Expansion and transmission dynamics of high risk carbapenem-resistant Klebsiella pneumoniae subclones in China: An epidemiological, spatial, genomic analysis.

AIMS: Carbapenem-resistant Klebsiella pneumonia (CRKP) is a global threat that varies by region. The global distribution, evolution, and clinical implications of the ST11 CRKP clone remain obscure. METHODS: We conducted a multicenter molecular epidemiological survey using isolates obtained from 28 provinces and municipalities across China between 2011 and 2021. We integrated sequences from public databases and performed genetic epidemiology analysis of ST11 CRKP. RESULTS: Among ST11 CRKP, KL64 serotypes exhibited considerable expansion, increasing from 1.54% to 46.08% between 2011 and 2021. Combining our data with public databases, the phylogenetic and phylogeography analyses indicated that ST11 CRKP appeared in the Americas in 1996 and spread worldwide, with key clones progressing from China's southeastern coast to the inland by 2010. Global phylogenetic analysis showed that ST11 KL64 CRKP has evolved to a virulent, resistant clade with notable regional spread. Single-nucleotide polymorphism (SNP) analysis identified BMPPS (bmr3, mltC, pyrB, ppsC, and sdaC) as a key marker for this clade. The BMPPS SNP clade is associated with high mortality and has strong anti-phagocytic and competitive traits in vitro. CONCLUSIONS: The high-risk ST11 KL64 CRKP subclone showed strong expansion potential and survival advantages, probably owing to genetic factors.

Substantial decline of organ preservation fluid contamination following adoption of ischemia-free liver transplantation: a post-hoc analysis.

INTRODUCTION: Preservation fluid (PF) contaminations are common in conventional liver transplantation (CLT) and presumably originate from organ or PF exposures to the external environment in a non-strict sterile manner. Such exposures and PF contamination may be avoided in ischaemia-free liver transplantation (IFLT) because of the strict sterile surgical procedures. In this study, the authors evaluated the impact of IFLT on organ PF contamination. METHODS: A post-hoc analysis using data from the first randomized controlled trial of IFLT was performed to compare the incidence, pathogenic spectrum of PF contamination, and incidence of early recipient infection between IFLT and CLT. Multivariable logistic regression was used to explore risk factors for PF contamination. RESULTS: Of the 68 cases recruited in the trial, 64 were included in this post-hoc analysis. The incidence of culture-positive PF was 9.4% (3/32) in the IFLT group versus 78.1% (25/32) in the CLT group ( P <0.001). Three microorganisms were isolated from PF in the IFLT group, while 43 were isolated in the CLT group. The recipient infection rate within postoperative day 14 was 3.1% (1/32) in the IFLT group vs 15.6% (5/32) in the CLT group, although this difference did not reach statistical significance ( P =0.196). Multivariate analysis revealed that adopting IFLT is an independent protective factor for culture-positive PF. CONCLUSION: PF contamination is substantially decreased in IFLT, and IFLT application is an independent protective factor for PF contamination. Using rigorous sterile measures and effective antibiotic therapy during IFLT may decrease PF contamination.

Prevalence and molecular characteristics of ceftazidime-avibactam resistance among carbapenem-resistant Pseudomonas aeruginosa clinical isolates.

OBJECTIVES: Resistance against ceftazidime-avibactam (CZA) in carbapenem-resistant Pseudomonas aeruginosa (CRPA) is emerging. This study was aimed at detecting the prevalence and molecular characteristics of CZA-resistant CRPA clinical isolates in Guangdong Province, China. METHODS: The antimicrobial susceptibility profile of these strains was determined. A subset of 16 CZA-resistant CRPA isolates was analysed by whole-genome sequencing (WGS). Genetic surroundings of carbapenem resistance genes and pan-genome-wide association analysis were further studied. RESULTS: Of the 250 CRPA isolates, CZA resistance rate was 6.4% (16/250). The minimum inhibitory concentration (MIC) of CZA range was from 0.25 to >256 mg/L. MIC50 and MIC90 were 2/4 and 8/4 mg/L, respectively. Among the 16 CZA-resistant CRPA strains, 31.3% (5/16) of them carried class B carbapenem resistance genes, including blaIMP-4, blaIMP-45, and blaVIM-2, located on IncP-2 megaplasmids or chromosomes, respectively. Pan-genome-wide association analysis of accessory genes for CZA-susceptible or -resistant CRPA isolates showed that PA1874, a hypothetical protein containing BapA prefix-like domain, was enriched in CZA-resistant group significantly. CONCLUSIONS: Class B carbapenem resistance genes play important roles in CZA resistance. Meanwhile, the PA1874 gene may be a novel mechanism involving in CZA resistance. It is necessary to continually monitor CZA-resistant CRPA isolates.

