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Abstract T cell engagers (TCE) such as chimeric antigen receptor (CAR) T cell therapy and bispecific antibodies (BiAbs) for the treatment of multiple myeloma (MM) have significantly improved clinical outcomes, but have also raised awareness for ensuing post-treatment secondary immunodeficiency and hypogammaglobulinemia (HG). As patients with MM live longer, recurrent infections become a significant component of therapy-associated morbidity and mortality. Treatment of HG with immunoglobulin G replacement therapy (IgG-RT) has been a mainstay of the primary immunodeficiency (PI) world, and extrapolation to MM has recently started to show promising clinical outcomes. However, IgG-RT initiation, dosing, route, timing, monitoring, and management in MM has not been standardized in the setting of TCE. Progress in MM treatment will involve greater recognition and screening of underlying secondary immunodeficiency, identification of risk-stratification markers, optimizing IgG-RT management, and implementing other approaches to decrease the risk of infection. In this review, we summarize infection risk, risk of HG, and management strategies for IgG-RT in patients with relapsed MM after TCE.

Linking outbreaks of Shigella spp. to specific foods is challenging due to poor selectivity of current enrichment media. We have previously shown that enrichment media, tailored to the genomically-predicted antimicrobial resistance (AMR) of Shiga toxigenic E. coli strains, enhances their isolation from foods. This study investigates the application of this approach for Shigella isolation. The AMR gene profiles of 21,908 published S. sonnei genomes indicated a high prevalence of genes conferring resistance to streptomycin (aadA, aph(3″)-Ib, aph(6)-Id, 92.8%), sulfonamides (sul1, sul2, 74.8%), and/or trimethoprim (dfrA, 96.2%). Genomic analysis and antibiotic susceptibility testing conducted with a panel of 17 outbreak-associated S. sonnei strains confirmed the correlation of AMR gene detection with resistance phenotypes. Supplementation of Shigella Broth (SB) with up to 400 µg/mL of trimethoprim or sulfadiazine did not suppress the growth of sensitive strains, whereas 100 µg/mL of streptomycin increased the selectivity of this broth. All three antibiotics increased the selectivity of modified Tryptone Soya Broth (mTSB). Based on these results, supplemented media formulations were developed and assessed by measuring the relative growth of S. sonnei in cultures coinoculated with a strain of bacteriocin-producing E. coli that is inhibitory to Shigella growth. S. sonnei was not recovered from cocultures grown in SB or mTSB without antibiotics. In contrast, media supplemented with streptomycin at 50 and 100 µg/mL, trimethoprim at 25 and 50 µg/mL, and sulfadiazine at 100 µg/mL increased the relative proportion of S. sonnei in postenrichment cultures. The enhanced recovery of resistant S. sonnei strains achieved in this study indicates that, in cases where genomic data are available for clinical S. sonnei isolates, customization of selective enrichment media based on AMR gene detection could be a valuable tool for supporting the investigation of foodborne shigellosis outbreaks.

Shigella spp. are Gram-negative gastrointestinal bacterial pathogens that cause bacillary dysentery or shigellosis in humans. Isolation of Shigella from outbreak-associated foods is often problematic due to the lack of selectivity of cultural enrichment broths. To facilitate Shigella recovery from foods, we have developed strain-specific enrichment media based on the genomically-predicted antimicrobial resistance (AMR) features of an outbreak-associated Shigella sonnei strain harboring resistance genes for streptomycin (STR) and trimethoprim (TMP). To assess performance of the method, baby carrots were artificially contaminated with the S. sonnei strain at low (2.4 CFU), medium (23.5 CFU), and high levels (235 CFU) along with 10-fold higher levels of a Shigella-inhibiting Escherichia coli strain. The target S. sonnei strain was successfully recovered from artificially-contaminated baby carrots when enriched in modified Tryptone Soya Broth (mTSB) supplemented with TMP, whereas Shigella was not recovered from Shigella broth (SB) or SB supplemented with STR. Quantitative PCR analysis indicated that supplementation of the enrichment broths with TMP or STR increased the relative proportion of S. sonnei in enrichment cultures, except at the lowest inoculation level for STR. Microbiome profiling of the baby carrot enrichment cultures conducted by 16S rRNA gene sequencing indicated that both SB-STR and mTSB-TMP repressed the growth of competing Enterobacteriaceae in the enrichment cultures, relative to SB without supplementation. Overall, improved Shigella recovery was achieved with the addition of the appropriate custom selective agent during cultural enrichments demonstrating that genomically informed custom selective enrichment of Shigella could be a valuable tool for supporting future foodborne shigellosis outbreak investigations.

