HERMES: a molecular-formula-oriented method to target the metabolome.

Comprehensive metabolome analyses are essential for biomedical, environmental, and biotechnological research. However, current MS1- and MS2-based acquisition and data analysis strategies in untargeted metabolomics result in low identification rates of metabolites. Here we present HERMES, a molecular-formula-oriented and peak-detection-free method that uses raw LC/MS1 information to optimize MS2 acquisition. Investigating environmental water, Escherichia coli, and human plasma extracts with HERMES, we achieved an increased biological specificity of MS2 scans, leading to improved mass spectral similarity scoring and identification rates when compared with a state-of-the-art data-dependent acquisition (DDA) approach. Thus, HERMES improves sensitivity, selectivity, and annotation of metabolites. HERMES is available as an R package with a user-friendly graphical interface for data analysis and visualization.

Quality check: concordance between two monitoring systems for postoperative organ/space-surgical site infections in rectal cancer surgery. Linkage of data from the Catalan Cancer Plan and the VINCat infection surveillance programme.

BACKGROUND: The Catalan Cancer Plan (CCP) undertakes periodic audits of cancer treatment outcomes, including organ/space surgical site infections (O/S-SSI) rates, while the Catalan Healthcare-associated Infections Surveillance Programme (VINCat) carries out standardized prospective surveillance of surgical site infections (SSI) in colorectal surgery. This cohort study aimed to assess the concordance between these two monitoring systems for O/S-SSI following primary rectal cancer surgery. METHODS: The study compared O/S-SSI incidence data from CCP clinical audits versus the VINCat Programme in patients undergoing surgery for primary rectal cancer, in 2011-12 and 2015-16, in publicly funded centres in Spain. The main outcome variable was the incidence of O/S-SSI in the first 30 days after surgery. Concordance between the two registers was analysed using Cohen's kappa. Discordant cases were reviewed by an expert, and the main reasons for discrepancies evaluated. RESULTS: Pooling data from both databases generated a sample of 2867 patients. Of these, O/S-SSI was detected in 414 patients-235 were common to both registry systems, with satisfactory concordance (κ = 0.69, 95% confidence interval 0.65-0.73). The rate of discordance from the CCP (positive cases in VINCat and negative in CCP) was 2.7%, and from VINCat (positive in CCP and negative in VINCat) was 3.6%. External review confirmed O/S-SSI in 66.2% of the cases in the CCP registry and 52.9% in VINCat. CONCLUSIONS: This type of synergy shows the potential of pooling data from two different information sources with a satisfactory level of agreement as a means to improving O/S-SSI detection. CLINICALTRIALS: gov Identifier: NCT06104579. Registered 30 November 2023.

Contemporary management of concomitant gallstones and common bile duct stones: a survey of Spanish surgeons.

BACKGROUND: Concomitant gallstones and common bile duct stones (CBDS) is a relatively frequent presentation. The optimal treatment remains controversial and the debate persists between two strategies. The one-stage approach: laparoscopic cholecystectomy with laparoscopic common bile duct exploration (LCBDE) has been shown to be equally safe and more cost-effective than the more traditional two-stage approach: endoscopic retrograde cholangiography followed by laparoscopic cholecystectomy (ERCP + LC). However, many surgeons worldwide still prefer the two-stage procedure. This survey evaluated contemporary management of CBDS in Spain and assessed the impact of surgeon and hospital factors on provision of LCBDE. METHODS: A 25-item, web-based anonymous survey was sent to general surgeons members of the Spanish Surgeons Association. Descriptive statistics were applied to summarize results. RESULTS: Responses from 305 surgeons across 173 Spanish hospitals were analyzed. ERCP is the initial approach for preoperatively suspected CBDS for 86% of surgeons. LCBDE is the preferred method for only 11% of surgeons and only 11% treat more than 10 cases per year. For CBDS discovered intraoperatively, 59% of respondents attempt extraction while 32% defer to a postoperative ERCP. The main reasons cited for not performing LCBDE were lack of equipment, training and timely availability of an ERCP proceduralist. Despite these barriers, most surgeons (84%) responded that LCBDE should be implemented in their departments. CONCLUSIONS: ERCP was the preferred approach for CBDS for the majority of respondents. There remains limited use of LCBDE despite many surgeons indicating it should be implemented. Focused planning and resourcing of both training and operational demands are required to facilitate adoption of LCBDE as option for patients.

