Varicella Zoster viral encephalitis without herpes: diagnosis by metagenomic next-generation sequencing of cerebrospinal fluid.

Acute Varicella Zoster viral encephalitis in immunocompetent adult patients without cutaneous herpes has rarely been reported. A 24-year-old female was hospitalized for a headache with a fever but without other obvious symptoms. Multiple routine examinations showed no abnormalities. Lumbar puncture indicated intracranial hypertension. The examination of cerebrospinal fluid by metagenomic next-generation sequencing demonstrated acute Varicella Zoster viral encephalitis. The patient's condition improved by treatment with acyclovir for antiviral therapy and mannitol dehydration to lower cranial pressure. Central Varicella Zoster viral infection should be emphasized as it is easily misdiagnosed and rare in clinical settings. Metagenomic next-generation sequencing of cerebrospinal fluid has significant advantages in the diagnosis of Varicella Zoster viral encephalitis.

Genome Analysis of ST1 Bartonella henselae, a Zoonotic Pathogen Causing Endocarditis in an Elderly Patient in China.

Infective endocarditis (IE) is a rare disease but with high associated mortality. Currently, the mainstays of diagnosis are still echocardiography and blood cultures. Here, we reported a case of infective endocarditis with negative blood cultures, and blood and aortic valve tissue metagenomic next-generation sequencing (mNGS) results suggested Bartonella henselae. In addition, we obtained the whole genomic sequence of B. henselae ZJBH strain. To our knowledge, this is the first report of B. henselae genomic analysis isolated from clinic in China. Furthermore, we described the whole genome sequencing (WGS) data incorporating all B. henselae from diverse sources worldwide and shed light on underlying risk of B. henselae transmitted between cats and humans.

Identification of Talaromyces marneffei Infection in an HIV-Negative Patient by ITS Sequencing.

Disseminated ankle mycosis is a life-threatening systemic infection caused by the emerging opportunistic and lethal fungal pathogen Talaromyces marneffei which is more common in HIV-positive patients. However, an increasing number of infections are occurring in HIV-negative patients. Here, we report a case of Talaromyces marneffei infection in HIV-negative patient. A 50s HIV-negative male patient with fever, cough, bloody sputum expectoration, pulmonary sarcoidosis and body rashes was hospitalized at Zhejiang Provincial People's Hospital. CT scanning showed pulmonary multiple nodules with apical bronchial occlusion, patchy infiltration and pathological biopsy demonstrated bronchiolitis obliterans with organized pneumonia and chronic active inflammation of lung tissue with infiltration of numerous lymphocytes, plasma cells, phagocytes and neutrophils. Laboratory tests revealed significantly increased white blood cells count 18.3 ×109/L, neutrophil count 15.34 ×109/L, monocyte count 0.66 ×109/L, platelet count 517 ×109/L, C-reactive protein 116 mg/L, erythrocyte sedimentation rate 112mm/h. The ß-D-glucan test was negative (33.06 pg/mL) while fungal culture of broncho alveolar lavage fluid revealed colonies with temperature-dependent dimorphic growth character and Talaromyces marneffei was confirmed by ITS sequencing of the colonies. The patient exhibited radiological improvement and clinical recuperation after intravenously guttae of voriconazole. Talaromycosis in immunocompetent and HIV-negative individuals is relatively rare and is characterized by an insidious onset, various clinical manifestations, and is clinically challenging. Fungal culture and ITS sequencing are warranted for diagnosis Talaromyces marneffei infection. This is the first report on identification of Talaromyces marneffei infection in an HIV-negative patient with skin involvement by ITS sequencing in Zhejiang.

Successful treatment with amoxicillin-clavulanic acid: cutaneous nocardiosis caused by Nocardia brasiliensis.

AIM: To emphasize the role of non-sulfonamides in the treatment of Nocardia infection and reduce the adverse reactions caused by sulfonamides. METHODS: We retrospectively analyzed a case of cutaneous nocardiosis in an immunocompetent individual. The colonies obtained by staining the pus in the lesion with antacid and culturing the agar plates were identified by flight mass spectrometry. The pathogenic identification showed Nocardia brasiliensis infection and the patient was treated with amoxicillin-clavulanic acid. RESULTS: After treatment with amoxicillin and clavulanic acid, the ulcer gradually peeled and crusted, leaving dark pigmentation. The patient has finally recovered. CONCLUSION: Sulfonamides are the first-line antibacterial agents for years in treatment of nocardiosis but are of great toxicity and side effects. This patient was successfully treated with amoxicillin-clavulanic acid and it provided a reference protocol for patients with sulfonamide-resistant Nocardia or sulfonamides intolerance.

