Etiological diagnostic performance of probe capture-based targeted next-generation sequencing in bloodstream infection

Background

A rapid and precise etiological diagnosis is crucial for the effective treatment of bloodstream infection (BSI). In this study, the performance of probe capture-based targeted next-generation sequencing (tNGS) was compared to that of blood culture and metagenomic next-generation sequencing (mNGS) in detecting potential pathogens in patients with BSI.

Methods

A total of 80 patients with suspected BSI were prospectively enrolled from 24 November 2023 to 30 December 2023 at Zhongshan Hospital, Shanghai, China. All 80 participants underwent simultaneous blood culture, blood mNGS, and blood tNGS after admission when febrile, and the results were compared.

Results

Among the 80 participants, 11 were clinically diagnosed with noninfectious fever, and 69 were diagnosed with BSI. Blood tNGS had a higher sensitivity for the diagnosis of BSI than blood culture (91.3% vs. 23.2%, P<0.001) and blood mNGS (91.3% vs. 69.6%, P=0.001). There was no significant difference in specificity between blood mNGS and tNGS (81.8% vs. 100.0%, P=0.13). Blood tNGS demonstrated a faster turnaround time than blood culture and blood mNGS. In 22 (31.9%) patients with BSI, targeted adjustment of the anti-infectious therapy according to the blood tNGS results resulted in clinical improvement.

Conclusions

Blood tNGS may be a promising tool for detecting potential pathogens in patients with BSI. The application of blood tNGS for BSI could guide anti-infectious treatment strategies and might improve clinical outcomes.

Accurate etiological diagnosis of Mycoplasma hominis mediastinitis in immunocompetent patients using metagenomic next-generation sequencing: a case series and literature review

Background

As a culture-independent method, metagenomic next-generation sequencing (mNGS) is widely used in microbiological diagnosis with advantages in identifying potential pathogens, guiding antibiotic therapy, and improving clinical prognosis, especially in culture-negative cases. Mycoplasma hominis (M. hominis) mediastinitis is a rare and severe disease for which etiological diagnosis is important but challenging. The application of mNGS in the etiological diagnosis of mediastinitis has seldom been studied.

Methods

By searching the electronic medical history retrieval system with "Mycoplasma hominis" and "mediastinitis", seven patients diagnosed with M. hominis mediastinitis were reviewed in Zhongshan Hospital, Fudan University, Shanghai from 9 December 2020 to 14 February 2023. Microbiological cultures and mNGS were conducted for blood, abscess, and/or mediastinal fluid. Adjustment of the antibiotic therapy due to mNGS was assessed. A literature review was conducted in the PubMed database beginning in 1970 for M. hominis infection and mediastinitis.

Results

For the seven patients, cultures of blood, abscess, and mediastinal fluid were negative whereas mNGS identified M. hominis in serum, abscess, and/or mediastinal fluid and was used to guide specific antibiotic therapy. The stringent mapped reads number of genera (SMRNG), stringent mapped reads number of species (SMRN), and coverage rate of M. hominis detection by mNGS were significantly higher in body fluid (abscess or mediastinal fluid) than in serum. All seven patients had underlying heart diseases and underwent previous cardiac surgery. The most common symptoms were fever and sternal pain. After detection of M. hominis, antibiotics were adjusted to quinolones or doxycycline except for one patient, whose diagnosis was clarified after death. Two patients died. Literature review since 1970 identified 30 cases of extra-genital infection caused by M. hominis. Including our seven new cases, 2 (5.4%) were neonates and 35 (94.6%) were adults. Thirty (81.1%) cases were postoperative infection and 15 (40.5%) had implanted devices. Five patients (13.5%) died.

Conclusions

mNGS might be a promising technology in the detection of fastidious pathogens such as M. hominis. Accurate etiological diagnosis by mNGS could guide antibiotic therapy and facilitate clinical management.

Mechanism of benzoxazinoids affecting the growth and development of Fusarium oxysporum f. sp. fabae

Continuous cropping of faba bean (Vicia faba L.) has led to a high incidence of wilt disease. The implementation of an intercropping system involving wheat and faba bean can effectively control the propagation of faba bean wilt disease. To investigate the mechanisms of wheat in mitigating faba bean wilt disease in a wheat-faba bean intercropping system. A comprehensive investigation was conducted to assess the temporal variations in Fusarium oxysporum f. sp. fabae (FOF) on the chemotaxis of benzoxazinoids (BXs) and wheat root through indoor culture tests. The effects of BXs on FOF mycelial growth, spore germination, spore production, and electrical conductivity were examined. The influence of BXs on the ultrastructure of FOF was investigated through transmission electron microscopy. Eukaryotic mRNA sequencing was utilized to analyze the differentially expressed genes in FOF upon treatment with BXs. FOF exhibited a significant positive chemotactic effect on BXs in wheat roots and root secretions. BXs possessed the potential to exert significant allelopathic effects on the mycelial growth, spore germination, and sporulation of FOF. In addition, BXs demonstrated a remarkable ability to disrupt the structural integrity and stability of the membrane and cell wall of the FOF mycelia. BXs possessed the capability of posing threats to the integrity and stability of the cell membrane and cell wall. This ultimately resulted in physiological dysfunction, effectively inhibiting the regular growth and developmental processes of the FOF.

Benzoxazinoids secreted by wheat root weaken the pathogenicity of Fusarium oxysporum f. sp. fabae by inhibiting linoleic acid and nucleotide metabolisms

KEY MESSAGE

The regulatory action of BXs secreted by wheat on the pathogenicity of FOF causing Fusarium wilt in faba bean were analyzed. DIMBOA and MBOA weakened the pathogenicity of FOF. A large number of pathogenic bacteria in continuous cropping soil infect faba bean plants, leading to the occurrence of wilt disease, which restricts their production. Faba bean-wheat intercropping is often used to alleviate this disease. This study investigates the effect of benzoxazinoids (BXs) secreted by wheat root on the pathogenicity of Fusarium oxysporum f. sp. Fabae (FOF) and underlying molecular mechanisms. The effects of DIMBOA(2,4-dihydroxy-7-methoxy-1,4-benzoxazine-4-one) and MBOA(6-methoxybenzoxazolin-2-one) on the activity of cell-wall-degrading enzymes in FOF(cellulase, pectinase, amylase, and protease), FOF Toxin (fusaric acid, FA) content were investigated through indoor culture experiments. The effect of BXs on the metabolic level of FOF was analyzed by metabonomics to explore the ecological function of benzoxazines intercropping control of Fusarium wilt in faba bean. The results show that the Exogenous addition of DIMBOA and MBOA decreased the activity of plant-cell-wall-degrading enzymes and fusaric acid content and significantly weakened the pathogenicity of FOF. DIMBOA and MBOA significantly inhibited the pathogenicity of FOF, and metabolome analysis showed that DIMBOA and MBOA reduced the pathogenicity of FOF by down-regulating related pathways such as nucleotide metabolism and linoleic acid metabolism, thus effectively controlling the occurrence of Fusarium wilt in faba bean.

Oral Simnotrelvir for Adult Patients with Mild-to-Moderate Covid-19

BACKGROUND

Simnotrelvir is an oral 3-chymotrypsin-like protease inhibitor that has been found to have in vitro activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and potential efficacy in a phase 1B trial.

METHODS

In this phase 2-3, double-blind, randomized, placebo-controlled trial, we assigned patients who had mild-to-moderate coronavirus disease 2019 (Covid-19) and onset of symptoms within the past 3 days in a 1:1 ratio to receive 750 mg of simnotrelvir plus 100 mg of ritonavir or placebo twice daily for 5 days. The primary efficacy end point was the time to sustained resolution of symptoms, defined as the absence of 11 Covid-19-related symptoms for 2 consecutive days. Safety and changes in viral load were also assessed.

RESULTS

A total of 1208 patients were enrolled at 35 sites in China; 603 were assigned to receive simnotrelvir and 605 to receive placebo. Among patients in the modified intention-to-treat population who received the first dose of trial drug or placebo within 72 hours after symptom onset, the time to sustained resolution of Covid-19 symptoms was significantly shorter in the simnotrelvir group than in the placebo group (180.1 hours [95% confidence interval {CI}, 162.1 to 201.6] vs. 216.0 hours [95% CI, 203.4 to 228.1]; median difference, -35.8 hours [95% CI, -60.1 to -12.4]; P = 0.006 by Peto-Prentice test). On day 5, the decrease in viral load from baseline was greater in the simnotrelvir group than in the placebo group (mean difference [±SE], -1.51±0.14 log10 copies per milliliter; 95% CI, -1.79 to -1.24). The incidence of adverse events during treatment was higher in the simnotrelvir group than in the placebo group (29.0% vs. 21.6%). Most adverse events were mild or moderate.

CONCLUSIONS

Early administration of simnotrelvir plus ritonavir shortened the time to the resolution of symptoms among adult patients with Covid-19, without evident safety concerns. (Funded by Jiangsu Simcere Pharmaceutical; ClinicalTrials.gov number, NCT05506176.).

