We investigated the infectivity of 128 severe acute respiratory disease coronavirus 2–associated deaths and evaluated predictive values of standard diagnostic procedures. Maintained infectivity (20%) did not correlate with viral RNA loads but correlated well with anti-S antibody levels. Sensitivity >90% for antigen-detecting rapid diagnostic tests supports their usefulness for assessment. Deaths associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have raised concerns that contact with the corpses of deceased persons might pose a risk for transmitting infection   , panel Apies/mL) , panel B7 copies/mL, IQR 3.7 × 104–3.3 × 108) among culture-positive corpses did not differ significantly from PMI  and RNA loads  among culture-negative corpses (4 copies/mL), in contrast with previous findings among living patients , indicative of potentially decreased infectivity.Virus isolation proved infectivity was maintained in 26/128 (20%) corpses . PMI  (We confirmed seroconversion in 18/44 (41%) blood samples, 15/43 (35%) anti-nucleocapsid positive and 17/44 (39%) anti-spike positive  , panel C = 0.23) , panel Chttps://www.abbott.com), sensitivity was 80.3% (95% CI 72.3%–86.4%) and specificity 100.0% (95% CI 95.0%–100.0%); for the SARS-CoV-2 Rapid Antigen Test (Roche https://www.roche.com), sensitivity was 86.4% (95% CI 79.1%–91.9%) and specificity 98.6% (95% CI 93.0%–100.0%); and for the SARS-CoV-2 Antigen Rapid Test (MEDsan https://www.medsan.eu), sensitivity was 84.1% (95% CI 76.6%–90.0%) and specificity 95.8% (95% CI 88.0%–99.0%) .Antigen-detecting rapid diagnostic tests (Ag-RDTs) are considered adequate alternative swift diagnostic tools in living patients (6 RNA copies/mL (n = 74) revealed 100% (95% CI 95.1%–100.0%) sensitivity in Abbott (n = 74) and Roche and MEDsan (n = 73 each) assays. In contrast, neither PMI (p = 0.34) nor putrefactive changes (p = 0.90) were predictive for testing positive in Ag-RDTs . Ag-RDT sensitivity in infectious corpses was 92.3% (95% CI 74.9%–99.1%) for Abbott, 96.2% (95% CI 80.4%–99.9%) for Roche, and 96.2% (95% CI 80.4%–99.9%) for MEDsan. We detected 2 SARS-CoV-2 variants of concern despite relatively low viral RNA loads (4.83 log10); the 2 samples tested positive by Abbott and Roche but were missed by MEDsan.We found SARS-CoV-2 RNA load correlated with Ag-RDT positivity in univariate and multivariate analyses (p<0.001), thereby confirming their predictive value (The first limitation of our study is that blood was not available from all corpses, and the serologic assays and Ag-RDTs used are not approved for cadaveric samples. Furthermore, because of a shortage of reagents and supplies, we had to use different tests to quantify RNA, and slight deviations cannot be ruled out.In summary, we show that cadavers from SARS-CoV-2–associated deaths remain infectious long after death in a considerable proportion of cases. Postmortem infectivity does not correlate with PMI or viral RNA load but correlates with the absence of virus-specific antibodies. Ag-RDTs performed well, enabling rapid on-site detection. Because previous studies among living patients indicate that Ag-RDTs reliably detect all SARS-CoV-2 variants (Additional information about study of infectivity of cadavers from SARS-COV-2 deaths


Klebsiella pneumoniae (hvKp), unlike classical K. pneumoniae (cKp), are often responsible for community-acquired infections in otherwise healthy individuals. The acquisition of hypervirulence genes by sequence type 11 (ST11) carbapenem-resistant (CR) Kp endemic in Asia is a grave threat. Aztreonam-avibactam (ATM-AVI) is a monobactam combined with a β-lactamase inhibitor for the treatment of infections caused by Enterobacterales isolates that carry Class A, B, C and some Class D β-lactamases.Hypervirulent K. pneumoniae isolates were collected from 17 sites in China in 2019 as a part of the ATLAS global surveillance study. 220 isolates with MICs >1 µg/ml to meropenem (MEM), ceftazidime or ATM were selected for whole genome sequencing (Illumina Hiseq 2x150 bp reads). Analyses were carried out using the CLC Genomics Workbench (Qiagen). Presence of the aerobactin synthesis locus differentiated hvKp and cKp. Antimicrobial susceptibility was determined by CLSI broth microdilution.487 90 values for ATM-AVI  were lower than those for any comparator tested, with only two isolates testing with MIC >4 µg/ml. Of the isolates sequenced, 82/220 (37.3%) were ST11. 53/82 (64.6%) of these ST11 isolates were hvKp  and showed percentages of susceptibility < 90% to three last-line agents (0% MEM-susceptible (S); 18.9% amikacin (AMK)-S; 88.7% tigecycline (TGC)-S). Isolates of other STs (Non-ST11) were less frequently identified as hvKp  and more Non-ST-11 hvKp and cKp alike were S to MEM and AMK relative to isolates of ST11 . Likewise, the ATM-AVI MIC90 value (0.25 µg/ml) was 4-fold lower for Non-ST11 isolates.Of the 487 isolates, MICResults Tablein vitro activity against these isolates which displayed resistance to a range of last-line agents. CST and TGC also displayed some activity but are limited in utility due to nephrotoxicity and poor accumulation in blood, respectively. The spread of virulence factors leading to the complicated clinical presentation of hvKp infection into multidrug-resistant lineages warrants continued surveillance.CR ST11 hvKp represented at least 10.9% of the collected Kp isolates. ATM-AVI retained potent Mark Estabrook, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Krystyna Kazmierczak, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Francis Arhin, PhD, Pfizer, Inc. (Employee) Daniel F. Sahm, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor)


During the COVID-19 pandemic, a task force was assembled to collect data on patient characteristics and treatment exposures to assess what factors may contribute to patient outcomes, and to help develop institutional treatment guidelines. apriori. Covariates of interest included baseline comorbidities, admission level-of-care, vital signs, mortality outcomes, need for intubation, and specific pharmacological treatment exposures. Logistic regression was performed on our final model and reported as OR +/- 95% CI. A retrospective study was performed on COVID-19 inpatient admissions within a four-hospital community health system over a six-month period from April-October 2020. Positive COVID-19 immunology results and/in conjunction with an inpatient admission was criteria for inclusion. Covariates for age, gender, race were added A total of 349 patients met inclusion criteria. Pharmacotherapies were not associated with a difference in mortality in a four-hospital system. Corticosteroids (p = 0.99); Remdesivir (p = 0.79); hyrdroxychloroquine (p = 0.32); tocilizumab (p = 0.91); were not associated with mortality. ACE-inhibitor or angiotensin II receptor blockers OR 0.29 (0.09-0.93) (p = 0.03); convalescent plasma OR 7.85 (1.47-42.1) (p = 0.02); neuromuscular blocking agents (NMBA) OR 5.51 (1.28-23.8) (p = 0.02); vasopressors OR 17.6 (5.62-54.9) (p = 0.00) were associated with in-hospital mortality. Covariates that were associated with a difference in mortality were: age > 60 years OR 2.73 (1.04-7.14) (p = 0.04); structural lung disease OR 3.02 (1.28-7.10) (p = 0.01). Covariates not associated with mortality included African American race (p = 0.30); critical care admission (p = 0.19); obesity (p = 0.06); cardiovascular disease (p = 0.89); diabetes (p = 0.28).The use of corticosteroids, remdesivir, tocilizumab, and hydroxychloroquine, and admission to a critical care bed was not associated with a difference of in-hospital mortality. Patients who required vasopressors or NMBA were associated with in-hospital mortality. Despite national trends reporting increased mortality in patients with obesity, diabetes, cardiovascular disease, and of African American race, this was not observed in our health system safety net hospitals. All Authors: No reported disclosures


Achromobacter spp. is intrinsically resistant to multiple antibiotics, and the treatment options are limited. Cefiderocol (CFDC), a siderophore cephalosporin approved in US and EU, is active against a wide variety of aerobic Gram-negative bacteria, including carbapenem-resistant strains. In this study, in vitro and in vivo antibacterial activity of CFDC against Achromobacter spp. was evaluated.In vivo efficacy of CFDC was compared with meropenem (MEM), piperacillin-tazobactam (PIP/TAZ), ceftazidime (CAZ), and ciprofloxacin (CIP) in a neutropenic murine lung infection model (n=5), and compared with MEM in a immunocompetent rat lung infection model (n=3-7) caused by 2 A. xylosoxydans. In the murine model, treatment was given 2, 5, and 8 hours post-infection, and the numbers of viable cfu in lungs were determined 24 hours post-infection. In the rat model, the humanized PK in plasma resulting from CFDC 2 g every 8 h (3-h infusion) or meropenem 1 g every 8 h (0.5-h infusion) were recreated via continuous intravenous infusion for 4 days, following which cfu in lungs were determined.A total of 334 global isolates collected by IHMA from 39 countries in 2015-2019 were used. Minimum inhibitory concentrations (MICs) of CFDC and comparators were determined by broth microdilution method using iron-depleted CAMHB or CAMHB, respectively, as recommended by CLSI guidelines. in vitro activity with MIC50/90 of 0.06/0.5 µg/mL against 334 Achromobacter spp. Only 7 isolates (2.1%) had MICs > 4 µg/mL. These were the lowest values among all compound tested (Table). In the murine model, CFDC caused > 1.5 log10 decrease of viable cfu in lungs at 100 mg/kg dose (%fT >MIC: < 50%) from baseline control against both of strains (CFDC MIC: 0.5 and 2 µg/mL) (P< 0.05). No decrease of cfu in lungs was observed for the comparators at 100 mg/kg . In the rat model, humanized CFDC dosing reduced the viable cfu by >1 log10 CFU/lung compared with baseline controls (P< 0.05). MEM showed no significant activity.CFDC showed In vitro activity of CFDC and comparator agents against Achromobacter spp.334 Achromobacter spp. isolates collected from 2015 and 2019. The majority of isolates tested were A. xylosoxidans , followed by A. insolitus , Achromobacter sp. , A. denitrificans , and A. piechaudii .in vivo efficacy reflecting in vitro activity against A. xylosoxidans. The results suggested that CFDC has the potential to be an effective therapeutic option for Achromobacter spp. infections.CFDC showed potent Ryuichiro Nakai, MSc, Shionogi TechnoAdvance Research & Co., Ltd. (Employee) Ayaka makino, BSc, Shionogi TechnoAdvance Research & Co., Ltd. (Employee) Toriko Yoshitomi, -, Shionogi TechnoAdvance Research & Co., Ltd. (Employee) Rio Nakamura, BSc, Shionogi TechnoAdvance Research & Co., Ltd. (Employee) Meredith Hackel, PhD MPH, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Miki Takemura, MS, SHIONOGI & CO., LTD. (Employee) Daniel F. Sahm, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Yoshinori Yamano, PhD, Shionogi (Employee)