First report of Candida auris in Guangdong, China: clinical and microbiological characteristics of 7 episodes of candidemia.

Candida auris is an emerging multidrug-resistant fungal pathogen worldwide. To date, it has not been reported in Guangdong, China. For the first time, we reported 7 cases of C. auris candidemia from two hospitals in Guangdong. The clinical and microbiological characteristics of these cases were investigated carefully. Two geographic clades, i.e. III and I, were found popular in different hospitals by whole genome sequencing analyses. All C. auris isolates from bloodstream were resistant to fluconazole, 5 of which belonged to Clade III harbouring VF125AL mutation in the ERG11 gene. The isolates with Clade I presented Y132F mutation in the ERG11 gene as well as resistance to amphotericin B. All isolates exhibited strong biofilm-forming capacity and non-aggregative phenotype. The mean time from admission to onset of C. auris candidemia was 39.4 days (range: 12 - 80 days). Despite performing appropriate therapeutic regimen, 42.9% (3/7) of patients experienced occurrences of C. auris candidemia and colonization after the first positive bloodstream. C. auris colonization was still observed after the first C. auris candidemia for 81 days in some patient. Microbiologic eradication from bloodstream was achieved in 85.7% (6/7) of patients at discharge. In conclusion, this study offers a crucial insight into unravelling the multiple origins of C. auris in Guangdong, highlighting great challenges in clinical prevention and control.

Blood culture quality and turnaround time of clinical microbiology laboratories in Chinese Teaching Hospitals: A multicenter study.

PURPOSE: Blood culture (BC) remains the gold standard for the diagnosis of bloodstream infections. Improving the quality of clinical BC samples, optimizing BC performance, and accelerating antimicrobial susceptibility test (AST) results are essential for the early detection of bloodstream infections and specific treatments. METHODS: We conducted a retrospective multicenter study using 450,845 BC specimens from clinical laboratories obtained from 19 teaching hospitals between 1 January 2021 and 31 December 2021. We evaluated key performance indicators (KPIs), turnaround times (TATs), and frequency distributions of processing in BC specimens. We also evaluated the AST results of clinically significant isolates for four different laboratory workflow styles. RESULTS: Across the 10 common bacterial isolates (n = 16,865) and yeast isolates (n = 1011), the overall median (interquartile range) TATs of AST results were 2.67 (2.05-3.31) and 3.73 (2.98-4.64) days, respectively. The specimen collections mainly occurred between 06:00 and 24:00, and specimen reception and loadings mainly between 08:00 and 24:00. Based on the laboratory workflows of the BCs, 16 of the 19 hospitals were divided into four groups. Time to results (TTRs) from specimen collection to the AST reports were 2.35 (1.95-3.06), 2.61 (1.98-3.32), 2.99 (2.60-3.87), and 3.25 (2.80-3.98) days for groups I, II, III, and IV, respectively. CONCLUSION: This study shows the related BC KPIs and workflows in different Chinese hospitals, suggesting that laboratory workflow optimization can play important roles in shortening time to AST reports and initiation of appropriate timely treatment.

Microenvironment responsive charge-switchable nanoparticles act on biofilm eradication and virulence inhibition for chronic lung infection treatment.