Background and Aims: Secretion and transport of intestinal chylomicrons (CMs) via lymphatics to the blood circulation is stimulated primarily by fat ingestion, whereas several other factors have also been shown to play important roles in regulating CM secretion rate. Among these factors, active regulation of lymphatic pumping has not been appreciated to date. The gut peptide and intestinal growth factor glucagon-like peptide-2 (GLP-2) has emerged as a robust enhancer of intestinal lipid mobilization and secretion. The present study aims to elucidate GLP-2’s impact on lacteal contractility and assess enteric nervous system (ENS) involvement in GLP-2–induced effects on lipid mobilization. Methods: Using intravital imaging of a prospero-related homeobox 1-enhanced green fluorescent protein rat model, we assessed GLP-2’s effect on lacteal contractility, in the presence and absence of the ENS inhibitor mecamylamine (MEC). Concurrently, to explore the physiological relevance, we examined GLP-2’s impact on lymph flow and triglyceride (TG) output in vivo in a rat lymph fistula model. Results: GLP-2 significantly increased lacteal contractility, and this effect was inhibited by MEC. In the rat lymph fistula model, GLP-2 increased lymph flow, lymph volume, cumulative lymph volume, and TG output while reducing lymph TG concentration. MEC administration blocked these effects of GLP-2. Peak enhancement of lacteal contractility and enhancement of lymph flow in vivo occurred simultaneously with maximal effect at 15–20 minutes post GLP-2 administration, suggesting that GLP-2 enhances lipid transport by stimulating lymphatic contractility. Conclusion: For the first time, through imaging and concurrent rat lymphatic fistula studies, we demonstrated active regulation of lymphatic contractility as a key determinant of CM secretion and that intact ENS was required to observe this effect.

Abstract Background Although the spread of antimicrobial resistance (AMR) through food and its production poses a significant concern, there is limited research on the prevalence of AMR bacteria in various agri-food products. Sequencing technologies are increasingly being used to track the spread of AMR genes (ARGs) in bacteria, and metagenomics has the potential to bypass some of the limitations of single isolate characterization by allowing simultaneous analysis of the agri-food product microbiome and associated resistome. However, metagenomics may still be hindered by methodological biases, presence of eukaryotic DNA, and difficulties in detecting low abundance targets within an attainable sequence coverage. The goal of this study was to assess whether limits of detection of ARGs in agri-food metagenomes were influenced by sample type and bioinformatic approaches. Results We simulated metagenomes containing different proportions of AMR pathogens and analysed them for taxonomic composition and ARGs using several common bioinformatic tools. Kraken2/Bracken estimates of species abundance were closest to expected values. However, analysis by both Kraken2/Bracken indicated presence of organisms not included in the synthetic metagenomes. Metaphlan3/Metaphlan4 analysis of community composition was more specific but with lower sensitivity than the Kraken2/Bracken analysis. Accurate detection of ARGs dropped drastically below 5X isolate genome coverage. However, it was sometimes possible to detect ARGs and closely related alleles at lower coverage levels if using a lower ARG-target coverage cutoff (

Abstract Background Tetanus is a life-threatening vaccine-preventable disease found more commonly in tropical climates. It accounted for up to 60 deaths annually until the introduction of the tetanus toxoid. It is now rare in Canada by immunization. This study aims to describe a case of tetanus in Saskatchewan with possible occupational exposure. Case Report We describe the case of a vaccinated soil expert with tetanus resulting from skin abrasions. This report highlights the early diagnosis, atypical presentation with possible vaccine attenuation and management approach, including acute care, intensive care unit referral, surgical management and physical rehabilitation. We also describe the public health management provided in this case. Despite the severity, the patient returned to his previous home environment with minimal motor sequelae. Conclusion Occupational exposure to tetanus is an important risk, even in regions where the disease is rare. Prevention through vaccination is a key public health intervention that must be encouraged to avoid health complications that are often fatal.

Collateral sensitivity (CS), whereby resistance to one drug is accompanied by increased sensitivity to another, provides new opportunities for antimicrobial drug discovery. Here, Liu et al. screen large chemical libraries across 29 drug-resistant E. coli strains to identify multiple CS interactions, including natural products with potent CS activities against cephalosporin-resistant strains.

Understanding the role of foods in the emergence and spread of antimicrobial resistance necessitates the initial documentation of antibiotic resistance genes within bacterial species found in foods. Here, the NCBI Pathogen Detection database was used to query antimicrobial resistance gene prevalence in foodborne and human clinical bacterial isolates. Of the 1,843,630 sequence entries, 639,087 (34.7%) were assigned to foodborne or human clinical sources with 147,788 (23.14%) from food and 427,614 (76.88%) from humans. The majority of foodborne isolates were either Salmonella (47.88%), Campylobacter (23.03%), Escherichia (11.79%), or Listeria (11.3%), and the remaining 6% belonged to 20 other genera. Most foodborne isolates were from meat/poultry (95,251 or 64.45%), followed by multi-product mixed food sources (29,892 or 20.23%) and fish/seafood (6503 or 4.4%); however, the most prominent isolation source varied depending on the genus/species. Resistance gene carriage also varied depending on isolation source and genus/species. Of note, Klebsiella pneumoniae and Enterobacter spp. carried larger proportions of the quinolone resistance gene qnrS and some clinically relevant beta-lactam resistance genes in comparison to Salmonella and Escherichia coli. The prevalence of mec in S. aureus did not significantly differ between meat/poultry and multi-product sources relative to clinical sources, whereas this resistance was rare in isolates from dairy sources. The proportion of biocide resistance in Bacillus and Escherichia was significantly higher in clinical isolates compared to many foodborne sources but significantly lower in clinical Listeria compared to foodborne Listeria. This work exposes the gaps in current publicly available sequence data repositories, which are largely composed of clinical isolates and are biased towards specific highly abundant pathogenic species. We also highlight the importance of requiring and curating metadata on sequence submission to not only ensure correct information and data interpretation but also foster efficient analysis, sharing, and collaboration. To effectively monitor resistance carriage in food production, additional work on sequencing and characterizing AMR carriage in common commensal foodborne bacteria is critical.