Pseudomonas aeruginosa isolated from cystic fibrosis sputum. Short reads were de novo assembled into 190 contigs and scaffold assembled to a length of 6.26 Mbp. PhiSpy predicts that PA291 is free of prophages.Here, we report the genome sequence of PA291, a nonmucoid, multidrug-resistant strain of  Pseudomonas aeruginosa causes difficult-to-treat and often multidrug-resistant (MDR) infections, which severely impacts individuals with cystic fibrosis (CF) (sis (CF) , 2. CF psis (CF) . Phage tsis (CF) , 5; in pP. aeruginosa. The strain was named PA291 and found to have a nonmucoid phenotype, and a broth microdilution assay  revealed strong antibiotic resistance to ceftazidime (MIC > 16 μg/ml) and intermediate resistance to aztreonam , gentamicin , and meropenem . Moreover, PA291 was lysed by phages PAK_P1, E215, and E217, which are under investigation to treat P. aeruginosa infections  was cultured overnight on blood agar at 37°C, and matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry identified it as belonging to the species de novo assembled using SPAdes v3.14.1 (AE004091.2), W16407 (CP008869.2), VA-134 (CP013245.1), DVT779 (CP050330.1), SE5357 (CP054844.1), H47921 (CP008861.1), SE5443 (CP046405.1), PAO1161 (CP032126.1), PABL048 (CP039293.1), and PAC6 (CP053705.1). The quality and metrics were analyzed using QUAST v5.02   and alginate biosynthesis genes  , a polymyxin resistance gene (arnC), and a fosfomycin resistance gene (fosA). PhiSpy v4.2.6 (PA291 DNA extraction and purification was performed after overnight growth in Lennox broth (LB) at 37°C using the phenol-chloroform method . The DNA v3.14.1  into 190 v3.14.1  with the161 CP0326.1, PABLg, kinB)  were useP. aeruginosa strain isolated from CF sputum. The size of PA291 is consistent with that of other P. aeruginosa genomes, between 5.5 and 7 Mbp  under accession number SRR14436913. The RAST annotation of the genome is available on Zenodo (https://zenodo.org/record/5114517#.YPXHVehKguV). The genome sequence of P. aeruginosa PA291 was deposited in GenBank under accession number JAGYWJ000000000, where the Prokaryotic Genome Annotation Pipeline (PGAP) annotation is also available.Data for


Nosocomial pneumonia (NP) remains associated with excess morbidity and mortality. The effect of NP on other measures of outcome and quality, such as re-admission at 30 days, remains unclear. Moreover, differing types of NP may have varying impacts on re-admissions.We conducted a multicenter retrospective cohort study within the Premier Research database, a source containing administrative, pharmacy, and microbiology data. The rate of rehospitalization at 30 days following the index discharge served as our primary endpoint. We compared NP patients readmitted with pneumonia (RaP) as the principal diagnosis to those readmitted for other reasons (RaO). We also compared readmission rates as function of the type of NP: ventilator-associated bacterial pneumonia (VABP), ventilated hospital-acquired bacterial pneumonia (vHABP), and non-ventilated HABP (nvHABP).Among 17,819 patients with NP, 14,123 (79.3%) survived to discharge, of whom 2,151 (15.2%) required an acute readmission within 30 days of index discharge. Of these, 106 (4.9%) were RaP, and the remainder were RaO. At index hospitalization, RaP patients were older (mean age (SD) 67.4 (13.9] vs. 63.0 (15.2) years), more likely medical (44.3% vs. 36.7%), and less chronically ill (median [IQR] Charlson scores (3 [2-5] vs. 4 [2-5]) than persons with RaO. Bacteremia (10.4% vs. 17.5%), need for vasopressors (15.1% vs. 20.0%), dialysis (9.4% vs. 16.5%), and/or sepsis (9.4% vs. 16.5%) or septic shock 14.2% vs. 17.1%) occurred less frequently in the RaP group. With respect to NP type, nvHABP was most common in RaP (47.2%) and VABP in RaO (38.1%). One in seven survivors of a hospitalization complicated by NP requires an acute rehospitalization within 30 days. However, few of these readmissions had a principal diagnosis of pneumonia, irrespective of NP type. This suggests that short-term readmission does not capture the quality of care initially delivered to patients for their NP. Of the 5% of NP subjects with RaP, the plurality initially suffered from nvHABP. Marya Zilberberg, MD, MPH, Cleveland Clinic (Consultant)J&J (Shareholder)Lungpacer Merck (Grant/Research Support)scPharma (Consultant)Sedana Spero (Grant/Research Support) Brian Nathanson, PhD, Lungpacer (Grant/Research Support)Merck (Grant/Research Support)Spero (Grant/Research Support) Laura A. Puzniak, PhD, Merck & Co., Inc. (Employee) Andrew F. Shorr, MD, MPH, MBA, Merck (Consultant)


Children infected with SARS-CoV-2 often have mild or no symptoms, making symptom screening an ineffective tool for determining isolation precautions. As an infection control measure, universal pre-procedural and admission SARS-CoV-2 testing for pediatric patients was implemented in April and August 2020, respectively. Limited data exist on the utility screening programs in the pediatric population. We performed a retrospective cohort study of pediatric patients (birth to 18 years) admitted to a tertiary care academic medical center from April 2020 to May 2021 that had one or more SARS-CoV-2 point-of-care or polymerase chain reaction tests performed. We describe demographic data, positivity rates and repeat testing trends observed in our cohort.A total of 2,579 SARS-CoV-2 tests were performed among 1,027 pediatric inpatients. Of these, 51 tests (2%) from 45 patients (4.3%) resulted positive. Community infection rates ranged from 4.5-60 cases/100,000 persons/day during the study period. Hispanic patients comprised 16% of the total children tested, but were disproportionately overrepresented (40%) among those testing positive . Of 654 children with repeated tests, 7 (0.1%) converted to positive from a prior negative result. Median days between repeat tests was 12 (IQR 6-45), not necessarily performed during the same hospital stay. Five of these 7 patients had tests repeated < 3 days from a negative result, of which only 2 had no history of recent infection by testing performed at an outside facility. Pre-procedural tests accounted for 35% of repeat testing, of which 0.9% were positive. Repeated tests were most frequently ordered for patients in hematology/oncology (35%) and solid organ transplant/surgical (33%) wards, each with < 3% positive conversion rate. Notably, no hematopoietic stem cell transplant patients tested positive for SARS-CoV-2 during the study period.Pediatric SARS-CoV-2 Testing Distributed by Race/EthnicityThe positivity rate of universal pre-procedural and admission SARS-CoV-2 testing in pediatric patients was low in our inpatient cohort. Tests repeated < 3 days from a negative result were especially low yield, suggesting limited utility of this practice. Diagnostic testing stewardship in certain populations may be useful, especially as community infection rates decline.Michael J. Smith, MD, M.S.C.E, Merck (Grant/Research Support)Pfizer (Grant/Research Support) Rebekah W. Moehring, MD, MPH, UpToDate, Inc.


Staphylococcus aureus (MRSA) is a prominent colonizer in cystic fibrosis (CF) patients that causes acute pulmonary exacerbation (APE). Vancomycin is the first line treatment for APE of CF; however, optimal alternatives remain poorly defined. The goal of this study was to determine the safety and efficacy of ceftaroline in CF patients presenting with an APE caused by MRSA.Methicillin-resistant > 10% lower than the patient’s baseline. A positive MRSA culture within 90 days before or 21 days after hospital admission and receipt of > 7 days of either vancomycin or ceftaroline was required for inclusion. Patients were excluded for receipt of a lung transplant, > 48 hours of alternative MRSA therapy, renal replacement therapy, or an APE secondary to fungal or mycobacterium infection. The primary outcome was the return to > 90% of baseline lung function measured by discharge %FEV1 in comparison to baseline %FEV1.This study was a single-center, retrospective cohort study from January 1, 2011 to January 1, 2020. The study included adult CF patients admitted for APE with %FEV1 Clostridioides difficile infection 0 (0%) vs. 1 (3%), P = >0.99; or acute kidney injury 2 (9%) vs. 5 (15%), P = 0.69. Fifty-six patients were included in the analysis . There were no differences in baseline characteristics (Table 1). Eleven (50%) patients in the ceftaroline group and 19 (56%) in the vancomycin group met the primary outcome (P = 0.79) . FEV1 measurements at baseline, admission, and discharge were not different between treatments . Patients treated with ceftaroline had a longer length of stay during hospital admission, 14 days (IQR 13-14) vs.10 days (IQR 7-14), P = 0.01. Other secondary outcomes were similar between the ceftaroline and vancomycin groups, respectfully, including 30-day readmission rate, 6 (27%) vs. 12 (35%), P = 0.57; 30-day mortality, 0 (0%) vs. 2 (6%), P = 0.51; neutropenia 3 (12%) vs. 1 (3%), P = 0.29; Table 1. Baseline characteristics for ceftaroline and vancomycin treated patients1Lumacaftor/ivacaftor, tezacaftor/ivacaftor; 2Piperacillin/tazobactam, aminoglycoside, furosemide, contrast dye, lisinopril, NSAIDs, colistin, phenylephrine; 3Methimazole, sulfasalazine, trimethoprim/sulfamethoxazole; 4Albuterol, hypertonic saline, dornase alpha, azithromycin, ibuprofen, inhaled aminoglycoside, inhaled colistin, corticosteroid; 5Azithromycin, aminoglycoside, fluroquinolone, cephalosporin, carbapenem, piperacillin/tazobactam. Data represents n (%) unless noted. CFTR=cystic fibrosis transmembrane conductance regulator.Figure 1. %FEV1 trend from baseline to discharge in patients treated with ceftaroline or vancomycin(A) Percentage (%) of patients who met the primary outcome in each group; (B) Mean %FEV1 change between ceftaroline (square) and vancomycin (circle) with error bars representing standard deviationsThis study found no difference in safety and efficacy outcomes between vancomycin and ceftaroline. Our small cohort supports ceftaroline as an alternative agent for the treatment of MRSA mediated APE of CF. All Authors: No reported disclosures