Pacemaker Associated Aspergillus fumigatus Endocarditis: A Case Report.

Aspergillus endocarditis (AE) is a highly fatal infection that can occur in heart valve replacement, pacemaker implantation and other heart surgeries, and early recognition and sufficient diagnosis are challenging. Here, we report the case of a 68-year-old male with a history of dilated cardiomyopathy and pacemaker implantation who had a repeated fever with failed antibacterial treatment and sterile blood culture. He developed endocarditis, and the culture and biopsy of vegetation tissue showed the abundant presence of septate hyphae, which was subsequently identified as Aspergillus fumigatus by internal transcribed spacer (ITS) sequencing. Although the patient had serious side effects from voriconazole, he had a good prognosis following surgery and prolonged caspofungin antifungal therapy of 42 consecutive days. We discuss the diagnosis and treatment strategy of AE, and recommend galactomannan assays and next-generation sequencing for a timely diagnosis. Early surgical intervention combined with prompt antifungal therapy appears significant for survival.

Whole genome sequence of EC16, a blaNDM-5-, blaCTX-M-55-, and fosA3-coproducing Escherichia coli ST167 clinical isolate from China.

OBJECTIVES: Escherichia coli sequence type 167 (ST167) is an international multiresistant high-risk clone associated with New Delhi metallo-beta-lactamase (NDM) carbapenemase. Here, we report the whole genome sequence of an ST167 clinical isolate (EC16), obtained from a patient with abdominal infection in China, coharbouring the blaNDM-5, blaCTX-M-55, fosA3, aac(3)-IV, and qnrS1 genes. METHODS: E. coli strain EC16 was subjected to antimicrobial susceptibility testing by the broth microdilution method. Whole-genome sequencing of E. coli EC16 was performed using both Oxford Nanopore PromethION and Illumina NovaSeq 6000 platforms. De novo hybrid assembly of short Illumina reads and long PromethION reads was performed using Unicycler. Genome annotation was performed using Prokka 1.14.6, and further whole-genome sequence data analyses were performed. Easyfig 2.2.3 was used to analyse the genetic surroundings of blaNDM-5 and the homologous regions of the blaNDM-5-carrying plasmid pEC16-NDM-5 in E. coli EC16. RESULTS: The complete genome sequence of E. coli EC16 consists of six contigs comprising 5 317 797 bp, including one chromosome and five plasmids. Whole-genome sequencing and further bioinformatics analysis revealed that E. coli EC16 belonged to serotype O101:H9, fumC11 type, and ST167.blaNDM-5 was carried by a novel 145,550-bp IncFII-type plasmid pEC16-NDM-5 within a Tn2-IS26-ISAba125- blaNDM-5- bleMBL-trpF-dsbD-IS91 cassette. CONCLUSION: In this study, we report a clinical E. coli ST167 strain carrying a novel IncFII-type blaNDM-5 plasmid obtained from abdominal infection in China. The presented genome sequences of the blaNDM-5-producing E. coli strain ST167 could provide further insight into the acquisition of multiple resistance genes by this successful lineage.

Identification of sacrococcygeal and pelvic abscesses infected with invasive Mycoplasma hominis by MALDI-TOF MS.

