Metagenomic next-generation sequencing for the identification of infections caused by Gram-negative pathogens and the prediction of antimicrobial resistance.

OBJECTIVE: The aim of this study was to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) for the identification of Gram-negative bacteria (GNB) infections and the prediction of antimicrobial resistance. METHODS: A retrospective analysis was conducted on 182 patients with diagnosis of GNB infections who underwent mNGS and conventional microbiological tests (CMTs). RESULTS: The detection rate of mNGS was 96.15%, higher than CMTs (45.05%) with a significant difference (χ 2 = 114.46, P < .01). The pathogen spectrum identified by mNGS was significantly wider than CMTs. Interestingly, the detection rate of mNGS was substantially higher than that of CMTs (70.33% vs 23.08%, P < .01) in patients with but not without antibiotic exposure. There was a significant positive correlation between mapped reads and pro-inflammatory cytokines (interleukin-6 and interleukin-8). However, mNGS failed to predict antimicrobial resistance in 5 of 12 patients compared to phenotype antimicrobial susceptibility testing results. CONCLUSIONS: Metagenomic next-generation sequencing has a higher detection rate, a wider pathogen spectrum, and is less affected by prior antibiotic exposure than CMTs in identifying Gram-negative pathogens. The mapped reads may reflect a pro-inflammatory state in GNB-infected patients. Inferring actual resistance phenotypes from metagenomic data remains a great challenge.

Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing for Pathogen Detection in Patients with Suspected Infectious Diseases: A Retrospective Study from a Large Tertiary Hospital.

Purpose: Metagenomic next-generation sequencing (mNGS) is a powerful yet unbiased method to identify pathogens in suspected infections. However, little is known about its clinical effectiveness. The present study aimed to assess the efficacy of mNGS in routine clinical practice. Patients and Methods: In this single-center retrospective cohort study, 518 patients with suspected infectious diseases were assessed for inclusion. Among them, each patient had undergone mNGS testing; 407 patients had undergone both microbial culture and mNGS testing. The result of mNGS testing was compared to microbial culture performed concurrently. The diagnostic performance of mNGS was evaluated using the comprehensive clinical diagnosis as the reference standard. Results: There was a significant difference in the positive detection rates of pathogens between mNGS and culture (331/407, 81.3% vs 79/407, 19.4%, P < 0.001). The sensitivity of mNGS was much higher than the culture method (79.5% vs 21.3%, P < 0.001), especially in sample types of sputum and bronchoalveolar lavage fluid (BALF). Notably, the sensitivity of blood mNGS was relatively lower than other sample types (67.4% vs 88.9-93.8%). Pathogen cfDNA load based on standardized stringently mapped read number at the species level of microorganisms (SDSMRN) was significantly lower in blood than in other sample types from the same patient (P = 0.0003). Importantly, mNGS directly led to a change of treatment regimen in 142 (27.4%) cases, including antibiotic escalation (15.3%), antibiotic de-escalation (9.1%), and early definitive diagnosis to initiate appropriate treatment (3.1%). Conclusion: Our in-house mNGS platform significantly improved the sensitivity for the diagnosis of infectious diseases. mNGS has the potential to improve clinical outcomes by optimizing antimicrobial therapy.

Comparison of electromagnetic and optical navigation assisted Endo-TLIF in the treatment of lumbar spondylolisthesis.

Uniportal full endoscopic posterolateral transforaminal lumbar interbody fusion (Endo-TLIF) with percutaneous pedicle screw fixation is a promising, minimally invasive method for the treatment of lumbar spondylolisthesis. However, repeated radiation exposure from X-rays and the steep learning curve remain to be improved.

mNGS helped diagnose scrub typhus presenting as a urinary tract infection with high D-dimer levels: a case report.

BACKGROUND: Scrub typhus is caused by O. tsutsugamushi and spreads through mite larvae biting the skin. Classic symptoms of the disease are eschar and lymphadenopathy. Previous reports have revealed clinical manifestations of scrub typhus, including gastrointestinal symptoms, meningoencephalitis, ocular flutter, pneumonitis, acute respiratory distress syndrome, and acute kidney injury. However, cases of scrub typhus presenting as a urinary tract infection (UTI) with high D-dimer levels could be easily misdiagnosed when clinical attention is insufficient, resulting in difficulty in making a timely diagnosis of the infection. Metagenomics next-generation sequencing (mNGS) is a revolutionary and highly sensitive method that may help in diagnosing atypical cases, even when trace amounts of pathogens are present. CASE PRESENTATION: A 52-year-old female presented with a 10-day history of fever, chills, headache and myalgia. She was initially diagnosed with influenza at a local clinic. Various antibacterials were used on the 2nd-12th day onwards; however, her symptoms persisted and were followed by increased urination duration, frequency, urgency and dysuria for 2 days. Orientia tsutsugamushi was confirmed as the pathogen responsible for the infection through mNGS analysis of her blood samples from Day 13 onwards. The patient's temperature changed remarkably 24 h after the initiation of doxycycline. Over the next 48 h (i.e., Day 15 onwards), the patient showed clinical improvement. She recovered and was discharged from the hospital. CONCLUSIONS: Scrub typhus can present atypical clinical symptoms, such as UTIs, in a febrile patient. mNGS may be a useful method for identifying O. tsutsugamushi infection in patients with atypical clinical manifestations.