Incidence and risk factors for trocar-site incisional hernia detected by clinical and ultrasound examination: a prospective observational study.

BACKGROUND: Trocar site incisional hernia (TSIH) is the most frequent complication associated with laparoscopic surgery. Few studies currently describe its incidence or risk factors. The aim of this report is to determine the real incidence of TSIH and to identify risk factors. METHODS: A cross-sectional prospective study was performed including consecutive patients who underwent a laparoscopic procedure during a 4 months period. All the patients were assessed both clinically (TSIHc) and by an ultrasonographic examination (TSIHu). The main variable studied was the incidence of TSIH. A multivariate analysis was performed to identify risk factors. RESULTS: 76 patients were included. 27.6% of patients were clinically diagnosed as having TSIH (TSIHc) but only 23.7% of those cases were radiologically confirmed (TSIHu). In the logistic regression analysis, age > 70 years (OR 3.462 CI 1.14-10.515, p = 0.028) and body mass index (BMI) ≥ 30 kg/m2 (OR 3.313 CI 1.037-10.588, p = 0.043) were identified as risk factors for TSIH. The size of the trocar also showed statistically significant differences (p < 0.001). Mean follow-up time was 34 months. CONCLUSIONS: TSIH is under-diagnosed due to the lack of related symptomatology and the inadequacy of the postoperative follow-up period. We detected discrepancies between the clinical and ultrasonographic examinations. TSIHu should be considered as the gold standard for the diagnosis of TSIH. Risk factors such as age, BMI and size of the trocar were confirmed. Patients should be followed-up for a minimum of 2 years. Trial registration The study has been retrospectively registered in Clinicaltrials.gov on June 4, 2020 under registration number: NCT04410744.

Recommendations of «not-to-do¼: Proposals of the Spanish Association of Surgeons to the project «Commitment to quality of scientific societies¼. / Recomendaciones de «no hacer¼: propuestas de la Asociación Española de Cirujanos al proyecto de «Compromiso por la calidad de las sociedades científicas¼.

INTRODUCTION: The initiative of the Spanish Ministry of Health «Commitment to quality of scientific societies¼, aims to reduce unnecessary interventions of healthcare professionals. METHODS: The Spanish Association of Surgeons has selected 22 experts from the different sections that have participated in the identification of 26 proposals «do not do¼ to be ordered by the expected impact its implementation would have according to the GRADE methodology. From these proposals, the Delphi technique was used to select 5 recommendations presented in more detail in this article. RESULTS: The 5 selected recommendations are: Do not perform cholecystectomy in patients with asymptomatic cholelithiasis; do not keep bladder catheterization more than 48hours; do not extend antibiotic prophylaxis treatments more than 24hours after a surgical procedure; do not perform routine antibiotic prophylaxis for uncomplicated clean and no prosthetic surgery; and do not use antibiotics postoperatively after uncomplicated appendicitis. CONCLUSION: The Spanish Association of Surgeons's participation in this campaign has allowed a reflection on those activities that do not add value in the field of surgery and it is expected that the spread of this process serves to reduce its performance.

Surgical protocol for confirmed or suspected cases of Ebola and other highly transmissible diseases.

Outbreaks of viral haemorrhagic fevers such as Ebola can lead to imported cases in Europe and America. The eventuality of surgery in the setting of Ebola Virus Disease (EVD) is low, but the Spanish Association of Surgeons elaborated a surgical protocol for EVD. INDICATION: Elective surgical procedures are not indicated. Emergency cases can be considered in: persons under investigation, possible cases and early confirmed cases. In some conditions usually treated by surgery a medical treatment can be tested. HOSPITALS AND TEAMS: All cases must be treated in high technology hospitals. These hospitals must be equipped with adequate means for healthcare provider's protection. All members of the healthcare team should practice thorough simulation prior to caring for a possible Ebola patient. SURGICAL PROTOCOL: This protocol is based on international guidelines on use of Personal Protective Equipment, protocols of other scientific societies, and specific recommendations for the operating room environment.

[Prevention of surgical site infection in abdominal surgery. A critical review of the evidence]. / Medidas de prevención de la infección del sitio quirúrgico en cirugía abdominal. Revisión crítica de la evidencia.

