Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

Background Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide.Methods A multimethods analysis was performed as part of the GlobalSurg 3 study-a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital.Findings Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3.85 [95% CI 2.58-5.75]; p<0.0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63.0% vs 82.7%; OR 0.35 [0.23-0.53]; p<0.0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer.Interpretation Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised

Strain Specific Phage Treatment for Staphylococcus aureus Infection Is Influenced by Host Immunity and Site of Infection.

The response to multi-drug resistant bacterial infections must be a global priority. While mounting resistance threatens to create what the World Health Organization has termed a "post-antibiotic era", the recent discovery that antibiotic use may adversely impact the microbiome adds further urgency to the need for new developmental approaches for anti-pathogen treatments. Methicillin-resistant Staphylococcus aureus (MRSA), in particular, has declared itself a serious threat within the United States and abroad. A potential solution to the problem of antibiotic resistance may not entail looking to the future for completely novel treatments, but instead looking into our history of bacteriophage therapy. This study aimed to test the efficacy, safety, and commercial viability of the use of phages to treat Staphylococcus aureus infections using the commercially available phage SATA-8505. We found that SATA-8505 effectively controls S. aureus growth and reduces bacterial viability both in vitro and in a skin infection mouse model. However, this killing effect was not observed when phage was cultured in the presence of human whole blood. SATA-8505 did not induce inflammatory responses in peripheral blood mononuclear cultures. However, phage did induce IFN gamma production in primary human keratinocyte cultures and induced inflammatory responses in our mouse models, particularly in a mouse model of chronic granulomatous disease. Our findings support the potential efficacy of phage therapy, although regulatory and market factors may limit its wider investigation and use

SATA 8505 Effectively Kills USA 300 and Reduces its Viability in vitro.

<p>(a) Average colony forming unit (CFU) counts for USA300 cultured with SATA-8505 for up to four hours at ratios of <i>S</i>. <i>aureus</i>:Phage of 1:1, 1:10, or 1:100 (MOI 1, 10, 100 respectively). (b) Images of surviving colony morphology of USA300 grown in TSB after exposure to BHI (diluent) or SATA-8505. (c) Regrowth of surviving colonies pictured in panel b, <i>S</i>. <i>aureus</i> grown in TSB after prior exposure to BHI (diluent) or SATA-8505 run in triplicate culture. Data shown are representative of 3 or more independent experiments and displayed as mean <u>+</u> s.e.m. **** = p<0.0001.</p

SATA-8505 Does Not Impact USA300 Growth in Human Blood.

<p>(a) Hourly quantification of starting culture of 10⁶ CFU USA300 in three parts TSB and one part whole blood from healthy donor or a patient with CGD, grown with or without 10⁸ PFU SATA-8505 in duplicate. (b) Regrowth of surviving colonies from whole blood culture run in triplicate. One colony of <i>S</i>. <i>aureus</i> previously grown in 3:1 TSB:Whole blood without phage was subsequently grown in TSB with SATA-8505 (TSB/Phage) or without phage (TSB/TSB); one colony of the surviving <i>S</i>. <i>aureus</i> previously grown in the presence of SATA-8505 was subsequently grown in TSB with SATA-8505 (Phage/Phage) or without phage (Phage/TSB). (c) Average quantification of starting culture of 10¹⁰ CFU of USA300 grown in either 3:1 TSB:Whole blood or 3:1 TSB:HBSS, with or without 10⁷ PFU SATA-8505. (d) Average quantification of starting culture of 10⁷ CFU of USA300 grown in three parts TSB with either one part whole blood, HBSS, serum, or peripheral mononuclear cells (PBMC) in equivalent volume HBSS. Data shown are representative of 2–3 independent experiments using 3 or more different healthy volunteers and 2 patients with CGD. Data is displayed as mean + s.e.m. ** = p<0.01.</p

SATA-8505 Induces Interferon Gamma in Primary Human Keratinocytes.

<p>Human peripheral mononuclear cells (PBMC) were cultured in triplicate at 2⁶/mL with SATA-8505 at 1 PFU/mL to 10⁸ PFU/mL at ten-fold increments or diluent derived from the supernatant of an overnight culture of SA that had been pelleted and filter sterilized in a manner similar to the phage-containing media. At 72 hours supernatants were harvested and analyzed for IL-1ß (a), IL-6 (b), IL-17A (c), and IFN gamma (d). Human keratinocytes from primary foreskins (foreskin keratinocytes; FSKC) or the HaCaT cell line were cultured to confluence on 6-well plates and incubated in triplicate with SATA-8505 at 10⁴ PFU/mL to 10⁸ PFU/mL at ten-fold increments or TSB diluent. At 24 hours supernatants were harvested and analyzed for IL-1ß (e), IL-6 (f), and IFN gamma (g). Phage for all experiments was diluted in TSB from overnight culture of USA300 that was centrifuged at 5000rpm for 12 minutes and filter-sterilized through a 0.44 micrometer filter. Data shown are representative of 3 independent experiments using 3 different healthy volunteers (a-d) or a pool of 5 or more foreskin samples (e-g) and displayed as mean <u>+</u> s.e.m. * = p <0.05.</p

SATA-8505 Fails to Improve MRSA Skin Infection at High MOI.

