SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission.

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 lineages that have spread throughout the world. In this study, we investigated 129 RNA-seq data sets and 6928 consensus genomes to contrast the intra-host and inter-host diversity of SARS-CoV-2. Our analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights intra-host single nucleotide variant (iSNV) and SNP similarity, albeit with differences in C > U changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of insertions and deletions contribute to the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.

The impact of preoperative biliary drainage on postoperative healthcare-associated infections and clinical outcomes following pancreaticoduodenectomy: a ten-year retrospective analysis.

BACKGROUND: Pancreaticoduodenectomy (PD) is a complex procedure and easily accompanied by healthcare-associated infections (HAIs). This study aimed to assess the impact of PBD on postoperative infections and clinical outcomes in PD patients. METHODS: The retrospective cohort study were conducted in a tertiary hospital from January 2013 to December 2022. Clinical and epidemiological data were collected from HAIs surveillance system and analyzed. RESULTS: Among 2842 patients who underwent PD, 247 (8.7%) were diagnosed with HAIs, with surgical site infection being the most frequent type (n = 177, 71.7%). A total of 369 pathogenic strains were detected, with Klebsiella pneumoniae having the highest proportion, followed by Enterococcu and Escherichia coli. Although no significant association were observed generally between PBD and postoperative HAIs, subgroup analysis revealed that PBD was associated with postoperative HAIs in patients undergoing robotic PD (aRR = 2.174; 95% CI:1.011-4.674; P = 0.047). Prolonging the interval between PBD and PD could reduce postoperative HAIs in patients with cholangiocarcinoma (≥4 week: aRR = 0.292, 95% CI 0.100-0.853; P = 0.024) and robotic PD (≤2 week: aRR = 3.058, 95% CI 1.178-7.940; P = 0.022). PBD was also found to increase transfer of patients to ICU (aRR = 1.351; 95% CI 1.119-1.632; P = 0.002), extended length of stay (P < 0.001) and postoperative length of stay (P = 0.004). CONCLUSION: PBD does not exhibit a significant association with postoperative HAIs or other outcomes. However, the implementation of robotic PD, along with a suitable extension of the interval between PBD and PD, appear to confer advantages concerning patients' physiological recuperation. These observations suggest potential strategies that may contribute to enhanced patient outcomes.

Effects of neighborhood built environment on cognitive function in older adults: a systematic review.

BACKGROUND: In the background of an aging population, the risk of cognitive impairment in the older population is prominent. Exposure to complex neighborhood built environments may be beneficial to the cognitive health of older adults, and the purpose of this study was to systematically review the scientific evidence on the effects of neighborhood built environments on cognitive function in older adults. METHODS: Keywords and references were searched in Web of Science, Pubmed, PsycINFO, and MEDLINE. Studies examining the relationship between the built environment and cognitive function in older adults were included. The neighborhood built environment as an independent variable was classified according to seven aspects: density, design, diversity, destination accessibility, public transportation distance, blue/green space, and built environment quality. The cognitive function as the dependent variable was classified according to overall cognitive function, domain-specific cognitive function, and incidence of dementia. The quality of the included literature was assessed using the National Institutes of Health's Observational Cohort and Cross-Sectional Study Quality Assessment Tool. RESULTS: A total of 56 studies were included that met the inclusion criteria, including 31 cross-sectional studies, 23 longitudinal studies, 1 cross-sectional study design combined with a case-control design, and 1 longitudinal study design combined with a case-control design. Most of the studies reviewed indicate that the built environment factors that were positively associated with cognitive function in older adults were population density, street connectivity, walkability, number of public transportation stops around the residence, land use mix, neighborhood resources, green space, and quality of the neighborhood built environment. Built environment factors that were negatively associated with cognitive function in older adults were street integration, distance from residence to main road. The relationship between residential density, destination accessibility, and blue space with cognitive function in older adults needs to be further explored. CONCLUSION: Preliminary evidence suggests an association between the neighborhood built environment and cognitive function in older adults. The causal relationship between the built environment and cognitive function can be further explored in the future using standardized and combined subjective and objective assessment methods, and longitudinal or quasi-experimental study designs. For public health interventions on the cognitive health of older adults, it is recommended that relevant authorities include the neighborhood built environment in their intervention programs.