Bambusa oldhamii Munro, known as “green bamboo”, is famous for its edible bamboo shoots and fast-growing timber. The green and yellow striped-culm B. oldhamii variety, named B. oldhamii f. revoluta W.T. Lin & J. Y. Lin, is an attractive system for researching the culm color variation of B. oldhamii.The clumping bamboo 1, GA3, GA4, and GA7 was performed using HPLC–MS/MS platforms.Millions of clean reads were generated and assembled into 604,900 transcripts, and 383,278 unigenes were acquired with RNA-seq technology. The quantification of ABA, IAA, JA, GAB. oldhamii f. revoluta. Phytohormone contents, especially GA1 and GA7, were higher in B. oldhamii. Approximately 21 transcription factors (TFs) were differentially expressed between the two groups: the bZIP, MYB, and NF-YA transcription factor families had the most DEGs, indicating that those TFs play important roles in B. oldhamii culm color variation. RNA-seq data were confirmed by quantitative RT-PCR analysis of the selected genes; moreover, phytohormone contents, especially those of ABA, GA1 and GA7, were differentially accumulated between the groups. Our study provides a basal gene expression and phytohormone analysis of B. oldhamii culm color variation, which could provide a solid fundamental theory for investigating bamboo culm color variation.Differential expression analysis showed that 449 unigenes were differentially expressed genes (DEGs), among which 190 DEGs were downregulated and 259 DEGs were upregulated in  Dendrocalamus latiflorus, Bambusa oldhamii, and Bambusa chungii; and running bamboos , such as Phyllostachys edulis  and fast-growing culm timber  (Paeonia suffruticosa (Rosa chinensis (m timber . B. oldholorata) , Paeoniaruticosa , and Roshinensis .Basidiomycota phylum; they comprise red to red-violet betacyanins and yellow-orange betaxanthins  and jasmonic acid (JA) could promote anthocyanin biosynthesis, while auxin and gibberellin (GA) could inhibit anthocyanin biosynthesis . Abscisike genes . JA treake genes . JA treake genes . The accke genes . The plake genes . GA3 incing time . Treatmeotenoids .MdDFR and MdUFGT and influence fruit coloration  were labeled LZ_1, LZ_2, and LZ_3, and those from B. oldhamii f. revoluta W.T. Lin & J. Y. Lin (HLZ) were labeled HLZ_1, HLZ_2, and HLZ_3, representing three biological replicates of each type of bamboo. The culm skin samples were frozen in liquid nitrogen immediately for further phytohormone detection, RNA-seq, and relative gene expression. Total RNA was isolated using plant RNA isolation kits .The middle and lower culm internode epidermis samples that were removed from https://www.illumina.com) at Wuhan Metware Biotechnology Co., Ltd. . The output data contained raw reads in fastq format, that were then processed for quality control, including filtering and trimming of low confidence bases, biased nucleotide composition, adapters, duplicates and low-quality reads to acquire clean reads. Trinity (2.6.6) (Library construction and sequencing steps were performed based on the Illumina HiSeq platform for RNA-seq protocols ( (2.6.6)  and Cors (2.6.6)  were usee-value = 1e−5, and the Pfam annotation was performed using the hmmscan command of the HMMER 3.2 package with e-value = 0.01. Transcription factor annotation was performed with iTAK (1.7a) (Nr (NCBI nonredundant protein sequences), Pfam (Protein family), KOG (Protein family), Swiss-Prot, Trembl, KEGG (Kyoto Encyclopedia of Genes and Genomes), and GO (Gene Ontology) were used for gene annotation. The Nr, KOG, Swiss-Prot, Trembl, KEGG, and GO annotations were performed using BLAST (v2.7.1) with an K (1.7a)  with defWe used the assembled transcriptome of Trinity as a reference and then mapped the clean reads of each sample to the reference with RSEM software. FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values were calculated to estimate gene expression and abundance after normalization of the mapped reads and transcript lengths. The R package Pheatmap was used to draw a heatmap with normalized log2(FPKM+1) data and clusters of expression patterns with kmeans_k = 10. The color from red to blue indicates gene expression from high to low.After acquiring the abundance information and performing normalization, gene expression between the groups was compared. DESeq2 (1.22.2) was used to calculate the differentially expressed genes between the LZ and HLZ groups, which were corrected with FDR  by Benjamini–Hochberg methods. Differentially expressed genes were filtered with the condition of —log2(Fold Change)— ≥ 1 and FDR < 0.05.® II Q RT SuperMix for qPCR . Quantitative Real-Time PCR (qRT-PCR) was performed on a LightCycler® 480 II Real-Time PCR system  using the Unique Aptamer™ qPCR SYBR® Green Master Mix. The components of the qRT-PCR were as follows: SYBR Premix Ex Taq (2x) (10 µl), forward primers (0.5 µM), reverse primers (0.5 µM), cDNA template (2 µl), and ddH2O to 20 µl. Then, qRT-PCR was performed as follows: initial denaturation at 95 °C for 5 min; 40 cycles of denaturation at 95 °C for 10 s and annealing at 72 °C; and finally, steps for melt-curve analysis . Actin was used as the internal control  was performed by Genepioneer Biotechnologies Co., Ltd.  using an HPLC–MS/MS platform.The quantification of endogenous abscisic acid (ABA), auxin , jasmonic acid (JA), and gibberellic acid (GAn = 9) with a significant difference (p < 0.05) according to unpaired t-tests.The enrichment of up- and downregulated genes was determined using GOseq and KOBAS . The corB. oldhamii (LZ) is a species of clumping bamboo (B. oldhamii variety referred to as B. oldhamii f. reboluta W.T. Lin & J. Y. Lin (HLZ) has green culms with yellow stripes of random widths. The culm skin was removed from LZ and HLZ to research the correlation of culm color variation on the phytohormone contents and gene expression levels.g bamboo  and it hB. oldhamii with three biological replicates marked LZ_1 - LZ_3 and from B. oldhamii f. revoluta with three biological replicates marked HLZ_1 - HLZ_3. After the cDNA library was constructed and sequenced, approximately 282 million raw sequence reads were obtained from the RNA-seq experiment, and 267 million clean sequence reads remained after filtering with a Q20 above 98% after quality control was performed. The error correction and GC content are shown as follows . The annotation results produced 38.64%, 70.18%, 44.92%, 69.23%, 40.03%, 57.24%, and 47.26% unigenes annotated in the KEGG, NR, SwissProt, Trembl, KOG, GO, and Pfam databases, respectively. Approximately 274,681 unigenes were annotated in at least one database.All of the unigenes were annotated using seven databases  (https:/The unigenes annotated with GO functions were assigned to three main ontologies: molecular function (MF), cellular component (CC), and biological process (BP). The terms cellular process (GO:0009987), metabolic process (GO:0008152), biological regulation (GO:0065007), and response to stimulus (GO:0050896) were the most common BP ontologies; the terms cell (GO:0005623), cell part (GO:0044464), and organelle (GO:0043226) were the most common CC ontologies; and binding (GO:0005488), catalytic activity (GO: 0003824), transporter activity (GO:0005215), and transcription regulator activity (GO:0140110) were the most common MF ontologies . The uniunigene-21666.123476) annotated with metallothionein that was highly expressed in all six samples, and cluster 1 included 8 genes that were more highly expressed in LZ samples. unigene-21666.69211 (mitogen-activated protein kinase kinase kinase ANP1), unigene-21666.134631 (SAUR family protein), unigene-21666.128797 (EREBF-like factor), and others without a specific annotation were included. The upregulated genes in HLZ were classified into 10 clusters , unigene-21666.90795 ; unigene-21666.169778 (serine/threonine-protein kinase PBS1), unigene-21666.167280 (granule-bound starch synthase), unigene-21666.149531 (acyl-[acyl-carrier-protein] desaturase), unigene-21666.125526 (anthranilate O-methyltransferase), unigene-21666.107961 (serine/threonine-protein kinase PBS1), and others without specific annotations , metabolic process (GO:0008152), response to stimulus (GO:0050896), and biological regulation (GO:0065007) terms were the most common BP ontologies; cell (GO:0005623), cell part (GO:0044464), organelle (GO:0043226), and membrane (GO:0016020) were the most common CC ontologies; and binding (GO:0005488) and catalytic activity (GO:0003824) were the most common MF ontologies . For theDifferential expression analysis between the LZ and HLZ groups showed that 190 and 259 DEGs were down- and upregulated in the HLZ culm skin samples. The GO functional enrichment revealed that the downregulated DEGs were more enriched in monocarboxylic acid transport (GO:0008028), transporter complex (GO:1990351), transmembrane transporter complex (GO:1902495), replication fork (GO:0005657), organelle envelope lumen (GO:0031970), lipid transporter activity (GO:0005319), and monocarboxylic acid transmembrane transporter activity (GO:0008028) .The upregulated DEGs were more enriched in biological processes and molecular functions. In particular, the top three terms were L-phenylalanine metabolic process (GO:0006558), L-phenylalanine catabolic process (GO:0006559), and entrainment of the circadian clock (GO:0009649), followed by photoreceptor activity (GO:0009881), phenylalanine ammonia-lyase activity (GO:0045548), NAD(P)H dehydrogenase (quinone) activity (GO:0003955), and carbon-nitrogen lyase activity (GO:0016840) .The downregulated DEGs were enriched in the alpha-linolenic acid metabolism pathway (ko00592) , and theB. oldhamii, the content of endogenous abscisic acid (ABA), auxin , jasmonic acid (JA), and gibberellic acid  was detected  and gene expression was analyzed with corresponding samples. There were 18 genes whose expression was significantly related to ABA accumulation patterns (1 (7 (1 and GA7 were more enriched in the GO terms of chloride channel complex (GO:0034707), ion channel complex (GO:0034702), protein kinase complex (GO:1902911), transporter complex (GO:1990351), anion channel activity (GO:0005253), chloride channel activity (GO:0005254), phosphatidylinositol bisphosphate binding (GO:1902936), and phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)  pathway (ko04712) (unigene-21666.126192 and unigene-21666.239597) and protein FLOWERING LOCUS T (FT) (unigene-54902.0) were up-regulated. Moreover, the expression of genes significantly related to ABA, GA1 and GA7 showed that unigene-21666.90795  was relatively highly expressed in HLZ  . All theko04712) . In the d in HLZ . The genunigene-21666.57044 (bHLH), unigene-21666.218036 (MYB-related), and unigene-21666.41135 (SBP) were not detected in the HLZ samples and were only detected in the LZ samples. bHLH transcription factors can interact with MYB transcription factors to regulate anthocyanin biosynthesis (unigene-21666.194872 (FAR1), unigene-21666.98709 (MADS-M-type), unigene-21666.139384 (MYB), and unigene-21666.212035 (TRAF) were not detected in the LZ samples and were only detected in the HLZ samples. MADS-box transcription factors are involved in flower promotion and development, and simultaneous death usually follows after mass production of bamboo flowers  were annotated as the transcription factor HY5. The target genes of HY5 participate in many biological signaling processes, such as light signaling, circadian clock, anthocyanin biosynthesis, and chlorophyll biosynthesis , CHI , and FLS (flavonol synthase) to regulate anthocyanin biosynthesis  that were members of the MYB transcription factor family. MYB transcription factors could regulate anthocyanin biosynthesis . The psbP protein is required for the photosystem II complex and normal thylakoid architecture in Arabidopsis thaliana (unigene-54902.0 (FT) gene is upregulated in the circadian rhythm (plant) pathway. The FT gene (FLOWERING LOCUS T), a mobile stimulus expressed in leaves and then translocated to the shoot apex, is essential for floral induction in Arabidopsis (unigene-21666.98709 (MADS-M-type) is relatively highly expressed in HLZ. MADS-box genes are essential for flower induction, promotion, and maturation . These proteins are usually divided into four classes: (1) R2R3-MYB, (2) 1R-MYB, MYB-related, and others, (3) 3R-MYB, and (4) 4R-MYB . Among tis genes .unigene-21666.57044, was differentially expressed. These results demonstrate that MYB and bHLH transcription factors could regulate the color variation of bamboos. However, how the crosstalk among the transcription factors and hormone regulation influences color variation still needs further investigation.The family of Basic Helix-Loop-Helix (bHLH) transcription factors contains approximately 60 conserved amino acid domains that bind to the promoter of E-box cis-elements to regulate downstream genes , and theB. oldhamii via combined RNA-seq and endogenous phytohormone content variation analyses. The results showed that bZIP, MYB, HY5, and other differentially expressed transcription factors play a role in B. oldhamii culm color variation. Moreover, phytohormone contents, especially GA1 and GA 7, were more highly accumulated in LZ, but many flower-regulated genes were more highly expressed in HLZ, which indicates that HLZ may flower more rapidly than LZ and that the senescence pathways may be involved in bamboo culm color variation. The transcription factors HY5, MYB, and bHLH participate in culm color variation by regulating pigment biosynthesis pathways to cause bamboo culm color variation, but how the regulatory pathways between transcription factors and phytohormones influence culm color variation still needs to be deeply investigated.This paper focused on investigating the culm color variation of the clumping bamboo 10.7717/peerj.12796/supp-1Supplemental Information 1Click here for additional data file.10.7717/peerj.12796/supp-2Supplemental Information 2Click here for additional data file.10.7717/peerj.12796/supp-3Supplemental Information 3Click here for additional data file.10.7717/peerj.12796/supp-4Supplemental Information 4Click here for additional data file.10.7717/peerj.12796/supp-5Supplemental Information 5Click here for additional data file.10.7717/peerj.12796/supp-6Supplemental Information 6Click here for additional data file.10.7717/peerj.12796/supp-7Supplemental Information 7Click here for additional data file.10.7717/peerj.12796/supp-8Supplemental Information 8Click here for additional data file.10.7717/peerj.12796/supp-9Supplemental Information 9Click here for additional data file.10.7717/peerj.12796/supp-10Supplemental Information 10Click here for additional data file.10.7717/peerj.12796/supp-11Supplemental Information 11Click here for additional data file.10.7717/peerj.12796/supp-12Supplemental Information 12Click here for additional data file.10.7717/peerj.12796/supp-13Supplemental Information 13Click here for additional data file.10.7717/peerj.12796/supp-14Supplemental Information 14Click here for additional data file.10.7717/peerj.12796/supp-15Supplemental Information 15Click here for additional data file.10.7717/peerj.12796/supp-16Supplemental Information 16Click here for additional data file.10.7717/peerj.12796/supp-17Supplemental Information 17Click here for additional data file.10.7717/peerj.12796/supp-18Supplemental Information 18Click here for additional data file.10.7717/peerj.12796/supp-19Supplemental Information 19Click here for additional data file.10.7717/peerj.12796/supp-20Supplemental Information 20Click here for additional data file.10.7717/peerj.12796/supp-21Supplemental Information 21Click here for additional data file.10.7717/peerj.12796/supp-22Supplemental Information 22Click here for additional data file.