Proteomic analysis of the faba bean-wheat intercropping system in controlling the occurrence of faba bean fusarium wilt due to stress caused by Fusarium oxysporum f. sp. fabae and benzoic acid

BACKGROUND

In faba bean, continuous cropping severely affects plant growth and increases the incidence of fusarium wilt due to the accumulation of pathogens and autotoxic substances. The intercropping of faba bean and wheat is commonly used to alleviate the occurrence of fusarium wilt in the faba bean.

OBJECTIVE

To investigate the role of Fusarium oxysporum f. sp. Fabae(FOF) and benzoic acid in the occurrence of faba bean fusarium wilt and unravel the potential mechanism of intercropping in alleviating its occurrence.

METHODS

Hydroponic experiment was carried out using monocropping faba bean (M) and intercropping faba bean and wheat (I) patterns under FOF alone stress (M + F, I + F), FOF and benzoic acid double stress (M + F + B, I + F + B). The growth of faba bean seedlings under FOF and benzoic acid dual stresses were analyzed as well as the protein expression profile of monocropping and intercropping faba bean roots.

RESULT

Under FOF stress, the growth of faba bean seedlings was inhibited, and the inhibitory effect was enhanced under the dual stress of FOF and benzoic acid. However, faba bean-wheat intercropping alleviated the inhibitory effect of FOF and benzoic acid on faba bean growth. In faba bean, the up-regulated protein was involved in different functions, such as redox, hydrogen peroxide decomposition, and metabolic processes under FOF stress (M + F, I + F) compared to the control. Compared with FOF stress (M + F, I + F), under the dual stress of FOF and benzoic acid (M + F + B, I + F + B), the up-regulated protein in faba bean were involved in intracellular redox balance, defense, and maintenance of cell integrity. Compared with monocropping (M, M + F, M + F + B), the up-regulated protein function of intercropping(I, I + F, I + F + B) was mainly involved in the biosynthesis of secondary metabolites, redox balance, biological carbon fixation of photosynthesis, and so on. KEGG enrichment analysis results showed that intercropping increased ethylene and jasmonic acid synthesis and other related pathways to improve resistance against fusarium wilt in the faba bean.

CONCLUSION

The growth of faba bean was inhibited under FOF stress and the inhibitory effect was enhanced under the dual stress of FOF and benzoic acid, which promoted the occurrence of faba bean fusarium wilt. This might be due to the down-regulation of energy and cytoplasmic matrix proteins under FOF and benzoic acid stress. The faba bean wheat intercropping alleviated the inhibition of FOF and benzoic acid stress by up-regulating the biosynthesis of secondary metabolites, redox homeostasis, photosynthetic carbon fixation, and other related proteins. Besides, it also promoted the biosynthesis of ethylene, and jasmonic acid, improved the resistance of faba bean plants, and alleviated the occurrence of faba bean fusarium wilt. This provides a theoretical basis for the determination of jasmonic acid and ethylene content.

Contamination of personal protective equipment and environmental surfaces in Fangcang shelter hospitals

BACKGROUND

Fangcang shelter hospitals emerged as a new public health concept after COVID-19. Data regarding contamination of Fangcang shelter environments remains scarce. This study aims to investigate the extent of SARS-CoV-2 contamination on personal protective equipment and surfaces in Fangcang hospitals.

METHODS

Between March and May 2022, during wave of omicron variant, a prospective study was conducted in 2 Fangcang hospitals in Shanghai, China. Swabs of personal protective equipment worn and environmental surfaces of contaminated areas, doffing rooms, and potentially contaminated areas were collected. SARS-CoV-2 RNA was detected by reverse transcription quantitative polymerase chain reaction. If viral RNA was detected, sampling was repeated after cleaning and disinfection.

RESULTS

A total of 602 samples were collected. 13.3% of the personal protective equipment were contaminated. Positive rate was higher in the contaminated areas (48.4%) than in the doffing rooms (11.7%) and the potentially contaminated areas (0; P<.05). Contamination was highest in patient occupied areas (67.5%). After cleaning, samples taken at previously contaminated surfaces are all negative.

CONCLUSIONS

SARS-CoV-2 RNA contamination is prevalent in Fangcang hospitals and healthcare workers are under risk of infection. Potentially contaminated areas and surfaces after cleaning and disinfection are negative, underlying the importance of infection control policy.

Guidelines for the diagnosis, treatment, prevention and control of infections caused by carbapenem-resistant gram-negative bacilli

The dissemination of carbapenem-resistant Gram-negative bacilli (CRGNB) is a global public health issue. CRGNB isolates are usually extensively drug-resistant or pandrug-resistant, resulting in limited antimicrobial treatment options and high mortality. A multidisciplinary guideline development group covering clinical infectious diseases, clinical microbiology, clinical pharmacology, infection control, and guideline methodology experts jointly developed the present clinical practice guidelines based on best available scientific evidence to address the clinical issues regarding laboratory testing, antimicrobial therapy, and prevention of CRGNB infections. This guideline focuses on carbapenem-resistant Enterobacteriales (CRE), carbapenem-resistant Acinetobacter baumannii (CRAB), and carbapenem-resistant Pseudomonas aeruginosa (CRPA). Sixteen clinical questions were proposed from the perspective of current clinical practice and translated into research questions using PICO (population, intervention, comparator, and outcomes) format to collect and synthesize relevant evidence to inform corresponding recommendations. The grading of recommendations, assessment, development and evaluation (GRADE) approach was used to evaluate the quality of evidence, benefit and risk profile of corresponding interventions and formulate recommendations or suggestions. Evidence extracted from systematic reviews and randomized controlled trials (RCTs) was considered preferentially for treatment-related clinical questions. Observational studies, non-controlled studies, and expert opinions were considered as supplementary evidence in the absence of RCTs. The strength of recommendations was classified as strong or conditional (weak). The evidence informing recommendations derives from studies worldwide, while the implementation suggestions combined the Chinese experience. The target audience of this guideline is clinician and related professionals involved in management of infectious diseases.

Epidemiology of Clinically Significant Aspergillus Species from a Large Tertiary Hospital in Shanghai, China, for the Period of Two Years

Background

Aspergillus species are becoming a major public health concern worldwide due to the increase in the incidence of aspergillosis and emergence of antifungal resistance. In this study, we surveyed all Aspergillus species isolated from aspergillosis patients in Zhongshan Hospital Fudan University, Shanghai, China, from 2019 to 2021.

Methods

We characterized the susceptibility profiles of these Aspergillus species to medical azoles (voriconazole, itraconazole and posaconazole) using YeastOne^TM broth microdilution system. To determine the underlying antifungal resistance mechanisms in azole-resistant A. fumigatus (ARAf) isolates, we characterized mutations in the cyp51A gene. Genotypic diversity of sampled A. fumigatus was investigated using CSP-typing.

Results

A total of 112 Aspergillus isolates (81 A. fumigatus, 17 A. flavus, 5 A. niger, 2 A. terreus, 2 A. lentulus, 2 A. oryzae, 1 A. nidulans, 1 A. versicolor and 1 A. sydowii) from 105 patients diagnosed with aspergillosis (including proven or probable invasive aspergillosis, chronic pulmonary aspergillosis, allergic bronchopulmonary aspergillosis and cutaneous aspergillosis) were obtained. Eight isolates (7 A. fumigatus and 1 A. niger) from seven patients were either azole non-susceptible or non-wild type. Azole non-susceptible or non-wild type rate was 7.1%/isolate and 6.7%/patient analysed. Four ARAf harbored TR34/L98H mutation, whereas one carried TR46/Y121F/T289A allele. The 81 A. fumigatus isolates were spread across 8 CSP types with t01 to be the predominant type (53.1%). ARAf isolates were distributed over CSP types t01, t02, t04A and t11.

Conclusion

Results from this study provided us with an understanding of the antifungal resistance and related characteristics of Aspergillus species in Eastern China. Further comparisons of our results with those in other countries reflect potential clonal expansion of A. fumigatus in our region. Further surveillance study is warranted to guide antifungal therapy and for epidemiological purposes.

Anxiety and depression among patients with non-tuberculous mycobacterial disease in Shanghai: a cross-sectional study

Objective

To understand the mental health status and its influencing factors among patients with non-tuberculous mycobacterial disease and to provide a reference for medical staff to formulate scientific and feasible intervention strategies.

Methods

A total of 114 patients diagnosed with non-tuberculous mycobacillosis during hospitalization in the Department of Infection from September 2020 to April 2021 were selected as the research participants. Participants' mental health status and related factors were evaluated using a self-made general patient information questionnaire, self-rating Anxiety Scale (SAS), and self-rating Depression Scale (SDS).

Results

Among 114 patients with non-tuberculous mycosis, 61 (53.51%) exhibited depressive symptoms, and the SDS score was 51.15 ± 13.04, which was higher than the national norm of 41.88 ± 10.57 (p < 0.05); further, 39 patients (34.21%) showed anxiety symptoms, and the SAS score was 45.75 ± 10.81, which was significantly higher than the national norm of 29.78 ± 10.07 (p < 0.05). Body mass index and monthly household income had significant effects on depression in patients with non-tuberculous mycobacterial disease (p < 0.05). Educational level had a significant effect on the anxiety state of patients with non-tuberculous mycobacterial disease (p < 0.05).

Conclusion

Patients with non-tuberculous mycobacterial disease are prone to depression and anxiety. Nurses should pay attention to it in clinical work for the timely identification of and intervention for anxiety and depression and intervene.

