectively, while EC50 of NVP measured by the recombinant virus assay and live virus assay was 0.36 micromol/L, 0.23 micromol/L, respectively. The recombinant virus assay showed good reproducibility with coefficient variation of 0, however coefficient variation of live virus assay reached to 60%. ED50 of IDV and NVP measured by the recombinant virus assay were 70.6 nmol/L and 0.62 micromol/L, respectively. Coefficient variations for IDV and NVP were 14.3% and 9.7%, respectively. CONCLUSION: The pseudoviruses could be used in evaluating anti-HIV-1 drugs. The recombinant virus assay showed good reproducibility and could calculate not only the EC50 but also the ED50 of drugs.

[A study on the prevalence rates of human immunodeficiency virus, hepatitis B virus and hepatitis C virus infections in intravenous drug users].

OBJECTIVE: To study HIV, HBV and HCV infections in intravenous drug users. METHODS: 2025 blood samples from intravenous drug users were collected from Sichuan, Hunan, Guangxi and Xinjiang regions, and tested for anti-HIV, anti-HCV, HBsAg using enzyme-linked immuno-sobent assays (ELISAs). RESULTS: The positive rates of anti-HIV,anti-HCV and HBsAg were14.7%-30.4%, 60.7%-85.5% and 6.6%-22.4% in the intravenous drug users, respectively. The co-infection rates of HIV/HBV, HIV/HCV, HCV/HBV and HIV/HCV/HBV were 0%-0.4%, 11.6%-27.2%, 2.3%-14.3% and 1.6%-4.8% respectively in this population. CONCLUSION: The infection rates of HIV, HBV and HCV were higher in the intravenous drug users than that in general populations in the same regions, and HIV/HCV co-infection appeared most frequent in this population.

[Effects of diethylhexyl phthalate on lipid peroxidation and the life-span in Drosophila melanogaster].

OBJECTIVE: To observe the effects of diethlhexyl phthalate (DEHP) on lipid peroxidation and the life span in Drosophila melanogaster. METHODS: Fed Drosophila with the concentration 0.20% DEHP of exposure after 0, 14, 28 days, the activity of total superoxide dismutase (SOD), CuZn-SOD and the concentration of malondialdehyde were determined. At the same time, the longevity test was carried out to examine the effect of DEHP on the Drosophila's lifespan. RESULTS: The lifespan of Drosophila was shortened in a dose of DEHP exposed groups. The indexes of mean life span (MLS), 50% lethal time and mean maximum life span in three DEHP-treated groups (concentration of 0.05%, 0.10% and 0.20%) were lower than those of the controlled group respectively (P < 0.01 or P < 0.05). The MLS of both Drosophila sexes were reduced from the control of 64 days and 59 days to the test 60 days-52 days and 54 days-49 days respectively. DEHP decreased the activity of SOD (P < 0.01 or P < 0.05), and lead to a time-dependent relation and an increase in the concentration of malondialdehyde (P < 0.01 or P < 0.05) in the DEHP-exposed Drosophila groups. CONCLUSION: DEHP might promote the process of lipid peroxidation and shorten the life span in Drosophila melanogaster. It should be one of the reasons in the senescence of Drosophila.

[Capacity of HIV enzyme immunoassay diagnostic kits to detect antibodies against different genotypes of HIV].

OBJECTIVE: To investigate the capacity of commercial HIV enzyme immunoassay (EIA) diagnostic kits to detect antibodies against different genotypes of HIV. METHODS: HIV RNA was detected with RT-PCR from samples positive for HIV antibody. The purified PCR products were sequenced directly and the genotypes of HIV from samples were analyzed. The samples for each genotype of HIV were diluted and the diluted samples were detected with different HIV EIA diagnostic kits. RESULTS: All 20 samples positive for HIV antibody were also positive for HIV RNA; 9 of 20 isolates were genotype B, 9 of them were genotype C or CRF BC, 2 of them were CRF AE. The sensitivity of different HIV EIA diagnostic kits to detect antibodies against different genotypes of HIV was not significantly different. CONCLUSION: The capacity of commercial HIV diagnostic kits to detect antibodies against different HIV genotypes may not be significantly different.