Surgical site infection (SSI) is associated with prolonged hospital stay, increased morbidity, mortality and sanitary costs, and reduced patients quality of life. Many hospitals have adopted guidelines of scientifically-validated processes for prevention of surgical site and central-line catheter infections and sepsis. Most of these guidelines have resulted in an improvement in postoperative results. A review of the best available evidence on these measures in abdominal surgery is presented. The best measures are: avoidance of hair removal from the surgical field, skin decontamination with alcoholic antiseptic, correct use of antibiotic prophylaxis (administration within 30-60 min before incision, use of 1(st) or 2(nd) generation cephalosporins, single preoperative dosis, dosage adjustments based on body weight and renal function, intraoperative re-dosing if the duration of the procedure exceeds 2 half-lives of the drug or there is excessive blood loss), prevention of hypothermia, control of perioperative glucose levels, avoid blood transfusion and restrict intraoperative liquid infusion.

Surgical management of acute cholecystitis. Results of a nation-wide survey among Spanish surgeons.

There is a wide variability in the management of acute cholecystitis. A survey among the members of the Spanish Association of Surgeons (AEC) analyzed the preferences of Spanish surgeons for its surgical management. The majority of the 771 responders didn't declare any subspecialty (41.6%), 21% were HPB surgeons, followed by colorectal and upper-GI specialities. Early cholecystectomy during the first admission is the preferred method of management of 92.3% of surgeons, but only 42.7% succeed in adopting this practice. The most frequent reasons for changing their preferred practice were: Patients not fit for surgery (43.6%) and lack of availability of emergency operating room (35.2%). A total of 88.9% perform surgery laparoscopically. The majority of AEC surgeons advise index admission cholecystectomy for acute cholecystitis, although only half of them succeed in its actual implementation. There is room for improvement in the management of acute cholecystitis in Spanish hospitals.

Appropriate Use of Antibiotics in Acute Pancreatitis: A Scoping Review.

BACKGROUND: While selective use of antibiotics for infected pancreatic necrosis (IPN) in acute pancreatitis (AP) is recommended, studies indicate a high rate of inadequate treatment. METHODS: A search of PubMed, Scopus, and Cochrane databases was conducted, focusing on primary research and meta-analyses. Data were categorized based on core concepts, and a narrative synthesis was performed. RESULTS: The search identified a total of 1016 publications. After evaluating 203 full texts and additional sources from the grey literature, 80 studies were included in the review. The answers obtained were: (1) Preventive treatment does not decrease the incidence of IPN or mortality. Given the risks of bacterial resistance and fungal infections, antibiotics should be reserved for highly suspected or confirmed IPN; (2) The diagnosis of IPN does not always require microbiological samples, as clinical suspicion or computed tomography signs can suffice. Early diagnosis and treatment may be improved by using biomarkers such as procalcitonin and novel microbiological methods; (3) When indicated, early initiation of antibiotics is a key determinant in reducing mortality associated with IPN; (4) Antibiotics with good penetration into pancreatic tissue covering Gram-negative and Gram-positive bacteria should be used. Routine antifungal therapy is not recommended; (5) The step-up approach, including antibiotics, is the standard for IPN management; (6) Antibiotic duration should be kept to a minimum and should be based on the quality of source control and patient condition. CONCLUSIONS: Early antibiotic therapy is essential for the treatment of IPN, but prophylactic antibiotics are not recommended in AP. High-quality randomized controlled trials are required to better understand the role of antibiotics and antifungals in AP management.

Comparison of two bundles for reducing surgical site infection in colorectal surgery: multicentre cohort study.