Helicobacter pylori (H.pylori) may cause dyspepsia and/or unexplained functional nonspecific, gastrointestinal complaints of the irritable bowel syndrome (IBS) spectrum. Hitherto, in H. pylori infected patients with symptoms of the IBS spectrum the occurrence of additional food intolerance/malabsorption is not evaluated. We used a retrospective analysis of charts from 548 patients who presented with gastrointestinal complaints of the irritable bowel syndrome spectrum. An enzyme-linked IgA immunosorbent assay or histologic evaluation of gastric mucosa were used to detect H. pylori infection. A hydrogen breath (H2) test was performed to evaluate fructose malabsorption (FM) and lactose intolerance (LIT). Serum diamine oxidase value of <10 U/ml and a response to a histamine-reduced diet was used to identify histamine intolerance (HIT). We found 293 patients infected with H. pylori, within these were 58 H. pylori patients with LIT, 23 H. pylori LIT patients with FM and 46 H. pylori LIT patients with HIT. Additionally, 13 H. pylori, lactose- and histamine intolerance patients also had FM. The Kruskal Wallis test and pairwise comparison were used to analyze differences of the area under the curve of expiratory hydrogen. In lactose H2 breath tests compared with LIT-only patients, LIT with H. pylori, LIT and H. pylori with HIT, LIT and H. pylori with FM showed significantly higher exhaled H2 levels (p=0.022). Pairwise comparison demonstrated H. pylori infected patients with LIT exhaled more H2 compared to LIT-only (p=0.029). H. pylori with lactose- and histamine intolerance, and H. pylori with lactose-, histamine intolerance and FM compared to H. pylori-only patients indicated a significantly higher occurrence of stomach pain during lactose H2 breath tests . We demonstrate that LIT patients with high expiratory H2 levels in lactose breath tests may have H. pylori infection and possibly additional food intolerance/malabsorption. Subsequently, besides H. pylori eradication, a dietician is necessary for an individually tailored reduction- or exclusion diet of symptom triggering food components.Infection with  AUC, Area under the curve; DAO, diamine oxidase; FM, fructose malabsorption; GI, gastrointestinal; HIT, histamine intolerance; IBS, irritable bowel syndrome; LIT, lactose intolerance.Helicobacter pylori (H. pylori) infection is the most prevalent human pathogen and is present in more than 50 % of worldwide populations. If H. pylori is detected, then an eradication therapy is mandatory. Some association of H. pylori infection and dyspepsia and/or unexplained functional, nonspecific, non-allergic gastrointestinal (GI) complaints of the irritable bowel syndrome (IBS) spectrum is documented. Reduction of these symptoms due to H. pylori eradication has been shown . Based al., 2019).Unexplained functional, nonspecific, non-allergic GI complaints and dyspepsia, including IBS and IBS-like syndromes, are widespread and costly, and a main reason for consultations in primary care settings . GeneraH. pylori-infected patients for additional food intolerance/malabsorption, including CD, FM, HIT and LIT. All included patients presented with dyspepsia/unexplained functional, nonspecific, non-allergic GI complaints of the IBS spectrum. Compared to LIT-only, patients with LIT and H. pylori combined with or without additional food intolerance/malabsorption demonstrated significantly higher expiratory hydrogen (H2) values during lactose tolerance breath tests. In this study we have evaluated H. pylori infection. 293 were infected with H. pylori and in 255 H. pylori was not found. Eradication therapy was started after performance of H2 breath tests and included in this evaluation were only patients who took part in all tests. Patients with alarming symptoms, such as vomiting, rectal bleeding or unintentional weight loss were excluded.During the retrospective evaluation, we found 548 patients who presented with dyspepsia/unexplained functional, nonspecific, non-allergic GI complaints of the IBS spectrum. Main symptoms included abdominal pain, diarrhea, loose stools, bloating, constipation and postprandial fullness. They were examined for additional food intolerance/malabsorption, including CD, FM, HIT, and LIT. In evaluated patients, either an enzyme-linked IgA immunosorbent assay  or a histologic evaluation of gastric mucosa was used to detect 2 breath tests  were used for LIT and FM testing as described earlier .Hal., 2020). After A thorough anamnesis, concerning abdominal complaints, and a timely relation to the ingestion of food or drinks, including pharmaceutical treatments that might influence dyspepsia/unexplained functional, nonspecific, non-allergic GI complaints of the IBS spectrum was performed. A registered dietitian was consulted to implement and monitor an individualized diet to reduce and/or eliminate symptom-triggering foods. For screening of celiac disease, antibodies against tissue transglutaminase were measured with the anti-tTG IgA ELISA  method. The study follows the ethical guidelines of the Declaration of Helsinki and was approved by the Ethical Committee of the Johannes Kepler University in Linz, Austria (No. K-107-16).2 breath tests were calculated and compared with the Kruskal-Wallis test, and pairwise comparison. The Chi-square and the Fisher's exact test were applied for evaluation of symptoms. The level of significance was set to 5 %. The Bonferroni correction was used for multiple testing.Descriptive statistics are presented as medians with interquartile ranges (IQR). The data distribution was assessed with a Shapiro Wilk test. For not normally distributed data non-parametric tests were applied. The areas under the curve (AUC) of exhaled hydrogen during HStatistical analyses were performed with IBM SPSS statistics version 25.0 , and GraphPad Prism version 9.0.0.  was used for the generation of figures. H. pylori, male/female 93/200, median age 50 years (IQR 21), age range 17-93 years. We identified 68 patients with H. pylori infection only (12.4 %) - male/female 25/43, median age 56 years (IQR 22), age range 25-93 years. Hydrogen breath tests neither showed LIT nor FM in these patients, and serum DAO values were within normal >10 IU/mL (median 17.9 IU/mL (IQR 12.1), range 10.1-63.4 IU/mL). 58 patients with H. pylori had additional LIT (10.6 %) - male/female 20/38, median age 50 years (IQR 17), age range 22-84 years. Hydrogen breath tests did not show FM in these patients, and DAO values were >10 IU/mL (median 17 IU/mL (IQR 9.5), range 10.5-80 IU/mL). 17 H. pylori patients had only additional FM (3.1 %), male/female 3/14, median age 57 years (IQR 15), age range 23-78 years. Hydrogen breath tests did not show LIT in these patients, and DAO values were >10 IU/mL (median 14.7 IU/mL (IQR 5.6), range 10.7-30.6 IU/mL). However, 47 H. pylori patients had additional HIT (8.6 %), male/female 12/35, median age 50 years (IQR 22), age range 24-91 years. Their DAO values were <10 IU/mL (median 5 IU/mL (IQR 5.2), range 1.5-9.7 IU/mL). Moreover, hydrogen breath tests did show neither LIT nor FM in this group. For this retrospective evaluation, we used 548 patients with IBS spectrum symptoms. We found 293 infected withH. pylori combined with LIT and FM (4.2 %) - male/female 6/17, median age 45 years (IQR 21), and age range 17-82 years. Their DAO values were >10 IU/mL (median 16.6 IU/mL (IQR 9.5), range 12.4-71 IU/mL). In 46 patients we found H. pylori combined with LIT and HIT (8.4 %) - male/female 17/29, median age 43 years (IQR 21), age range 22-83 years. Accordingly, their DAO values were <10 IU/mL (median 6.6 IU/mL (IQR 3.0), range 1.5-9.9 IU/mL) and hydrogen breath tests did not show FM. In 17 H. pylori patients we found additional FM combined with HIT (3.1 %) - male/female 6/11, median age 54 years (IQR 22), age range 28-79 years. Their DAO values were <10 IU/mL (median 4.1 IU/mL (IQR 6.7), range 1.5-10 IU/mL). Hydrogen breath tests did not show LIT in these patients. 13 patients with H. pylori had LIT and FM combined with HIT (2.4 %). Their DAO values were <10 IU/mL (median 7.8 IU/mL (IQR 3.5), range 2.1-9.9 IU/mL). Antibodies against tissue transglutaminase were not detectable in 289 H. pylori patients. Four patients with H. pylori infection demonstrated celiac disease (0.8 %) with elevated tissue transglutaminase antibodies and following histologic diagnosis of the duodenal mucosa as shown in Table 1Additionally, 23 patients showed 2 breath tests. 102 patients (18.6 %) were positive for FM , range 19-91 years). Their DAO values were > 10 IU/mL, with median 16.9 IU/mL (IQR 7.9) and range 10.2-62.5 IU/mL and they did not show LIT in lactose H2 breath tests. In all of these 255 patients neither antibodies against H. pylori nor tissue transglutaminase were detected.In 153 (27.9 %) patients , age range 16-84 years, LIT only was diagnosed. Their DAO values were >10 IU/mL (median 16.6U/ml (IQR 10.2), range 10.2-80 IU/mL) and they did not show FM in fructose HH. pylori, to H. pylori, LIT with HIT and, to H. pylori, LIT with FM demonstrated significantly higher exhaled hydrogen values (p=0.022) , corrected for multiple testing (test statistic 35.206 and standard error 12.48). Due to the low number of H. pylori patients with LIT, FM and HIT these were not included in Figure 1The Kruskal Wallis test for the comparison of the AUCs of LIT-only, to patients with LIT and  Figure 1. PairwisH. pylori and LIT patients were abdominal pain, bloating, diarrhea, and increased bowel movements. Other GI symptoms included nausea, heartburn, belching, fullness, and excessive mucus in the throat. Extra-intestinal symptoms were headache, fatigue, vertigo and one eczema. Various double and few triple combinations of these symptoms were indicated. GI-symptoms were indicated by 160 of 279 LIT patients (57 %) during H2 breath tests. As shown in Figure 2H. pylori with LIT and FM, and H. pylori with LIT, FM and HIT compared to H. pylori-only patients demonstrate significantly higher occurrence of stomach pain . Patients with H. pylori-only infection did specify symptoms, although neither bloating nor diarrhea were mentioned during lactose breath tests. All patients >50 years old were screened by colonoscopy and no pathology was present.During performed lactose breath tests patients specified their GI and extra-intestinal symptoms on paper. Indicated GI symptoms by H. pylori in 262 patients, male/female 84/178, median age 51 years (IQR 22), age range 17-93 years, with mean 77.2 IU/mL (range 21-200 IU/mL) IgA antibodies. 63 patients had H. pylori only, male/female 25/38, median age 53 years (IQR 24), age range 25-93 years, and they had mean 73.9 IU/mL (range 21-200 IU/mL) IgA antibodies. 45 patients had H. pylori combined with LIT, male/female 17/28, median age 49 years (IQR 16), age range 26-86 years, with mean 63.8 IU/mL (range 21-200 IU/mL) IgA antibodies. 46 were H. pylori and HIT patients male/female 9/37, median age 49.5 years (IQR 24), age range 24-91 years, they had IgA antibodies mean 65.3 IU/mL (range 22-200 IU/mL). 19 were H. pylori and FM patients, male/female 3/16, and median age 56 years (IQR 17), age range 23-78 years, with mean 74.1 IU/mL (range 21-200 IU/mL) IgA antibodies. 44 were H. pylori and LIT with HIT patients, male/female 17/27, median age 43 years (IQR 18), age range 22-83 years, IgA antibodies with mean 84.9 IU/mL (range 21-200 IU/mL). 19 were H. pylori patients with LIT and FM male/female 6/13, median age 51 years (IQR 21), age range 17-79 years, with mean 111 IU/mL (range 34-200 IU/mL) IgA antibodies. 15 were H. pylori, FM and HIT patients male/female 5/10, median age 54 years (IQR 28), age range 28-58 years, IgA antibodies with mean 95.3 IU/mL (range 24-200 IU/mL). 11 H. pylori, LIT, HIT with FM patients, male/female 2/9, median age 41 years (IQR 32), age range 24-83 years, with mean 92.8 IU/mL (range 25-200 IU/mL) IgA antibodies.The enzyme-linked IgA immunosorbent assay  detected IgA antibodies against H. pylori significant different among all groups (p=0.044). Patients with H. pylori, LIT and FM had the highest quantity of IgA antibodies. Pairwise comparisons showed significantly lower antibody values comparing H. pylori, LIT and FM to H. pylori and LIT (p=0.005), to H. pylori and HIT (p=0.005), to H. pylori with FM (p=0.034) and, to H. pylori only (p=0.016). However, correction for multiple testing showed no significance.As shown in Figure 32 (p=0.39) comparing all groups (data not shown). Fructose malabsorption breath tests (n=159), using the Kruskall-Wallis test for evaluation of AUCs, showed no differences of exhaled HSee also the Supplementary data.From a clinical perspective, considerable overlap exists between food intolerance/ malabsorption and unexplained dyspepsia/ functional, nonspecific, non-allergic GI complaints and disorders, including IBS and IBS-like disorders. Currently, IBS is classified as a functional gastrointestinal disorder, according to Rome IV criteria, but new disease models are being proposed continuously Talley, 2020). Food i020. FoodH. pylori, the hormone gastrin and the biogenic amine histamine are main stimulants of gastric acid secretion . In patal., 2018). Due toal., 2018), we useal., 2020).H. pylori infection and its association with deficiencies of micronutrients, minerals and vitamins was reported . A relaley, 2020). Succesal., 2000). Additial., 2020). Severakas, 2020). FinallH. pylori patients with dyspepsia/functional, nonspecific, non-allergic GI complaints of the IBS spectrum, besides a thorough anamnesis, it seems useful to include examinations for food intolerance/malabsorption with FM- and lactose intolerance H2 breath tests, serum DAO determination and screening for celiac disease . 2 production. Therefore, the clinical diagnosis of LIT and FM is primarily performed with H2 breath tests. Impaired degradation of ingested histamine due to an anticipated gastrointestinal DAO deficiency, promotes HIT. So far, serum DAO is not established to reflect GI histamine-degrading DAO activity , fermen al. 2021). Noneth al. 2021; Mušič e al. 2021). Althou al. 2021).Generally, only few studies have reported on combined occurrence of food intolerance/malabsorption. Nonetheless, more than 30 % of patients with dyspepsia/ unexplained functional, nonspecific, non-allergic GI complaints and carbohydrate intolerance/malabsorption may have combinations of these . Next tH. pylori, the presence of additional food intolerance/ malabsorption induced significantly increased expiratory H2 values . In thikas, 2020).H. pylori patients when this infection is combined with LIT and FM or with LIT, FM and HIT . HoweveH. pylori infection may have additional food intolerance/malabsorption. Moreover, we show that in LIT the presence of H. pylori infection causes significantly higher expiratory H2 values in lactose tolerance breath tests. Subsequently, besides eradication, a registered and experienced dietician is essential for the development of an individually tailored reduction- or exclusion diet of symptom triggering food components.In conclusion, we describe, that patients with dyspepsia/unexplained functional, nonspecific, non-allergic GI complaints of the IBS spectrum having LIT and We are indebted to Mrs. Katharina Schnedl, Cardiff University, Cardiff, UK, who performed English language corrections.Wolfgang J. Schnedl received speaking honoraria from Sciotec. The other authors have no conflict of interest.