Chronic pulmonary infection caused by Pseudomonas aeruginosa (P. aeruginosa) is a common lung disease with high mortality, posing severe threats to public health. Highly resistant biofilm and intrinsic resistance make P. aeruginosa hard to eradicate, while powerful virulence system of P. aeruginosa may give rise to the recurrence of infection and eventual failure of antibiotic therapy. To address these issues, infection-microenvironment responsive nanoparticles functioning on biofilm eradication and virulence inhibition were simply prepared by electrostatic complexation between dimethylmaleic anhydride (DA) modified negatively charged coating and epsilon-poly(l-lysine) derived cationic nanoparticles loaded with azithromycin (AZI) (DA-AZI NPs). Charge reversal responsive to acidic condition enabled DA-AZI NPs to successively penetrate through both mucus and biofilms, followed by targeting to P. aeruginosa and permeabilizing its outer/inner membrane. Then in situ released AZI, which was induced by the lipase-triggered NPs dissociation, could easily enter into bacteria to take effects. DA-AZI NPs exhibited enhanced eradication activity against P. aeruginosa biofilms with a decrease of >99.999% of bacterial colonies, as well as remarkable inhibitory effects on the production of virulence factors and bacteria re-adhesion & biofilm re-formation. In a chronic pulmonary infection model, nebulization of DA-AZI NPs into infected mice resulted in prolonged retention and increased accumulation of the NPs in the infected sites of the lungs. Moreover, they significantly reduced the burden of P. aeruginosa, effectively alleviating lung tissue damages and inflammation. Overall, the proposed DA-AZI NPs highlight an innovative strategy for treating chronic pulmonary infection.

IL-27 in combination with anti-PD-1 can be anti-cancer or pro-cancer.

Interleukin-27 (IL-27) is known to play opposing roles in immunology. The present paper considers, specifically, the role IL-27 plays in cancer immunotherapy when combined with immune checkpoint inhibitor anti-PD-1. We first develop a mathematical model for this combination therapy, by a system of Partial Differential Equations, and show agreement with experimental results in mice injected with melanoma cells. We then proceed to simulate tumor volume with IL-27 injection at a variable dose F and anti-PD-1 at a variable dose g. We show that in some range of "small" values of g, as f increases tumor volume decreases as long as fFc(g), where Fc(g) is a monotone increasing function of g. This demonstrates that IL-27 can be both anti-cancer and pro-cancer, depending on the ranges of both anti-PD-1 and IL-27.

Cylin-Painting: Seamless 360° Panoramic Image Outpainting and Beyond.

Image outpainting gains increasing attention since it can generate the complete scene from a partial view, providing a valuable solution to construct 360° panoramic images. As image outpainting suffers from the intrinsic issue of unidirectional completion flow, previous methods convert the original problem into inpainting, which allows a bidirectional flow. However, we find that inpainting has its own limitations and is inferior to outpainting in certain situations. The question of how they may be combined for the best of both has as yet remained under-explored. In this paper, we provide a deep analysis of the differences between inpainting and outpainting, which essentially depends on how the source pixels contribute to the unknown regions under different spatial arrangements. Motivated by this analysis, we present a Cylin-Painting framework that involves meaningful collaborations between inpainting and outpainting and efficiently fuses the different arrangements, with a view to leveraging their complementary benefits on a seamless cylinder. Nevertheless, straightforwardly applying the cylinder-style convolution often generates visually unpleasing results as it discards important positional information. To address this issue, we further present a learnable positional embedding strategy to incorporate the missing component of positional encoding into the cylinder convolution, which significantly improves the panoramic results. It is noted that while developed for image outpainting, the proposed algorithm can be effectively extended to other panoramic vision tasks, such as object detection, depth estimation, and image super-resolution. Code will be made available at https://github.com/KangLiao929/Cylin-Painting.

Whole genome analysis of echinocandin non-susceptible Candida Glabrata clinical isolates: a multi-center study in China.

