Cell atlas of CCl 4-induced progressive liver fibrosis reveals stage-specific responses.

Chronic liver injury leads to progressive liver fibrosis and ultimately cirrhosis, a major cause of morbidity and mortality worldwide. However, there are currently no effective anti-fibrotic therapies available, especially for late-stage patients, which is partly attributed to the major knowledge gap regarding liver cell heterogeneity and cell-specific responses in different fibrosis stages. To reveal the multicellular networks regulating mammalian liver fibrosis from mild to severe phenotypes, we generated a single-nucleus transcriptomic atlas encompassing 49 919 nuclei corresponding to all main liver cell types at different stages of murine carbon tetrachloride (CCl 4)-induced progressive liver fibrosis. Integrative analysis distinguished the sequential responses to injury of hepatocytes, hepatic stellate cells and endothelial cells. Moreover, we reconstructed cell-cell interactions and gene regulatory networks implicated in these processes. These integrative analyses uncovered previously overlooked aspects of hepatocyte proliferation exhaustion and disrupted pericentral metabolic functions, dysfunction for clearance by apoptosis of activated hepatic stellate cells, accumulation of pro-fibrotic signals, and the switch from an anti-angiogenic to a pro-angiogenic program during CCl 4-induced progressive liver fibrosis. Our dataset thus constitutes a useful resource for understanding the molecular basis of progressive liver fibrosis using a relevant animal model.

A localized small-scale external quality assessment (EQA) for PCR testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the molecular laboratories.

The aim of this study was to estimate the PCR results for SARS-CoV-2 testing in 32 participating laboratories in a localized small-scale external quality assessment (EQA) scheme. EQA samples were distributed to the participants and detected immediately on the day of delivery. Qualitative results were submitted to the EQA provider, including negative or positive results along with cycle threshold (Ct) values for different target genes. Although the variability of Ct values differed among the laboratories in the EQA, a total of 32 (100 %) participants reported correct qualitative results. The study showed that the mean loads of N or E gene were higher than those of ORF1ab in SARS-CoV-2 RNA samples. Regardless of the analyzed gene target, the mean Ct values for weak positive and positive samples varied by fewer than 1.74 and 1.91 cycles, respectively. Less than 12 % of reported Ct values for ORF1ab and N genes deviated by more than ±4 cycles (maximum: -9.92 cycles), while none deviated by more than ±4 cycles for the E gene. The current EQA program can provide a robust practical basis for follow-up planning to conduct evaluations for SARS-CoV-2 PCR testing and other novel emerging pathogens in the future.

Clinician-collected urethra swab: A good alternative sample type using cobas 4800 system for Chlamydia trachomatis and Neisseria gonorrhoeae in men.

BACKGROUND: Nucleic acid amplification tests (NAATs) are being used increasing to detection of CT (Chlamydia trachomatis) and NG (Neisseria gonorrhoeae) infections for superior sensitivity and specificity than other tests. Male first-void urine (FVU) sample is the optimal sample type for detection of CT and NG by NAATs. Although not being the recommended by NAATs, clinician-collected urethra swab (CCUS) is perhaps a good alternative sample type compared with the FVU sample in men. METHODS: Paired samples (FVU and CCUS) from one hundred male outpatients were simultaneously detected by urine pattern and swab pattern using cobas 4800 CT/NG assay on cobas 4800 system for the detection of CT and NG, respectively. And twenty-one positive controls were also detected on cobas 4800 system. RESULTS: The CT/NG cycle thresholds (Ct) value of urine pattern is lower than that of swab pattern for the same positive samples (clinical samples and positive controls) on the cobas 4800 CT/NG assay. The final CT/NG results of two sample patterns from patients were highly consistent except for four discordant results. CONCLUSION: CCUS is validated for a good alternative sample type for the CT/NG detection on the cobas 4800 system in this study.

Prevalence and antimicrobial susceptibility of Ureaplasma urealyticum and Mycoplasma hominis in female outpatients, 2009-2013.

PURPOSE: The aim of this study was to estimate the prevalence and antimicrobial susceptibility of Ureaplasma urealyticum and Mycoplasma hominis among female outpatients treated for genital infection at a Chinese hospital from January 1, 2009 to December 31, 2013. METHODS: Samples from 6051 female outpatients were analyzed using Mycoplasma Identification and Antimicrobial Susceptibility Testing (ID/AST). RESULTS: The overall prevalence of U. urealyticum was higher than the prevalence of single M. hominis infection (31.2% vs 0.7%) and coinfections (31.2% vs. 1.9%). The percentage of U. urealyticum and/or M. hominis detected in the 30-39 year age group was greater than in the other age groups. More than 94.6% of the U. urealyticum isolates, 100% of the M. hominis isolates, and 84.3% of the isolates from coinfections were susceptible to doxycycline, minocycline, and tetracycline. More than 69.2% of the U. urealyticum isolates were susceptible to azithromycin, erythromycin, clarithromycin, and roxithromycin, but > 95.6% of the M. hominis isolates and 89.6% of the isolates from coinfections were resistant to these antibiotics. Acetylspiramycin, sparfloxacin, levofloxacin, ciprofloxacin, and ofloxacin were inactive against more than one-half of the isolates. More than 75.6% of the M. hominis isolates were susceptible to spectinomycin, but > 87.1% of the U. urealyticum and 93.3% of the coinfection isolates were resistant to this antibiotic. Isolates from three coinfections were completely resistant to the 14 antibiotics. CONCLUSION: The determination of antimicrobial susceptibility of these mycoplasma species is often crucial for optimal antimicrobial therapy of infected outpatients.

Urinary tract infection caused by Enterococcus isolates: aetiology and antimicrobial resistance patterns.

The purpose of this study was to analyse the data on resistance in Enterococcus faecalis and E. faecium isolated from urine samples of inpatients from January 2010 to December 2013. Compared to E. faecalis, E. faecium isolates were significantly more resistant to ampicilin, nitrofurantoin, and ciprofloxacin in the antimicrobial agents evaluated. Both species showed higher resistance to high-level gentamicin. The rate of vancomycin-resistant enterococci (VRE) in E. faecium was higher as compared to that of E. faecalis, and we found that apparent increase in the frequency of VRE E. faecalis clinical isolates in the 4-year study period. In our study, analysis of the antimicrobial resistance trends showed resistance to linezolid and vancomycin were <30.2% and <20.3% in both species, respectively. Of noteworthy is the high rate of MDR in two species from inpatients. This study highlights that it is of importance for clinicians to promote rational drug utilization and delay the emergence of resistant organisms.