Isolation, whole genome sequencing and application of a broad-spectrum Salmonella phage.

Salmonella is considered as one of the most common zoonotic /foodborne pathogens in the world. The application of bacteriophages as novel antibacterial agents in food substrates has become an emerging strategy. Bacteriophages have the potential to control Salmonella contamination.We have isolated and characterized a broad-spectrum Salmonella phage, SP154, which can lyse 9 serotypes, including S. Enteritidis, S. Typhimurium, S. Pullorum, S. Arizonae, S. Dublin, S. Cholerasuis, S. Chester, S. 1, 4, [5], 12: i: -, and S. Derby, accounting for 81.9% of 144 isolates. SP154 showed a short latent period (40 min) and a high burst size (with the first rapid burst size at 107 PFUs/cell and the second rapid burst size at approximately 40 PFUs/cell). Furthermore, SP154 activity has higher survival rates across various environmental conditions, including pH 4.0-12.0 and temperatures ranging from 4 to 50 °C for 60 min, making it suitable for diverse food processing and storage applications. Significant reductions in live Salmonella were observed in different foods matrices such as milk and chicken meat, with a decrease of up to 1.9 log10 CFU/mL in milk contamination and a 1 log10 CFU/mL reduction in chicken meat. Whole genome sequencing analysis revealed that SP154 belongs to the genus Ithacavirus, subfamily Humphriesvirinae, within the family Schitoviridae. Phylogenetic analysis based on the terminase large subunit supported this classification, although an alternate tree using the tail spike protein gene suggested affiliation with the genus Kuttervirus, underscoring the limitations of relying on a single gene for phylogenetic inference. Importantly, no virulence or antibiotic resistance genes were detected in SP154. Our research highlights the potential of using SP154 for biocontrol of Salmonella in the food industry.

Fluorescent immunoassay for chloramphenicol based on the label-free polyadenine-mediated spherical nucleic acids triggered signal amplification.

A fluorescent immunosorbent assay incorporating signal amplification away from the surface of spherical nucleic acid (SNA) was developed for the detection of chloramphenicol (CAP). Through the conjugation of antibodies and poly-adenine (polyA) DNA onto the surface of gold nanoparticles (AuNPs), the fabrication of the nano-immunoprobe was achieved in a more straightforward and cost-effective manner. Moreover, a strategy utilizing the hybridization chain reaction (HCR) in the amplification step was devised, with particular attention given to the enzyme inhibition associated with SNA. The results demonstrated good performance on CAP detection with a linear range of 0.01-5 ng/L with a detection limit of 0.005 ng/L. The significance of this work mainly lies in the polyA-SNA-based immunoprobe and the thoughtful design to prevent enzyme inhibition.

ELL associated factor 2 is a potential diagnostic and prognostic indicator: evidence from the in silico and in vitro experiments.

Due to the lack of sensitive biomarkers, cancer disease kill 9.6 million individuals each year around the globe. The present study aimed to explore the association between ELL Associated Factor 2 (EAF2) expression and its diagnostic and prognostic landscape across different human cancers using an in silico and in vitro approach. To achieve the defined goals of this study, we used the following online sources: UALCAN, KM plotter, TNMplot, cBioPortal, STRING, DAVID, MuTarget, Cytoscape, and CTD. In addition to this, we also used additional The Cancer Genome Atlas (TCGA) datasets via TIMER2, GENT2, and GEPIA to confirm the expression of EAF2 on additional cohorts. Finally, we performed RNA sequencing (RNA-seq) and targeted bisulfite sequencing (bisulfite-seq) techniques-based analysis using A549, ABC-1, EBC-1, LK-2 lung cancer cell lines, and MRC-9 normal control lung cell line for further validation of the results. On balance, EAF2 was elevated in 19 types of human cancers and its up-regulation was significantly correlated with shorter overall survival (OS), relapse-free survival (RFS), and metastasis in Liver Hepatocellular Carcinoma (LIHC) and Lung Squamous Cell Carcinoma (LUSC) patients. We further evaluated that EAF2 expression was also elevated across LIHC and LUSC patients belonging to different clinicopathological features. Through pathway analysis, EAF2 associations were observed with four important pathways. Moreover, some worth noticing correlations were also documented between EAF2 expression and its promoter methylation level, genetic alterations, other mutant genes, tumor purity, and different immune cells infiltration. The higher EAF2 expression contributes significantly to the tumorigenesis and metastasis of LIHC and LUSC. Therefore, it can be used as a common biomarker in these cancers.