BACKGROUND: Candida glabrata is an important cause of invasive candidiasis. Echinocandins are the first-line treatment of invasive candidiasis caused by C. glabrata. The epidemiological echinocandin sensitivity requires long-term surveillance and the understanding about whole genome characteristics of echinocandin non-susceptible isolates was limited. RESULTS: The present study investigated the echinocandin susceptibility of 1650 C. glabrata clinical isolates in China from August 2014 to July 2019. The in vitro activity of micafungin was significantly better than those of caspofungin and anidulafungin (P < 0.001), assessed by MIC50/90 values. Whole genome sequencing was conducted on non-susceptible isolates and geography-matched susceptible isolates. Thirteen isolates (0.79%) were resistant to at least one echinocandin. Six isolates (0.36%) were solely intermediate to caspofungin. Common evolutionary analysis of echinocandin-resistant and echinocandin-intermediate isolates revealed genes related with reduced caspofungin sensitivity, including previously identified sphinganine hydroxylase encoding gene SUR2. Genome-wide association study identified SNPs at subtelometric regions that were associated with echinocandin non-susceptibility. In-host evolution of echinocandin resistance of serial isolates revealed an enrichment for non-synonymous mutations in adhesins genes and loss of subtelometric regions containing adhesin genes. CONCLUSIONS: The echinocandins are highly active against C. glabrata in China with a resistant rate of 0.79%. Echinocandin non-susceptible isolates carried common evolved genes which are related with reduced caspofungin sensitivity. In-host evolution of C. glabrata accompanied intensive changing of adhesins profile.

Different mechanisms of CD200-CD200R induce diverse outcomes in cancer treatment.

The CD200 is a cell membrane protein expressed by tumor cells, and its receptor CD200 receptor (CD200R) is expressed by immune cells including macrophages and dendritic cells. The formation of CD200-CD200R inhibits the cellular functions of the targeted immune cells, so CD200 is one type of the immune checkpoint and blockade CD200-CD200R formation is a potential cancer treatment. However, the CD200 blockade has opposite treatment outcomes in different types of cancers. For instance, the CD200R deficient mice have a higher tumor load than the wild type (WT) mice in melanoma suggesting that CD200-CD200R inhibits melanoma. On the other hand, the antibody anti-CD200 treatment in pancreatic ductal adenocarcinoma (PDAC) and head and neck squamous cell carcinoma (HNSCC) significantly reduces the tumor load indicating that CD200-CD200R promotes PDAC and HNSCC. In this work, we hypothesize that different mechanisms of CD200-CD200R in tumor microenvironment could be one of the reasons for the diverse treatment outcomes of CD200 blockade in different types of cancers. We create one Ordinary Differential Equations (ODEs) model for melanoma including the inhibition of CCL8 and regulatory T cells and the switching from M2 to M1 macrophages by CD200-CD200R to capture the tumor inhibition by CD200-CD200R. We also create another ODEs model for PDAC and HNSCC including the promotion of the polarization and suppressive activities of M2 macrophages by CD200-CD200R to generate the tumor promotion by CD200-CD200R. Furthermore, we use these two models to investigate the treatment efficacy of the combination treatment between the CD200-CD200R blockade and the other immune checkpoint inhibitor, anti-PD-1. Our result shows that different mechanisms of CD200-CD200R can induce different treatment outcomes in combination treatments, namely, only the CD200-CD200R blockade reduces tumor load in melanoma and only the anti-PD-1 and CD200 knockout decrease tumor load in PDAC and HNSCC. Moreover, in melanoma, the CD200-CD200R mainly utilizes the inhibitions on M1 macrophages and dendritic cells to inhibit tumor growth, instead of M2 macrophages.

Dynamic evolution of ceftazidime-avibactam resistance due to interchanges between blaKPC-2 and blaKPC-145 during treatment of Klebsiella pneumoniae infection.