Patients hospitalized with SARS-CoV-2 infections are major contributors to morbidity and mortality in health care settings. Our understanding of the distribution of this virus in the built health care environment and wastewater, and relationship to disease burden, is limited. We performed a prospective multi-center study of environmental sampling of SARS-CoV-2 from hospital surfaces and wastewater and evaluated their relationships with regional and hospital COVID-19 burden. We validated a qPCR-based approach to surface sampling and collected swab samples weekly from different locations and surfaces across two tertiary care hospital campuses for a 10-week period during the pandemic, along with wastewater samples. Over the 10-week period, 963 swab samples were collected and analyzed. We found 61 (6%) swabs positive for SARS-CoV-2, with the majority of these (n = 51) originating from floor samples. Wards that actively managed patients with COVID-19 had the highest frequency of positive samples. Detection frequency in built environment swabs was significantly associated with active cases in the hospital throughout the study. Wastewater viral signal changes appeared to predate change in case burden. Our results indicate that environment sampling for SARS-CoV-2, in particular from floors, may offer a unique and resolved approach to surveillance of COVID-19.

BackgroundSARS-CoV-2 can be detected from the built environment (e.g., floors), but it is unknown how the viral burden surrounding an infected patient changes over space and time. Characterizing these data can help advance our understanding and interpretation of surface swabs from the built environment.MethodsWe conducted a prospective study at two hospitals in Ontario, Canada between January 19, 2022 and February 11, 2022. We performed serial floor sampling for SARS-CoV-2 in rooms of patients newly hospitalized with COVID-19 in the past 48 hours. We sampled the floor twice daily until the occupant moved to another room, was discharged, or 96 hours had elapsed. Floor sampling locations included 1 metre (m) from the hospital bed, 2 m from the hospital bed, and at the room's threshold to the hallway (typically 3 to 5 m from the hospital bed). The samples were analyzed for the presence of SARS-CoV-2 using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR). We calculated the sensitivity of detecting SARS-CoV-2 in a patient with COVID-19, and we evaluated how the percentage of positive swabs and the cycle threshold of the swabs changed over time. We also compared the cycle threshold between the two hospitals.ResultsOver the 6-week study period we collected 164 floor swabs from the rooms of 13 patients. The overall percentage of swabs positive for SARS-CoV-2 was 93% and the median cycle threshold was 33.4 (interquartile range [IQR]: 30.8, 37.2). On day 0 of swabbing the percentage of swabs positive for SARS-CoV-2 was 88% and the median cycle threshold was 33.6 (IQR: 31.8, 38.2) compared to swabs performed on day 2 or later where the percentage of swabs positive for SARS-CoV-2 was 98% and the cycle threshold was 33.2 (IQR: 30.6, 35.6). We found that viral detection did not change with increasing time (since the first sample collection) over the sampling period, Odds Ratio (OR) 1.65 per day (95% CI 0.68, 4.02; p = 0.27). Similarly, viral detection did not change with increasing distance from the patient's bed (1 m, 2 m, or 3 m), OR 0.85 per metre (95% CI 0.38, 1.88; p = 0.69). The cycle threshold was lower (i.e., more virus) in The Ottawa Hospital (median quantification cycle [Cq] 30.8) where floors were cleaned once daily compared to the Toronto hospital (median Cq 37.2) where floors were cleaned twice daily.ConclusionsWe were able to detect SARS-CoV-2 on the floors in rooms of patients with COVID-19. The viral burden did not vary over time or by distance from the patient's bed. These results suggest floor swabbing for the detection of SARS-CoV-2 in a built environment such as a hospital room is both accurate and robust to variation in sampling location and duration of occupancy.

Bacterial pathogens, such as Shiga toxin-producing Escherichia coli (STEC) and Shigella spp., are important causes of foodborne illness internationally. Recovery of these organisms from foods is critical for food safety investigations to support attribution of illnesses to specific food commodities; however, isolation of bacterial cultures can be challenging. Methods for the isolation of STEC and Shigella spp. from foods typically require enrichment to amplify target organisms to detectable levels. Yet, during enrichment, target organisms can be outcompeted by other bacteria in food matrices due to faster growth rates, or through production of antimicrobial agents such as bacteriocins or bacteriophages. The purpose of this study was to evaluate the occurrence of Shigella and STEC inhibitors produced by food microbiota. The production of antimicrobial compounds in cell-free extracts from 200 bacterial strains and 332 food-enrichment broths was assessed. Cell-free extracts produced by 23 (11.5%) of the strains tested inhibited growth of at least one of the five Shigella and seven STEC indicator strains used in this study. Of the 332 enrichment broths tested, cell-free extracts from 25 (7.5%) samples inhibited growth of at least one of the indicator strains tested. Inhibition was most commonly associated with E. coli recovered from meat products. Most of the inhibiting compounds were determined to be proteinaceous (34 of the 48 positive samples, 71%; including 17 strains, 17 foods) based on inactivation by proteolytic enzymes, indicating presence of bacteriocins. The cell-free extracts from 13 samples (27%, eight strains, five foods) were determined to contain bacteriophages based on the observation of plaques in diluted extracts and/or resistance to proteolytic enzymes. These results indicate that the production of inhibitors by food microbiota may be an important challenge for the recovery of foodborne pathogens, particularly for Shigella sonnei. The performance of enrichment media for recovery of Shigella and STEC could be improved by mitigating the impact of inhibitors produced by food microbiota during the enrichment process.