Enhanced production of D-psicose from D-fructose by a redox-driven multi-enzyme cascade system.

D-Psicose, a new-generation sugar substitute, has been enzymatically synthesized through D-fructose isomerization. However, isomerization often causes low yields due to unfavorable thermodynamic equilibria, which limited its further industrial application. In this study, we present a redox-driven multi-enzyme cascade, two-step biotransformation system to produce D-psicose from D-fructose. Compared to D-fructose isomerization, this method has a maximized theoretical conversion rate of 100%. D-Psicose-3-epimerase from Clostridiales (CBDPE), ribitol 2-dehydrogenase from Providencia alcalifaciens (PRDH), and formate dehydrogenase from Starkeya (SFDH) were co-expressed in Escherichia coli in the first step to produce D-allitol from D-fructose. Afterward, NADH oxidase from Streptococcus pyogenes (SPNOX), and ribitol 2-dehydrogenase from Rubrivivax sp. (RSRDH) were co-expressed in E. coli to oxidize D-allitol into D-psicose in the second step. The two-step biotransformation system was optimized to maximize the D-fructose-to-D-psicose conversion rate (up to 90%), corresponding to a concentration of 450 mM. This study suggests that this redox-driven multi-enzyme cascade strategy through a sugar-to-alcohol-to-sugar pathway has the advantage of great application for enhanced production of D-psicose and other rare sugars.

Characterization and genomic analysis of a Demerecviridae phage SP76 with lytic multiple-serotypes of Salmonella.

With the increase in antimicrobial resistance of Salmonella, phages have been paid more attention to as an alternative to antibiotics. In this study, a phage designated as SP76 was isolated from sewage. It can lyse several serotypes of Salmonella, including S. typhimurium (21/33), S. enteritidis (7/7), S. dublin (4/4), S. pullorum (2/2) and S. choleraesuis (1/2). SP76 showed a latent time of about 10 min, and maintained good lytic activity at a pH range of 3-10 and temperatures between 4 and 37 °C. Moreover, its optimal multiplicity of infection (MOI) was 0.0001. Based on the results of genomic sequence and analysis, SP76 was found to have a genome of 111,639 bp that encoded 166 predicted ORFs and belong to the Demerecviridae family, order Caudovirales. No virulence or lysogen formation gene clusters were identified in the SP76 genome. A pan-genome analysis based on 100 phages within the subfamily Markadamsvirinae indicated that SP76 had 23 core genes and 1199 accessory genes. We grouped the subfamily Markadamsvirinae and found that the main difference was in group III. In vitro bacteriostasis, experiments showed that the phage SP76 reduced planktonic bacteria by 1.52 log10 CFU/mL, and biofilms (24 h old) by 0.372 log10 CFU/mL, respectively. Thus, we isolated a safe and efficient phage that might be a good antibacterial agent.

Influenza virus subtype/lineage-specific seasonal patterns and age-related infection risk, in Eastern China.

INTRODUCTION: Differences in seasonal pattern and age-related infection risk have been reported between Influenza type A and B, but have not been elaborated at subtype/lineage level. METHODOLOGY: All laboratory-confirmed influenza cases reported in the influenza surveillance system of Jiangsu Province, China from January 2011 to August 2019 were analyzed. Influenza seasonality was characterized using the Seasonal Decomposition method. Binary and multinomial logistic regressions were employed to calculate the odds ratios of influenza subtypes/lineages in relation to age. RESULTS: A total of 28,772 confirmed influenza cases were included. Among them, a majority (64.1%) were influenza A infections. One annual peak was observed for A (H1N1) pdm and B-Yamagata in winter months, and for B-Victoria in spring months, while biannual peaks were observed for A (H3N2) in winter and summer months. Using all ages as the reference, children younger than 5 years and adults of 25-59 years were more likely to infect with A (H1N1) pdm. Older children aged 5-14 years had significantly higher odds of infection with influenza B of both lineages, while individuals aged 15-24 years had higher odds for A (H3N2) and B-Victoria. The elderly (60 years or older) were prone to be infected with A (H3N2) and B-Yamagata. For a specific age group, their likelihood of getting infected with an influenza subtype or lineage was related to the co-circulating influenza subtype or lineage. CONCLUSIONS: Influenza viruses have divergent seasonal peak times and age-related infection risk at subtype/lineage level.

