Dear Editor, Recently, the novel coronavirus disease (COVID-19) has broken out worldwide, 1 with rapid increase of infected patients. COVID-19 dominantly leads to pneumonia. 2 Among these COVID-19 patients, some appears to be severe symptoms with acute respiratory distress syndrome, organ failure, 2 and further present a poor outcome. Previous studies have been reported that immune patterns are closely associated with disease progression of patients infected with other viruses. 3 The correlation between immune signatures and outcome of severe and critical COVID-19 cases was not well illuminated. Therefore, we aimed to evaluate the correlation between immune characteristics, especially levels of lymphocytes and cytokines in peripheral blood, and clinical parameters in severe and critical COVID-19 patients, in order to find critical indicators of disease progression and to provide important guides for therapeutic strategy. Thirty-six adult cases with severe and critical COVID-19 were enrolled. The disease outcome, immune patterns, microbiota infection, coagulation profile, and organ dysfunction biomarkers were analyzed and collected. This project was approved by the Ethics Committee of our hospital (No. 2020-KY-060), and all patients signed the informed consent. We found that the cell numbers of lymphocytes in these patients were obviously decreased compared to that in healthy donors, including total lymphocytes, total T, CD4 + T, CD8 + T, B and NK cells (Fig. 1a), and the percentage of lymphocytes in COVID-19 patients was also significantly decreased except B cells (Supplementary Fig. S1a, b), with an increased ratio of CD4 + /CD8 + T cells (Supplementary

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BackgroundCTX-M-55 extended-spectrum beta-lactamases are being rapidly disseminated and transmitted in clinical practices around the world. The genetic contexts of the transferable plasmid-mediated blaCTX-M-55 gene in Enterobacteriaceae were detected and characterized in this study.MethodsIsolates were obtained from the First Affiliated Hospital of Zhengzhou University between September 2015 and March 2016. Based on polymerase chain reaction and BLAST analysis, resistance genes and genetic context of the blaCTX-M-55 gene were investigated. Conjugation experiments and multilocus sequence typing were performed to demonstrate plasmid-mediated blaCTX-M-55 transmission.ResultsThirteen blaCTX-M-55-positive isolates of Enterobacteriaceae were obtained. Seven isolates were Escherichia coli, 3 were Klebsiella pneumoniae, 1 was Citrobacter freundii, 1 was Morganella morganii and 1 was Serratia marcescens. The blaCTX-M-55 gene has not previously been identified from C. freundii and M. morganii. Four different blaCTX-M-55 genetic contexts were identified, and all of them harbored ISEcp1 in the region upstream of blaCTX-M-55 (in two cases, ISEcp1 was truncated by IS26, and in one case, it was truncated by IS1294), whereas ORF477 was detected downstream of the blaCTX-M-55 gene from 12 of 13 strains. The novel genetic context of ISEcp1∆-blaCTX-M-55-∆IS903 was firstly detected the IS903 element which was identified downstream of blaCTX-M-55. A conjugation assay revealed that all blaCTX-M-55 plasmids were quickly and easily transferable to recipient E. coli, which then presented resistance to multiple antibiotics.ConclusionsNumerous blaCTX-M-55-positive strains were isolated in a short period of 7 months. The findings indicate that blaCTX-M-55 was rapidly disseminated. The genetic context and conjugative transfer found in this study demonstrate that there is active transmission of blaCTX-M-55 among strains of Enterobacteriaceae in China, which could give rise to an urgent global public health threat.

To investigate the occurrence and genetic characteristics of the bla IMP-26-positive plasmid from a multidrug-resistant clinical isolate, Enterobacter hormaechei L51. Methods: Species identification was determined by MALDI-TOF MS and Sanger sequencing. Antimicrobial susceptibility testing was performed by the agar dilution and broth microdilution. Whole-genome sequencing was conducted using Illumina HiSeq 4000-PE150 and PacBio Sequel platforms, and the genome was annotated by the RAST annotation server. The ANI analysis of genomes was performed using OAT. Phylogenetic reconstruction and analyses were performed using the Harvest suite based on the core-genome SNPs of 61 publicly available E. hormaechei genomes. Results: The E. hormaechei L51 genome consists of a 5,018,729 bp circular chromosome and a 343,918 bp conjugative IncHI2/2A plasmid pEHZJ1 encoding bla IMP-26 which surrounding genetic context was intI1-bla IMP-26-ltrA-qacEΔ1-sul1. A new sequence type (ST1103) was assigned for the isolate L51 which was resistant to cephalosporins, carbapenems, but sensitive to piperacillin-tazobactam, amikacin, tigecycline, trimethoprimsulfamethoxazole and colistin. Phylogenetic analysis demonstrated that E. hormaechei L51 belonged to the same subspecies as the reference strain E. hormaechei SCEH020042, however 18,248 divergent SNP were identified. Resistance genes in pEHZJ1 including aac (3)-IIc, aac(6ʹ)-IIc, bla SHV-178 , bla DHA-1 , bla TEM-1 , bla IMP-26 , ereA2, catII, fosA5, qnrB4, tet(D), sul1 and dfrA19. Conclusion: In our study, we identified a conjugative IncHI2/2A plasmid carrying bla IMP-26 and bla SHV-178 in E. hormaechei ST1103, a novel multidrug-resistant strain isolated from China, and describe the underlying resistance mechanisms of the strain and detailed genetic context of mega plasmid pEHZJ1.