Bacterial carbapenem resistance is a major public health concern since these antimicrobials are often the last resort to treat serious human infections. To evaluate methodologies for detection of carbapenem resistance, carbapenem-tolerant bacteria were isolated from wastewater treatment plants in Toronto, Ottawa, and Arnprior, Ontario. A total of 135 carbapenem-tolerant bacteria were recovered. Polymerase chain reaction (PCR) indicated the presence of carbapenem hydrolysing enzymes KPC (n = 10), GES (n = 5), VIM (n = 7), and IMP (n = 1), and β-lactamases TEM (n = 7), PER (n = 1), and OXA-variants (n = 16). A subset of 46 isolates were sequenced and analysed using ResFinder and CARD-RGI. Both programs detected carbapenem resistance genes in 35 sequenced isolates and antimicrobial resistance genes (ARGs) conferring resistance to multiple class of other antibiotics. Where β-lactamase resistance genes were not initially identified, lowering the thresholds for ARG detection enabled identification of closely related β-lactamases. However, no known carbapenem resistance genes were found in seven sequenced Pseudomonas spp. isolates. Also of note was a multi-drug-resistant Klebsiella pneumoniae isolate from Ottawa, which harboured resistance to seven antimicrobial classes including β-lactams. These results highlight the diversity of genes encoding carbapenem resistance in Ontario and the utility of whole genome sequencing over PCR for ARG detection where resistance may result from an assortment of genes.

Abstract A strain profile measurement technique using a chirped fibre Bragg grating (CFBG) sensor by implementing an integration of differences (IOD) method is reported in this paper. Using the IOD method the spatial distribution of strain along the length of the CFBG is extracted from its power reflectance spectra. As a proof of concept demonstration, the developed technique is applied to measure the polymerisation shrinkage strain profile of a photo-cured polymer dental composite which exhibits a non-uniform strain distribution attributed to the curing lamp characteristics. The result from the CFBG technique is compared with that of an FBG array embedded in the dental composite and is correlated with the degree of conversion of the material which also depends on the curing lamp intensity distribution. This technology will have significant impact and applications in a range of medical, materials and engineering areas where strain or temperature gradient profile measurement is required in smaller scales.

Introduction Gender affirming hormone therapy (GAHT) is increasingly used by transgender individuals and leads to shifts in sex hormone levels. Skeletal muscle is highly responsive to hormone activity, with limited data on the effects of GAHT on different human tissues. Here, we present the protocol for the GAME study (the effects of Gender Affirming hormone therapy on skeletal Muscle training and Epigenetics), which aims to uncover the effects of GAHT on skeletal muscle ‘omic’ profiles (methylomics, transcriptomics, proteomics, metabolomics) and markers of skeletal muscle health and fitness.Methods and analysis This study is a prospective age-matched cohort study in transgender adults commencing GAHT (n=80) and age-matched individuals not commencing GAHT (n=80), conducted at Austin Health and Victoria University in Victoria, Australia. Assessments will take place prior to beginning GAHT and 6 and 12 months into therapies in adults commencing GAHT. Age-matched individuals will be assessed at the same time points. Assessments will be divided over three examination days, involving (1) aerobic fitness tests, (2) muscle strength assessments and (3) collection of blood and muscle samples, as well as body composition measurements. Standardised diets, fitness watches and questionnaires will be used to control for key confounders in analyses. Primary outcomes are changes in aerobic fitness and muscle strength, as well as changes in skeletal muscle DNA methylation and gene expression profiles. Secondary outcomes include changes in skeletal muscle characteristics, proteomics, body composition and blood markers. Linear mixed models will be used to assess changes in outcomes, while accounting for repeated measures within participants and adjusting for known confounders.Ethics and dissemination The Austin Health Human Research Ethics Committee (HREC) and Victoria University HREC granted approval for this study (HREC/77146/Austin-2021). Findings from this project will be published in open-access, peer-reviewed journals and presented to scientific and public audiences.Trial registration number ACTRN12621001415897; Pre-results.

In light of the rising prevalence of antimicrobial resistance (AMR) and the slow pace of new antimicrobial development, there has been increasing interest in the development of adjuvants that improve or restore the effectiveness of existing drugs. Here, we use a novel small RNA (sRNA) screening approach to identify genes whose knockdown increases ciprofloxacin (CIP) sensitivity in a resistant strain of Escherichia coli. 5000 sRNA constructs were initially screened on a gyrA S83L background, ultimately leading to 30 validated genes whose disruption reduces CIP resistance. This set includes genes involved in DNA replication, repair, recombination, efflux, and other regulatory systems. Our findings increase understanding of the functional interactions of DNA Gyrase, and may aid in the development of new therapeutic approaches for combating AMR.