Association between the overall burden of comorbidity and Ct values among the older patients with Omicron infection: Mediated by inflammation

Objectives

To investigate the associations between the overall burden of comorbidity, inflammatory indicators in plasma and Ct values among the elderly with COVID-19.

Methods

We conducted a retrospective observational study. The results of each nucleic acid test of during hospitalization were obtained. Linear regression models assessed the associations between the overall burden of comorbidity, inflammatory indicators in plasma and Ct values among the elderly. A causal mediation analysis was performed to assess the mediation effects of inflammatory indicators on the association between the overall burden of comorbidity and Ct values.

Results

A total of 767 COVID-19 patients aged ≥ 60 years were included between April 2022 and May 2022. Patients with a high burden of comorbidity had significantly lower Ct values of the ORF gene than subjects with a low burden of comorbidity (median, 24.81 VS 26.58, P &lt; 0.05). Linear regression models showed that a high burden of comorbidity was significantly associated with higher inflammatory responses, including white blood cell count, neutrophil count and C-reactive protein. Also, white blood cell count, neutrophil count, C-reactive protein and the overall burden of comorbidity assessed by age-adjusted Charlson comorbidity index were independent risk factors for the Ct values. A mediation analysis detected the mediation effect of white blood cells on the association between the burden of comorbidity and Ct values, with the indirect effect estimates of 0.381 (95% CI: 0.166, 0.632, P &lt; 0.001). Similarly, the indirect effect of C-reactive protein was -0.307 (95% CI: -0.645, -0.064, P = 0.034). White blood cells and C-reactive protein significantly mediated the relationship between the burden of comorbidity and Ct values by 29.56% and 18.13% of the total effect size, respectively.

Conclusions

Inflammation mediated the association between the overall burden of comorbidity and Ct values among elderly with COVID-19, which suggests that combined immunomodulatory therapies could reduce the Ct values for such patients with a high burden of comorbidity.

Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing

Background

The application of clinical mNGS for diagnosing respiratory infections improves etiology diagnosis, however at the same time, it brings new challenges as an unbiased sequencing method informing all identified microbiomes in the specimen.

Methods

Strategy evaluation and metagenomic analysis were performed for the mNGS data generated between March 2017 and October 2019. Diagnostic strengths of four specimen types were assessed to pinpoint the more appropriate type for mNGS diagnosis of respiratory infections. Microbiome complexity was revealed between patient cohorts and infection types. A bioinformatic pipeline resembling diagnosis results was built based upon multiple bioinformatic parameters.

Results

The positive predictive values (PPVs) for mNGS diagnosing of non-mycobacterium, Nontuberculous Mycobacteria (NTM), and Aspergillus were obviously higher in bronchoalveolar lavage fluid (BALF) demonstrating the potency of BALF in mNGS diagnosis. Lung tissues and sputum were acceptable for diagnosis of the Mycobacterium tuberculosis (MTB) infections. Interestingly, significant taxonomy differences were identified in sufficient BALF specimens, and unique bacteriome and virome compositions were found in the BALF specimens of tumor patients. Our pipeline showed comparative diagnostic strength with the clinical microbiological diagnosis.

Conclusions

To achieve reliable mNGS diagnosis result, BALF specimens for suspicious common infections, and lung tissues and sputum for doubtful MTB infections are recommended to avoid the false results given by the complexed respiratory microbiomes. Our developed bioinformatic pipeline successful helps mNGS data interpretation and reduces manual corrections for etiology diagnosis.

Prolonged Use of Surgical Masks and Respirators Affects the Protection and Comfort for Healthcare Workers

This study explored the ideal period for wearing masks to prevent the physiological and psychological problems associated with long-term face mask use during respiratory infections by healthcare workers. Breathing simulators, surgical masks (SM) and medical respirators (PM) were prepared for two to eight hours. Changes in the comfort of masks (facial skin temperature, breathing resistance, and moisture permeability) and protection (filtration efficiency, resistance to blood penetration, and colony count) were assessed. The results demonstrated that the masks offered efficient liquid-particle filtering even after eight hours of use. However, the number of bacterial colonies using PM and SM grew significantly after two and four hours, respectively. Concerning comfort, the inspiratory resistance of masks rose dramatically after two hours, whereas the moisture permeability declined considerably after four hours. In addition, skin temperature had a significant increase within two hours, which may result in facial discomfort. When conditions permitted, the hospital staff was instructed to replace their masks every two hours.

Characterization of Phage Resistance and Their Impacts on Bacterial Fitness in Pseudomonas aeruginosa

The emergence and spread of antibiotic resistance pose serious environmental and health challenges. Attention has been drawn to phage therapy as an alternative approach to combat antibiotic resistance with immense potential. However, one of the obstacles to phage therapy is phage resistance, and it can be acquired through genetic mutations, followed by consequences of phenotypic variations. Therefore, understanding the mechanisms underlying phage-host interactions will provide us with greater detail on how to optimize phage therapy. In this study, three lytic phages (phipa2, phipa4, and phipa10) were isolated to investigate phage resistance and the potential fitness trade-offs in Pseudomonas aeruginosa. Specifically, in phage-resistant mutants phipa2-R and phipa4-R, mutations in conferring resistance occurred in genes pilT and pilB, both essential for type IV pili (T4P) biosynthesis. In the phage-resistant mutant phipa10-R, a large chromosomal deletion of ~294 kb, including the hmgA (homogentisate 1,2-dioxygenase) and galU (UTP-glucose-1-phosphate uridylyltransferase) genes, was observed and conferred phage phipa10 resistance. Further, we show examples of associated trade-offs in these phage-resistant mutations, e.g., impaired motility, reduced biofilm formation, and increased antibiotic susceptibility. Collectively, our study sheds light on resistance-mediated genetic mutations and their pleiotropic phenotypes, further emphasizing the impressive complexity and diversity of phage-host interactions and the challenges they pose when controlling bacterial diseases in this important pathogen. IMPORTANCE Battling phage resistance is one of the main challenges faced by phage therapy. To overcome this challenge, detailed information about the mechanisms of phage-host interactions is required to understand the bacterial evolutionary processes. In this study, we identified mutations in key steps of type IV pili (T4P) and O-antigen biosynthesis leading to phage resistance and provided new evidence on how phage predation contributed toward host phenotypes and fitness variations. Together, our results add further fundamental knowledge on phage-host interactions and how they regulate different aspects of Pseudomonas cell behaviors.

Diagnostic accuracy of metagenomic next-generation sequencing for cryptococcosis in immunocompetent and immunocompromised patients

OBJECTIVE

To compare the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for cryptococcosis in patients with different immune statuses with that of conventional detection.

METHODS

A total of 1442 specimens including 71 specimens from patients with cryptococcosis were analyzed in the study. The chi square test was used to screen the sensitivity and specificity of different detection methods for different specimen types. One-way ANOVA was used to compare the mNGS results with age, CD4, lymphocytes, IFN, IL-6, IL-2 and serum antigen assay.

RESULTS

The sensitivity of mNGS was 44.29% in Cryptococcus infection cases. The positive rate of mNGS results for bronchoalveolar lavage fluid (BALF, 87.50%) from immunocompromised patients was higher than that of BALF from immunocompetent patients (40.00%, p=0.04). The sensitivity of the serum Cryptococcus capsular antigen assay was 80.00% in immunocompetent patients and 96.42% in immunocompromised patients (p = 0.049). A positive rate of detection of Cryptococcus from mNGS was higher when cryptococcal antigen ≥1:160 (p=0.022) in immunocompromised patients. A positive rate of detection of Cryptococcus from mNGS was higher when lymphocyte counts were lower in both immunocompetent patients(p=0.017) and in immunocompromised patients(p=0.029).

CONCLUSIONS

The sensitivity of mNGS is lower than that of serum cryptococcal antigen assay and histopathology in immunocompetent patients. However, BALF detection is recommend for immunocompromised patients compared with tissue and CSF. The positive mNGS result was correlated with lower lymphocyte counts, higher IL-2 and higher serum antigen assay in immunocompromised patients.

Expert Consensus on Diagnosis and Treatment of End-Stage Liver Disease Complicated with Infections

Abstract

End-stage liver disease (ESLD) is a life-threatening clinical syndrome that markedly increases mortality in patients with infections. In patients with ESLD, infections can induce or aggravate the occurrence of liver decompensation. Consequently, infections are among the most common complications of disease progression. There is a lack of working procedure for early diagnosis and appropriate management for patients with ESLD complicated by infections as well as local and international guidelines or consensus. This consensus assembled up-to-date knowledge and experience across Chinese colleagues, providing data on principles as well as working procedures for the diagnosis and treatment of patients with ESLD complicated by infections.

[Diagnostic efficacy of indirect haemagglutination assay for detection of Schistosoma japonicum infections among boatmen and fishermen in the Dongting Lake region]

OBJECTIVE

To evaluate the diagnostic efficacy of indirect haemagglutination assay (IHA) for detection of Schistosoma japonicum infections among boatmen and fishermen in Dongting Lake region, so as to provide insights into improving the schistosomiasis surveillance program among boatmen and fishermen.