Multi-omics analysis identifies rare variation in leptin/PPAR gene sets and hypermethylation of ABCG1 contribute to antipsychotics-induced metabolic syndromes.

Antipsychotic-induced metabolic syndrome (APs-induced Mets) is the most common adverse drug reaction, which affects more than 60% of the psychiatric patients. Although the etiology of APs-induced Mets has been extensively investigated, there is a lack of integrated analysis of the genetic and epigenetic factors. In this study, we performed genome-wide, whole-exome sequencing (WES) and epigenome-wide association studies in schizophrenia (SCZ) patients with or without APs-induced Mets to find the underlying mechanisms, followed by in vitro and in vivo functional validations. By population-based omics analysis, we revealed that rare functional variants across in the leptin and peroxisome proliferator-activated receptors (PPARs) gene sets were imbalanced with rare functional variants across the APs-induced Mets and Non-Mets cohort. Besides, we discovered that APs-induced Mets are hypermethylated in ABCG1 (chr21:43642166-43642366, adjusted P < 0.05) than Non-Mets, and hypermethylation of this area was associated with higher TC (total cholesterol) and TG (triglycerides) levels in HepG2 cells. Candidate genes from omics studies were furtherly screened in C. elegans and 17 gene have been verified to associated with olanzapine (OLA) induced fat deposit. Among them, several genes were expressed differentially in Mets cohort and APs-induced in vitro/in vivo models compared to controls, demonstrating the validity of omics study. Overexpression one of the most significant gene, PTPN11, exhibited compromised glucose responses and insulin resistance. Pharmacologic inhibition of PTPN11 protected HepG2 cell from APs-induced insulin resistance. These findings provide important insights into our understanding of the mechanism of the APs-induced Mets.

Epidemiology of healthcare-associated infections and outcomes among open and robotic pancreatoduodenectomy: A retrospective study from 2013 to 2022.

BACKGROUND AND AIM: Healthcare-associated infections (HAIs) after pancreaticoduodenectomy (PD) are one of the common postoperative complications. This study aims to investigate the epidemiology of postoperative HAIs in patients with open pancreaticoduodenectomy (OPD) and robotic pancreaticoduodenectomy (RPD). METHODS: This retrospective cohort study described the trend of HAIs in patients undergoing PD from January 2013 to December 2022 at a tertiary hospital. Patients were divided into OPD and RPD, and the HAIs and outcomes were compared. RESULTS: Among 2632 patients who underwent PD, 230 (8.7%, 95% confidence interval [CI] 7.7-9.9%) were diagnosed with HAIs, with a decreasing trend from 2013 to 2022 (P < 0.001 for trend). The incidence of postoperative HAIs was significantly higher in patients with OPD than RPD (9.6% vs 5.8%; P = 0.003). The incidence of HAIs for patients with OPD showed a decreasing trend (P = 0.001 for trend), and the trend for RPD was not significant (P = 0.554 for trend). Logistic regression showed that RPD was significantly associated with postoperative HAIs after adjusting for covariates (adjusted odds ratio = 0.654; 95% CI 0.443-0.965; P = 0.032), especially in the subgroup of patients without preoperative biliary drainage (adjusted odds ratio = 0.486; 95% CI 0.292-0.809; P = 0.006). Regarding clinical outcomes, RPD has a shorter length of stay and a more expensive charge than OPD (all P < 0.05). CONCLUSION: Postoperative HAIs in patients with PD showed a decreasing trend in recent years, especially in OPD. RPD was significantly associated with reduced postoperative HAIs and length of stay, although the charge is more expensive. Attention should be paid to postoperative HAIs in OPD, and it is imperative to continue reducing the costs of RPD.