The rise in antimicrobial resistant bacteria is limiting the number of effective treatments for bacterial infections. Escherichia coli and Pseudomonas aeruginosa are two of the pathogens with the highest prevalence of resistance, and with the greatest need for new antimicrobial agents. Combinations of antimicrobial peptides (AMPs) and antibiotics that display synergistic effects have been shown to be an effective strategy in the development of novel therapeutic agents. In this study, we investigated the synergy between the AMP LL-37 and various classes of antibiotics against E. coli and P. aeruginosa strains. Of the six antibiotics tested (ampicillin, tetracycline, ciprofloxacin, gentamicin, aztreonam, and polymyxin B (PMB)), LL-37 displayed the strongest synergy against E. coli MG1655 and P. aeruginosa PAO1 laboratory strains when combined with PMB. Given the strong synergy, the PMB + LL-37 combination was chosen for further examination where it demonstrated synergy against multidrug-resistant and clinical E. coli isolates. Synergy of PMB + LL-37 towards clinical isolates of P. aeruginosa varied and showed synergistic, additive, or indifferent effects. The PMB + LL-37 combination treatment showed significant prevention of biofilm formation as well as eradication of pre-grown E. coli and P. aeruginosa biofilms. Using the Galleria mellonella wax worm model, we showed that the PMB + LL-37 combination treatment retained its antibacterial capacities in vivo. Flow analyses were performed to characterize the mode of action. The results of the present study provide proof of principle for the synergistic response between LL-37 and PMB and give novel insights into a promising new antimicrobial combination against gram-negative planktonic and biofilm cells.

The aim of this study was to characterize the prevalence of fecal carriage of extended-spectrum beta-lactamases and carbapenemase-producing Gram-negative bacteria among healthy humans in Tunisia. Fifty-one rectal swabs of healthy volunteers were plated on MacConkey agar plates supplemented with cefotaxime or imipenem. The occurrences of resistance genes, integrons, and phylogroup typing were investigated using PCR and sequencing. The genetic relatedness of isolates was determined by pulsed-field-gel-electrophoresis (PFGE) and multilocus-sequence-typing (MLST). Whole-genome-sequencing (WGS) was performed for the carbapenem-resistant isolate. Sixteen ESBL-producing Escherichia coli isolates and one carbapenem-resistant Enterobacter bugandensis were detected out of the fifty-one fecal samples. The ESBL-producing E. coli strains contained genes encoding CTX-M-15 (n = 9), CTX-M-1 (n = 3), CTX-M-27 (n = 3), and CTX-M-55 (n = 1). Three CTX-M-1-producers were of lineages ST131, ST7366, and ST1158; two CTX-M-15-producers belonged to lineage ST925 and ST5100; one CTX-M-27-producer belonged to ST2887, and one CTX-M-15-producer belonged to ST744. Six isolates contained class 1 integrons with the following four gene cassette arrangements: dfrA5 (two isolates), dfrA12-orf-aadA2 (two isolates), dfrA17-aadA5 (one isolate), and aadA1 (one isolate). E. bugandensis belonged to ST1095, produced IMI-2 carbapenemase, and contained qnrE1 and fosA genes. A genome-sequence analysis of the E. bugandensis strain revealed new mutations in the blaACT and qnr genes. Our results reveal an alarming rate of ESBL-E. coli in healthy humans in Tunisia and the first description of IMI-2 in E. bugandensis.

Abstract Background Hepatitis B (HBV) and Human Immunodeficiency Virus (HIV) share common risk factors for exposure. Co-infected patients have an increased liver-related mortality risk and may have accelerated HIV progression. The epidemiology and demographic characteristics of HIV-HBV co-infection in Canada remain poorly defined. We compared the demographic and clinical characteristics and factors associated with advanced hepatic fibrosis between HIV and HIV-HBV co-infected patients. Methods A retrospective cohort analysis was conducted using data from the Canadian Observational Cohort (CANOC) Collaboration, including eight sites from British Columbia, Quebec, and Ontario. Eligible participants were HIV-infected patients who initiated combination ARV between January 1, 2000 and December 14, 2014. Demographic and clinical characteristics were compared between HIV-HBV co-infected and HIV-infected groups using chi-square or Fisher exact tests for categorical variables, and Wilcoxon’s Rank Sum test for continuous variables. Liver fibrosis was estimated by the AST to Platelet Ratio Index (APRI). Results HBV status and APRI values were available for 2419 cohort participants. 199 (8%) were HBV co-infected. Compared to HIV-infected participants, HIV-HBV co-infected participants were more likely to use injection drugs (28% vs. 21%, p = 0.03) and be HCV-positive (31%, vs. 23%, p = 0.02). HIV-HBV co-infected participants had lower baseline CD4 T cell counts (188 cells/mm3, IQR: 120–360) compared to 235 cells/mm3 in HIV-infected participants (IQR: 85–294) (p = 0.0002) and higher baseline median APRI scores (0.50 vs. 0.37, p

