SAM-TB: a whole genome sequencing data analysis website for detection of Mycobacterium tuberculosis drug resistance and transmission.

Whole genome sequencing (WGS) can provide insight into drug-resistance, transmission chains and the identification of outbreaks, but data analysis remains an obstacle to its routine clinical use. Although several drug-resistance prediction tools have appeared, until now no website integrates drug-resistance prediction with strain genetic relationships and species identification of nontuberculous mycobacteria (NTM). We have established a free, function-rich, user-friendly online platform for MTB WGS data analysis (SAM-TB, http://samtb.szmbzx.com) that integrates drug-resistance prediction for 17 antituberculosis drugs, detection of variants, analysis of genetic relationships and NTM species identification. The accuracy of SAM-TB in predicting drug-resistance was assessed using 3177 sequenced clinical isolates with results of phenotypic drug-susceptibility tests (pDST). Compared to pDST, the sensitivity of SAM-TB for detecting multidrug-resistant tuberculosis was 93.9% [95% confidence interval (CI) 92.6-95.1%] with specificity of 96.2% (95% CI 95.2-97.1%). SAM-TB also analyzes the genetic relationships between multiple strains by reconstructing phylogenetic trees and calculating pairwise single nucleotide polymorphism (SNP) distances to identify genomic clusters. The incorporated mlstverse software identifies NTM species with an accuracy of 98.2% and Kraken2 software can detect mixed MTB and NTM samples. SAM-TB also has the capacity to share both sequence data and analysis between users. SAM-TB is a multifunctional integrated website that uses WGS raw data to accurately predict antituberculosis drug-resistance profiles, analyze genetic relationships between multiple strains and identify NTM species and mixed samples containing both NTM and MTB. SAM-TB is a useful tool for guiding both treatment and epidemiological investigation.

[Effect of pertussis vaccination on clinical manifestations of infants and young children with pertussis].

OBJECTIVE: To study the effect of pertussis vaccination on the clinical manifestations of infants and young children with pertussis. METHODS: A retrospective analysis was performed to investigate the differences in clinical manifestations and peripheral blood cell levels between pertussis children with different pertussis vaccination status. RESULTS: A total of 1 083 children with pertussisat at age of < 3 years were enrolled, with 551 children in the unvaccinated group and 532 in the vaccinated group. Of all the children, 392 had an age of onset of < 3 months (372 were unvaccinated and 20 were vaccinated) and 691 children had an age of onset of ≥ 3 months (179 were unvaccinated and 512 were vaccinated). Compared with the vaccinated group, the unvaccinated group had a longer length of hospital stay and a higher incidence rate of respiratory failure (P < 0.05). Among the children ≥ 3 months of age, the incidence of severe pneumonia in the unvaccinated group was higher than that in the vaccinated group (P < 0.05), and the incidence of severe pneumonia was the highest in the unvaccinated group (10.6%) and the lowest in the 4-dose vaccination group (1.2%). Among the 101 patients with severe pneumonia, 80 (79.2%) were observed in the unvaccinated group and only 21 (20.8%) in the four different doses vaccination groups. For the children with an age of onset of ≥ 3 months, the unvaccinated group had higher white blood cell count, absolute value of lymphocytes, and platelet count than the vaccinated group (P < 0.05). CONCLUSIONS: Pertussis vaccination can reduce the incidence of severe pneumonia and respiratory failure and alleviate the severity of respiratory complications in infants and young children with pertussis.

Risk Factors for Carbapenem-resistant Pseudomonas aeruginosa Infection in Children.

BACKGROUND: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is rapidly emerging as a life-threatening nosocomial infection. The study aimed to identify the risk factors for CRPA infection in children, especially antimicrobials use and invasive procedures. METHODS: A retrospective study was conducted in the Children's Hospital of Chongqing Medical University, which involved a cohort of patients with PA infection from January 2016 to December 2020. Patients were assigned to a carbapenem-susceptible PA group or to a CRPA group and matched using propensity-score matching. Univariate analysis and multivariate analysis were performed to estimate the risk factors of CRPA. RESULTS: One-thousand twenty-five patients were included in the study but 172 children were analyzed. Several factors were associated with CRPA infection according to univariate analysis ( P < 0.05), such as prior treatment with some antimicrobials and invasive procedures. However, only prior exposure to carbapenems (odds ratio [OR]: 0.102; confidence interval [CI]: 0.033-0.312; P < 0.001) and bronchoscopy (OR: 0.147; CI: 0.032-0.678; P = 0.014) during time at risk, previous invasive therapy in the last year (OR: 0.353; CI: 0.159-0.780; P = 0.013), and previous use of ß-lactams/ß-lactamase inhibitors within the last 90 days (OR: 0.327; CI: 0.121-0.884; P = 0.03) were considered independent risk factors by multivariate analysis. CONCLUSIONS: Those who had prior exposure to carbapenems and bronchoscopy were high-risk population to develop CRPA infection. The spread of CRPA could be influenced by invasive therapy, and we need pay attention to it. Moreover, we should take restrictions in the clinical use of carbapenems into account.

Case report: A case of severe acute hepatitis of unknown origin.

According to analyses of etiology, clinical features, diagnostic methods, and treatment strategies by summarizing a case of unexplained acute hepatitis recently experienced, we are aiming to provide some information to enrich the clinical experience in diagnosis and treatment of severe acute hepatitis of unknown etiology in young children. A boy, aged 10 years and 6 months old, was admitted to the hospital due to acute abdominal pain, jaundice, and exceptionally high levels of ALT and AST. A range of measures, including patient history, physical examination, and routine laboratory testing, were performed. Furthermore, strategies such as trio-based next-generation sequencing (Trio-NGS) and liver biopsy, as well as metagenomic NGS (mNGS) of blood and liver samples were also performed. In summary, this case was an acute severe non-A-E hepatitis that is a probable case with hepatitis of unknown origin. Immunohistochemical analysis showed an immune injury in liver tissues. Torque teno virus (TTV) sequences were detected by mNGS assay. As for treatment strategies, in addition to general treatment, this patient also underwent plasmapheresis and methylprednisolone treatment due to disease deterioration. The patient's liver function was improved afterward and discharged after one month of treatment. Taken together, this work reported the clinical feature and treatment of severe acute hepatitis with non-A-E hepatitis in detail. The potential mechanism of liver damage might be due to an immune attack in which TTV might play a role as a co-factor.