METHODS

The boatmen and fishermen were detected for S. japonicum infections using IHA and Kato-Katz technique or miracidium hatching test nylon gauze simultaneously at schistosomiasis testing sites in the anchor sites for boatmen and fishermen in the Dongting Lake region during the period from 2014 to 2016, and using IHA for serological screening followed by parasitological testing of seropositives during the period from 2017 to 2019. The sensitivity and specificity of IHA were evaluated for detection of S. japonicum infections among boatmen and fishermen, with the 2014-2016 parasitological testing results as a gold standard. In addition, the seroprevalence of S. japonicum infections was compared among boatmen and fishermen with different characteristics and among years.

RESULTS

A total of 306 schistosomiasis testing sites were assigned for boatmen and fishermen, and a total of 143 360 person-time boatmen and fishermen were tested for S. japonicum infections in the Dongting Lake region from 2014 to 2019. The sensitivity and specificity of IHA were 69.9%, 97.3% and 96.1% (χ² = 74.6, P < 0.05), and 70.9%, 74.5% and 71.9% for detection of S. japonicum infections from 2014 to 2016 (χ² = 29.4, P < 0.05), respectively. The seroprevalence of S. japonicum infections reduced from 30.3% in 2014 to 1.8% in 2019 among boatmen and fishermen, appearing an overall tendency towards a decline (Z = 1 552.4, P < 0.05). In addition, male, individuals at ages of 45 to 60 years, full-time boatmen and fishermen were more likely to be seropositive for S. japonicum infections (all P values < 0.05).

CONCLUSIONS

The seroprevalence of S. japonicum infections appeared a tendency towards a decline among boatmen and fishermen in the Dongting Lake region year by year from 2014 to 2019. IHA presented a high efficacy for screening of S. japonicum infections among boatmen and fishermen in the Dongting Lake region.

Isolation and Characterization of Novel Phages Targeting Pathogenic Klebsiella pneumoniae

Klebsiella pneumoniae is a dominant cause of community-acquired and nosocomial infections, specifically among immunocompromised individuals. The increasing occurrence of multidrug-resistant (MDR) isolates has significantly impacted the effectiveness of antimicrobial agents. As antibiotic resistance is becoming increasingly prevalent worldwide, the use of bacteriophages to treat pathogenic bacterial infections has recently gained attention. Elucidating the details of phage-bacteria interactions will provide insights into phage biology and the better development of phage therapy. In this study, a total of 22 K. pneumoniae isolates were assessed for their genetic and phenotypic relatedness by multi-locus sequence typing (MLST), endonuclease S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), and in vitro antibiotic susceptibility testing. In addition, the beta-lactamase gene (bla_KPC) was characterized to determine the spread and outbreak of K. pneumoniae carbapenemase (KPC)-producing enterobacterial pathogens. Using these ST11 carbapenem-resistant K. pneumoniae isolates, three phages (NL_ZS_1, NL_ZS_2, and NL_ZS_3) from the family of Podoviridae were isolated and characterized to evaluate the application of lytic phages against the MDR K. pneumoniae isolates. In vitro inhibition assays with three phages and K. pneumoniae strain ZS15 demonstrated the strong lytic potential of the phages, however, followed by the rapid growth of phage-resistant and phage-sensitive mutants, suggesting several anti-phage mechanisms had developed in the host populations. Together, this data adds more comprehensive knowledge to known phage biology and further emphasizes their complexity and future challenges to overcome prior to using phages for controlling this important MDR bacterium.

Interactions between the Prophage 919TP and Its Vibrio cholerae Host: Implications of gmd Mutation for Phage Resistance, Cell Auto-Aggregation, and Motility

Prophage 919TP is widely distributed among Vibrio cholera and is induced to produce free φ919TP phage particles. However, the interactions between prophage φ919TP, the induced phage particle, and its host remain unknown. In particular, phage resistance mechanisms and potential fitness trade-offs, resulting from phage resistance, are unresolved. In this study, we examined a prophage 919TP-deleted variant of V. cholerae and its interaction with a modified lytic variant of the induced prophage (φ919TP cI^-). Specifically, the phage-resistant mutant was isolated by challenging a prophage-deleted variant with lytic phage φ919TP cI^-. Further, the comparative genomic analysis of wild-type and φ919TP cI^--resistant mutant predicted that phage φ919TP cI^- selects for phage-resistant mutants harboring a mutation in key steps of lipopolysaccharide (LPS) O-antigen biosynthesis, causing a single-base-pair deletion in gene gmd. Our study showed that the gmd-mediated O-antigen defect can cause pleiotropic phenotypes, e.g., cell autoaggregation and reduced swarming motility, emphasizing the role of phage-driven diversification in V. cholerae. The developed approach assists in the identification of genetic determinants of host specificity and is used to explore the molecular mechanism underlying phage-host interactions. Our findings contribute to the understanding of prophage-facilitated horizontal gene transfer and emphasize the potential for developing new strategies to optimize the use of phages in bacterial pathogen control.

The clinical value of valve metagenomic next-generation sequencing when applied to the etiological diagnosis of infective endocarditis

Background

Metagenomic next-generation sequencing (mNGS) is widely applied in the etiological diagnosis of infectious diseases. However, the clinical practice of mNGS in infective endocarditis (IE) is relatively less studied. This research aimed to assess the etiological diagnostic value of valve mNGS in IE.

Methods

We retrospectively analyzed 49 IE patients who underwent cardiac valve surgery in Zhongshan Hospital, Fudan University, Shanghai from 1 June 2018 to 30 November 2020. Among these IE patients, 28 were culture positive and 21 were culture negative. The culture results of the culture-positive IE patients were set as gold standard to assess the sensitivity and specificity of valve mNGS in the etiological diagnosis of IE. We studied the positive detection rate of pathogens by valve mNGS among the culture-negative IE patients. During the same period, we also collected the resected valves of 8 patients with non-infective valvular diseases for mNGS as negative controls.

Results

The valve mNGS results of the culture-positive IE patients were the exact same as their culture results. Both the sensitivity and specificity of valve mNGS were 100%. The positive detection rate of pathogens by valve mNGS was 100% among the culture-negative IE patients. The stringent mapped reads number of genera (SMRNG), relative abundance of genera, stringent mapped reads number of species (SMRN), relative abundance of species, and coverage rate of valve mNGS results were significantly higher in culture-positive IE participants than in culture-negative IE participants. The valve mNGS results of the 8 participants with non-infective valvular diseases were all negative.

Conclusions

Valve mNGS is a promising technology for the etiological diagnosis of IE, especially culture-negative IE, and it may be used to guide precise antibiotic treatment after surgery.

Low CD4 T cell count predicts radiological progression in severe and critically ill COVID-19 patients: a case control study

Background

Novel coronavirus disease (COVID-19) has spread globally and caused over 3 million deaths, posing great challenge on public health and medical systems. Limited data are available predictive factors for disease progression. We aim to assess clinical and radiological predictors for pulmonary aggravation in severe and critically ill COVID-19 patients.

Methods

Patients with confirmed COVID-19 in Renmin Hospital of Wuhan University, China, between Feb. 6th, 2020 and Feb. 21st, 2020 were retrospectively collected. Enrolled patients were divided into non-progression group and progression group based on initial and follow-up chest CTs. Clinical, laboratory, and radiological variables were analyzed.

Results

During the study period, 162 patients were identified and a total of 126 patients, including 97 (77.0%) severe cases and 29 (23.0%) critically ill cases were included in the final analysis. Median age was 66.0 (IQR, 56.0–71.3) years. Median time from onset to initial chest CT was 15.0 (IQR, 12.0–20.0) days and median interval to follow-up was 7.0 (IQR, 5.0–7.0) days. Compared with those who did not progress (n=111, 88.1%), patients in the progression group (n=15, 11.9%) had significantly higher percentage of peak body temperature >38 °C (P=0.002), lower platelet count (P=0.011), lower CD4 T cell count (P=0.002), lower CD8 count (P=0.011), higher creatine kinase level (P=0.002), and lower glomerular filtration rate (P=0.018). On both univariate and multivariable analysis, only CD4 T cell count <200/µL was significant (OR, 6.804; 95% CI, 1.450–31.934; P=0.015) for predicting pulmonary progression.

Conclusions

Low CD4 T cell count predicts progression of pulmonary change in severe and critically ill patients with COVID-19.

Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii

Mycobacterium kansasii can cause serious pulmonary disease. It belongs to a group of closely-related species of non-tuberculous mycobacteria known as the M. kansasii complex (MKC). Here, we report a population genomics analysis of 358 MKC isolates from worldwide water and clinical sources. We find that recombination, likely mediated by distributive conjugative transfer, has contributed to speciation and on-going diversification of the MKC. Our analyses support municipal water as a main source of MKC infections. Furthermore, nearly 80% of the MKC infections are due to closely-related M. kansasii strains, forming a main cluster that apparently originated in the 1900s and subsequently expanded globally. Bioinformatic analyses indicate that several genes involved in metabolism (e.g., maintenance of the methylcitrate cycle), ESX-I secretion, metal ion homeostasis and cell surface remodelling may have contributed to M. kansasii's success and its ongoing adaptation to the human host.