Summary: Synthetic proteins with high affinity and selectivity for a protein target can be used as research tools, biomarkers, and pharmacological agents, but few methods exist to design such proteins de novo. To this end, the In-Silico Protein Synthesizer (InSiPS) was developed to design synthetic binding proteins (SBPs) that bind pre-determined targets while minimizing off-target interactions. InSiPS is a genetic algorithm that refines a pool of random sequences over hundreds of generations of mutation and selection to produce SBPs with pre-specified binding characteristics. As a proof of concept, we design SBPs against three yeast proteins and demonstrate binding and functional inhibition of two of three targets in vivo. Peptide SPOT arrays confirm binding sites, and a permutation array demonstrates target specificity. Our foundational approach will support the field of de novo design of small binding polypeptide motifs and has robust applicability while offering potential advantages over the limited number of techniques currently available. : Biological Sciences; Bioinformatics; Protein Family Determination Subject Areas: Biological Sciences, Bioinformatics, Protein Family Determination

Whole-genome sequencing (WGS) is used increasingly in public-health laboratories for typing and characterizing foodborne pathogens. To evaluate the performance of existing bioinformatic tools for in silico prediction of antimicrobial resistance (AMR) and serotypes of Salmonella enterica, WGS-based genotype predictions were compared with the results of traditional phenotyping assays. A total of 111 S. enterica isolates recovered from a Canadian baseline study on broiler chicken conducted in 2012-2013 were selected based on phenotypic resistance to 15 different antibiotics and isolates were subjected to WGS. Both SeqSero2 and SISTR accurately determined S. enterica serotypes, with full matches to laboratory results for 87.4 and 89.2% of isolates, respectively, and partial matches for the remaining isolates. Antimicrobial resistance genes (ARGs) were identified using several bioinformatics tools including the Comprehensive Antibiotic Resistance Database – Resistance Gene Identifier (CARD-RGI), Center for Genomic Epidemiology (CGE) ResFinder web tool, Short Read Sequence Typing for Bacterial Pathogens (SRST2 v 0.2.0), and k-mer alignment method (KMA v 1.17). All ARG identification tools had ≥ 99% accuracy for predicting resistance to all antibiotics tested except streptomycin (accuracy 94.6%). Evaluation of ARG detection in assembled versus raw-read WGS data found minimal observable differences that were gene- and coverage- dependent. Where initial phenotypic results indicated isolates were sensitive, yet ARGs were detected, repeat AMR testing corrected discrepancies. All tools failed to find resistance-determining genes for one gentamicin- and two streptomycin-resistant isolates. Further investigation found a single nucleotide polymorphism (SNP) in the nuoF coding region of one of the isolates which may be responsible for the observed streptomycin-resistant phenotype. Overall, WGS-based predictions of AMR and serotype were highly concordant with phenotype determination regardless of computational approach used.

ABSTRACT Ionophores are the second most widely used class of antibiotic in agriculture, with over 4 million kilograms sold in the United States in 2016. Because ionophores are not used in humans, it is widely assumed that their agricultural use will not impact human health. Consequently, these drugs have not been subject to the same regulations as medically important antibiotics. Here, I argue that the current evidence base is insufficient to conclude that ionophores do not contribute to human relevant antimicrobial resistance. It is unclear whether ionophore resistance can result in cross-resistance to medically important antibiotics. Moreover, recent evidence suggests that ionophore use may coselect for resistance to vancomycin in some cases. Systematic investigation of the consequences of agricultural ionophore use for human health is therefore imperative.

The evolution of antibiotic resistance is influenced by a variety of factors, including the availability of resistance mutations, and the pleiotropic effects of such mutations. Here, we isolate and characterize chromosomal quinolone resistance mutations in E. coli, in order to gain a systematic understanding of the rate and consequences of resistance to this important class of drugs. We isolated over fifty spontaneous resistance mutants on nalidixic acid, ciprofloxacin, and levofloxacin. This set of mutants includes known resistance mutations in gyrA, gyrB, and marR, as well as two novel gyrB mutations. We find that, for most mutations, resistance tends to be higher to nalidixic acid than relative to the other two drugs. Resistance mutations had deleterious impacts on one or more growth parameters, suggesting that quinolone resistance mutations are generally costly. Our findings suggest that the prevalence of specific gyrA alleles amongst clinical isolates are driven by high levels of resistance, at no more cost than other resistance alleles.

Background/Aims: This study tested the hypothesis that individuals with chronic obstructive pulmonary disease (COPD) have more small vessel disease and more severe disease than an age- and gender- matched hospital patient comparison group. Methods: This was a single centre, case-control study of 151 individuals with COPD (FEV1/VC) Results: Patients with COPD had more microvascular retinopathy (121, 80% and 76, 50%; OR 3.98, 95%CI 2.39 to 6.64) and more severe disease (42, 28% and 18, 12%; OR 2.85, 95% CI 1.55 to 5.23) than other hospital patients. COPD remained an independent determinant of microvascular retinopathy (OR 4.56, 95%CI 2.49 to 8.36) after adjusting for gender, hypertension, smoking, and diabetes duration. Retinal arterioles and venules were wider in patients with COPD than other hospital patients (mean difference +6.5µm, 95% confidence interval 1.4 to 11.6; and +17.4µm, 95%CI 9.4 to 25.5, respectively). Larger venules were more common in younger individuals (+0.6 µm, 0.1 to 1.17) with more cigarette exposure (+0.3 µm, 0.2 to 0.5) or a lower serum albumin (+23.0 µm, 6.0 to 40.0). Venular calibre was not different in current and former smokers (p=0.77). There were trends for venules to be larger with more severe COPD (lower FEV1/VC, p=0.09) and with CT-demonstrated emphysema (p=0.06). Conclusions: Hypertensive/microvascular disease is more common and more severe in patients with COPD. This is likely to contribute to the associated increase in cardiac risk.