<p>Lesion size (a), CFU (b), PFU (c), and transcript data (d-f) for mice injected with 10⁹ plaque-forming units (PFU) of SATA-8505 immediately prior to subcutaneous injections of 10⁷ CFU of USA300 processed in an identical manner as MOI of 1 experiments. Data shown are representative of 2–3 independent experiments using 5 or more mice per group, and displayed as mean + s.e.m. Differences were calculated by ANOVA with Bonferroni correction and depict differences from diluent treated wild type unless otherwise noted. ns = not significant, * = p <0.05, ** = p<0.01, *** = p<0.001.</p

SATA-8505 Improves MRSA Skin Infection at Low MOI.

<p>Mice were injected intraperitoneally (I.P.) with 10⁷ plaque-forming units (PFU) of SATA-8505 immediately prior to subcutaneous injections of 10⁷ CFU of USA300. (a) Lesion size progression over following six days. On day 6, skin biopsies were homogenized for culture, total bacterial (b) and phage burden (c) were calculated for individual mice. (d) mRNA transcript levels for IL-1ß, IL-6, and IL-17A in individual CGD mice relative to wild type controls, standardized to GAPDH. (e-g) mRNA transcript levels for IL-1ß, IL-6, and IL-17A in CGD and wild type mice with and without SATA-8505 treatment relative to wild type controls injected with diluent, standardized to GAPDH. Data shown are representative of 2–3 independent experiments using 5 or more mice per group, and displayed as mean + s.e.m. Differences were calculated by ANOVA with Bonferroni correction and depict differences from diluent treated wild type unless otherwise noted. ns = not significant, * = p <0.05, ** = p<0.01.</p

SATA-8505 Exhibits Commercial Viability but Significant Strain Limitations.

<p>(a) SATA-8505 quantified over up to sixty days after storage at either room temperature (RT), 4 degrees Celsius (4^°C), or frozen at -80^°C. (b) Average hourly quantification of 10⁸–10⁹ CFU of USA100 <i>S</i>. <i>aureus</i> or a vancomycin resistant variant of USA100 (VRSA) cultured with up to 10¹¹ PFU of SATA-8505. Data shown are a representative of 2 independent experiments.</p

Evolution of NLR genes in genus Arachis reveals asymmetric expansion of NLRome in wild and domesticated tetraploid species

Abstract Arachis hypogaea is an allotetraploid crop widely grown in the world. Wild relatives of genus Arachis are the rich source of genetic diversity and high levels of resistance to combat pathogens and climate change. The accurate identification and characterization of plant resistance gene, nucleotide binding site leucine rich repeat receptor (NLRs) substantially contribute to the repertoire of resistances and improve production. In the current study, we have studied the evolution of NLR genes in genus Arachis and performed their comparative genomics among four diploids (A. duranensis, A. ipaensis, A. cardenasii, A. stenosperma) and two tetraploid (wild: A. monticola and domesticated: A. hypogaea) species. In total 521, 354, 284, 794, 654, 290 NLR genes were identified from A. cardenasii, A. stenosperma and A. duranensis, A. hypogaea, A. monticola and A. ipaensis respectively. Phylogenetic analysis and classification of NLRs revealed that they belong to 7 subgroups and specific subgroups have expanded in each genome leading towards divergent evolution. Gene gain and loss, duplication assay reveals that wild and domesticated tetraploids species have shown asymmetric expansion of NLRome in both sub-genome (AA and BB). A-subgenome of A. monticola exhibited significant contraction of NLRome while B-subgenome shows expansion and vice versa in case of A. hypogaea probably due to distinct natural and artificial selection pressure. In addition, diploid species A. cardenasii revealed the largest repertoire of NLR genes due to higher frequency of gene duplication and selection pressure. A. cardenasii and A. monticola can be regarded as putative resistance resources for peanut breeding program for introgression of novel resistance genes. Findings of this study also emphasize the application neo-diploids and polyploids due to higher quantitative expression of NLR genes. To the best of our knowledge, this is the first study that studied the effect of domestication and polyploidy on the evolution of NLR genes in genus Arachis to identify genomic resources for improving resistance of polyploid crop with global importance on economy and food security

Dynamic Evolution of <i>NLR</i> Genes in Dalbergioids

Dalbergioid is a large group within the family Fabaceae that consists of diverse plant species distributed in distinct biogeographic realms. Here, we have performed a comprehensive study to understand the evolution of the nucleotide-binding leucine-rich repeats (NLRs) gene family in Dalbergioids. The evolution of gene families in this group is affected by a common whole genome duplication that occurred approximately 58 million years ago, followed by diploidization that often leads to contraction. Our study suggests that since diploidization, the NLRome of all groups of Dalbergioids is expanding in a clade-specific manner with fewer exceptions. Phylogenetic analysis and classification of NLRs revealed that they belong to seven subgroups. Specific subgroups have expanded in a species-specific manner, leading to divergent evolution. Among the Dalbergia clade, the expansion of NLRome in six species of the genus Dalbergia was observed, with the exception of Dalbergia odorifera, where a recent contraction of NLRome occurred. Similarly, members of the Pterocarpus clade genus Arachis revealed a large-scale expansion in the diploid species. In addition, the asymmetric expansion of NLRome was observed in wild and domesticated tetraploids after recent duplications in the genus Arachis. Our analysis strongly suggests that whole genome duplication followed by tandem duplication after divergence from a common ancestor of Dalbergioids is the major cause of NLRome expansion. To the best of our knowledge, this is the first ever study to provide insight toward the evolution of NLR genes in this important tribe. In addition, accurate identification and characterization of NLR genes is a substantial contribution to the repertoire of resistances among members of the Dalbergioids species