Diagnosis and Management of Intraabdominal Infection: Guidelines by the Chinese Society of Surgical Infection and Intensive Care and the Chinese College of Gastrointestinal Fistula Surgeons

The Chinese guidelines for IAI presented here were developed by a panel that included experts from the fields of surgery, critical care, microbiology, infection control, pharmacology, and evidence-based medicine. All questions were structured in population, intervention, comparison, and outcomes format, and evidence profiles were generated. Recommendations were generated following the principles of the Grading of Recommendations Assessment, Development, and Evaluation system or Best Practice Statement (BPS), when applicable. The final guidelines include 45 graded recommendations and 17 BPSs, including the classification of disease severity, diagnosis, source control, antimicrobial therapy, microbiologic evaluation, nutritional therapy, other supportive therapies, diagnosis and management of specific IAIs, and recognition and management of source control failure. Recommendations on fluid resuscitation and organ support therapy could not be formulated and thus were not included. Accordingly, additional high-quality clinical studies should be performed in the future to address the clinicians' concerns.

Infection Control in the Era of Antimicrobial Resistance in China: Progress, Challenges, and Opportunities

More than 3 decades have passed since infection control was implemented nationwide in China in 1986. A comprehensive set of regulations and guidelines has been developed, and almost all hospitals have established infection control teams. However, compliance is variable and is usually suboptimal. The incidence of certain multidrug-resistant organisms (MDROs), including carbapenem-resistant Acinetobacter baumannii (CRAB) and carbapenem-resistant Klebsiella pneumoniae (CRKP), is increasing, and associated infections are mainly hospital-acquired in China. Carbapenem-resistant Pseudomonas aeruginosa has remained relatively stable, whereas methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterobacter faecium have been decreasing. The spread of CRAB and CRKP in China is largely mediated by dominant high-risk lineages, namely, clonal complex 92 for CRAB and sequence type 11 for CRKP. However, challenges owing to MDROs bring opportunities for rethinking, taking coordinated action, building capacity, changing behavior, and performing studies that reflect everyday situations in the Chinese healthcare system.

Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai

Background

In COVID-19 patients, information regarding superinfection, antimicrobial assessment, and the value of metagenomic sequencing (MS) could help develop antimicrobial stewardship.

Method

This retrospective study analyzed 323 laboratory-confirmed COVID-19 patients for co-infection rate and antimicrobial usage in the Shanghai Public Health Clinical Center (SPHCC) from January 23rd to March 14th 2020. The microbiota composition was also investigated in patients with critically severe COVID-19.

Results

The total population co-infection rate was 17/323 (5.3%) and 0/229 (0), 4/78 (5.1%), and 13/16 (81.3%) for the mild, severe, and critically severe subgroups, respectively. Proven fungal infection was significantly associated with a higher mortality rate (p = 0.029). In critically severe patients, the rate of antimicrobials and carbapenem usage were 16/16 (100%) and 13/16 (81.3%), respectively, in which the preemptive and empiric antimicrobial days accounted for 51.6% and 30.1%, respectively. Targeted therapy only accounted for 18.3%. MS was implemented to detect non-COVID-19 virus co-existence and the semi-quantitative surveillance of bacteremia, with clear clinical benefit seen in cases with MS-based precision antimicrobial management. Airway microbiome analysis suggested that the microbiota compositions in critically severe COVID-19 patients were likely due to intubation and mechanical ventilation.

Conclusions

In the SPHCC cohort, we observed a non-negligible rate of super-infection, especially for the critically ill COVID-19 patients. Fungal co-infection requires intensive attention due to the high risk of mortality, and the clinical benefit of MS in guiding antimicrobial management warrants further investigation.

Review and Prospects of Pathogen Detection Related to Autopsy of Coronavirus Infectious Diseases

Abstract

In the past, coronavirus caused two serious human-to-human pandemics in the world, including severe acute respiratory syndrome （SARS） and Middle East respiratory syndrome （MERS）. In late 2019, coronavirus disease 2019 （COVID-19） caused another major global public health event. Due to the strong infectivity of novel coronavirus, it is difficult to carry out the autopsy of related death cases widely. This paper reviews the previous status of the pathogen detection related to the autopsy of coronavirus infection diseases, and introduces the ongoing detection methods of novel coronavirus in clinical practice, in order to provide reference for the pathogen detection and study related to autopsy of COVID-19.

High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings

The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.

[The observation of secretogranin Ⅲ in the peripheral blood and vitreous of patients with diabetic retinopathy]

Objective: To study the expression levels of secretogranin Ⅲ (SCG3) in the peripheral blood and vitreous of patients with diabetic retinopathy (DR). Methods: Cross-sectional research. A total of 77 patients (41 men and 36 women, 77 eyes) received vitrectomy in Tianjin Medical University Eye Hospital from May to December 2018, with an average age of (60.75±11.34) years. According to the blood glucose level, diabetes history and fundus status, all the patients were divided into the DR group and the non-diabetic group. According to the patients' blood lipids and body mass index (BMI), patients were further divided into subgroups of high blood lipids, normal blood lipids, high BMI and normal BMI. All patients were tested with eye examinations, height and weight to calculate the BMI, and blood lipid levels in the peripheral blood. The vitreous was collected during the vitrectomy surgery, and the levels of SCG3 in the vitreous and peripheral blood were analyzed by ELISA. All the data were analyzed statistically with Wilcoxon rank sum test. Results: There were 43 patients in the DR group, among whom 25 had hyperlipidemia, 18 had normal blood lipids, 22 had a high BMI, and 21 had a normal BMI. There were 34 patients in the non-diabetic group, among whom 13 had hyperlipidemia, 21 had normal blood lipids, 17 had a high BMI, and 17 had a normal BMI. The level of SCG3 in the DR group [6.02 (4.34, 11.76) ng/ml] was higher than that in the non-diabetic group [4.30 (3.20, 10.78) ng/ml] (Z=-2.339, P =0.019). The level of SCG3 in the hyperlipidemia subgroup of the DR patients [7.94 (5.33, 13.51) ng/ml] was higher than that in the normal blood lipid subgroup of the non-diabetic patients [4.04 (3.12, 7.77) ng/ml] (Z=-3.473, P=0.001), and higher than that in the DR patients without hyperlipidemia [4.45 (3.71, 9.14) ng/ml] (Z=-2.511, P=0.012). The level of SCG3 in the DR patients with a high BMI [7.12 (4.56, 13.12) ng/ml] was higher than that in the non-diabetic patients with a normal BMI [3.53 (3.16, 4.38) ng/ml] (Z=-3.767, P =0.000). The level of SCG3 in the DR patients with a normal BMI [5.72 (4.10, 11.60) ng/ml] was higher than that in the non-diabetic patients with a normal BMI (Z=-2.862, P = 0.004). SCG3 in the plasma was rare or can not be detected. Conclusions: The concentration of SCG3 in the vitreous increase in DR patients. However, SCG3 can not be detected in the healthy vascular system. (Chin J Ophthalmol, 2020, 56: 933-937).

Efficacy of early hydroxychloroquine treatment in preventing COVID-19 pneumonia aggravation, the experience from Shanghai, China

The aim of this study is to assess the efficacy of multiple treatments, especially hydroxychloroquine, used in different disease stages of coronavirus disease 2019 (COVID-19). All consecutive patients with COVID-19 admitted to Shanghai Public Health Clinical Center (Shanghai, China) between January 20, 2020, and April 30, 2020, were enrolled, and their clinical data were retrospectively collected. Binary logistic regression was used to screen the factors associated with disease aggravation, and multivariable analyses with the Cox proportional hazards model were used to estimate the effects of prognostic factors on the improvement time and PCR conversion days in throat swabs and stool swabs. A total of 616 patients, including 50 (8.11%) severe and 18 (2.92%) critical patients, were enrolled in our retrospective cohort study. The early use of hydroxychloroquine was a protective factor associated with disease aggravation (95% CI: 0.040-0.575, p = 0.006). Clinical improvement by 20 days was significantly different between patients with hydroxychloroquine used early and those with hydroxychloroquine not used (p = 0.016, 95% CI: 1.052-1.647). The median time to clinical improvement was 6 days in the hydroxychloroquine used early group, compared with 9 days in the without hydroxychloroquine used group and 8 days in the with hydroxychloroquine not used early group (p < 0.001). Hydroxychloroquine used early was associated with earlier PCR conversion in both throat swabs (HR = 1.558, p = 0.001) and stool swabs (HR = 1.400, p = 0.028). The use of hydroxychloroquine at an early stage is a potential therapeutic strategy for treating patients before irreversible severe respiratory complications occur. The early use of hydroxychloroquine decreased the improvement time and the duration of COVID-19 detection in throat and stool swabs.

Beneficial aspects of high dose intravenous vitamin C on patients with COVID-19 pneumonia in severe condition: a retrospective case series study

BACKGROUND

Coronavirus disease 2019 (COVID-19) is a global public health event without specific therapeutic agents till now. We aim to determine if high dose intravenous vitamin C (HDIVC) was effective for COVID-19 patients in severe condition.

METHODS

COVID-19 patients admitted in Shanghai Public Health Clinical Center from January 22, 2020 to April 11, 2020 were retrospectively scrolled. The enrolled patients were those with confirmed diagnosis of severe or critical COVID-19 pneumonia, who received HDIVC within 24 hours after disease aggravation. Main clinical outcomes obtained from 3-5 days (day 3) and 7-10 days (day 7) after HDIVC were compared to the ones just before (day 0) HDIVC.