Background: The emergence of ceftazidime-avibactam (CZA) resistance among carbapenem-resistant Klebsiella pneumoniae (CRKP) is of major concern due to limited therapeutic options. Methods: In this study, 10 CRKP strains were isolated from different samples of a patient with CRKP infection receiving CZA treatment. Whole-genome sequencing (WGS) and conjugation experiments were performed to determine the transferability of the carbapenem resistance gene. Results: This infection began with a KPC-2-producing K. pneumoniae (CZA MIC = 2 µg/mL, imipenem MIC ≥ 16 µg/mL). After 20 days of CZA treatment, the strains switched to the amino acid substitution of T263A caused by a novel KPC-producing gene, blaKPC-145, which restored carbapenem susceptibility but showed CZA resistance (CZA MIC ≥ 256 µg/mL, imipenem MIC = 1 µg/mL). The blaKPC-145 gene was located on a 148,185-bp untransformable IncFII-type plasmid. The subsequent use of carbapenem against KPC-145-producing K. pneumoniae infection led to a reversion of KPC-2 production (CZA MIC = 2 µg/mL, imipenem MIC ≥ 16 µg/mL). WGS analysis showed that all isolates belonged to ST11-KL47, and the number of SNPs was 14. This implied that these blaKPC-positive K. pneumoniae isolates might originate from a single clone and have been colonized for a long time during the 120-day treatment period. Conclusion: This is the first report of CZA resistance caused by blaKPC-145, which emerged during the treatment with CZA against blaKPC-2-positive K. pneumoniae-associated infection in China. These findings indicated that routine testing for antibiotic susceptibility and carbapenemase genotype is essential during CZA treatment.

Metabolomic and transcriptomice analyses of flavonoid biosynthesis in apricot fruits.

Introduction: Flavonoids, as secondary metabolites in plants, play important roles in many biological processes and responses to environmental factors. Methods: Apricot fruits are rich in flavonoid compounds, and in this study, we performed a combined metabolomic and transcriptomic analysis of orange flesh (JN) and white flesh (ZS) apricot fruits. Results and discussion: A total of 222 differentially accumulated flavonoids (DAFs) and 15855 differentially expressed genes (DEGs) involved in flavonoid biosynthesis were identified. The biosynthesis of flavonoids in apricot fruit may be regulated by 17 enzyme-encoding genes, namely PAL (2), 4CL (9), C4H (1), HCT (15), C3'H (4), CHS (2), CHI (3), F3H (1), F3'H (CYP75B1) (2), F3'5'H (4), DFR (4), LAR (1), FLS (3), ANS (9), ANR (2), UGT79B1 (6) and CYP81E (2). A structural gene-transcription factor (TF) correlation analysis yielded 3 TFs (2 bHLH, 1 MYB) highly correlated with 2 structural genes. In addition, we obtained 26 candidate genes involved in the biosynthesis of 8 differentially accumulated flavonoids metabolites in ZS by weighted gene coexpression network analysis. The candidate genes and transcription factors identified in this study will provide a highly valuable molecular basis for the in-depth study of flavonoid biosynthesis in apricot fruits.

Exploring the third-generation tetracycline resistance of multidrug-resistant livestock-associated methicillin-resistant Staphylococcus aureus ST9 across healthcare settings in China.

BACKGROUND: The overuse of antibiotics in livestock is contributing to the burden of antimicrobial resistance in humans, representing a One Health challenge. Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has recently become a growing concern, and ST9 is the major LA-MRSA lineage in China and has emerged in clinical settings. METHODS: Antimicrobial susceptibility testing was used to evaluate the tetracycline resistance of ST9 MRSA collections, and gene cloning experiments were performed to explore the resistance mechanisms. Whole-genome sequencing and comparative genomics were used to analyse the genetic features of clinical ST9 isolates. A phylogenetic tree was constructed to investigate the relationship of human- and livestock-derived ST9 isolates. RESULTS: Clinical ST9 isolates were found to possess several types of resistance genes and resistance-related mutations and were multidrug-resistant. Notably, all clinical ST9 isolates were resistant to third-generation tetracyclines. Cloning experiments showed that both the acquisition of the tetracycline resistance gene tet(L)/tet(63) and a mutation in the rpsJ gene contributed to third-generation tetracycline resistance. Phylogenetic analysis showed that the ST9 isolates collected in healthcare systems were probably transmitted from livestock. The ST9 lineage underwent multiple interspecies recombination events and gained many resistance elements. Furthermore, the resistance to third-generation tetracyclines may have evolved under tetracycline pressure in livestock. CONCLUSIONS: The evolution of ST9 MRSA in livestock and transmission of this clone between humans and livestock highlight the importance of establishing control strategies with the One Health approach to reduce the burden of antibiotic resistance.