Characterization of Human Origin Salmonella Serovar 1,4,[5],12:i:- in Eastern China, 2014 to 2018.

The prevalence of Salmonella serovar 1,4,[5],12:i:- among diarrhea patients has increased considerably in many countries around the world, including China. However, the characterization of this serovar of human origin has been less reported from China. We characterized 76 isolates of Salmonella 1,4,[5],12:i:- gained from diarrhea patients from 2014 to 2018 in the Jiangsu Province of eastern China. These isolates fell into a single-sequence type (ST34) determined by multilocus sequence typing (MLST), and into 44 pulsed-field gel electrophoresis band patterns, with 1 pattern (JSSMM015) comprising 12 isolates (15.9%). By means of PCR-based assays, the seven prophage located virulence genes were detected in our Salmonella 1,4,[5],12:i:- isolates with a high rate of gipA, gtgB, sspH1, sspH2, sodC1, and gtgE (93.4-97.4%), and with a moderate rate of sopE (42.1%). In contrast, none of the five plasmid-borne virulence genes (spvC, pefA, mig5, rck, and srgA) was identified. We tested the isolates' susceptibility to 18 antibiotics of 9 categories using the VITEK 2 system. A high proportion (89.5%) of the isolates were multidrug resistant (MDR) strains with full resistance to cefazolin, cefotetan, amikacin, gentamycin, and tobramycin, followed by resistance to ampicillin (88.2%) and ampicillin/sulbactam (80.3%). The resistance to piperacillin/tazobactam, ceftazidime, cefepime, and levofloxacin was scarce (2.6-9.2%). Notably, an isolate from 2018 was resistant to carbapenems. blaTEM-1B and aac(6')-Ib-cr were the most common drug resistance genes presented in cephalosporin- and fluoroquinolone-resistant strains. All Salmonella 1,4,[5],12:i:- isolates were capable of forming biofilm, with 13.2% of them having strong ability. However, no association was indicated between the scale of biofilm formation ability and MDR. Our results indicate that the combination of these characteristics may together provide a selective and competitive advantage to those Salmonella 1,4,[5],12:i:- isolates, contributing to their increasing prevalence observed worldwide.

Semisynthesis of CRV431.

The non-immune-suppressive cyclophilin inhibitor CRV431 is a clinical candidate to cure nonalcoholic steatohepatitis (NASH) and has the potential to treat liver fibrosis and cancer incidence. Herein we report a concise chemical semisynthesis of CRV431 in four steps from the commercially available cyclosporine, featuring in this the flow-chemistry-based methylenation an intermolecular ring-closing metathesis and a Rh-catalyzed diastereoselective hydrogenation.

CDH1 Gene rs1801552 C/T Polymorphism Increases Susceptibility to Esophageal Squamous Cell Carcinoma but Not to Gastric Cardiac Adenocarcinoma.

PURPOSE: The present study aimed to investigate whether the single nucleotide polymorphism (SNP) rs1801552 C/T in CDH1 gene is correlated with the risk of esophageal squamous cell carcinoma (ESCC) and gastric cardiac adenocarcinoma (GCA), as a preliminary study. METHODS: The rs1801552 C/T polymorphism was genotyped by the method of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 1316 cancer patients (810 ESCC and 506 GCA) and 1966 controls in north China. We performed two case-control studies, each of which included a population-based set and a hospital-based set. RESULTS: The data showed that the rs1801552 C/T polymorphism was associated with the risk of ESCC. Allelotype and genotype distributions of the rs1801552 C/T polymorphism in ESCC patients of high-incidence region and hospital were significantly different from that in their respective controls (p < 0.05). Compared with C/C genotype, T/T genotype increased the risk of ESCC in high-incidence region and hospital (age, sex, smoking status and family history of UGIC adjusted odds ratio (OR) = 1.79 and 2.10, 95% confidence interval (CI) = 1.23-2.60 and 1.10-4.04, respectively). Allelotype and genotype distributions of the rs1801552 C/T polymorphism in GCA patients were not significantly different from that in their controls, respectively (p > 0.05). CONCLUSIONS: The findings in the present pilot study suggest that the rs1801552 C/T polymorphism was associated with the risk of ESCC, but was not associated with the risk of GCA in high-incidence region and hospital.