The relationship between sleep status and activity of daily living: based on China Hainan centenarians cohort study.

OBJECTIVE: This study, based on the China Hainan Centenarians Cohort Study (CHCCS), aims to comprehensively describe the characteristic of daytime, night and total sleep duration, sleep quality and different sleep mode of Hainan centenarians and their associations with activity of daily living (ADL) functions. METHOD: The baseline data of CHCCS was used. ADL function was evaluated the Bathel index, sleep quality was evaluated by Pittsburgh sleep quality index (PSQI), sleep status including daytime, night and total sleep duration as well as sleep quality and sleep mode. Multivariate logistic regression model was used to explore the association between sleep status and ADL disability and ADL moderate & severe disability. RESULTS: A total of 994 centenarians were included in this study with the age range 100-116 years old. Compared with the centenarians who sleep 6-9 h at night and < 2 h in the daytime, the adjusted OR between sleep > 9 h at night and sleep ≥ 2 h in the daytime and ADL disability was 2.93 (95% CI: 1.02-8.44), and adjusted OR of ADL moderate & severe disability was 2.75 (95% CI: 1.56-4.83). Compared with centenarians who sleep for 7-9 h and have good sleep quality, centenarians who sleep for > 9 h and have poor sleep quality have an increased risk of ADL moderate & severe disability (OR = 3.72, 95% CI: 1.54-9.00). CONCLUSION: Relation between sleep duration and ADL disability was more significant compared with sleep quality in Hainan centenarians. Poor sleep quality can aggravate the relationship between sleep duration and ADL moderate & severe disability.

Genome-wide analysis of tandem duplicated genes and their contribution to stress resistance in pigeonpea (Cajanus cajan).

Pigeonpea is the main protein source for more than one billion people, and it shows a strong adaptation to biotic stress and abiotic stress. Gene duplication is a fundamental process in genome evolution. Although the draft sequence of the pigeonpea genome has been available since 2011, further analysis of tandem duplicated genes (TDGs) and their contribution to the evolution of pigeonpea has not been reported. In this study, we identify 3211 TDGs in the pigeonpea genome and KEGG enrichment analysis of these genes shows that the TDGs are significantly enriched in resistance-related pathways. In addition, we find that TDGs are more abundant in retrotransposon-related genes in pigeonpea than in the other species included in our study. These results indicate that stress resistance in pigeonpea may be ascribed to resistance-related pathways and retrotransposons originating from tandem duplications. Our study will provide an important basis for further research in pigeonpea breeding.

Metabolic alterations provide insights into Stylosanthes roots responding to phosphorus deficiency.

BACKGROUND: Phosphorus (P) deficiency is one of the major constraints limiting plant growth, especially in acid soils. Stylosanthes (stylo) is a pioneer tropical legume with excellent adaptability to low P stress, but its underlying mechanisms remain largely unknown. RESULTS: In this study, the physiological, molecular and metabolic changes in stylo responding to phosphate (Pi) starvation were investigated. Under low P condition, the growth of stylo root was enhanced, which was attributed to the up-regulation of expansin genes participating in root growth. Metabolic profiling analysis showed that a total of 256 metabolites with differential accumulations were identified in stylo roots response to P deficiency, which mainly included flavonoids, sugars, nucleotides, amino acids, phenylpropanoids and phenylamides. P deficiency led to significant reduction in the accumulation of phosphorylated metabolites (e.g., P-containing sugars, nucleotides and cholines), suggesting that internal P utilization was enhanced in stylo roots subjected to low P stress. However, flavonoid metabolites, such as kaempferol, daidzein and their glycoside derivatives, were increased in P-deficient stylo roots. Furthermore, the qRT-PCR analysis showed that a set of genes involved in flavonoids synthesis were found to be up-regulated by Pi starvation in stylo roots. In addition, the abundances of phenolic acids and phenylamides were significantly increased in stylo roots during P deficiency. The increased accumulation of the metabolites in stylo roots, such as flavonoids, phenolic acids and phenylamides, might facilitate P solubilization and cooperate with beneficial microorganisms in rhizosphere, and thus contributing to P acquisition and utilization in stylo. CONCLUSIONS: These results suggest that stylo plants cope with P deficiency by modulating root morphology, scavenging internal Pi from phosphorylated metabolites and increasing accumulation of flavonoids, phenolic acids and phenylamides. This study provides valuable insights into the complex responses and adaptive mechanisms of stylo roots to P deficiency.