BACKGROUND: Mycoplasma hominis is the smallest prokaryotic microorganism with no cell wall, high pleomorphism, and slower reproduction than bacteria. It is difficult for clinical technicians to find M. hominis through the negative Gram staining of specimens. Therefore, it is likely to miss detection in routine clinical smear etiological examination. M. hominis is generally considered to be a common colonizing bacterium in urogenital tract with low pathogenicity, and it is usually difficult to invade submucosal tissue and enter the bloodstream. METHODS: The abscesses of the patient were examined histopathologically, and the pus in the abscesses was extracted for etiological examination. MALDI-TOF MS was used to identify and confirmed the pathogens in the specimens. The commercial Mycoplasma isolation, culture, and drug sensitivity kit was used to determine antibiotic susceptibility. RESULTS: No pathogens were found after pathological and smear microscopic examination of the puncture fluid from the sacrococcygeal and pelvic abscesses. Until 48 h later, small, translucent, and gray-white colonies were observed in the blood plate culture results. The laboratory physician ultimately determined that the pathogen was M. hominis by MALDI-TOF MS. CONCLUSION: We report a case of extra-urogenital cystic abscesses infected by M. hominis, in order to improve clinicians' comprehensive understanding of the pathogenicity of Mycoplasma. In addition, the clinical laboratory technician should pay attention to the role of Wright-Giemsa staining of puncture fluid smear in the preliminary detection and the application of MALDI-TOF MS in identification of uncommon pathogenic microorganisms.

A multiple-dimension model for microbiota of patients with colorectal cancer from normal participants and other intestinal disorders.

Gut microbiota is a primary driver of inflammation in the colon and is linked to early colorectal cancer (CRC) development. Thus, a novel and noninvasive microbiome-based model could promote screening in patients at average risk for CRC. Nevertheless, the relevance and effectiveness of microbial biomarkers for noninvasive CRC screening remains unclear, and researchers lack the data to distinguish CRC-related gut microbiome biomarkers from those of other common gastrointestinal (GI) diseases. Microbiome-based classification distinguishes patients with CRC from normal participants and excludes other CRC-relevant diseases (e.g., GI bleed, adenoma, bowel diseases, and postoperative). The area under the receiver operator characteristic curve (AUC) was 92.2%. Known associations with oral pathogenic features, benefits-generated features, and functional features of CRC were confirmed using the model. Our optimised prediction model was established using large-scale experimental population-based data and other sequence-based faecal microbial community data. This model can be used to identify the high-risk groups and has the potential to become a novel screening method for CRC biomarkers because of its low false-positive rate (FPR) and good stability. KEY POINTS: • A total of 5744 CRC and non-CRC large-scale faecal samples were sequenced, and a model was constructed for CRC discrimination on the basis of the relative abundance of taxonomic and functional features. • This model could identify high-risk groups and become a novel screening method for CRC biomarkers because of its low FPR and good stability. • The association relationship of oral pathogenic features, benefits-generated features, and functional features in CRC was confirmed by the study.

A rare case of pulmonary nocardiosis comorbid with Sjogren's syndrome.

BACKGROUND: Nocardia is an opportunistic pathogen, which occurs in patients with autoimmune diseases and immune dysfunction, and can cause bacteremia and other life-threatening complications. The clinical manifestations of Nocardia pneumonia are similar to tuberculous and other clinical common bacterial pneumonia, but its antibacterial treatments are different and detection methods are unique, which may lead patients to suffer for many years due to clinical misdiagnosis and missed diagnosis. METHODS: Imaging and laboratory examinations were performed for preliminary diagnosis, and next-generation sequencing was used to identify the exact species type of Nocardia in the bronchoalveolar lavage fluid (BALF) of the patient. RESULTS: Imaging and laboratory parameters preliminarily implied that the patient was infected with Nocardia with Sjogren's syndrome (SS), and NGS showed that the strain was N. terpenica. CONCLUSIONS: Accurate etiological diagnosis and corresponding antibiotics are key to improve the prognosis of pulmonary nocardiosis in this case. Nocardia pneumonia is rare in clinical practice; it is of great medical significance to improve the understanding of pulmonary nocardiosis.

Penicillium janthinellum Pneumonia in an SLE Patient: A Case Study.

