Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Seaweed extracts as antimicrobial agents in aquaculture

Author's accepted version (post-print).The final publication is available at Springer via http://dx.doi.org/10.1007/s10811-014-0506-0.In the last 20 years, there has been an increasing interest in using various seaweed extracts as prophylactic and/or therapeutic agents in aquaculture. Up until now, most studies on the direct antimicrobial effect of seaweeds have taken place in various parts of Asia, particularly in India. All groups of seaweeds exhibit significant antimicrobial properties against many infectious agents of fish and shrimp, but the genera that appear to exhibit a broader range of antibacterial properties are Asparagopsis spp. (red seaweed) and Sargassum spp. (brown seaweed). The activity can be affected by many factors and the method of extraction is one of the most important ones, as the extracts that are produced using organic solvents appear more efficient. In fish, almost all published information on bacterial pathogens comes from in vitro screenings, where extracts of different seaweed species were tested against many bacterial species. On the other hand, in shrimp, the studies have been focusing on the antimicrobial effects of seaweed extracts mainly against many Vibrio species. Regarding the viral pathogens, in fish, there is only one published study on fish viruses (IHNV and IPNV), while in shrimp there are many studies on WSSV. There are only two published studies on fish parasites (Ichthyophonus hoferi and Neobendenia spp.) and no studies on pathogenic fish and shrimp fungi. Interestingly, there are no published studies on salmons and carps, the main fish species that are extensively farmed. When the antimicrobial properties were studied in vivo, the seaweed extracts were either incorporated directly in the feeds (dry or live) or added directly into the water in which the fish and shrimp were reared. In the last case, the water-soluble antimicrobial seaweed substances affected the communication between the bacterial pathogens, rather than their growth. The development of parasites was also affected. In addition, one study indicated that short-term immersion of shrimp in seaweed extracts appeared to have a therapeutic effect against Vibrio parahaemolyticus. On the other hand, incorporation of the extracts into the feeds appeared to be an effective delivery method for the prevention and treatment of different infectious diseases. Up until now, there are no complete studies on the pharmacodynamics and pharmacokinetics of seaweed extracts in fish or shrimp. However, the findings indicate that they can reduce the bacterial load within the tissues. Another issue that has not been examined yet is the applicability of using these extracts on a commercial scale. Currently, the increased extraction cost inhibits the extensive use of these extracts. Other methodologies, such the production of synthetic analogues with similar properties, may decrease the production cost. Based on the published studies, seaweed extracts exhibit promising antimicrobial properties, but further research is needed before the complete potential of seaweed extracts is assessed

Correction: Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

International audienc

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

BackgroundWe previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in similar to 80% of cases.MethodsWe report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.ResultsNo gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P=1.1x10(-4)) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR=3.70[95%CI 1.3-8.2], P=2.1x10(-4)). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR=19.65[95%CI 2.1-2635.4], P=3.4x10(-3)), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR=4.40[9%CI 2.3-8.4], P=7.7x10(-8)). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD]=43.3 [20.3] years) than the other patients (56.0 [17.3] years; P=1.68x10(-5)).ConclusionsRare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old