OBJECTIVES/SPECIFIC AIMS: Examine data from PNID patients to evaluation the strength of associations between pre-operative and post-operative levels of pain, quality of life, and emotional reactions to pain to determine if one or more can serve as better predictors of surgical success than pain. METHODS/STUDY POPULATION: In our preliminary study, we gathered data from a pre-existing database of 464 PNID patients that contains self-reported visual analog scale scores (VAS) of pain intensity, QoL, and depression. We measured these variables at three time points: pre-operatively, post-operatively, and at the final visit. We used the Wilcoxon signed rank test to determine if each of these three variables differed significantly between the pre-operative visit and the post-operative visit period and from the pre-operative visit to the final visit. RESULTS/ANTICIPATED RESULTS: Median time from the pre-operative visit to surgery was 9 weeks; median time from surgery to the post-operative visit was 4 weeks; and median time from the post-operative visit to the final visit was 23.5 weeks. There was a clinically meaningful difference in pain scores between the pre-operative and post-operative visits (median difference 1.15; 95% CI 0.75-1.55). In the period between the post-operative visit and the final visit there was also a decrease in pain (0.90; 95% CI 0.55-1.30). The magnitude of change in median difference of 1.85 (95% CI 1.50-2.20) between the pre-operative visit and the final visit was larger than the change in median difference of 0.90 (95% CI 0.55-1.30) between the post-operative visit and the final visit. The pre-operative visit median QoL score was higher than the median score at the post-operative visit (1.65; 95% CI 1.25-2.10). The smallest median difference in QoL of occurred between the post-operative and the final visit (1.10; 95% CI 0.60-1.45). As seen with the pain scores, the magnitude of change in median difference of 2.50 (95% CI 2.20-2.85) for QoL was greatest between the pre-operative and the final visit. Depression scores showed the least amount of change amongst all the variables, between the pre-operative and the post-operative visit (1.00; 95% CI (0.70-1.40), and similarly between the post-operative visit and the final visit (0.15; 95% CI (0-.40). The median differences between the pre-operative and final visit were greatest in QoL (2.50; 95% CI 2.20-2.85), followed by pain scores (1.85; 95% CI 1.50-2.20), and finally, depression (1.05; 95% CI 0.70-1.40). DISCUSSION/SIGNIFICANCE OF IMPACT: Our results show that all three variables measured improve with surgery and continue to improve over the post-operative course to the final visit. This suggest that the relationships between pain, QoL, and depression should be further investigated. We are hopeful that elucidating how these variables interact in the PNID patient population, will encourage peripheral nerve surgeons to use these parameters in conjunction with pain intensity to measure outcomes. A follow-up study expanding on these results and including measures of anger and frustration in a larger sample is underway.

Background: People with disabilities, who face multiple barriers to care, experience health disparities, yet few studies have measured health literacy in this population. Objective: This study evaluated functional literacy, health literacy, fluid cognitive function, and self-reported health in people who live in community dwellings with spinal cord injury, stroke, or traumatic brain injury. Methods: Participants with a traumatic spinal cord injury, stroke, or traumatic brain injury, one-year postinjury, and age 18 to 85 years, completed a battery of instruments at three medical centers in the Midwestern U.S.: functional literacy (word recognition, vocabulary knowledge), health literacy (comprehension of prose, document, and quantitative health information), fluid cognitive function (memory, executive function, and processing speed), and patient-reported outcomes (mobility, fatigue, sadness, anxiety, social function, and overall health). Key Results: There were strong correlations between functional literacy, health literacy, and fluid cognitive function. After adjustment for sociodemographic and clinical characteristics, higher health literacy was associated with better mobility, less anxiety, and better overall health; higher functional literacy was associated with less anxiety and better overall health; and higher fluid cognitive function was associated with better mobility, less sadness, better social function, and better overall health. Conclusions: To effectively address limited health literacy among people with spinal cord injury, stroke, and traumatic brain injury, and ensure that they are able to be informed partners in their health care, intervention is required at the level of patients, providers, and health care delivery systems. A special consideration is to ensure that health information is both well-targeted to people's health literacy levels and accessible for people with a range of physical, cognitive, and sensory limitations. The multimedia self-administered health literacy measure used in this study could be useful to rehabilitation providers and designers of health information and interfaces.

Interest in the evolution of protein-protein and genetic interaction networks has been rising in recent years, but the lack of large-scale high quality comparative datasets has acted as a barrier. Here, we carried out a comparative analysis of computationally predicted protein-protein interaction (PPI) networks from five closely related yeast species. We used the Protein-protein Interaction Prediction Engine (PIPE), which uses a database of known interactions to make sequence-based PPI predictions, to generate high quality predicted interactomes. Simulated proteomes and corresponding PPI networks were used to provide null expectations for the extent and nature of PPI network evolution. We found strong evidence for conservation of PPIs, with lower than expected levels of change in PPIs for about a quarter of the proteome. Furthermore, we found that changes in predicted PPI networks are poorly predicted by sequence divergence. Our analyses identified a number of functional classes experiencing fewer PPI changes than expected, suggestive of purifying selection on PPIs. Our results demonstrate the added benefit of considering predicted PPI networks when studying the evolution of closely related organisms.