RESULTS

Totally, twelve patients were enrolled including six severe [age of mean, 56; interquartile range (IQR), 32-65 years, 3 men] and six critical (age of mean, 63; IQR, 60-82 years, 4 men) patients. The dosage of vitamin C [median (IQR), mg/kg (body weight)/day] were [162.7 (71.1-328.6)] for severe and [178.6 (133.3-350.6)] for critical patients. By Generalized estimating equation (GEE) model, C-reactive protein (CRP) was found to decrease significantly from day 0 to 3 and 7 (severe: 59.01±37.9, 12.36±22.12, 8.95±20.4; critical: 92.5±41.21, 33.9±30.2, 59.56±41.4 mg/L). Lymphocyte and CD4+ T cell counts in severe patients reached to normal level since day 3. Similar improving trends were observed for PaO2/FiO2 (severe: 209.3±111.7, 313.4±146, 423.3±140.8; critical: 119.9±52.7, 201.8±86.64, 190.5±51.99) and sequential organ failure assessment score (severe: 2.83±1.72, 1.33±1.63, 0.67±1.03; critical: 6.67±2.34, 4.17±2.32, 3.83±2.56). Better improving effect was observed in severe than critical patients after HDIVC.

CONCLUSIONS

HDIVC might be beneficial in aspects of inflammatory response, immune and organ function for aggravation of COVID-19 patients. Further clinical trials are in warrant.

TRIAL REGISTRATION

This trial has been retrospectively registered in Chinese Clinical Trail Registry (ChiCTR2000032716) on May 8, 2020. http://www.chictr.org.cn/showproj.aspx?proj=53389.

Diagnostic accuracy of metagenomic next-generation sequencing for active tuberculosis in clinical practice at a tertiary general hospital

Background

To evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for active tuberculosis (TB).

Methods

We retrospectively collected 820 samples at Zhongshan Hospital, Fudan University in Shanghai, China, between 1 April 2017 and 31 March 2018. They were classified into TB cases (125, 15.2%) and NOT TB cases (695, 84.8%) according to the clinical diagnosis. Specimens were evaluated by a regular clinical microbiological assay and mNGS performed in parallel.

Results

Sixty-one confirmed TB cases and 64 clinical TB cases were included. The overall sensitivity of mNGS was 49.6% [95% confidence interval (95% CI), 40.6–58.6%], and the specificity was 98.3% (95% CI, 96.9–99.1%), with peak sensitivities of 88.9% (95% CI, 50.7–99.4%) for lung tissue, 55.0% (95% CI, 32.0–76.2%) for bronchoalveolar lavage fluid (BALF), and 50.0% (95% CI, 32.8–67.2%) for serous fluids. The overall sensitivity of mNGS was superior to that of the culture assay (35.2%, 95% CI, 27.0–44.3), but no superior sensitivity for sputum was observed in mNGS compared with the culture assay (mNGS: 52.3%, 95% CI, 31.1–72.6%; culture: 60.9%, 95% CI, 38.8–79.5%). In clinical TB cases, mNGS detected additional positive results (40.6%, 26/64). mNGS reduced the turnaround time from 2–6 weeks to 32–36 hours.

Conclusions

mNGS may be a promising technology for the early auxiliary diagnosis of active TB, especially sputum-negative pulmonary TB (PTB) and tuberculous serous effusion.

D-dimer as a biomarker for disease severity and mortality in COVID-19 patients: a case control study

Background

Over 5,488,000 cases of coronavirus disease-19 (COVID-19) have been reported since December 2019. We aim to explore risk factors associated with mortality in COVID-19 patients and assess the use of D-dimer as a biomarker for disease severity and clinical outcome.

Methods

We retrospectively analyzed the clinical, laboratory, and radiological characteristics of 248 consecutive cases of COVID-19 in Renmin Hospital of Wuhan University, Wuhan, China from January 28 to March 08, 2020. Univariable and multivariable logistic regression methods were used to explore risk factors associated with in-hospital mortality. Correlations of D-dimer upon admission with disease severity and in-hospital mortality were analyzed. Receiver operating characteristic curve was used to determine the optimal cutoff level for D-dimer that discriminated those survivors versus non-survivors during hospitalization.

Results

Multivariable regression that showed D-dimer > 2.0 mg/L at admission was the only variable associated with increased odds of mortality [OR 10.17 (95% CI 1.10–94.38), P = 0.041]. D-dimer elevation (≥ 0.50 mg/L) was seen in 74.6% (185/248) of the patients. Pulmonary embolism and deep vein thrombosis were ruled out in patients with high probability of thrombosis. D-dimer levels significantly increased with increasing severity of COVID-19 as determined by clinical staging (Kendall’s tau-b = 0.374, P = 0.000) and chest CT staging (Kendall’s tau-b = 0.378, P = 0.000). In-hospital mortality rate was 6.9%. Median D-dimer level in non-survivors (n = 17) was significantly higher than in survivors (n = 231) [6.21 (3.79–16.01) mg/L versus 1.02 (0.47–2.66) mg/L, P = 0.000]. D-dimer level of > 2.14 mg/L predicted in-hospital mortality with a sensitivity of 88.2% and specificity of 71.3% (AUC 0.85; 95% CI = 0.77–0.92).

Conclusions

D-dimer is commonly elevated in patients with COVID-19. D-dimer levels correlate with disease severity and are a reliable prognostic marker for in-hospital mortality in patients admitted for COVID-19.

[Progress of schistosomiasis control in Dongting Lake regions]

As an ancient parasitic disease, schistosomiasis has been endemic in Dongting Lake areas for more than 2 100 years. In the early 20th century, the first human case of schistosomiasis in China was reported in Dongting Lake areas, which was paid extensive attention. After the founding of the People's Republic of China, large-scale schistosomiasis control activities were launched promptly in Dongting Lake areas, and great successes have been achieved following the three stages of control efforts, including the snail control-based stage, synchronous chemotherapy for humans and livestock-based control stage and infectious source control-based control stage. In 2015, transmission control of schistosomiasis was achieved in Hunan Province. This paper comprehensively describes the discovery and control of schistosomiasis, analyzes the challenges for the current schistosomiasis control programs and proposes the emphasis for future control activities in Dongting Lake areas, so as to provide insights into the schistosomiasis control program in this area.

[Challenges and countermeasures of schistosomiasis control in Hunan Province in the new era]

This paper describes the current epidemic characteristics and endemic status of schistosomiasis, analyzes the main challenges of schistosomiasis control and proposes the emphasis and interventions for future schistosomiasis control activities in Hunan Province, so as to provide insights into the elimination of schistosomiasis in Hunan Province.

[Implications, spiritual characteristics and practical significance of Chinese schistosomiasis control culture]

The culture of schistosomiasis control is specific in the history of Chinese culture. Broadly speaking, the culture of schistosomiasis control is a summary of specific social mood, social consciousness and material culture created by Chinese populations during the progress of schistosomiasis control since the founding of the People's Republic of China. Narrowly speaking, the culture of schistosomiasis control is the spiritual culture that is jointly created and nurtured by schistosomiasis control workers since the founding of the People's Republic of China. The spiritual features of Chinese schistosomiasis control culture are characterized by the patriotism and care about the people, the matter-to-fact attitude, the pioneering and enterprising spirit, and the spirit of sacrifice and dedication. The ultimate goal of the research on the culture of schistosomiasis control is to facilitate the achievement of the strategic goal of Healthy China 2030 as scheduled, accelerate the progress towards elimination of schistosomiasis, and to promote the sustainable development of schistosomiasis control in China.

A rare case of adrenal gland abscess due to anaerobes detected by metagenomic next-generation sequencing

A 50-year-old woman presented with right back pain, low fever, leukocytosis, a high level of C-reactive protein and a high erythrocyte sedimentation rate. Abdominal magnetic resonance imaging (MRI) revealed a hypodense lesion in the right suprarenal region, while PET/CT showed mildly increased metabolic activity. A CT-guided percutaneous puncture was performed, and foul-smelling thick pus was removed, which indicated an anaerobic infection. A smear of the pus showed both gram-positive and gram-negative microorganisms. Traditional culture only detected Escherichia coli, Proteus mirabilis, and Actinomyces turicensis. While surprisingly, metagenomic next-generation sequencing (mNGS) of both the pus and blood showed high reads of multiple pathogens, including anaerobes and the three culture-positive pathogens. Thus, adrenal gland abscess was confirmed, and a combination therapy of catheter drainage and effective antimicrobial treatment was started. Six days later, the patient had clinically improved and mNGS showed dramatically decreased reads of all pathogens. A follow-up lab examination of inflammatory biomarkers was normal, and the adrenal mass was reduced radiographically.