Mycobacterium smegmatis mc2 155 host. The genome of JeTaime is 75,099 bp (142 predicted genes), and that of Luna22 is 53,730 bp (87 predicted genes). Both phages exhibit Siphoviridae morphology.The mycobacteriophages JeTaime (E cluster) and Luna22 (Q cluster) were isolated from soil in Providence, Rhode Island, and Charleston, South Carolina, respectively, using a  Mycobacterium smegmatis mc2 155, as described in the SEA-PHAGES Phage Discovery Guide  program through the Howard Hughes Medical Institute (HHMI) . The phale tails .de novo into a single contig using Newbler v2.9 (https://cpt.tamu.edu/computer-resources/pause), genome termini with 3′ cohesive overhangs were identified, as follows: JeTaime, 5′-CGCTTGTCA-3′; Luna22, 5′-TAAGCCGCGCGGTA-3′. The Promega Wizard DNA cleanup system was used to extract DNA from phage lysates, and sequencing libraries were prepared with a NEBNext Ultra II DNA library prep kit v3). Libraries for each phage were independently generated, and genomes were sequenced separately. Sequencing was performed at the Pittsburgh Bacteriophage Institute on an Illumina MiSeq system (MiSeq reagent kit v3) , TOPCONS v2 (https://phagesdb.org/DNAMaster). All programs used default settings.Each genome was annotated on PECAAN  using GLPCONS v2 , and thePCONS v2 . tRNAs aPCONS v2  and tRNAPCONS v2 , and comKT222941) genomes. The other 103 published E-cluster members typically contain endonuclease VII and/or DNA methylase in that genome region. Also, the JeTaime gp89 (unidentified function) is rare, occurring in only one other E-cluster bacteriophage, 244 (GenBank accession number DQ398041). Whole-genome BLASTn alignment (NC_004681.1) (99.24% identity and 96% coverage), Phrux (GenBank accession number NC_021309.1) (99.20% identity and 95% coverage), and ShereKhan (GenBank accession number MH513983.1) (99.10% identity and 95% coverage).JeTaime is an E-cluster phage with 142 predicted protein-coding genes (54 assigned functions), while Luna22 is a Q-cluster phage with 87 predicted protein-coding genes (42 assigned functions) . Intereslignment  revealedMT114159) and New Zealand  (GenBank accession number MK494095) retain >98% nucleotide sequence identity to the Luna22 genome. Also, the genome of Giles (GenBank accession number EU203571) is nearly identical to that of Luna22 (99.96% identity and 100% coverage)  –21; the Individual GenBank and SRA numbers are listed in


Defining the metabolic syndrome (MetS) in children remains challenging. Furthermore, a dichotomous MetS diagnosis can limit the power to study associations. We sought to characterize the serum metabolite signature of the MetS in early childhood using high-throughput metabolomic technologies that allow comprehensive profiling of metabolic status from a biospecimen.In the Family Atherosclerosis Monitoring In earLY life (FAMILY) prospective birth cohort study, we selected 228 cases of MetS and 228 matched controls among children age 5 years. In addition, a continuous MetS risk score was calculated for all 456 participants. Comprehensive metabolite profiling was performed on fasting serum samples using multisegment injection-capillary electrophoresis-mass spectrometry. Multivariable regression models were applied to test metabolite associations with MetS adjusting for covariates of screen time, diet quality, physical activity, night sleep, socioeconomic status, age, and sex.Compared to controls, thirteen serum metabolites were identified in MetS cases when using multivariable regression models, and using the quantitative MetS score, an additional eight metabolites were identified. These included metabolites associated with gluconeogenesis (glucose (odds ratio (OR) 1.55 [95% CI 1.25–1.93]) and glutamine/glutamate ratio (OR 0.82 [95% CI 0.67–1.00])) and the alanine-glucose cycle ), amino acids metabolism (tyrosine (OR 1.33 [95% CI 1.10–1.63]), threonine (OR 1.24 [95% CI 1.02–1.51]), monomethylarginine (OR 1.33 [95% CI 1.09–1.64]) and lysine (OR 1.23 [95% CI 1.01–1.50])), tryptophan metabolism (tryptophan (OR 0.78 [95% CI 0.64–0.95])), and fatty acids metabolism (carnitine (OR 1.24 [95% CI 1.02–1.51])). The quantitative MetS risk score was more powerful than the dichotomous outcome in consistently detecting this metabolite signature.A distinct metabolite signature of pediatric MetS is detectable in children as young as 5 years old and may improve risk assessment at early stages of development.The online version contains supplementary material available at 10.1186/s12916-021-02162-7. Obesity and related metabolic sequelae such as type 2 diabetes are increasingly prevalent among children in high-income countries , 2. The N-oxide or TMAO) Additional file 2. Supplemental Methods [IDEFICS MetS definitions and MSI-CE-MS data processing]Additional file 3: Table S1. [Serum metabolites characteristics]Additional file 4: Table S2. [Unadjusted and intermediate adjusted models]Additional file 5: Table S3. [Pathway analysis]Additional file 6: Fig. S2. [Clustering of MetS cases]