Background. Hepatitis C virus (HCV) coinfection occurs in 20–30% of Canadians living with HIV and is responsible for a heavy burden of morbidity and mortality. Purpose. To update national standards for management of HCV-HIV coinfected adults in the Canadian context with evolving evidence for and accessibility of effective and tolerable DAA therapies. The document addresses patient workup and treatment preparation, antiviral recommendations overall and in specific populations, and drug-drug interactions. Methods. A standing working group with HIV-HCV expertise was convened by The Canadian Institute of Health Research HIV Trials Network to review recently published HCV antiviral data and update Canadian HIV-HCV Coinfection Guidelines. Results. The gap in sustained virologic response between HCV monoinfection and HIV-HCV coinfection has been eliminated with newer HCV antiviral regimens. All coinfected individuals should be assessed for interferon-free, Direct Acting Antiviral HCV therapy. Regimens vary in content, duration, and success based largely on genotype. Reimbursement restrictions forcing the use of pegylated interferon is not acceptable if optimal patient care is to be provided. Discussion. Recommendations may not supersede individual clinical judgement. Treatment advances published since December 2015 are not considered in this document.

Burn injuries are a leading cause of morbidity including prolonged hospitalization, disfigurement, and disability. Currently there is no Food and Drug Administration-approved burn therapeutics. A clinical distinction of burn injuries from other acute wounds is the event of the so-called secondary burn wound progression within the first week of the injury, in which a burn expands horizontally and vertically from its initial boundary to a larger area. Therefore, an effective therapeutics for burns should show dual abilities to prevent the burn wound progression and thereafter promote burn wound healing. Herein we report that topically applied F-5 fragment of heat shock protein-90α is a dual functional agent to promote burn wound healing in pigs. First, F-5 prevents burn wound progression by protecting the surrounding cells from undergoing heat-induced caspase 3 activation and apoptosis with increased Akt activation. Accordingly, F-5–treated burn and excision wounds show a marked decline in inflammation. Thereafter, F-5 accelerates burn wound healing by stimulating the keratinocyte migration-led reepithelialization, leading to wound closure. This study addresses a topical agent that is capable of preventing burn wound progression and accelerating burn wound healing.

The putative role of nitric oxide (3333333333333333335) in modulating adipogenesis was investigated in cultured preadipocytes derived from rat white adipose tissue. The NO releasing reagent, hydroxylamine (HA), and nitric oxide synthase (NOS) substrate l-arginine (Arg) had no influence on cell replication. However, both HA and Arg exhibited significant induction on differentiation, as evidenced by increased lipoprotein lipase (LPL) and glycerol-3-phosphate dehydrogenase (GPDH) activities, as well as accelerated triacylglycerol (TG) accumulation. These observations suggested a positive role of NO in modulating adipogenesis. Preadipocytes were found to produce NO, and a ∼50% increase over basal level was observed on the first 2 days of differentiation. Deprivation of endogenous NOS activity by a non-selective NOS inhibitor, NG-monomethyl-l-arginine (NMMA), partially abrogated the differentiation process, implicating a role for endogenous NO to stimulate preadipocyte differentiation. Both NOS isoforms, eNOS and iNOS, were detected in differentiating preadipocytes.Specific iNOS inhibitors (1400W and aminoguanidine) had little influence on NO production and differentiation, suggesting that eNOS rather than iNOS may be the major isoform involved in modulating adipogenesis.

The Asian tiger mosquito (Aedes albopictus) is an important vector for pathogens that affect human health, including the viruses that cause dengue and Chikungunya fevers. It is also one of the world's fastest-spreading invasive species. For these reasons, it is crucial to identify strategies for controlling the reproduction and spread of this mosquito. During mating, seminal fluid proteins (Sfps) are transferred from male mosquitoes to females, and these Sfps modulate female behavior and physiology in ways that influence reproduction. Despite the importance of Sfps on female reproductive behavior in mosquitoes and other insects, the identity of Sfps in Ae. albopictus has not previously been reported. We used transcriptomics and proteomics to identify 198 Sfps in Ae. albopictus. We discuss possible functions of these Sfps in relation to Ae. albopictus reproduction-related biology. We additionally compare the sequences of these Sfps with proteins (including reported Sfps) in several other species, including Ae. aegypti. While only 72 (36.4%) of Ae. albopictus Sfps have putative orthologs in Ae. aegypti, suggesting low conservation of the complement of Sfps in these species, we find no evidence for an elevated rate of evolution or positive selection in the Sfps that are shared between the two Aedes species, suggesting high sequence conservation of those shared Sfps. Our results provide a foundation for future studies to investigate the roles of individual Sfps on feeding and reproduction in this mosquito. Functional analysis of these Sfps could inform strategies for managing the rate of pathogen transmission by Ae. albopictus.