Guide to the Forensic Pathology Practice on Death Cases Related to Corona Virus Disease 2019 （COVID-19） （Trial Draft）

Abstract

Autopsy is of great significance to the elucidation of the pathological changes, pathogeneses and causes of death of corona virus disease 2019 （COVID-19） and can provide theoretical basis for more scientific and accurate prevention and control of the outbreak. Based on related laws and regulations, such as the Law of the People's Republic of China on Prevention and Control of Infectious Diseases, the clinical manifestations and epidemiological characteristics of COVID-19, and the related guidelines on the prevention and control of the outbreak, combined with the practical work of forensic pathology examination, the Guide to the Forensic Pathology Practice on Death Cases Related to Corona Virus Disease 2019 （COVID-19） （Trial Draft） has been developed. This guide includes information on the background investigation of the cases, autopsy room requirements, personal prevention and protections, external examinations, autopsy, auxiliary examinations, and so on. This guide can be used as a reference by forensic and pathological examination institutions, as well as examination staff.

Colonization of Toxigenic Clostridium difficile Among Intensive Care Unit Patients: A Multi-Centre Cross-Sectional Study

Background:Clostridium difficile (CD) is a major cause of healthcare-associated infections and antibiotic-associated diarrhea in hospitalized patients worldwide. Carriers of toxigenic CD (tCD) have a higher risk of developing CD infections and can transmit CD to the environment and susceptible patients. However, little is known regarding the carriers and transmission of tCD in China.

Methods: A multi-center cross-sectional study of tCD colonization (tCDC) was conducted from October 24 to 31, 2014, at 33 hospitals in Shanghai, China. Rectal swabs or stool samples were collected and tested, and the clinical and demographic status, epidemiological data, and blood parameters of 531 participants were recorded. The status of tCDC was defined by a positive result on the nucleic acid amplification test for the tcdA (toxin A), tcdB (toxin B), and cdtAB (toxin CDT) genes after positive bacterial culture.

Results: The overall prevalence of CD colonization (CDC) was 19.02%, tCDC accounted for 92.08%, and A+B+CDT– was the dominant genotype (87.13%). The CD infection (CDI) prevalence was 1.51%. Potential tCDC-associated factors were admission to secondary grade hospitals, a body mass index <18.5, hospitalization during the previous 30 days, underlying diseases (including hypertension, diabetes mellitus, coronary heart disease, and respiratory failure), diarrhea during the previous 7 days, and exposure to fluoroquinolones or lansoprazole.

Conclusions: This study reveals the prevalence of CDC and tCDC in Shanghai, elucidates several associated factors, contributes to the awareness of the current epidemiology in parts of eastern China and provides new insights for further study and infection control practices.

Increased multidrug resistant isolates: new clinical burdens for 66 hospitals in Shanghai, 2015 to 2017

Background

To investigate the etiology of urinary tract and respiratory infections and the rate of drug resistant bacteria in Shanghai from 2015 to 2017, provide the support to the promotion of the correct clinical etiological specimens detection.

Methods

The retrospective questionnaire survey was conducted to obtain the antibiotic prescription rate, pathogen detection rate, and isolation rate of drug-resistant bacteria of the inpatients in 66 hospitals of Shanghai in 2015 and 2017.

Results

Although the detection rate of multidrug-resistant bacteria in sputum specimens has decreased, the clinical pathogen detection still relied mainly on sputum specimens in 2017. Among the sputum specis, the detection rates of extended-spectrum β-lactamase-producing Escherichia (ESBL-ESC), extended-spectrum β-lactamase Klebsiella pneumoniae (ESBL-KP), carbapenem-resistant Acinetobacter baumannii (CRAB), carbapenem-resistant Pseudomonas aeruginosa (CRPA) and methicillin-resistant Staphylococcus aureus (MRSA) in 2017 were 66.67%, 32.46%, 61.74%, 32.01% and 58.55% respectively. The detection rates of ESBL-ESC, ESBL-KP, CRAB, CRPA in 2017 were increased while the MRSA was decreased than 2015 (P<0.001). Among the blood samples, the detection rates of ESBL-ESC, ESBL-KP, CRAB, CRPA, MRSA and vancomycin-resistant Enterococcus sp (VRE) in 2017 were 53.71%, 31.43%, 50.80%, 19.43%, 43.87% and 0.55% respectively. The detection rates of ESBL-KP, CRAB, CRPA and MRSA increased while the rates of ESBL-ESC and VRE decreased compared with 2015 (P<0.005). The pathogens of multi-drug resistant bacteria were mainly detected from sputum specimens in 2017, which were all higher than detected from the blood specimens (P<0.001).

Conclusions

Most of the multi-drug resistant bacteria in Shanghai, especially in Acinetobacter baumannii or Pseudomonas aeruginosa are mainly detected from sputum specimens, indicating that the actual drug resistance may be overestimated.

D-dimer as a biomarker for disease severity and mortality in COVID-19 patients: a case control study

BACKGROUND

Over 5,488,000 cases of coronavirus disease-19 (COVID-19) have been reported since December 2019. We aim to explore risk factors associated with mortality in COVID-19 patients and assess the use of D-dimer as a biomarker for disease severity and clinical outcome.

METHODS

We retrospectively analyzed the clinical, laboratory, and radiological characteristics of 248 consecutive cases of COVID-19 in Renmin Hospital of Wuhan University, Wuhan, China from January 28 to March 08, 2020. Univariable and multivariable logistic regression methods were used to explore risk factors associated with in-hospital mortality. Correlations of D-dimer upon admission with disease severity and in-hospital mortality were analyzed. Receiver operating characteristic curve was used to determine the optimal cutoff level for D-dimer that discriminated those survivors versus non-survivors during hospitalization.

RESULTS

Multivariable regression that showed D-dimer > 2.0 mg/L at admission was the only variable associated with increased odds of mortality [OR 10.17 (95% CI 1.10-94.38), P = 0.041]. D-dimer elevation (≥ 0.50 mg/L) was seen in 74.6% (185/248) of the patients. Pulmonary embolism and deep vein thrombosis were ruled out in patients with high probability of thrombosis. D-dimer levels significantly increased with increasing severity of COVID-19 as determined by clinical staging (Kendall's tau-b = 0.374, P = 0.000) and chest CT staging (Kendall's tau-b = 0.378, P = 0.000). In-hospital mortality rate was 6.9%. Median D-dimer level in non-survivors (n = 17) was significantly higher than in survivors (n = 231) [6.21 (3.79-16.01) mg/L versus 1.02 (0.47-2.66) mg/L, P = 0.000]. D-dimer level of > 2.14 mg/L predicted in-hospital mortality with a sensitivity of 88.2% and specificity of 71.3% (AUC 0.85; 95% CI = 0.77-0.92).

CONCLUSIONS

D-dimer is commonly elevated in patients with COVID-19. D-dimer levels correlate with disease severity and are a reliable prognostic marker for in-hospital mortality in patients admitted for COVID-19.

Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice

Background

Metagenomic next-generation sequencing (mNGS) was suggested to potentially replace traditional microbiological methodology because of its comprehensiveness. However, clinical experience with application of the test is relatively limited.

Methods

From April 2017 to December 2017, 511 specimens were collected, and their retrospective diagnoses were classified into infectious disease (347 [67.9%]), noninfectious disease (119 [23.3%]), and unknown cases (45 [8.8%]). The diagnostic performance of pathogens was compared between mNGS and culture. The effect of antibiotic exposure on detection rate was also assessed.

Results

The sensitivity and specificity of mNGS for diagnosing infectious disease were 50.7% and 85.7%, respectively, and these values outperformed those of culture, especially for Mycobacterium tuberculosis (odds ratio [OR], 4 [95% confidence interval {CI}, 1.7-10.8]; P < .01), viruses (mNGS only; P < .01), anaerobes (OR, ∞ [95% CI, 1.71-∞]; P < .01) and fungi (OR, 4.0 [95% CI, 1.6-10.3]; P < .01). Importantly, for mNGS-positive cases where the conventional method was inconclusive, 43 (61%) cases led to diagnosis modification, and 41 (58%) cases were not covered by empirical antibiotics. For cases where viruses were identified, broad-spectrum antibiotics were commonly administered (14/27), and 10 of 27 of these cases were suspected to be inappropriate. Interestingly, the sensitivity of mNGS was superior to that of culture (52.5% vs 34.2%; P < .01) in cases with, but not without, antibiotic exposure.

Conclusions

mNGS could yield a higher sensitivity for pathogen identification and is less affected by prior antibiotic exposure, thereby emerging as a promising technology for detecting infectious diseases.

A survey of sharps injuries and occupational infections among healthcare workers in Shanghai

Background

Healthcare workers (HCWs) are at greater risk of occupational exposure to sharp injuries in their daily routine work, which is extremely worrying due to the potential risk of transmitting bloodborne pathogens. This study aims to assess what procedures and factors present the greatest risk of sharp injuries to HCWs in Shanghai and to provide an evidence base for improving measures to reduce sharps injuries.

Methods

A cross-sectional study was administered to all HCW who might be exposed to sharp instruments in 81 hospitals in Shanghai. According to the voluntary, investigate as many HCWs as possible and get feedbacks N=61,309. The survey addressed the sharp injury (SI) incidents, SIs of common instruments, SIs of common locations, SIs of operating procedures, SIs of common instruments and common sources of SI occurrences. Statistical analysis was performed using the SPSS program.