Orgyia postica. The complete mitochondrial genome was a circular molecule with 15,258 bp in full-length, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes (rRNAs). The nucleotide composition of O. postica mitogenome was A: 37.6%, C: 7.9%, G: 14.8%, T: 39.7%. In addition, the results of the phylogenetic analysis indicate that O. postica had the closest relationship with Laelia suffusa. Our study will contribute to further research on the evolution of Lymantriidae and the identification of larva species.The high-throughput sequencing method was used for the first time to determined complete mitochondrial genome of  Orgyia postica Walker, 1855 (Lepidoptera: Lymantriidae) is a crop pest that mainly damages stamens and leaves, It mainly damages more than 70 crops such as tea, cotton, strawberries, loofah, asparagus, radishes, peaches, grapes, pears, citrus, mangoes, causing poor growth, reduced production and even death . The specimen was deposited at the Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety  (Voucher specimen number: FDSW202318382-1r) and identified by the head of herbarium Mr Li (Email: lijunlijun1981@163.com). Genomic DNA was extracted using Genomic DNA Kit  and constructed the libraries with an average length of 350 bp using the NexteraXT DNA Library Preparation Kit . Then the libraries were sequenced on Illumina Novaseq 6000 platform, 9.23 Gb clean data was assembled by SPAdes (version 3.11.0) . The original sequencing data were uploaded to the NCBI database (https://www.ncbi.nlm.nih.gov/sra/) with the accession number SRR15041082. The complete mitochondrial genome was assigned Genbank accession number MW355619.The sample of O. postica is a closed circular molecule of 15,258 bp, consisting of complex I (NADH dehydrogenase), complex IV (cytochrome C oxidase), ATP synthase, transfer RNAs, ribosomal RNAs and other genes, with the base content of A 37.6%, C 7.9%, G 14.8%, and T 39.7%. The A + T content is 77.3%, showing a strong AT skew. The genome encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). With the gene rrnS as a starting point, the gene order of complete mitochondrial is rrnS, trnV-TAC, rrnL, trnL-TAG, ND1, trnS-TGA, CYTB, ND6, trnP-TGG, trnT-TGT, ND4L, ND4, trnH-GTG, ND5, trnF-GAA, trnE-TTC, trnS-GCT, trnN-GTT, trnR-TCG, trnA-TGC, ND3, trnG-TCC, COX3, ATP6, ATP8, trnD-GTC, trnK-CTT, COX2, trnL-TAA, COX1, trnY-GTA, trnC-GCA, trnW-TCA, ND2, trnQ-TTG, trnI-GAT, trnM-CAT. Among these genes, the shortest and longest were 62 (trnR-TCG) and 1692 bp (ND5), and the average gene length was 390.78 bp.The mitochondrial genome of O. postica within lepidoptera. 21 published complete mitochondrial genome sequences from lepidoptera including Euproctis pseudoconspersa (KJ716847.1), Euproctis cryptosticta (KY996558.1), Anarta trifolii (MN715147.1), Sesamia inferens (JN039362.1), Spodoptera littoralis (MT816470.1), Spodoptera litura (JQ647918.1), Spodoptera frugiperda (KM362176.1), Spodoptera exigua (JX316220.1), Spodoptera exempta (MT906792.1), Parasa consocia (KX108765.1), Aglaomorpha histrio (KY800518.1), Spilarctia subcarnea (KT258909.1), Lemyra melli (KP307017.1), Hyphantria cunea (GU592049.1), Amata formosae (KC513737.1), Euproctis similis (KT258910.1), Euproctis seitzi (MN916588.1), Lymantria dispar (FJ617240.1), Laelia suffusa (MN908152.1), Lymantria umbrosa (KY923066.1) and Lymantria sugii (MT265380.1) species were collected and aligned with O. postica by MAFFT7.037 (Katoh and Standley, L. suffusa has the closest relationship with O. postica.To confirm the phylogenetic position and understand the relationship of


Women aged 65 and older experience nearly three-fourths of the 2 million osteoporotic fractures annually in the US, yet whether accelerometer-measured volumes and intensities of physical activity and sedentary behavior (SB) are associated with reduced fracture risk is understudied. We investigated associations of accelerometer-measured light physical activity (LPA), moderate-to-vigorous physical activity (MVPA), sedentary time (ST), and mean sedentary bout duration (MBD) with incident clinical fractures  in the WHI OPACH cohort. Participants  without prior hip fracture wore the ActiGraph GT3X+ for 7 days between May 2012-April 2014 and were followed through March 2020 for incident clinical fracture (N=711). Cox models estimated hazard ratios (HR) and 95% confidence intervals (CI), adjusting for age, race-ethnicity, education, alcohol, smoking, height, weight, falls history, RAND-36 physical function, diabetes, thiazide use, prescription osteoporotic therapy, and age at menopause. The HR(95% CI) across MVPA quartiles was 1.00(reference), 1.15(0.93-1.41), 0.90(0.72-1.13), and 0.79(0.61-1.02); p-trend=0.01. The HR(95% CI) for a one-interquartile range increment in MVPA (42 minutes/day) was 0.86(0.76-0.97). Associations were modified by prescription osteoporotic therapy  and varied in magnitude by age, BMI , and race-ethnicity . LPA, ST, or MBD were not associated with incident fractures. These data suggest that MVPA may reduce and not increase fracture risk and that LPA and SB do not increase fracture risk.


Scientific Reports 10.1038/s41598-021-81257-w, published online 18 January 2021Correction to: This Article contains an error, where Supplementary Data files Supplementary Data 1.Supplementary Data 2.Supplementary Data 3.


Monarda (family Lamiaceae) contains 22 species of which three are native to southern Alabama, M. citriodora, M. fistulosa, and M. punctata. Several species of Monarda have been used in traditional medicines of Native Americans, and this present study is part of an ongoing project to add to our understanding of Native American pharmacopeia. Plant material from M. citriodora, M. fistulosa, and M. punctata was collected in south Alabama and the essential oils obtained by hydrodistillation. The essential oils were analyzed by gas chromatographic techniques to determine the chemical compositions as well as enantiomeric distributions. The compounds thymol, carvacrol, p-cymene, and their derivatives were the primary terpenoid components found in the essential oils. The known biological activities of these compounds are consistent with the traditional uses of Monarda species to treat wounds, skin infections, colds, and fevers.The genus  Monarda L. (Lamiaceae) species, 18 of which occur in the United States [Monarda species native to south Alabama, namely Monarda citriodora Cerv. ex Lag., Monarda fistulosa L., and Monarda punctata L.  and carvacrol (RIdb = 1296). The other major components were p-cymene (RIdb = 1024) and thymol methyl ether (RIdb = 1239).The M. citriodora essential oils revealed the (+)-enantiomers to be the major stereoisomers for α-thujene, α-pinene, β-pinene, α-phellandrene, δ-3-carene, α-terpinene, cis-sabinene hydrate, trans-sabinene hydrate, α-terpineol, α-copaene, (E)-β-caryophyllene, and germacrene D. On the other hand, the (−)-enantiomer was dominant for β-phellandrene, borneol, carvone, and δ-cadinene. Limonene showed variation in the enantiomeric distributions with (+)-limonene in 26.7%, 63.3%, and 57.3% for aerial parts #1, #2, and roots essential oils, respectively. Likewise, linalool also showed variation with (+)-linalool of 71.9%, 49.7%, and 50.1%. (+)-Terpinen-4-ol was the predominant enantiomer in the aerial parts essential oils (60.2% and 58.5%), but (−)-terpinen-4-ol (79.1%) was dominant in the root essential oil.Chiral gas chromatography–mass spectrometry (GC-MS) analysis of the Monarda fistulosa essential oils were obtained in 2.66–4.83% yields as bright orange oils. The chemical compositions of the essential oils from the aerial parts of M. fistulosa are summarized in db = 1289) dominated the compositions  with lesser quantities of p-cymene , limonene , carvacrol , and thymoquinone . Curiously, sample #3, although qualitatively similar, had a very different quantitative composition with thymoquinone as the most abundant constituent (41.3%) followed by p-cymene (21.9%), but with lower concentrations of thymol (8.9%) and carvacrol (1.6%).M. citriodora essential oils, in M. fistulosa essential oils, the (+)-enantiomer was the major for α-thujene, α-pinene, β-pinene, α-phellandrene, δ-3-carene, α-terpinene, cis-sabinene hydrate, trans-sabinene hydrate, α-terpineol, α-copaene, (E)-β-caryophyllene, and germacrene D, while the (−)-enantiomer was predominant for β-phellandrene and borneol. (−)-Limonene (97.4–99.5%) and (−)-linalool (62.1–62.5%) dominated in all three M. fistulosa samples. (+)-Camphene (100%), (+)-sabinene (58.4–59.0%), and (+)-terpinen-4-ol (63.2–63.3%) were also dominant.As was observed in M. punctata aerial parts gave bright orange essential oils in 0.781% and 0.658% yield. The most abundant components in the essential oils were thymol , p-cymene , γ-terpinene , and carvacrol  (see Hydrodistillation of two samples of wild-growing .1%) see .M. punctata essential oils were analogous to those observed for M. citriodora and M. fistulosa oils with the exception of limonene, which was virtually racemic in sample #1, but 100% (−)-limonene in sample #2.The enantiomeric distributions of terpenoids in Monarda citriodora and M. fistulosa have been introduced throughout temperate regions of the world as popular herbal medicines as well as ornamentals [M. citriodora in the present study were rich in both thymol and carvacrol, whereas essential oils from Europe and Asia were dominated by thymol with much lower concentrations of carvacrol. Monarda fistulosa, in particular, showed wide variation with at least three different chemotypes  in this study fit into the thymol-rich chemotype. Interestingly, there was a high concentration of thymoquinone in M. fistulosa sample #3, with concomitant lower concentrations of thymol and carvacrol. Thymol was reported as the major component of M. punctata in two old reports [M. punctata from China was rich in thymol (75.2%), which is in agreement with the aerial parts essential oils from Alabama.amentals ,5,6. The reports ,12. Consp-cymene are consistent with the traditional uses of Monarda spp. to treat skin infections, wounds, fevers, and respiratory problems. Thymol [p-cymene [The high concentrations of thymol, carvacrol, and . Thymol , carvacr. Thymol , and p-cp-cymene  have demp-cymene ,35, as wp-cymene . Thymol p-cymene  and carvp-cymene , in addip-cymene , have shp-cymene . Furtherp-cymene  and carvp-cymene  have shop-cymene .Monarda species. Several investigations on the enantiomeric distributions in other members of the Lamiaceae have been reported in the literature, however. There seems to be much variation in the enantiomeric distribution of monoterpenoids across the family. Consistent with what was observed in Monarda essential oils, (+)-α-pinene was the major enantiomer found in Coridothymus capitatus [Rosmarinus officinalis [Lepechinia heteromorpha [Ocimum canum, and Ocimum kilimandscharicum [C. capitatus [Monarda essential oils. On the other hand, (−)-β-pinene dominates in R. officinalis [Lepechinia mutica [Mentha × piperita) and spearmint (Mentha spicata) have shown nearly racemic mixtures of α- and β-pinenes [Monarda essential oils. In marked contrast, however, (−)-α-phellandrene and (+)-β-phellandrene predominated in L. mutica essential oil [M. fistulosa essential oil, peppermint (M. piperita) and spearmint (M. spicata) essential oils [C. capitatus [O. canum, and O. kilimandscharicum [R. officinalis) essential oil [C. capitatus [Salvia schimperi [Pycnanthemum incanum [O. canum, and O. kilimandscharicum [Lavandula angustifolia [R. officinalis [As far as we are aware, this work presents the first chiral analysis of terpenoid constituents of apitatus , Rosmariicinalis , Lepechiromorpha , Ocimum charicum . Likewisapitatus  as well icinalis  and Lepea mutica . The ess-pinenes . (+)-α-Ptial oil . (−)-Limial oils  whereas apitatus , O. canucharicum , and a ntial oil . (+)-Linapitatus , Salvia chimperi , Pycnant incanum , O. canucharicum , whereasstifolia  and R. oicinalis .Monarda citriodora was cultivated in Kirkland Gardens, Newville, AL, USA  from seeds . The cultivated Monarda spp. were grown in loamy clayey-sand and fertilized with chicken manure, kelp meal, and bone meal at planting in full sun. The aerial parts of M. citriodora were collected from separate plants on separate occasions . The roots of M. citriodora were obtained from plant #2.Monarda fistulosa was cultivated in Kirkland Gardens, Newville, AL, USA  from seedlings  as above. The aerial parts of three different plant samples were collected on 25 June 2020.Monarda punctata was collected from wild-growing plants near Newville, AL, USA ; the edge of a planted pine forest, disturbed grassland, full/partial sun, sandy-clay soil that had been intentionally burned (prescribed burn) 1.5 years before collection. The aerial parts of two different plants were collected on 1 June 2020.M. citriodora (SKL61820), M. fistulosa (SKL72020), and M. punctata (SKL9620). The Monarda plant materials were allowed to dry in the shade for several days, the air-dried plant materials were pulverized and subjected to hydrodistillation using a Likens-Nickerson apparatus with continuous extraction with dichloromethane (Plants were identified by S.K. Lawson and a voucher specimen of each plant was deposited in the University of Alabama in Huntsville Herbarium (HALA); voucher numbers for omethane .The essential oils were analyzed by gas chromatography–mass spectrometry (GC-MS), gas chromatography with flame ionization detection (GC-FID), and chiral GC-MS as previously reported .n-alkanes. Compounds identified by comparison of the MS fragmentation and retention indices with those in the databases [Shimadzu GCMS-QP2010 Ultra, ZB-5ms GC column, GC oven temperature 50 °C–260 °C (2 °C/min), 1-μL injection of 5% solution of EO in dichloromethane . Retention indices (RIs) were determined with reference to a homologous series of atabases ,8,9,10.Shimadzu GC 2010, FID detector, ZB-5 GC column, GC oven temperature 50 °C–260 °C (2.0 °C/min). The percent compositions were determined from raw peak areas without standardization.Shimadzu GCMS-QP2010S, Restek B-Dex 325 column, GC oven temperature 50 °C–120 °C (1.5 °C/min) then 120 °C–200 °C (2.0 °C/min), 0.1 μL injection of 5% solution of EO in dichloromethane . The enantiomeric distributions were determined by comparison of retention times with authentic samples obtained from Sigma-Aldrich . Relative enantiomer percentages were calculated from peak areas.Monarda growing in south Alabama. In addition, the enantiomeric distribution of terpenoids was also carried out. This work illustrates the wide variation in essential oil compositions based on geographical location as well as variations in enantiomeric distribution. It would be interesting to compare enantiomeric distributions for Monarda essential oils from other geographical locations and for other Monarda species. Nevertheless, the phenolic monoterpenoids thymol and/or carvacrol were found to dominate the compositions of M. citriodora, M. fistulosa, and M. punctata and support the traditional medicinal uses of these plants.This study presents, for the first time, analyses of the essential oils of three species of