The risk of opportunistic fungal infections is high in immunocompromised patients. The Penicillium genus is common and diverse in nature. However, it rarely causes infection in humans. Here, we reported a case of Penicillium janthinellum pneumonia in a systemic lupus erythematosus (SLE) patient, and the morphological characteristics of P. janthinellum were also described. The patient was a 64-year-old female. She had been diagnosed with SLE and membranous lupus nephritis 10 months previously. Her medications included methylprednisolone, cyclosporine, and hydroxychloroquine. She was admitted because of fever and diagnosed with pneumonia. P. janthinellum was isolated from sputum and bronchoalveolar lavage (BAL) samples. BAL fluid stained with multiple stains showed the presence of somewhat dichotomously branching septate fungal hyphae. P. janthinellum was identified, and its morphological features were described. Antibiotic susceptibility profiles showed that this strain had higher minimum inhibitory concentration (MIC) values in response to multiple antifungal drugs. The patient died 10 days after diagnosis. To the best of our knowledge, this report is the second to demonstrate that P. janthinellum causes infection and is the first to present an infection (pneumonia) caused by P. janthinellumi in an SLE patient. Clinical and laboratory personnel should be aware that the Penicillium genus also contains pathogenic bacteria that cannot simply be treated as contaminants, especially in immunosuppressed patients.

Whole genome sequence of an Escherichia coli ST131 strain isolated from a patient with bloodstream infection in China co-harbouring blaKPC-2, blaCTX-M-3, blaCTX-M-14, qnrS1, aac(3)-IIa and aac(6')-Ib-cr genes.

OBJECTIVES: Escherichia coli sequence type 131 (ST131) is an international multiresistant high-risk clone associated with a large number of clinical infections. Here we report the draft genome sequence of a ST131 clinical isolate (EC538) obtained from a patient with bloodstream infection (BSI) in China co-harbouring the blaKPC-2, blaCTX-M-3, blaCTX-M-14, qnrS1, aac(3)-IIa and aac(6')-Ib-cr genes. METHODS: Antimicrobial susceptibility testing of E. coli EC538 was performed. DNA of E. coli EC538 was extracted and was sequenced using an Illumina HiSeqTM X Ten platform. Generated sequence reads were assembled using CLC Genomics Workbench. Contigs were annotated using Rapid Annotation using Subsystem Technology (RAST), and further bioinformatics analyses were performed. RESULTS: The total number of assembled bases was 5 420 040bp, with 5611 protein-coding sequences. Escherichia coli EC538 belongs to ST131 by multilocus sequence typing (MLST). The presence of blaKPC-2, blaCTX-M-3 and blaCTX-M-14 genes was detected in addition to other antimicrobial resistance genes conferring resistance to fluoroquinolones, aminoglycosides, trimethoprim, sulfonamides, tetracyclines, macrolides and rifampicin. CONCLUSION: To our knowledge, this is the first report of an E. coli ST131 strain from a BSI co-harbouring blaKPC-2, blaCTX-M-3, blaCTX-M-14, qnrS1, aac(3)-IIa and aac(6')-Ib-cr genes in China. The presented genome sequence of a carbapenemase-producing E. coli ST131 strain could provide further insight into the genomic diversity of this highly virulent, multiresistant and successfully pandemic bacterial pathogen.

Mining TCGA database for tumor mutation burden and their clinical significance in bladder cancer.

BACKGROUND: Bladder cancer is the ninth most-common cancer worldwide and it is associated with high morbidity and mortality. Tumor mutational burden (TMB) is an emerging biomarker in cancer characterized by microsatellite instability. TMB has been described as a powerful predictor of tumor behavior and response to immunotherapy. METHODS: A total of 443 bladder cancer samples obtained from The Cancer Genome Atlas (TCGA) were analyzed for mutation types, TMB values, and prognostic value of TMB. Differentially expressed genes (DEGs) were identified from the TMB groupings. Functional analysis was performed to assess the prognostic value of the first 30 core genes. CIBERSORT algorithm was used to determine the correlation between the immune cells and TMB subtypes. RESULTS: Single nucleotide polymorphism (SNP) and C>T were reported as the most common missense mutations and we also identified a high rate of mutations in TP53, TTN, KMT2D. Bladder cancer patients with high TMB showed a better prognosis. Enrichment analysis of the DEGs revealed that they were involved in the regulation of the P13K-Akt signaling pathway, cytokine-cytokine receptor interaction, and Ras signaling pathway. The high expression of hub genes ADRA2A, CXCL12, S1PR1, ADAMTS9, F13A1, and SPON1 was correlated with poor overall survival. Besides, significant differences in the composition of the immune cells of T cells CD8, T cells CD4 memory activated, NK cells resting and Mast cells resting were observed. CONCLUSIONS: The present study provides a comprehensive and systematic analysis of the prediction of TMB in bladder cancer and its clinical significance. Also, the study provides additional prognostic information and opportunities for immunotherapy in bladder cancer.