Results

A total of 61,309 HCWs were surveyed for this study, and 935 (1.53%) HCWs experienced the various types of sharp injuries in one month. Of the 1,140 sharp injuries, 292 (25.61%) sharp injuries were reported, and 815 (71.49%) sharp injuries were traced to their sources. Interns experienced the highest proportion of sharps injuries (4.12%). General wards were the most common location where sharp injuries occurred to HCWs (36.05%), while disposable syringes were the most common medical devices that caused sharp injuries (32.11%). Nurses, doctors and logistical workers who did not receive relevant training had a higher incidence of SI (4.40%, 4.95% and 4.03%, respectively) than those who received training (1.58%, 1.03% and 0.67%, respectively, P<0.001). HBV infection was the main source of exposure to sharp injuries, with scalpel cuts being the most common related occurrence.

Conclusions

Sharp injuries occur among HCWs in Shanghai dented optimism. There are multiple high-risk factors for SI and exposure to blood-borne pathogens in their work such as interns, general wards, disposable syringes, and lack of relevant training. HBV infection was the main source of exposure to sharp injuries. As such, medical institutions shall pay closer attention to this topic.

2037. A Novel Strategy of Antimicrobial Stewardship in Shanghai: Preliminary Practice with Integration of Three Surveillance Networks

Background

The bacterial resistance surveillance networks, antimicrobial clinical use surveillance networks and provincial hospital-acquired infection (HAI) surveillance have been well established in China. They aim to inform the current situation of bacterial resistance, antimicrobial use and HAI, and to guide the rational use of antimicrobials. However, these three networks presently are running separately. To increase the data value in antimicrobial stewardship (AMS)practice, those three surveillance networks are integrated in Shanghai

Methods

The Committee of Rational Use of Antimicrobials and AMS of Shanghai Municipal Health Commission, consisting of health administrators, clinical physicians and microbiologists, clinical pharmacologists and infection control experts, was formed in 2017. The oversight committee developed a comprehensive AMS score index mainly based on the surveillance data of the three networks to evaluate the AMS requirements in the hospitals. The AMS score index consists of 3 surveillance network indexes: resistance weight index; antimicrobial weight index and HAI weight index; each of the indexes is further divided into two parts, namely the surveillance quality score and data-related score. For example, the data-related score in the resistance index is calculated for the prevalence of 6 most important MDR/XDR bacteria (CRKP, CRAB, CRPA, ESBL, MRSA, VRE). A multi-disciplinary AMS team was convened to provide expert on-site visit of the hospitals and offered AMS support in the form of practical guidance and advice.

Results

AMS score and detailed score such as the prevalence of CRKP were ranked among 50 hospitals within the networks. These scores will support the AMS team to find out the main drivers of resistance/antibiotic use and thereby support appropriate interventions during the on-site visit. For example, a hospital visited which had a high consumption of carbapenems (ranked third in Shanghai) and also had a high percentage of carbapenems used in the department of liver transplantation. The advice of the on-site visit team was to encourage a more diverse group of antibiotics so as to spare carbapenems.

Conclusion

Involvement of the multi-disciplinary team and integration of surveillance networks are very helpful in AMS practice.

Disclosures

All authors: No reported disclosures.

Arthritis caused by Legionella micdadei and Staphylococcus aureus: metagenomic next-generation sequencing provides a rapid and accurate access to diagnosis and surveillance

Legionella spp. is an important pulmonary pathogen but rarely causes extra-pulmonary infections. We report a case of joint infection caused by Legionella micdadei and Staphylococcus aureus in a 54-year-old male with medication history of oral steroid for systemic lupus erythematosus (SLE). He developed arthritis in his right metacarpophalangeal (MCP) joints without precursor pneumonia. In the joint aspirate, S. aureus was detected through culture. The existence of L. micdadei and S. aureus were indicated by metagenomic next-generation sequencing (mNGS) and confirmed by 16S rRNA sequence analysis. After oral levofloxacin treatment for 54 days, the patient's symptoms ameliorated and blood test results improved, which were consistent with the dynamic trend of reads numbers in mNGS data. Our case included, arthritis caused by Legionella spp. have been reported in 11 patients. However, our case is the first to report septic arthritis caused by L. micdadei in native joints and monitored by mNGS. This case demonstrated an application of mNGS for etiological diagnosis and semi-quantification in joint aspirate. mNGS may serve as a promising tool for rapid and accurate etiological diagnosis and surveillance, contributing to appropriate antimicrobial drug applications and timely medication adjustments when necessary.

Successful therapy for autoimmune myocarditis with pembrolizumab treatment for nasopharyngeal carcinoma

Immune checkpoint inhibitors (ICIs), including inhibitors of cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4), programmed death-1 (PD-1) and programmed death-ligand 1 (PD-L1) have demonstrated prominent clinical benefits in a variety of cancers and have been rapidly applied to treat a variety of carcinomas such as melanoma, non-small-cell lung cancer, and head and neck cancer. Meanwhile, the occurrence of immune-related adverse events (irAEs) has been increasing. In this case, we report a 45-year-old man with metastatic nasopharyngeal carcinoma suffering from pulmonary fibrosis and myocarditis on the 4th day after receiving pembrolizumab treatment which belongs to anti-PD-1 drugs. Although the endomyocardial biopsy (EMB) could not be performed, the strong temporal association with pembrolizumab treatment and the specific changes of electrocardiograph, echocardiography and cardiovascular magnetic resonance (CMR) suggest that the myocardial injury and edema were related to pembrolizumab-induced myocarditis. With glucocorticoid treatment, the symptoms and myocardium lesion were almost resolved and the patient agreed to tapered chemotherapy with steroid treatment.

[Microbiological profiles of pathogens causing nosocomial bacteremia in 2011, 2013 and 2016]

To dynamically investigate the distribution and antimicrobial resistance profiles of bacteremia pathogens isolated from different regions in China in 2011, 2013 and 2016. Non-repetitive isolates from nosocomial bloodstream infections were retrospectively collected and detected for antimicrobial susceptibility tests (AST) by agar dilution or microbroth dilution methods. Whonet 5.6 was used to analyze the AST data. Among 2 248 isolates, 1 657 (73.7%) were Gram-negative bacilli and 591 (26.3%) were Gram-positive cocci. The top five bacteremia pathogens were as follows, Escherichia coli (32.6%, 733/2 248), Klebsiella pneumoniae (14.5%, 327/2 248), Staphylococcus aureus (10.0%, 225/2 248), Acinetobacter baumannii (8.7%, 196/2 248) and Pseudomonas aeruginosa (6.2%, 140/2 248). Colistin (96.5%, 1 525/1 581, excluding innate resistant organisms), tigecycline (95.6%, 1 375/1 438, excluding innate resistant organisms), ceftazidine/clavulanate acid (89.2%, 1 112 /1 246), amikacin (86.4%, 1 382/1 599) and meropenem (85.7%, 1 376/1 605) showed relatively high susceptibility against Gram-negative bacilli. While tigecycline, teicoplanin and daptomycin (the susceptibility rates were 100.0%), vancomycin and linezolid (the susceptibility rates were 99.7%) demonstrated high susceptibility against Gram-positive cocci. The prevalence of extended-spectrum β-lactamases (ESBLs)-producing Enterobacteriaceae were 50.6% (206/407), 49.8% (136/273) and 38.9% (167/429) in 2011, 2013 and 2016 respectively; carbapenem-non-susceptible Enterobacteriaceae were 2.2% (9/408), 4.0% (16/402) and 3.9% (17/439) in 2011, 2013 and 2016 respectively; The prevalence of multidrug-resistant A. baumannii (MDRA) was 76.4% (55/72) in 2011, 82.7% (43/52) in 2013 and 87.5% (63/72) in 2016, respectively. The prevalence of multidrug-resistant P. aeruginosa (MDRP) was 9.8% (5/51) in 2011, 20.0% (7/35) in 2013 and 13.0% (7/54) in 2016, respectively. The prevalence of methicillin-resistant S. aureus (MRSA) was 51.9% (41/79) in 2011, 29.7% (19/64) in 2013 and 31.7% (26/82) in 2016, respectively. The prevalence of high level gentamicin resistance (HLGR) of Enterococcus faecium and Enterococcus faecalis were 43.2% (48/111) and 40.9% (27/66), respectively. The predominant organism of carbapenem-non-susceptible Enterobacteriaceae was K. pneumoniae with its proportion of 57.1% (24/42). Among 30 tigecycline-non-susceptible Enterobacteriaceae, K. pneumoniae was the most popular organism with 76.7% (23/30). Among 39 colistin-resistant Enterobacteriaceae, E. coli, Enterobacter cloacae and K. pneumoniae were constituted with the percent of 43.6 (17/39), 35.9 (14/39) and 15.4 (6/39), respectively. The Gram-negative bacilli (E. coli and K. pneumoniae were the major organisms) were the major pathogens of nosocomial bacteremia, to which tigecycline, colistin and carbapenems kept with highly in vitro susceptibility. Whereas, among the Gram-positive cocci, S. aureus was the top 1 isolated organism, followed by E. faecium, to which tigecycline, daptomycin, linezolid, vancomycin and teicoplanin kept with highly in vitro susceptibility. Isolation of colistin-resistant Enterobacteriaceae, tigecycline-non-susceptible Enterobacteriaceae, linezolid- or vancomycin-non-susceptible Gram-positive cocci suggests more attention should be paid to these resistant organisms and dynamic surveillance was essential.