Clinical Efficacy Study of the Quadrant Channel and Delta Large Channel Technique in the Treatment of Lumbar Degenerative Diseases.

OBJECTIVE: To compare the therapeutic effect of the quadrant channel and delta large channel techniques in lumbar degenerative diseases. METHODS: According to the inclusion criteria, 62 patients suffering from lumbar degenerative disease were selected for the present study, which was conducted from September 2018 to June 2020. Patients were divided into Group A (quadrant channel technology) and Group B (delta large channel technology), which comprised 28 and 34 patients, respectively. The factors compared between the two groups were operation time, length of incision, blood loss, ambulation time, length of hospitalization, visual analogue scale (VAS) preoperatively, 7 days postoperatively, and 30 days postoperatively, and Oswestry dysfunction score (ODI). RESULTS: The length of incision, blood loss, ambulation time, and length of hospitalization stay in Group A were significantly higher compared with Group B (P < 0.05). There was no significant difference between the two groups in operation time, preoperative ODI index, preoperative VAS scores, and thirty-day postoperative VAS scores (P > 0.05). The seven-day postoperative VAS score, seven-day postoperative ODI index, and thirty-day postoperative ODI index of Group A were significantly higher than those of Group B (P < 0.05). The preoperative VAS score and ODI index in both groups were significantly higher compared with after operation (P < 0.05). CONCLUSION: Both surgical methods achieved a good clinical outcome in the treatment of lumbar degenerative diseases. The delta large channel technique may offer some advantages over quadrant channel technology, such as less trauma and bleeding and faster recovery time.

Effects of application of corn straw on soil microbial community structure during the maize growing season.

This study investigated the influence of corn straw application on soil microbial communities and the relationship between such communities and soil properties in black soil. The crop used in this study was maize (Zea mays L.). The five treatments consisted of applying a gradient (50, 100, 150, and 200%) of shattered corn straw residue to the soil. Soil samples were taken from May through September during the 2012 maize growing season. The microbial community structure was determined using phospholipid fatty acid (PLFA) analysis. Our results revealed that the application of corn straw influenced the soil properties and increased the soil organic carbon and total nitrogen. Applying corn straw to fields also influenced the variation in soil microbial biomass and community composition, which is consistent with the variations found in soil total nitrogen (TN) and soil respiration (SR). However, the soil carbon-to-nitrogen ratio had no effect on soil microbial communities. The abundance of PLFAs, TN, and SR was higher in C1.5 than those in other treatments, suggesting that the soil properties and soil microbial community composition were affected positively by the application of corn straw to black soil. A Principal Component Analysis indicated that soil microbial communities were different in the straw decomposition processes. Moreover, the soil microbial communities from C1.5 were significantly different from those of CK (p < 0.05). We also found a high ratio of fungal-to-bacterial PLFAs in black soil and significant variations in the ratio of monounsaturated-to-branched fatty acids with different straw treatments that correlated with SR (p < 0.05). These results indicated that the application of corn straw positively influences soil properties and soil microbial communities and that these properties affect these communities. The individual PLFA signatures were sensitive indicators that reflected the changes in the soil environment condition.

[Meta-analysis of lumbar disc herniation in Chinese adolescents].

OBJECTIVE: To provide evidence-based medicine rationales for the diagnosis and treatment of lumbar disc herniation (LDH) in Chinese adolescents. METHODS: The related medical literature of pediatric LDH between January 1990 and December 2012 was collected by retrospective searches of WANGFANG and CNKI databases. The data concerning mechanism, clinical manifestations, diagnosis and treatment were recorded and analyzed. RESULTS: A total of 1208 cases of LDH in adolescents were retrieved from 45 articles. Most of them were males (74.2%). And the primary cause was trauma (65.9%). Their clinical presentations were characterized by mild symptoms and serious physical signs. And 87.0% of them had a positive straight-leg raising test. Single-level intervertebral disk protrusion accounted for 92%. And the levels were at L4-L5 (54.7%) and L5-S1 (37.6%). There was a higher incidence of lumbar scoliosis deformity (38.2%), lumbar spine physiological curvature change (41.4%) and loss of vertebral height (33.6%) in adolescents than adults. There were many different treatments for pediatric LDH. Each method had its own advantages and disadvantages. The success rates of micro endoscopic discectomy (MED) and open discectomy were more than 90%. CONCLUSION: Trauma is a common cause of pediatric LDH. Males are more frequently affected. The single-level protrusion of L4/5 or L5/S1 has a much higher incidence. Positive straight-leg raising test and imaging findings of lumbar scoliosis deformity, lumbar spine physiological curvature change and a loss of vertebral height may aid the diagnosis. Normally conservative treatment is offered. And chemonucleolysis, MED and open discectomy are alternative options.