TIM-3 polymorphism is involved in the progression of esophageal squamous cell carcinoma by regulating gene expression.

The T-cell immunoglobulin and mucin domain containing molecule 3 (TIM-3), a crucial immune regulatory molecule, is an emerging immune checkpoint target for cancer therapy. Our study aimed to investigate the association between TIM-3 polymorphisms (rs10053538 C > A, rs10515746 C > A, and rs1036199 A > C) and the susceptibility and prognosis of esophageal squamous cell carcinoma (ESCC). We further detect the effects of polymorphisms on TIM-3 expression. Two independent case-control sets (population-based and hospital-based sets) were performed in total 994 ESCC patients and 998 controls. TIM-3 polymorphisms were genotyped by polymerase chain reaction-ligase detection reaction (PCR). Survival data were available for 198 patients who received platinum-based chemotherapy after surgery. The regulation on TIM-3 expression by the polymorphisms was investigated in 35 patients using real-time quantitative PCR. The association between mRNA level of TIM-3 and survival was detected by using Kaplan-Meier plotter database. We found that for rs10053538 C > A polymorphisms, A allele was associated with significant increased risk of ESCC (odds ratios [OR] = 1.34, 95%CI = 1.05-1.72), and CA/AA genotypes enhanced susceptibility to ESCC for smokers (adjusted OR = 1.61, 95%CI = 1.00-2.59). The patients with AA genotypes had significantly poor prognosis (adjusted HR = 4.98, 95%CI = 1.14-21.71). The patients carrying CA/AA genotypes had significantly higher mRNA levels of TIM-3 than those carrying the CC genotype. Furthermore, high mRNA level of TIM-3 had a shorter overall survival in patients (HR = 2.56, 95%CI = 1.04-6.28). For rs10515746 C > A and rs1036199 A > C polymorphisms, there were no statistical correlation with the progression of ESCC. These data demonstrate that rs10053538 C > A polymorphisms may be associated with the susceptibility and prognosis of ESCC patients through regulating expression of TIM-3.

Detection of antibiotics in the urine of children and pregnant women in Jiangsu, China.

Exposure to low concentrations of antibiotics links to multiple health hazards, such as drug resistance of bacteria, and childhood obesity. In this study, seven antibiotics were measured in the urine of 107 children and 126 pregnant women in Jiangsu Province by ultra-performance liquid chromatography and tandem mass spectrometry (UPLC-MS/MS). The overall urinary antibiotics detection rate was 38.6%. Most (98.3%) of the participants' antibiotics concentrations were no more than 10 ng/mL. Children had a significantly higher detection rate than pregnant women (47.7% vs. 31.0%, P = 0.009), as well as the concentration (95th percentile: 6.49 vs. 4.08 ng/mL, P = 0.002). The detection rates of individual antibiotics ranged from 0.4% to 15.0%, and the concentrations ranged from lower than the limit of detection (LOD) through up to 31.96 ng/mL individually. Two or more antibiotics were detected in 11.2% of the urines. Tetracyclines were more frequently detected than phenicols (30.9% vs.12.4%). Oxytetracycline was the most frequently detected (15.0%). Multivariate logistic regression showed that consuming puffed food every day was associated with a significantly increased likelihood of detection, and higher concentration of overall antibiotics, and of doxycycline. Children were more likely to be detected of doxycycline and florfenicol, and to have elevated concentration of doxycycline, compared with pregnant women. This study highlights the relatively heavier antibiotics exposure in children, and a possible impact of puffed food on it, which needs to be warranted in future studies.

Development and validation of a sensitive UHPLC-MS/MS method for the measurement of ß-elemonic acid in rat plasma and tissues and its application to pharmacokinetics and tissue distribution study.