Ferrigenium kumadai An22T (= JCM 30584T = NBRC 112974T = ATCC TSD-51T) is a microaerophilic iron oxidizer isolated from paddy field soil and belongs to the family Gallionellaceae. Here, we report the complete genome sequence of F. kumadai An22T, which was obtained from the hybrid data of Oxford Nanopore long-read and Illumina short-read sequencing. Ferrigenium kumadai, isolated from paddy soil has been described (F. kumadai An22T (= JCM 30584T = NBRC 112974T = ATCC TSD-51T).Microaerophilic iron-oxidizing bacteria, which are capable of oxidizing ferrous iron (Fe) under circumneutral pH and microoxic conditions, are a key player in the Fe redox cycle in environments . Howeverescribed . Here, wT and DNA preparation were described previously  were removed with Sickle v1.33 (https://github.com/najoshi/sickle). Short ONT reads  were filtered out with Filtlong v0.2.0 (https://github.com/rrwick/Filtlong), and then error correction of the reads was carried out on FMLRC v0.1.2 (Betaproteobacteria. Genes were annotated with DFAST v10 (Sideroxydans lithotrophicus ES-1 (GenBank accession number CP001965.1), Rhodopseudomonas palustris TIE-1 (CP058907.1), Mariprofundus ferrooxydans PV-1T (DS022294.1), and Acidithiobacillus ferrooxidans ATCC 23270T (CP001219.1). An orthologous gene cluster table among the genome sequences used was created  was found as a sole candidate gene of Fe(II) oxidation.The genome size of strain An22F. kumadai An22T was deposited to the DDBJ database under the accession number AP019536.1. The raw sequencing data were deposited under BioProject accession number PRJDB7995 and SRA accession numbers DRR168795 and DRR168796.The genome sequence of


Elevated resistance rates have been reported in ICUs. Aztreonam (ATM) combined with avibactam (AVI) is being developed for use against drug-resistant Enterobacterales (Ebact), including metallo-β-lactamase (MBL)-positive isolates. We examined the activity of ATM-AVI and comparators against Ebact isolates collected from geriatric patients in ICU and non-ICU wards as part of the ATLAS surveillance program.Escherichia coli, Klebsiella spp. and Proteus mirabilis with ATM or ceftazidime MIC >1 µg/mL.23754 non-duplicate Ebact isolates were collected in 53 countries in Asia/Pacific (excluding mainland China and India), Europe, Latin America, and Middle East/Africa from patients ≥65 years with lower respiratory tract (LRTI), urinary tract (UTI), skin and soft tissue (SSTI), intra-abdominal (IAI), and bloodstream (BSI) infections. Susceptibility testing was performed by CLSI broth microdilution and values interpreted using CLSI 2021 breakpoints. PCR and sequencing were used to determine the β-lactamase genes present in isolates with meropenem MIC >1 µg/mL, and 90 values were up to 32-fold higher. ATM-AVI MIC90 values were within one doubling-dilution across all studied strata (0.12-0.25 µg/mL), were comparable to or lower than for meropenem in all strata, and were 2 to ≥9 dilutions lower than all other tested comparators. MBL-positive Ebact were found in 1.5% of LRTI (n=91), 1.2% of UTI (n=70), 1.1% of SSTI (n=52), 1.3% of BSI (n=49), and 0.7% of IAI isolates (n=22). MBL-positive rates were higher among ICU  than non-ICU isolates . ATM-AVI MIC90 values were 0.5 µg/mL against MBL-positive isolates from all ward and infection types except SSTI (MIC90 0.25 µg/mL) and BSI (MIC90 1 µg/mL), 2-4 dilutions lower than tigecycline and at least 5-10 dilutions lower than the other comparators.Susceptibility of the studied comparator agents was generally slightly lower among Ebact from BSI than other infection types (Table). Susceptibility was also generally lower among Ebact from ICU than non-ICU wards by up to 10 percentage points, and MICResults TableATM-AVI could provide a valuable therapeutic option for treatment of infections caused by Ebact in patients ≥65 years old in both ICU and non-ICU wards.Sibylle Lob, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Krystyna Kazmierczak, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor) Francis Arhin, PhD, Pfizer, Inc. (Employee) Daniel F. Sahm, PhD, IHMA (Employee)Pfizer, Inc. (Independent Contractor)


Rhizopus species is the primary fungi responsible for 70% of mucormycosis cases.During the second wave of the COVID-19 pandemic, an unusual increase in cases of mucormycosis was observed in India, owing to immunological dysregulation caused by the SARS-CoV-2 and the use of broad-spectrum antibiotics, particularly in patients with poorly controlled diabetes with ketoacidosis to have contributed to the rise, and it has been declared an epidemic in several states of India. Because of the black colouring of dead and dying tissue caused by the fungus, it was dubbed "black fungus" by several Indian media outlets. In this study, attempts were taken to unmask novel therapeutic options to treat mucormycosis disease. Rhizopus delemar such as CotH3, Lanosterol 14 alpha-demethylase and Mucoricin which plays a crucial role in the virulence of Mucorales. Initially, we explored the physiochemical, structural and functional insights of proteins and later using AutoDock Vina, we applied computational protein–ligand binding modelling to perform a virtual screening around 300 selected compounds against these three proteins, including FDA-approved drugs, FDA-unapproved drugs, investigational-only drugs and natural bioactive compounds. ADME parameters, toxicity risk and biological activity of those compounds were approximated via in silico methods. Our computational studies identified six ligands as potential inhibitors against Rhizopus delemar, including 12,28-Oxamanzamine A, vialinin B and deoxytopsentin for CotH3; pramiconazole and saperconazole for Lanosterol 14 alpha-demethylase; and Hesperidin for Mucoricin. Interestingly, 12,28-Oxamanzamine A showed a maximum binding affinity with all three proteins .We chose three important proteins from the In summary, our investigation identified 12,28-Oxamanzamine A, vialinin B, deoxytopsentin, pramiconazole, saperconazole and hesperidin as potent bioactive compounds for treating mucormycosis that may be considered for further optimisation techniques and in vitro and in vivo studies.The online version contains supplementary material available at 10.1186/s42269-022-00704-4. Rhizopus species are the most common fungi in the order of Mucorales responsible for over 70% of mucormycosis cases  and diabetic ketoacidosis. SARS-Cov-2, in addition to mucormycosis, is a fatal combination that has caused a considerable number of deaths, particularly in India  acts as a fungal ligand for host cell GRP78 and mediates pathogenic host-cell interactions. The presence of CotH3 in Mucorales also explained why DKA patients with high GRP78 levels are more susceptible to mucormycosis  require a thorough examination of their structure and function, which will bring unique insights into the development of an effective, low-cost medicine with minimal side effects. Therefore, the current study aims to collect 300 compounds  that exhibit antiviral, antifungal, antibacterial and antimicrobial properties have been identified through different literature reviews, and it was screened against CotH3, Lanosterol 14 alpha-demethylase and Mucoricin by applying several in silico tools, viz., protein modelling, binding pocket prediction, molecular docking, ADME and drug-likeness screening, bioactivity prediction and toxicity prediction , cytochrome P450 enzyme Lanosterol 14 alpha-demethylase (ACCESSION: EIE87079) and ricin-like toxin Mucoricin (ACCESSION: EIE81863) . Various physicochemical properties of the CotH3, Lanosterol 14 alpha-demethylase and Mucoricin were calculated using ExPasy's ProtParam tool   NPS@ .All three proteins  were subjected to 3D modelling. CotH3 was modelled via SWISS-MODEL  3.0 was used to predict probable binding pockets of the proteins , part of MGLTools  program  alpha helix, 13.95% (36 residues) extended strand, 2.71% (7 residues) beta turn and 43.02% (111 residues) random coil, while Lanosterol 14 alpha-demethylase showed to have 49.80% (254 residues) alpha helix, 10.78% (55 residues) extended strand, 3.14% (16 residues) beta turn and 36.27% (185 residues) random coil. Similarly, Mucoricin exhibited 5.44% (8 residues) alpha helix, 40.14% (59 residues) extended strand, 14.97% (22 residues) beta turns and 39.46% (58 residues) random coil.Bacillus cereus CotH kinase (PDB ID: 5JD9)  = 0.02 nM) and acts as a promising anti-allergic agent . The compound displayed potent low nanomolar inhibitory activity against MRSA PK with significant concomitant selectivity over human PK orthologues -dien-3, β-6α-diol and 14α-methylergosta-5,7,22,24(28)-tetraenol , Parsiguine (B), Haliclonacyclamine B (C), Vialinin B (D), 6-Deoxymanzamine X (E), Natamycin (F), Olorofim (G), Deoxytopsentin (H), Manzamine E (I), Fascioquinol A (J). Figure S2. 2D visualisation of docking analysis of Lanosterol 14 alpha-demethylase binding with Pramiconazole (A), 12,28-Oxamanzamine A (B), Fascioquinol D (C), Saperconazole (D), Nakadomarin A (E), Plakinamine A (F), Fascioquinol C (G), Parsiguine (H), Hesperidin (I), Epoxyazadiradione (J). Figure S3. 2D visualisation of docking analysis of Mucoricin binding with 12,28-Oxamanzamine A (A), Manzamine A (B), Parsiguine (C), Halicyclamine A (D), Tetrahydrohaliclonacyclamine A (E), Phaeosphenone (F), 6-Deoxymanzamine X (G), Goniodomin A (H), Hesperidin (I), Stelletin A (J).Additional file 2: Table S1. The variants of mucormycosis and the symptoms associated with the disease .Additional file 3: Data 1. Binding affinities of all bioactive compunds with our three target proteins.