Unusual findings of acute myeloid leukemia with inv(3)(q21q26.2) or t(3;3)(q21;q26.2): A multicenter study.

INTRODUCTION: AML with inv(3)(q21.3q26.2) or t(3;3)(q21.3;q26.2) [inv(3)/t(3;3)] was very rare. Currently, most reports of AML-inv(3)/t(3;3) were from Western countries, and few reports were from Asian countries. Racial differences in patients with AML-inv(3)/t(3;3) are still unknown. METHODS: Between January 1996 and April 2018, a total of 37 AML cases with inv(3)/t(3;3) were studied retrospectively. They were collected from 2229 primary AML cases performed with conventional cytogenetic analysis (37/2229, 1.66%). RESULTS: Here, some differences were found by comparing our data with those from Western countries. In our series, AML with inv(3)(q21q26) had a lower incidence than that with t(3;3)(q21;q26) (11 vs 26 cases). Our patients seemed to be more younger (median, 43 years) and have lower hemoglobin concentrations (median, 73 g/L) and higher platelet count (median, 351 × 109 /L). A higher incidence of acute monoblastic and monocytic leukemia (45.9%) was observed in our patients. Immunophenotypic studies showed that CD38 (30.8%) was not so frequently expressed as that in the earlier reports. Mutations analysis showed a high frequency of NRAS mutations (45.0%), followed by SF3B1(15.0%), GATA2(15.0%), FLT3-ITD(10.0%), C-Kit/D816(5.0%), and CEBPA(5.0%), without mutation of NPM1(Exon12)or JAK2V617. CONCLUSION: Ethnic differences do exist between the Chinese and Western patients with AML-inv(3)/t(3;3), and more attention should be paid involving different ethnic populations and geographic regions.

Detection and characterization of a clinical Escherichia coli ST3204 strain coproducing NDM-16 and MCR-1.

OBJECTIVES: A plasmid-mediated colistin resistance gene, mcr-1, has been reported worldwide and has caused concern regarding a major therapeutic challenge. Alarmingly, mcr-1 has spread into clinical carbapenem-resistant Enterobacteriaceae isolates, resulting in extensively drug-resistant and even pan drug-resistant isolates that can cause untreatable infections. In this study, we report isolation of an extensively drug-resistant Escherichia coli strain EC1188 that coproduces NDM-16 and MCR-1 from a urine sample taken from a patient with craniocerebral injury. MATERIALS AND METHODS: E. coli strain EC1188 was identified and subjected to genotyping, susceptibility testing and conjugation experiments. The genetic locations of blaNDM-16 and mcr-1 were established with southern blot hybridization. The complete genome sequence of this strain was obtained and the genetic characteristics of the mcr-1- and blaNDM-16-harboring plasmids were analyzed. In addition, comparative genetic analyses of mcr-1 and blaNDM-16 with closely related plasmids were also carried out. RESULTS: Whole-genome sequencing revealed that strain EC1188 possess various resistance genes and virulence genes. S1-pulsed-field gel electrophoresis and southern blot suggested that the blaNDM-16 and mcr-1 genes were located on an ~65 kb plasmid and an ~80 kb plasmid, respectively. Moreover, the two genes could successfully transfer their resistance phenotype to E. coli strain C600. Sequence analysis showed that these two plasmids possessed high sequence similarity to previously reported blaNDM-5-harboring and mcr-1-harboring plasmids in China. CONCLUSION: To the best of our knowledge, this is the first report to isolate an E. coli strain that coproduces NDM-16 and MCR-1. In addition, we characterized the blaNDM-16-harboring plasmid for the first time. Our study further emphasizes that the co-occurrence of the two prevalent transferrable resistance plasmids in a single isolate is highly significant because infections caused by MCR-1-producing carbapenem-resistant Enterobacteriaceae isolates are increasing each year. It is imperative to perform active surveillance to prevent further dissemination of MCR-1-producing CRE isolates.

Draft genome sequence of Escherichia coli ST977: A clinical multidrug-resistant strain harbouring blaNDM-3 isolated from a bloodstream infection.