Multicenter surveillance study of surgical site infection and its risk factors in radical resection of colon or rectal carcinoma.

BACKGROUND: Colorectal surgery is associated with high rates of surgical site infection (SSI). We investigated SSI in radical resection of colon or rectal carcinoma and its epidemiological distribution in 26 hospitals in China. METHODS: We conducted prospective surveillance of patients who underwent radical resection of colon or rectal carcinoma in 26 selected hospitals from January 2015 to June 2016.An information system monitored all of the surgical inpatients. Infection control professionals observed the inpatients with suspected SSI who had been screened by the system at the bedside. The infection status of the incisions was followed up by telephone 1 month after the operation. RESULTS: In total, 5729 patients were enrolled for the two operations; SSIs occurred in 206 patients, and the infection rate was 3.60%. The incidence of SSI after radical resection of rectal carcinoma (5.12%; 119/2323) was 2.1 times higher than that after radical resection of colon carcinoma (2.55%; 87/3406) (P < 0.0001). Additionally, in the colon versus rectal groups, the rate of superficial incisional SSI was 0.94% versus 2.28% (P < 0.0001), the rate of deep incisional SSI was 0.56% versus 1.11% (P = 0.018), and the rate of organ space SSI was 1.06% versus 1.72% (P = 0.031), respectively. The most common pathogens causing SSIs after radical resection of colon carcinoma were Escherichia coli (21/38) and Pseudomonas aeruginosa (5/38). Escherichia coli (24/65) and Enterococcus spp. (14/65) were the two most common pathogens in the rectal group. The multivariate logistic regression analysis showed that only the operating time and number of hospital beds were common independent risk factors for SSIs after the two types of surgery. CONCLUSION: This multicenter study showed that there were significant differences in the incidence of SSIs, three types of SSIs, and some risk factors between radical resection of colon carcinoma and rectal carcinoma.

The prevalence and clinical characteristics of tick-borne diseases at One Sentinel Hospital in Northeastern China.

Northeastern China is a region of high tick abundance, multiple tick-borne pathogens and likely human infections. The spectrum of diseases caused by tick-borne pathogens has not been objectively evaluated in this region for clinical management and for comparison with other regions globally where tick-transmitted diseases are common. Based on clinical symptoms, PCR, indirect immunofluorescent assay and (or) blood smear, we identified and described tick-borne diseases from patients with recent tick bite seen at Mudanjiang Forestry Central Hospital. From May 2010 to September 2011, 42% (75/180) of patients were diagnosed with a specific tick-borne disease, including Lyme borreliosis, tick-borne encephalitis, human granulocytic anaplasmosis, human babesiosis and spotted fever group rickettsiosis. When we compared clinical and laboratory features to identify factors that might discriminate tick-transmitted infections from those lacking that evidence, we revealed that erythema migrans and neurological manifestations were statistically significantly differently presented between those with and without documented aetiologies (P < 0.001, P = 0.003). Twelve patients (6.7%, 12/180) were co-infected with two tick-borne pathogens. We demonstrated the poor ability of clinicians to identify the specific tick-borne disease. In addition, it is necessary to develop specific laboratory assays for optimal diagnosis of tick-borne diseases.

Study on age-dependent pre-existing 2009 pandemic influenza virus T and B cell responses from Chinese population.