ß-Elemonic acid is one of the main active ingredients isolated from Boswellia carterii Birdw. which has been reported to exhibit potential anti-inflammatory and anti-cancer activities. There is few information about pharmacokinetics and tissue distribution of ß-elemonic acid by now. In this study, an ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-MS/MS) method has been developed and validated to determine ß-elemonic acid in rat plasma and various tissues after intragastric administration. Oleanolic acid was chosen as an internal standard (IS) and the plasma/tissue samples were pretreated with one-step liquid-liquid extraction. Chromatographic separation was accomplished on Eclipse Plus C18 analytical column (2.1 × 50 mm, 1.8 µm) utilizing a gradient mobile phase system consisting of water (with 0.1% ammonia-solution) and acetonitrile. ß-Elemonic acid and IS were detected and quantified using negative electrospray ionization in multiple reaction monitoring (MRM) mode with transitions of m/z 453.3 â†’ 423.5 for ß-elemonic acid and m/z 455.3 â†’ 407.6 for IS. ß-Elemonic acid showed good linearity over the investigated concentration range (r > 0.9934) in rat plasma and tissue sample. The method was successfully applied for determination of ß-elemonic acid in bio-samples. A bimodal phenomenon appeared in the plasma concentration-time curve of the ß-elemonic acid. The highest tissue concentrations were found in the intestine including jejunum, ileum and colon.

Identification of novel fibronectin-binding proteins by 2D-far Western blot in atypical enteropathogenic Escherichia coli serotype O55:H7.

Atypical enteropathogenic Escherichia coli (aEPEC) is a subgroup of EPEC, which is one of the major pathogens responsible for fatal diarrhoea in children. Compared with typical EPEC (tEPEC), aEPEC lack an EAF (EPEC adherence factor) plasmid (pEAF), which encodes a series of virulence-associated genes. The extracellular matrix (ECM) component of human cells has been reported to be an important element in the interaction between host and bacterial pathogens. In this research, a 2D-Far Western blot method was performed to identifiy the bacterial proteins that could bind to fibronectin, one of the most common constituents of ECM. A total of 17 protein spots were identified, including 4 outer membrane proteins (OMPs), namely, OmpC, OmpD, OmpX and LamB. In vitro studies were used to determine whether these OMPs were involved in the adherence process. Through indirect immunofluorescence assays, four OMPs could be observed on the surfaces of host cells. After incubating the cells with the recombinant proteins, the adhesion rate of the O55:H7 isolate was decreased. Furthermore, the deletion of OmpX and LamB can also decrease the adhesion rate of WT. Taken together, a high-throughput screening method for host ECM-binding proteins based on 2D Far-Western blot was established, and four outer membrane proteins identified by this method were found to be involved in the adherence process.

The COVID-19 Vaccine in Clinical Trials: Where Are We Now?

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to scale up around the world, costing severe health and economic losses. The development of an effective COVID-19 vaccine is of utmost importance. Most vaccine designs can be classified into three camps: protein based (inactivated vaccines, protein subunit, VLP and T-cell based vaccines), gene based (DNA or RNA vaccines, replicating or non-replicating viral/bacterial vectored vaccines), and a combination of both protein-based and gene-based (live-attenuated virus vaccines). Up to now, 237 candidate vaccines against SARS-CoV-2 are in development worldwide, of which 63 have been approved for clinical trials and 27 are evaluated in phase 3 clinical trials. Six candidate vaccines have been authorized for emergency use or conditional licensed, based on their efficacy data in phase 3 trials. This review summarizes the strengths and weaknesses of the candidate COVID-19 vaccines from various platforms, compares, and discusses their protective efficacy, safety, and immunogenicity according to the published clinical trials results.

Secondary attack rates of COVID-19 in diverse contact settings, a meta-analysis.

INTRODUCTION: The secondary attack rate (SAR) measures the transmissibility of an infectious agent. The reported SAR of COVID-19 varied in a broad range, and between different contact settings. METHODOLOGY: We conducted a meta-analysis on the SAR of COVID-19 with adherence to the PRISMA guideline. We searched published literatures and preprints in international databases of PubMed and medRxiv, and in five major Chinese databases as of 20 April 2020, using the following search terms: ("COVID-19" and "secondary attack rate") or ("COVID-19" and "close contact"). The random effect model was chosen for pooled analyses, using R (version 3.6.3). RESULTS: A total of 1,136 references were retrieved and 18 of them remained after screening. The pooled SAR of COVID-19 was 0.07 (95%: 0.03-0.12) in general. It differed significantly between contact settings, peaking in households (0.20, 95%: 0.15-0.28), followed by in social gatherings (0.06, 95%: 0.03-0.10). The point estimates of the pooled SARs in health facilities, transports, and work/study settings were all as low as 0.01. Among all the secondary cases, the proportion of asymptomatic infections was estimated to be 0.17 (95% CI: 0.09 - 0.34). The proportion was higher in households (0.26, 95% CI: 0.12-0.56), than in other contact settings. CONCLUSIONS: The transmission risk of SARS-CoV-2 is much higher in households than in other scenarios. Identification of asymptomatic secondary infections should be enhanced in households.