The emergence of carbapenem resistance (CR) caused by hydrolytic enzymes called carbapenemases has become a major concern worldwide. So far, CR genes have been widely detected in various bacteria. However, there is no report of CR gene harboring Comamonas thiooxydans. We first isolated a strain of an IMP-8-producing C. thiooxydans from a patient with urinary tract infection in China. Species identity was determined using MALDI-TOF MS analysis and carbapenemase-encoding genes were detected using PCR. The complete genomic sequence of C. thiooxydans was identified using Illumina Novaseq and Oxford Nanopore PromethION. Antimicrobial susceptibility analysis indicated that the C. thiooxydans strain ZDHYF418 was susceptible to imipenem, intermediate to meropenem, and was resistant to aztreonam, fluoroquinolones, and aminoglycosides. The blaIMP–8 gene was chromosomally located, and was part of a Tn402-like class 1 integron characterized by the following structure: DDE-type integrase/transposase/recombinase-tniB-tniQ-recombinase family protein-aac(6′)-Ib-cr-blaIMP–8-intI1. Phylogenetic analysis demonstrated that the closest relative of ZDHYF418 is C. thiooxydans QYY (accession number: CP053920.1). We detected 330 SNP differences between ZDHYF418 and C. thiooxydans QYY. Strain QYY was isolated from activated sludge in Jilin province, China in 2015. In summary, we isolated a strain of C. thiooxydans that is able to produce IMP-8 and a novel blaOXA. This is the first time that a CR gene has been identified in C. thiooxydans. The occurrence of the strain needs to be closely monitored.

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ObjectivesTo identify key genes involved in vascular invasion in hepatocellular carcinoma (HCC), to describe their regulatory mechanisms, and to explore the immune microenvironment of HCC.MethodologyIn this study, the genome, transcriptome, and immune microenvironment of HCC were assessed by using multi-platform data from The Cancer Genome Atlas (n = 373) and GEO data (GSE149614). The key regulatory networks, transcription factors and core genes related to vascular invasion and prognosis were explored based on the CE mechanism. Survival analysis and gene set enrichment were used to explore pathways related to vascular invasion. Combined with single-cell transcriptome data, the distribution of core gene expression in various cells was observed. Cellular communication analysis was used to identify key cells associated with vascular invasion. Pseudo-temporal locus analysis was used to explore the regulation of core genes in key cell phenotypes. The influence of core genes on current immune checkpoint therapy was evaluated and correlations with tumor stem cell scores were explored.ResultsWe obtained a network containing 1,249 pairs of CE regulatory relationships, including 579 differential proteins, 28 non-coding RNAs, and 37 miRNAs. Three key transcription factors, ILF2, YBX1, and HMGA1, were identified, all regulated by HCG18 lncRNA. ScRNAseq showed that HCG18 co-localized with macrophages and stem cells. CIBERSORTx assessed 22 types of immune cells in HCC and found that HCG18 was positively correlated with M0 macrophages, while being negatively correlated with M1 and M2 macrophages, monocytes, and dendritic cells. Cluster analysis based on patient prognosis suggested that regulating phenotypic transformation of macrophages could be an effective intervention for treating HCC. At the same time, higher expression of HCG18, HMGA1, ILF2, and YBX1 was associated with a higher stem cell score and less tumor differentiation. Pan cancer analysis indicated that high expression of HCG18 implies high sensitivity to immune checkpoint therapy.ConclusionHCG18 participates in vascular invasion of HCC by regulating macrophages and tumor stem cells through three key transcription factors, YBX1, ILF2, and HMGA1.

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