BACKGROUND: The outbreak of the 2009 H1N1 influenza pandemic (H1N1pdm) affected thousands of people in Mexico and the United States, and spread rapidly throughout the world from April 2009 to July 2010. To explore the age-specific prevalence of seroprotection against H1N1pdm infection, we estimated pre-existing humoral and cellular immunities of residents in Northern China against H1N1pdm and seasonal H1N1 virus in an age-dependent manner. METHODS: Anonymous serum samples were collected from 1425 to 1434 adult healthy individuals before and after the pandemic outbreak, and then grouped by birth year 1913-1990. The antibody titers of H1N1pdm and seasonal H1N1 were determined using microneutralization (MN) assays, and the proportion of seropositive was estimated based on the year of birth. Separately, another 63 blood samples were collected in 2006 and prepared for analysis of virus specific memory B and IFN-γ+ T cells using the ELISpot assays. RESULTS: The prevalence of pre-existing H1N1pdm-specific sero-antibodies in the elderly population (>60 years old) was 7.8%. The younger group, aged 19 to 60 years, exhibited a significant increase in seropositivity for H1N1pdm after the pandemic (4.9% before pandemic and 18.9% after pandemic, p < 0.05). The prevalence of H1N1pdm specific MBCs before the pandemic in the elderly (>60 years) and younger populations (<60 years) was 38% (8/21) and 48% (20/42), respectively (p = 0.6). The IFN-γ+ T cell responses to the pandemic and seasonal viruses were significantly lower in the elder group than those in the younger group (<60 years) (p < 0.05). CONCLUSIONS: Pre-existing serum antibodies and memory B cells against H1N1pdm were low in all age group, whereas diminished memory T cell responses to this virus were observed in the elderly population both before and after the pandemic.

Neohesperidin Exerts Lipid-Regulating Effects in vitro and in vivo via Fibroblast Growth Factor 21 and AMP-Activated Protein Kinase/Sirtuin Type 1/Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1α Signaling Axis.

The purpose of this study is to prove the lipid-regulating effects of neohesperidin (NHP) and explore the potential mechanisms related to fibroblast growth factor 21 (FGF21) and AMP-activated protein kinase (AMPK). Free fatty acids (FFAs)-induced lipid-accumulated HepG2 cells, acutely egg yolk-induced dyslipidemia and chronically diet-induced obese (DIO) model mice were treated with NHP. Biochemical analyses were carried out to determine the lipid profiles. Western blotting and real-time PCR were employed to analyze FGF21, AMPK and the related proteins or mRNA expressions. Body weight and food intake were measured in DIO mice. siRNA or inhibitors of FGF21 or AMPK were utilized in further study. NHP showed potent hypolipidemic effect in HepG2 cells loaded with FFAs and reversed the pathological changes of lipid in the acute or chronic dyslipidemia mouse model. It obviously improved the lipid profiles in plasma, liver and gastrocnemius muscles in DIO mice, and led to a significant body weight loss. Simultaneously, FGF21 protein expression or secretion, and AMPK/sirtuin type 1 (SIRT1)/peroxisome proliferator-activated receptor gamma coactivator 1α (PGC-1α) axis or related molecules, was improved by NHP in HepG2 cells and/or DIO mice. Furthermore, the siRNA or inhibitor targeting FGF21 or AMPK rejected the triglyceride-lowering effect of NHP. In conclusion, NHP regulates lipid metabolism in vivo and in vitro via FGF21 and AMPK/SIRT1/PGC-1α signaling axis.

Nosocomial Bloodstream Infection Due to Candida spp. in China: Species Distribution, Clinical Features, and Outcomes.