Deep Rotation Correction Without Angle Prior.

Not everybody can be equipped with professional photography skills and sufficient shooting time, and there can be some tilts in the captured images occasionally. In this paper, we propose a new and practical task, named Rotation Correction, to automatically correct the tilt with high content fidelity in the condition that the rotated angle is unknown. This task can be easily integrated into image editing applications, allowing users to correct the rotated images without any manual operations. To this end, we leverage a neural network to predict the optical flows that can warp the tilted images to be perceptually horizontal. Nevertheless, the pixel-wise optical flow estimation from a single image is severely unstable, especially in large-angle tilted images. To enhance its robustness, we propose a simple but effective prediction strategy to form a robust elastic warp. Particularly, we first regress the mesh deformation that can be transformed into robust initial optical flows. Then we estimate residual optical flows to facilitate our network the flexibility of pixel-wise deformation, further correcting the details of the tilted images. To establish an evaluation benchmark and train the learning framework, a comprehensive rotation correction dataset is presented with a large diversity in scenes and rotated angles. Extensive experiments demonstrate that even in the absence of the angle prior, our algorithm can outperform other state-of-the-art solutions requiring this prior. The code and dataset are available at https://github.com/nie-lang/RotationCorrection.

Evaluation of Implementation and Effectiveness of China's Antibiotic Stewardship in the First Affiliated Hospital of Sun Yat-sen University.

Antibiotic stewardship has been prioritized by governments and health care organizations in recent years as antibiotic resistance is markedly increasing. A tertiary hospital in Guangzhou, China was chosen as a study example to undertake an implementation and effectiveness evaluation of China's antibiotic stewardship to improve and promote antimicrobial stewardship nationwide. The general surgery department of the study hospital was utilized to examine surgical site infection, and samples from across the hospital were used to identify bloodstream infection. Data was analyzed using descriptive analysis, the Mann-Kendall trend test, logit model and panel data model, and t-tests. In terms of prophylactic and therapeutic antibiotic rational use, respectively, we evaluated implementation conditions, the correlation between implementation and corresponding disease progress, and the cost-effectiveness of China's antibiotic stewardship. For perioperative prophylactic antibiotic use, antibiotic stewardship was found to have been well-implemented, cost-effective, and reduced the incidence of surgical site infection. However, concerning therapeutic use and antibiotic-resistant bacterial infection prophylaxis, the complexity of influencing factors and the contradiction between stewardship implementation and clinical demand needs to be further evaluated.

Application of next-generation sequencing on diagnosis of bloodstream infection caused by Mycoplasma hominis in a patient with ANCA-associated vasculitis.

BACKGROUND: Mycoplasma hominis is one of the main opportunistic pathogenic mycoplasmas in humans which has a major impact on patients with bloodstream infections. Because it is difficult to detect or isolate, rapid and accurate diagnosis using improved methods is essential and still challenging for patients with bloodstream infection. CASE PRESENTATION: In this case, we reported the application of next -generation sequencing for the diagnosis of bloodstream infection caused by Mycoplasma hominis in a patient with Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis. After 9 days of combined treatment with levofloxacin, polymyxin B and meropenem, the patient's condition was gradually controlled and he was discharged without further complications. During the three-month outpatient follow-up, no recurrence of symptoms or clinical signs was reported. CONCLUSIONS: This successful application of next generation sequencing assisted the rapid diagnosis of Mycoplasma hominis bloodstream infection, provided a new perspective in the clinical approach and highlighted the potential of this technique in rapid etiological diagnosis.

Clinical Profiles and Prognoses of Adult Patients with Full-Frequency Sudden Sensorineural Hearing Loss in Combination Therapy.