OBJECTIVES: The emergence of carbapenem-resistant Escherichia coli has become a serious challenge to manage in the clinic because of multidrug resistance. Here we report the draft genome sequence of NDM-3-producing E. coli strain NT1 isolated from a bloodstream infection in China. METHODS: Whole genomic DNA of E. coli strain NT1 was extracted and was sequenced using an Illumina HiSeq™ X Ten platform. The generated sequence reads were assembled using CLC Genomics Workbench. The draft genome was annotated using Rapid Annotation using Subsystem Technology (RAST). Bioinformatics analysis was further performed. RESULTS: The genome size was calculated at 5,353 620bp, with 5297 protein-coding sequences and the presence of genes conferring resistance to aminoglycosides, ß-lactams, quinolones, macrolides, phenicols, sulphonamides, tetracycline and trimethoprim. In addition, genes encoding virulence factors were also identified. CONCLUSIONS: To our knowledge, this is the first report of an E. coli strain producing NDM-3 isolated from a human bloodstream infection. The genome sequence will provide valuable information to understand antibiotic resistance mechanisms and pathogenic mechanisms in this strain. Close surveillance is urgently needed to monitor the spread of NDM-3-producing isolates.

Draft genome sequence of Enterobacter cloacae HBY, a ST128 clinical strain co-producing KPC-2 and NDM-1 carbapenemases.

OBJECTIVES: Enterobacter cloacae is one of the major pathogens responsible for a variety of human infections. Here we report the draft genome sequence of multidrug-resistant E. cloacae strain HBY isolated from a female patient in China. METHODS: Whole genomic DNA of E. cloacae strain HBY was extracted and was sequenced using an Illumina HiSeq™ 2000 platform. The generated sequence reads were assembled using CLC Genomics Workbench. The draft genome was annotated using Rapid Annotations using Subsystems Technology (RAST), and the presence of antimicrobial resistance genes was identified. RESULTS: The 5799439-bp genome contains various antimicrobial resistance genes conferring resistance to aminoglycosides, ß-lactams, fosfomycin, macrolides, sulphonamides and fluoroquinolones. Notably, the strain was identified to carry two main carbapenemase genes (blaKPC-2 and blaNDM-1). CONCLUSIONS: The genome sequence reported in this study will provide valuable information to understand antibiotic resistance mechanisms in this strain. It is important to monitor the spread strains of Enterobacter sp. encoding both of these carbapenemase genes.

[Construction and identification of a mouse spermatocyte-derived cell line with a stable expression of PIAS-NY].

OBJECTIVE: To construct a lentiviral expression vector of the PIAS-NY gene, and establish a mouse spermatocyte-derived cell line with a stable overexpression of PIAS-NY. METHODS: PIAS-NY was synthesized, amplified by PCR and cloned into the lentiviral vector expression plasmid pGC-FU. After digestion and sequencing, pGC-FU-PIAS-NY, pHelper 1.0 and pHelper 2.0 were co-transfected into 293T cells. Then the lentiviral particles were used to transfect the mouse spermatocyte-derived cells. The expression of the PIAS-NY protein was detected by Western blot. RESULTS: We successfully constructed the lentiviral expression vector pGC-FU-PIAS-NY and established a mouse spermatocyte-derived cell line with a stable overexpression of PIAS-NY. CONCLUSION: The construction of the lentiviral expression vector pGC-FU-PIAS-NY and the obtainment of stably transfected mouse spermatocyte-derived cells have paved the way for further studies on the roles of the PIAS-NY gene in spermatogenesis.

Identification of Pold2 as a novel interaction partner of protein inhibitor of activated STAT2.

Pold2 is a subunit of the DNA polymerase δ complex, encoding a protein involved in DNA replication and repair. In this study, using a yeast two-hybrid screening technique and the common cDNA fragment of the mouse PIAS2 as a bait, Pold2 was found to interact with PIAS2. A direct interaction between Pold2 and PIAS2 was confirmed by direct yeast two-hybrid. In vivo evidence of Pold2 association with PIAS2 was obtained by co-immunoprecipitation using HEK-293 cells. Subcellular localization studies demonstrated that Pold2 and PIAS2 were partially co-localized in mammalian cells. Collectively, our results suggest that Pold2 interacts under physiological conditions with PIAS2.