A Two-Stage Method for Target Searching in the Path Planning for Mobile Robots.

The path planning for target searching in mobile robots is critical for many applications, such as warehouse inspection and caring and surveillance for elderly people in the family scene. To ensure visual complete coverage from the camera equipped in robots is one of the most challenging tasks. To tackle this issue, we propose a two-stage optimization model to efficiently obtain an approximate optimal solution. In this model, we first develop a method to determine the key locations for visual complete coverage of a two-dimensional grid map, which is constructed by drawing lessons from the method of corner detection in the image processing. Then, we design a planning problem for searching the shortest path that passes all key locations considering the frequency of target occurrence. The testing results show that the proposed algorithm can achieve the significantly shorter search path length and the shorter target search time than the current Rule-based Algorithm and Genetic Algorithm (GA) in various simulation cases. Furthermore, the results show that the improved optimization algorithm with the priori known frequency of occurrence of the target can further improve the searching with shorter searching time. We also set up a test in a real environment to verify the feasibility of our algorithm.

PARP1 Gene Polymorphisms and the Prognosis of Esophageal Cancer Patients from Cixian High-Incidence Region in Northern China.

OBJECTIVE: Poly (ADP-ribose) polymerase 1 (PARP1), as a key enzyme in the base excision repair pathway, plays a crucial role in tumorigenesis and progression. This study aimed to assess whether polymorphisms of PARP1 gene could be used as predictive biomarkers for the survival of esophageal squamous cell carcinoma (ESCC) patients from Cixian high-incidence region in northern China. METHODS: In 203 ESCC patients with survival information, PARP1 rs1136410 T/C and rs8679 T/C single nucleotide polymorphisms (SNPs) were genotyped by polymerase chain reaction ligase detection reaction (PCR-LDR) method. All statistical analyses were performed using the SPSS ver. 22.0 software package (SPSS, Chicago, IL, USA). RESULTS: The mean age ± standard deviation of the ESCC patients was 60.4 ± 7.9 years. There was no significant relation of sex, age, smoking status and upper gastrointestinal cancer family history with the survival time of the ESCC patients. The mean survival time of rs1136410 T/T, T/C and C/C genotype carriers were 43.3, 42.3 and 46.6 months, respectively. The rs1136410 was not associated with the survival time of the ESCC patients. For rs8679, the mean survival time of T/T genotype carriers was 43.7 months, which was not significantly different from that of the patients with T/C genotype (42.1 months). CONCLUSION: In Cixian high-incidence region from northern China, rs1136410 and rs8679 SNPs might not be used to predict survival of ESCC patients. There is a need to explore whether other SNPs of PARP1 gene have an effect on prognosis of ESCC patients.

A fatal paediatric case infected with reassortant avian influenza A(H5N6) virus in Eastern China.

Avian influenza A(H5N6) keeps evolving, causing outbreaks in birds and sporadic infections in human. Here, we report a fatal paediatric infection caused by a novel reassortant H5N6 virus. The patient was an obese 9-year-old girl. She initiated with fever and cough, then developed pneumonia, acute respiratory distress syndrome (ARDS) and respiratory failure. Lower respiratory tract aspirates and anal swabs were serially taken till the patient's death. Viral isolation, genome sequencing and phylogenetic analysis were conducted. A novel reassortant H5N6 virus was isolated from the patient. Except the PA gene, all other 7 genes of the virus belonged to H5N6 genotype A (S4-like virus). The PA gene was probably obtained from Eurasian waterfowl influenza viruses. The H5N6 virus was consistently detected from the patient's respiratory samples till the 17th day after symptom onset, but not from anal swabs or urine sample by real-time reverse transcription polymerase chain reaction (RT-PCR). Significantly elevated (32-fold) serum antibodies to H5N6 virus were observed during the patient's course of disease. Aside from the identified novel reassortant H5N6 viral strain, obesity, delayed confirmation of aetiology and specific antiviral treatment, and prolonged virus shedding could have contributed to the poor clinical outcome.