Literature on SARS-CoV-2 infection in cancer patients is scarce in Latin America. This population seems to have a higher risk for adverse outcomes. This study aims to correlate clinical characteristics with outcomes in patients with cancer in a referral center in Mexico.We included patients with cancer and confirmed SARS-CoV-2 infection, from April, 19 to December 30, 2020, at the Instituto Nacional de Cancerología, Mexico. Clinical information was obtained from medical and epidemiological records. We conducted a descriptive analysis. For the association between variables with hospitalization, invasive mechanical ventilation (IMV), and mortality; univariate and multivariate logistic regression was performed; odds ratios and 95% confidence intervals were calculated.Four hundred thirty-three patients were included; 268 (62%) were female, the median age was 55 years. One hundred thirty-five (31%), 130 (30%), and 93 (21%) patients had obesity, hypertension, and diabetes mellitus (DM), respectively. Three hundred forty-one (79%) had solid cancer; 82 (19%) hematological malignancy (HM), and 10 (2%) were under evaluation for cancer diagnosis. One hundred seventy (39%) had advanced or metastatic cancer. One hundred ninety-eight (46%) patients were hospitalized. Risk factors were: age (p= 0.001); woman (p=0.019); HM (p=0.050) and advanced or metastatic cancer (p= 0.041). Fourty-five (10%) patients required IMV. Age (p=0.018); DM (p=0.041); C-Reactive Protein (p= 0.002), and LDH (p= 0.033) were associated with invasive mechanical ventilation. Mortality within 30-days after diagnosis was 19% (82 cases). Associated characteristics were: age (p=0.041); lymphocytes (p=0.049); creatinine (p=0.005) and albumin (p=0.001).In this study, patients with cancer showed higher mortality, need of hospitalization, and invasive mechanical ventilation compared with groups of patients without cancer. We did not find an increased risk in mortality for hematological malignancies. Although our cohort was younger than others previously reported, age was a strong predictor of adverse outcomes. Variables associated with IMV and death were similar to those previously described in cancer patients with COVID-19.All Authors: No reported disclosures


Despite well-established guidelines for urinary tract infection (UTI) treatment, prescribing practices vary. We examined the association between inappropriate (IA) or suboptimal (SO) antibiotic (AB) prescribing (RX) and hospitalization, healthcare resource use (HRU), and costs among patients with uncomplicated UTI (uUTI) in the US.Table 1) were assessed from Optum claims data during index episode (within 28 days of index) and 12-month follow-up.This retrospective cohort study used linked Premier Healthcare/Optum claims data from female outpatients (≥ 12 years old) with a uUTI diagnosis . Patients with complicated UTIs  were excluded. HRU and costs between patients with IA/SO and appropriate and optimal (AP&OP) AB RX (defined in Table 1. Definitions of appropriateness of AB RXTable 2). During index episode, mean ambulatory care and pharmacy claims were significantly higher for IA/SO versus AP&OP AB RX , and total HRU cost per patient was higher for IA/SO (&2616) versus AP&OP AB RX . During follow-up, 267 (9.7%) patients with IA/SO AB RX had a UTI-related emergency department (ED) visit versus 202 (6.5%) patients with AP&OP AB RX (p < 0.001). Mean UTI-related HRU costs were significantly higher for IA/SO (&5048) versus AP&OP AB RX . After adjusting for patient characteristics, patients with IA/SO AB RX were 40% more likely than those with AP&OP AB RX to have a UTI-related ED visit  during follow-up (Table 3). Adjusted HRU costs for IA/SO AB RX (vs AP&OP) were numerically higher for index uUTI episode (by &1772), and UTI-related (by &1102) and all-cause (by &1528) charges during follow-up .Of 5870 patients, 1856 (31.6%) had IA and 1255 (21.4%) had SO AB RX. Patients with IA/SO AB RX (47.1%) were older and more likely to have a Charlson Comorbidity Index score > 0 than those with AP&OP AB RX , stratified by appropriateness of AB RX at index and during follow-upIA/SO AB RX was associated with higher overall and UTI-related HRU and costs during index episode and 12-month follow-up, highlighting a need for education on applying prescription guidelines and the use of culture-based RX.Rena Moon, MD, Premier Applied Sciences, Premier Inc. (Employee) Alen Marijam, MSc, GlaxoSmithKline plc.  Fanny S. Mitrani-Gold, MPH, GlaxoSmithKline plc.  Daniel C. Gibbons, PhD, GlaxoSmithKline plc.  Alex Kartashov, PhD, Premier Applied Sciences, Premier Inc. (Employee) Ning Rosenthal, MD, Premier Applied Sciences, Premier Inc.  Ashish V. Joshi, PhD, GlaxoSmithKline plc.


Oncogene (2020) 39:5616–5632, 10.1038/s41388-020-01388-8, published online 13 July 2020Correction to: Following the publication of the above article, the authors noted two errors in Fig. p < 0.05, ** p < 0.01.Supplemental Fig. 2: Overexpression of LINC01503 promotes NPC cell growth, migration, and invasion in vitro. (a) Relative expression of LINC01503 in 5-8F and HONE1 cells transfected with LINC01503-expressing plasmid and empty vector. (b) LINC01503 overexpression promoted cell growth of 5-8F and HONE1 cells as shown by CCK-8 assays. (c) LINC01503 overexpression facilitated cellular survival effects as evaluated by colony formation assays. (d) LINC01503 overexpression accelerated the movement of 5-8F and HONE1 cells as assessed by wound healing assays. Scale bar, 100 μm. (e) LINC01503 overexpression promoted the migration and invasion ability of 5-8F and HONE1 cells as determined by transwell assays. Scale bar, 100 μm. * The original article has been corrected.Supplementary Fig. 2


Hemophagocytic lymphohistiocytosis (HLH) is a disease that can affect both children and adults. HLH can be categorized as primary or secondary. Secondary HLH (sHLH) may be secondary to various viral infections. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infection is a pandemic with multi-system involvement. HLH in COVID-19 positive patients is a recognized entity. However, in post-COVID-19 patients who have recovered and are negative by serological tests and reverse transcription-polymerase chain reaction test may present with sHLH due to dysregulation of the immune system. We highlight this unusual finding of post-COVID-19 sHLH in two cases, who were diagnosed by the new revised H-score. Hemophagocytic lymphohistiocytosis (HLH) is a lethal disorder of varying etiology and encompasses a wide range of diseases. Familial HLH (FHLH) and immune-related HLH constitute the primary HLH spectrum whereas infections, drug-related and transplantation, malignancies, and macrophage activation syndrome (MAS) constitute the secondary HLH (sHLH) spectrum . LaboratCase 12 was 88%, and the temperature was 40̊C. On examination, pallor was present. Bilateral crepitations and rhonchi were present in respiratory system auscultation. The cardiovascular system was unremarkable and central nervous system examination showed no focal neurological deficit. Ultrasonography of the whole abdomen revealed hepatosplenomegaly. High-resolution computed tomography (HRCT) thorax showed CO-RADS category 6 and CT severity of 15/25. Bone marrow aspirate showed evidence of hemophagocytosis  and was hospitalized for 1.5 months. At presentation, the patient was conscious, alert, and oriented. Her blood pressure was 96/58 mmHg, pulse rate was 118 beats per minute, respiratory rate was 33/min and SPO3 /µL with differential leukocyte count (DLC) of N87L10M03E0, and platelet count of 20x103 /µL. Biochemical investigations revealed serum urea of 61 mg/dL (reference range [RR]: 17-45 mg/dL), serum creatinine of 0.9 mg/dL (RR: 0.6-1.4 mg/dL), D-dimer of 1.58 mg/L (RR: 0-0.5 mg/L), aspartate aminotransferase (AST) of 76 IU/L (RR: 5-40 IU/L), alanine aminotransferase (ALT) of 98 IU/L (RR: 5-55 IU/L), alkaline phosphatase (ALP) of 137 IU/L (RR: 20-140 IU/L), total bilirubin of 2.5 mg/dL (RR: up to 1.2 mg/dL), direct bilirubin of 1.3 mg/dL (RR: 0-0.2 mg/dL), IL-6 of 11.56 pg/mL (RR: 5-15 pg/mL), fibrinogen of 2.3 g/L (RR: 2-4 g/L), vitamin B12 of 489.5 pg/mL (RR: 160-950 pg/mL), ferritin of 170.2 ng/L (RR:12-250 ng/L), and C-reactive protein of 77mg/L (RR: 0-10 mg/L). Direct Coombs test was negative and indirect cold antibodies titer was more than 256 (RR: less than 164). All viral markers, anti-nuclear antibody (ANA), and glucose-6-phosphate dehydrogenase (G6PD) were negative. The H-score estimated as per the H-score of 2014 was 213 points with a probability of sHLH to be 93% to 96%  of 3.3 g%, total leukocyte count (TLC) of 18.3x10According to the protocols of our institute, the patient was isolated and started on intravenous steroids (dexamethasone acetate 10 mg/day), low molecular weight heparin (LMWH), antibiotics, and oxygen support. Considering the deranged kidney function, strict monitoring and adequate hydration were provided along with four units of whole blood transfusion. The patient developed congestive cardiac failure during the hospital stay and oral diuretics were initiated. The patient responded to treatment without the addition of etoposide and was hemodynamically stable. She was discharged after four weeks of hospital stay. The patient was reviewed after 14 days and was stable.Case 23 /µL with DLC N86L10M02E02, and platelet count of 60x103 /µL. Biochemical investigations showed serum ferritin of 188.0 ng/mL (RR: 7-140 ng/mL), IL-6 of 1,057 pg/mL (RR: 1-5 pg/mL), D-dimer of 1.76 mg/L (RR: 0-0.5 mg/L), AST of 182 IU/L (RR:10-40 IU/L), ALT of 77 IU/L (RR:10-40 IU/L), ALP of 77 IU/L (RR: <350 IU/L), C-reactive protein of 62.1 mg/L (RR: 0.02-14.5 mg/L), and fibrinogen of 2.13 g/L (RR: 2-4 g/L). Malaria, scrub typhus, HBsAg, anti-HCV were negative. Bone marrow aspirate revealed features of hemophagocytosis with increased iron , diarrhea, and vomiting for two days. The patient had no previous episodes in the past and developmental milestones were achieved at his age normally. On examination of muscle tone, neck control was decreased. A possible diagnosis of post-viral encephalitis was considered. The patient was positive for SARS-CoV-2 virus by RT-PCR and was admitted to COVID-19 designated hospital. He was discharged after testing negative for the SARS-CoV-2 virus. After two weeks of discharge, he presented with the above symptoms but was negative for COVID-19 by RAT and RT-PCR. MRI brain showed features suggestive of viral encephalitis with atrophy of cerebral hemispheres and peritrigonal white matter hyperintensities. Laboratory findings revealed Hb of 7.1 g%, TLC of 7.3x10The H-score estimated as per the H-score of 2014 was 239 points with a probability of sHLH to be 98% to 99% , laboratory , and histological parameters , which was modified in 2004 . The HLHThe optimal cut-off for a diagnosis of HLH was considered to be 169 by Fardet et al. with 93% sensitivity and 86% specificity . In our HLH in COVID-19 positive patients is reported in various case reports ,15. HoweSARS-CoV-2 infection is a recent pandemic with important complications inherent to its multisystemic affections. Recent information about etiopathogenesis, clinical signs and symptoms, and treatment protocols are getting highlighted. sHLH is a condition primarily occurring in COVID-19 positive patients; however, sHLH in post-COVID-19 patients is rare. Immune dysregulation following infection by the SARS-CoV-2 virus may be the prime reason for sHLH in such patients. We highlighted two such post-COVID-19 patients who were negative for COVID-19 at the time of presentation but were diagnosed as cases of sHLH based on the H-score.