We aimed to characterize the clinical profiles and short-term outcomes of adult patients with full-frequency idiopathic sudden sensorineural hearing loss (ISSNHL) treated uniformly with combination therapy, and to determine the prognostic predictors for the combination therapy. A total of 131 eligible cases hospitalized in our department from January 2018 to June 2021 were retrospectively reviewed. All enrolled cases received a standardized combination therapy employing intravenous methylprednisolone, batroxobin, and Ginkgo biloba extract during the 12 days of hospitalization. The clinical and audiometric profiles were compared between recovered patients and their unrecovered counterparts. The overall recovery rate was 57.3% in the study. Accompanying vertigo (odds ratio = 0.360, p = 0.006) and body mass index (BMI, odds ratio = 1.158, p = 0.016) were two independent predictors of hearing outcomes of the therapy. The male gender and cigarette-smoking history were marginally associated with good hearing prognosis (p = 0.051 and 0.070, respectively). Patients with BMI ≥ 22.4 kg/m2 had a better chance of hearing recovery (p = 0.02). Conclusions: Accompanying vertigo and low BMI (<22.4 kg/m2) were independently associated with poor prognosis for full-frequency ISSNHL in combination therapy. Male gender and cigarette-smoking history might be considered positive effects on hearing prognosis.

Metagenomic next-generation sequencing for the diagnosis of Pneumocystis jirovecii Pneumonia in critically pediatric patients.

OBJECTIVE: The aim of this study was to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) for the diagnosis of Pneumocystis jirovecii Pneumonia (PCP) in critically pediatric patients. METHODS: Seventeen critically pediatric patients with PCP and sixty patients diagnosed with non-PCP pneumonia who were admitted in pediatric intensive care unit between June 2018 and July 2021 were enrolled. Conventional methods and mNGS for detecting Pneumocystis jirovecii (P. jirovecii) were compared. The patients' demographics, comorbidities, laboratory test results, antibiotic treatment response and 30 day mortality were analyzed. RESULT: The mNGS showed a satisfying diagnostic performance with a sensitivity of 100% in detecting P. jirovecii compared with Gomori methenamine silver staining (5.9%), serum (1,3)-ß-D-glucan (86.7%) and and LDH (55.6%). The diagnostic specificity of mNGS for PCP was higher than that of serum BDG (56.7%) and LDH (71.4%). In PCP group, over one thirds' cases had mixed infections. Compared with survivors, non-survivors had higher stringently mapped read numbers (SMRNs) in bronchoalveolar lavage fluid (BALF) sample (P < 0.05), suggesting SMRNs were closely associated with the severity of response. The detection for P. jirovecii by mNGS both in BALF and blood samples reached a concordance rate of 100%, and the SMRNs in the BALF were remarkably higher than that in blood samples. Initial antimicrobial treatment was modified in 88.2% of PCP patients based on the mNGS results. CONCLUSION: The mNGS is a potential and efficient technology in diagnosing PCP and shows a satisfying performance in the detection of co-pathogens. Both blood and BALF samples for mNGS are suggested for the presumptive diagnosis of PCP.

A simple in-host model for COVID-19 with treatments: model prediction and calibration.

In this paper, we provide a simple ODEs model with a generic nonlinear incidence rate function and incorporate two treatments, blocking the virus binding and inhibiting the virus replication to investigate the impact of calibration on model predictions for the SARS-CoV-2 infection dynamics. We derive conditions of the infection eradication for the long-term dynamics using the basic reproduction number, and complement the characterization of the dynamics at short-time using the resilience and reactivity of the virus-free equilibrium are considered to inform on the average time of recovery and sensitivity to perturbations in the initial virus free stage. Then, we calibrate the treatment model to clinical datasets for viral load in mild and severe cases and immune cells in severe cases. Based on the analysis, the model calibrated to these different datasets predicts distinct scenarios: eradication with a non reactive virus-free equilibrium, eradication with a reactive virus-free equilibrium, and failure of infection eradication. Moreover, severe cases generate richer dynamics and different outcomes with the same treatment. Calibration to different datasets can lead to diverse model predictions, but combining long- and short-term dynamics indicators allows the categorization of model predictions and determination of infection severity.