OBJECTIVES: To investigate the distribution of Candida spp., predictors of mortality, and effects of therapeutic measures on outcomes of nosocomial bloodstream infection (BSI) due to Candida spp. METHODS: This retrospective, population-based study enrolled adult patients with Candida nosocomial BSI from January 2010 to December 2014 in one tertiary care hospital. The demographics, comorbidities, species distribution, risk factors, and effects of antifungal treatment were assessed. RESULTS: In total, 190 episodes of Candida BSI were identified. The most prevalent species was C. albicans (38.9 %), followed by C. parapsilosis (23.2 %) and C. tropicalis (20.5 %). In vitro susceptibility testing showed that 88.9 % of Candida isolates were susceptible to fluconazole. The 30-day hospital mortality was 27.9 %, while the early mortality (within 7 days) was 16.3 %. In a multivariate regression analysis, the Acute Physiology and Chronic Health Evaluation II score [odds ratio (OR) 1.23; 95 % confidence interval (CI) 1.080-1.390; P = 0.002] and severe sepsis or septic shock (OR 15.35; 95 % CI 2.391-98.502; P = 0.004) were independently correlated with early mortality. Severe sepsis or septic shock (OR 24.75; 95 % CI 5.099-120.162; P < 0.001) was an independent risk factor for 30-day mortality, while proven catheter-related candidemia (OR 0.16; 95 % CI 0.031-0.810; P = 0.027) was a positive factor for 30-day mortality. Early central venous catheter removal and adequate antifungal treatment were closely related to decreased mortality in patients with primary candidemia. CONCLUSION: The proportion of candidemia caused by C. albicans was lower than that caused by non-albicans species. The severity of illness influenced early mortality, and the origin of the central venous catheter remarkably affected 30-day mortality.

Real-time automatic hospital-wide surveillance of nosocomial infections and outbreaks in a large Chinese tertiary hospital.

BACKGROUND: We aimed to develop a real-time nosocomial infection surveillance system (RT-NISS) to monitor all nosocomial infections (NIs) and outbreaks in a Chinese comprehensive hospital to better prevent and control NIs. METHODS: The screening algorithm used in RT-NISS included microbiological reports, antibiotic usage, serological and molecular testing, imaging reports, and fever history. The system could, in real-time, identify new NIs, record data, and produce time-series reports to align NI cases. RESULTS: Compared with a manual survey of NIs (the gold standard), the sensitivity and specificity of RT-NISS was 98.8% (84/85) and 93.0% (827/889), with time-saving efficiencies of about 200 times. RT-NISS obtained the highest hospital-wide monthly NI rate of 2.62%, while physician and medical record reviews reported rates of 1.52% and 2.35% respectively. It took about two hours for one infection control practitioner (ICP) to deal with 70 new suspicious NI cases; there were 3,500 inpatients each day in the study hospital. The system could also provide various updated data (i.e. the daily NI rate, surgical site infection (SSI) rate) for each ward, or the entire hospital. Within 3 years of implementing RT-NISS, the ICPs monitored and successfully controlled about 30 NI clusters and 4 outbreaks at the study hospital. CONCLUSIONS: Just like the "ICPs' eyes", RT-NISS was an essential and efficient tool for the day-to-day monitoring of all NIs and outbreak within the hospital; a task that would not have been accomplished through manual process.

One-step electrodeposition of MWCNTs-Cu MOF films for the ratiometric electrochemical analysis of glyphosate.

Sensitive and accurate determination of glyphosate (GLYP) is vital for food safety and environmental protection. Herein, a novel electrochemical ratiometric biosensor was designed for the accurate quantification of GLYP through one-step electrodeposition of MWCNTs-Cu MOF films. MWCNTs-Cu MOF nanostructures were directly electro-synthesized in situ on the electrode from the precursor solution. The combination of Cu MOFs with MWCNTs not merely improved the conductivity of MOFs, but also enhanced the sensitivity of the biosensor. Furthermore, Cu sites within Cu MOFs were turned into CuCl to further amplify the current signal and enable the specific recognition of GLYP through competing reactions with the transformation of CuCl into non-electroactive Cu-GLYP. Meanwhile, internal reference molecules of methylene blue (MB) were incorporated to improve the measurement accuracy of GLYP for reducing unpredictable measurement errors aroused by environmental deviations. The ratiometric electrochemical sensor exhibited a high linearity with the logarithmic value of GLYP concentration from 0.5 nM to 400 nM. The detection limit was estimated to be as low as 0.014 nM. Finally, the present sensor with ratiometric signal export was applied for GLYP analysis in real samples with high sensitivity and accuracy. The simplicity and reliability of the ratiometric sensor make it a worthy and powerful tool for food and environmental monitoring. This design strategy also provides an avenue for the development of simple and efficient biosensors for other substances.

Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater.

Wastewater surveillance for SARS-CoV-2 provides early warnings of emerging variants of concerns and can be used to screen for novel cryptic linked-read mutations, which are co-occurring single nucleotide mutations that are rare, or entirely missing, in existing SARS-CoV-2 databases. While previous approaches have focused on specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and investigating their potential origin. We present Crykey, a tool for rapidly identifying rare linked-read mutations across the genome of SARS-CoV-2. We evaluated the utility of Crykey on over 3,000 wastewater and over 22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations in wastewater that represent potential circulating cryptic lineages, serving as a new computational tool for wastewater surveillance of SARS-CoV-2.

Elucidating important factors and corresponding method optimization for sensitive detection of small peptide drugs in human urine by solid-phase extraction and UPLC-HRMS: The influence of MS scan modes, protein precipitants, and ammonium formate.

Small peptide hormones are widely used in sports as performance-enhancing substances, making it crucial to develop sensitive analytical methods for their detection in doping control analysis. Various factors significantly affect analytical sensitivity, such as the selection of ultra-performance liquid chromatography (UPLC) mobile phase, high-resolution mass spectrometry (HRMS) scanning modes, and extraction solvents for pretreatment. Herein, comparative study approach was utilized to investigate the sensitivity of each peptide analyte under both full scan and parallel reaction monitoring (PRM) modes of HRMS and assess the effects of some protein precipitants as a part of extraction solvents on solid-phase extraction (SPE). The results showed that full scan should be selected as the primary scan mode of HRMS, and the combination with PRM mode could effectively compensate for the limitations of full scan, and the addition of protein precipitants would adversely affect the detection of certain small peptide analytes. Meanwhile, influences of ammonium formate in reverse UPLC mobile phase on the charge state distribution of small peptides were investigated and elucidated. Based on these findings, a sensitive and reliable UPLC-HRMS analytical method combining full scan and PRM mode was validated for screening and confirmation of 63 small peptide analytes after SPE, with limits of detection (LODs) ranging between 0.010 and 0.473 ng/ml and limits of identification (LOIs) ranging between 0.015 and 1.512 ng/ml. Additionally, suggestions were provided for the detection of [Arg8]-vasopressin, dermorphin, and its analogues.

Epidemiology and risk factors of nosocomial infections in a Chinese tertiary-care hospital: a 10-year retrospective case-control study.

BACKGROUND: Nosocomial infections (NIs) are the most frequent adverse events among patients and cause a heavy burden on both health and economics. To investigate epidemiology of NIs and identify risk factors for NIs by integrating continuous long-term surveillance data. METHODS: We performed an observational study among inpatients at the Chinese People's Liberation Army General Hospital between January 1, 2010, and December 31, 2019. Infection rates, mortality rates and percentage of NIs were calculated. Trends of yearly infection rates by pathogens were assessed using Mann-Kendall trend test. Controls were matched to cases (2:1) by age (±2 years), sex, admission date (±1 year) and admission diagnosis, and conditional logistic regression was used to estimate odds ratios. RESULTS: A total of 1,534,713 inpatients were included among which 33,468 NIs cases occurred with an infection rate of 2.18%. The most common infections were respiratory system infection (52.22%), bloodstream infection (17.60%), and genitourinary system infection (15.62%). Acinetobacter. baumannii (9.6%), Klebsiella. pneumoniae (9.0%), Pseudomonas. aeruginosa (8.6%), Escherichia. coli (8.6%) and Enterococcus. faecium (5.0%) were the top five isolated pathogens. Infection rates of K. pneumoniae and carbapenems-resistant K. pneumoniae significantly increased. Prior ICU stay, surgery, any device placement (including central venous catheter, mechanical ventilation, urinary catheter, and tracheotomy), prior use of triple or more antibiotics combinations, carbapenem, and ß-Lactamase inhibitors were significantly associated with NIs. CONCLUSION: K. pneumoniae has the potential to cause a clinical crisis with increasing infection rates and carbapenem resistance. Clinical management of invasive operations and antibiotics use should be further strengthened.

Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet.

Taxonomic profiling is a ubiquitous task in the analysis of clinical and environmental microbiomes. The advent of long-read sequencing of microbiomes necessitates the development of new taxonomic profilers tailored to long-read shotgun metagenomic datasets. Here, we introduce Lemur and Magnet, a pair of tools optimized for lightweight and accurate taxonomic profiling from long-read shotgun metagenomic datasets. Lemur is a marker-gene based method that leverages an EM algorithm to reduce false positive calls while preserving true positives; Magnet makes detailed presence/absence calls for bacterial genomes based on whole-genome read mapping. The tools work in sequence: Lemur estimates abundances conservatively, and Magnet operates on the genomes of identified organisms to filter out likely false positive taxa. The result is an increase in precision of as much as 70%, which far exceeds competing methods. By operating only on marker genes, Lemur is a comparatively lightweight software. We demonstrate that it can run in minutes to hours on a laptop with 32 GB of RAM, even for large inputs - a crucial feature given the portability of long-read sequencing machines. Furthermore, the marker gene database used by Lemur is only 4 GB and contains information from over 300,000 RefSeq genomes. The reference is available at https://zenodo.org/records/10802546, and the software is open-source and available at https://github.com/treangenlab/lemur.

Retrospective Analysis of Epidemiology, Risk Factors, and Outcomes of Health Care-Acquired Carbapenem-Resistant Klebsiella pneumoniae Bacteremia in a Chinese Tertiary Hospital, 2010-2019.

INTRODUCTION: In the present study, we aimed to describe the proportion of carbapenem-resistant Klebsiella pneumoniae bloodstream infection (CRKP-BSI) in KP-BSI in one Chinese tertiary hospital over 10 years and determine the risk factors and outcomes of CRKP-BSI. METHODS: We retrospectively analyzed clinical and microbiological data of patients with KP-BSI from January 2010 to December 2019 to identify risk factors, clinical features, and outcomes using multivariate logistic regression analysis. KP-BSI only included monomicrobial BSI and health care-acquired BSI. RESULTS: Among the total 687 isolates of KP-BSI in this study, the rate of CRKP was 39.0% (268/687); this rate in the intensive care unit (ICU) was 65.6% and that in seven high-risk departments (including four ICUs, respiratory medicine, gastroenterology medicine, and hepatobiliary surgery) was 74.6%. The annual rate of CRKP in KP-BSI ranged from 0.0% in 2010 to 54.5% in 2019. The 28-day mortality was 36.2% in patients with CRKP-BSI and 11.7% in those with carbapenem-susceptible K. pneumoniae (CSKP) BSI. Multivariable logistic regression analysis showed that prior ICU stay (odds ratio [OR] 2.485, P < 0.001), hospital stay ≥ 30 days prior to BSI (OR 1.815, P = 0.007), prior mechanical ventilation (OR 2.020, P = 0.014), prior urinary catheter (OR 1.999, P = 0.003), prior carbapenem use (OR 3.840, P < 0.001), hepatobiliary disease (OR 2.943, P < 0.001), pancreatitis (OR 2.700, P = 0.026), and respiratory disease (OR 2.493, P = 0.009) were risk factors of CRKP-BSI. Patients with a first admission (OR 0.662, P = 0.046) had a lower percentage of CRKP-BSI. CONCLUSION: The rapidly rising rate of CRKP-BSI in KP with high mortality requires increased attention. Exposure to carbapenems, ICU stay, invasive mechanical ventilation or urinary catheter, prolonged hospital stay, hepatobiliary disease, pancreatitis, and respiratory disease were found to be risk factors for CRKP-BSI. Strict control measures should be implemented to prevent the emergence and spread of CRKP, especially in high-risk departments.