BACKGROUND: There is controversy regarding the maximum number of elements that can be included in a surgical site infection prevention bundle. In addition, it is unclear whether a bundle of this type can be implemented at a multicentre level. METHODS: A pragmatic, multicentre cohort study was designed to analyse surgical site infection rates in elective colorectal surgery after the sequential implementation of two preventive bundle protocols. Secondary outcomes were to determine compliance with individual measures and to establish their effectiveness, duration of stay, microbiology and 30-day mortality rate. RESULTS: A total of 32 205 patients were included. A 50% reduction in surgical site infection was achieved after the implementation of two sequential sets of bundles: from 18.16% in the Baseline group to 10.03% with Bundle-1 and 8.19% with Bundle-2. Bundle-2 reduced superficial-surgical site infection (OR 0.74 (95% c.i. 0.58 to 0.95); P = 0.018) and deep-surgical site infection (OR 0.66 (95% c.i. 0.46 to 0.93); P = 0.018) but not organ/space-surgical site infection (OR 0.88 (95% c.i. 0.74 to 1.06); P = 0.172). Compliance increased after the addition of four measures to Bundle-2. In the multivariable analysis, for organ/space-surgical site infection, laparoscopy, oral antibiotic prophylaxis and mechanical bowel preparation were protective factors in colonic procedures, while no protective factors were found in rectal surgery. Duration of stay fell significantly over time, from 7 in the Baseline group to 6 and 5 days for Bundle-1 and Bundle-2 respectively (P < 0.001). The mortality rate fell from 1.4% in the Baseline group to 0.59% and 0.6% for Bundle-1 and Bundle-2 respectively (P < 0.001). There was an increase in Gram-positive bacteria and yeast isolation, and reduction in Gram-negative bacteria and anaerobes in organ/space-surgical site infection. CONCLUSIONS: The addition of measures to create a final 10-measure protocol had a cumulative protective effect on reducing surgical site infection. However, organ/space-surgical site infection did not benefit from the addition. No protective measures were found for organ/space-surgical site infection in rectal surgery. Compliance with preventive measures increased from Bundle-1 to Bundle-2.

Impact of an antimicrobial stewardship program indicator on the appropriateness of the empiric antibiotic treatment of urinary source Escherichia coli bacteraemia.

A prospective multicentre study was carried out between 2017 and 2021 to assess (1) the appropriateness of the empirical treatment to the local guidelines of urinary source Escherichia coli bacteraemia, (2) the appropriateness of empirical treatment to antibiotic sensitivity results and (3) the degree of error in the local guidelines regarding the antibiotic sensitivity reported in acute care hospitals enrolled in the vigilància de les infeccions relacionades amb l'atenció sanitària de Catalunya program. During the study period, 79.0% of the empirical treatments analysed complied with the guidelines and 88.1% were appropriate in view of the in vitro activity of the isolated strain. The rate of appropriateness rose from 73.8% in 2017 to 81.0% in 2021 (P < 0.001). The degree of error in the recommendations regarding the in vitro activity of the isolated strains was 5.9% and remained stable during the study period. Antibiotic families correctly prescribed according to the guidelines were third-generation cephalosporins (54.9%), carbapenems (16.8%) and combinations of penicillins and beta-lactamase inhibitors (16.4%). Of the 8009 E. coli strains, 19.0% were extended-spectrum beta-lactamases producers, 36.8% were resistant to quinolones and 0.5% were resistant to carbapenems. The broad implementation of an antimicrobial stewardship program with quality indicators of antibiotic use improved compliance to local guidelines in the empiric treatment of urinary tract E. coli bacteraemia. The degree of error in local guidelines was low but higher in more complex hospitals and in healthcare-associated infections. Guidelines need to be constantly updated with the use of epidemiological data, rapid diagnostic tests and the analysis of patient risk factors specific to each geographical area.

Assessment of the effectiveness of a polypropylene onlay mesh in the prevention of laparoscopic trocar-site incisional hernia in high-risk patients. A randomized clinical trial.

PURPOSE: Trocar site incisional hernia (TSIH) is a common complication of laparoscopic surgery. In the scientific literature there are few descriptions of methods or tools for its prevention. The aim of this report was to assess the effectiveness and safety of a prophylactic measure designed to lower rates of TSIH. METHODS: A multicenter randomized double-blinded clinical trial was performed in high-risk patients (diabetes mellitus and/or age ≥ 70 years and/or BMI ≥ 30 kg/m2 and/or extended incision for specimen retrieval) who underwent either elective or emergency laparoscopic cholecystectomy. Patients were assigned to prophylactic onlay polypropylene mesh fixation (intervention) or to standard trocar closure (control). The main aim was to analyze the efficacy of the intervention, taking occurrence of TSIH as the primary outcome. Clinical and radiological follow up lasted at least one year after surgery. Secondary endpoints were technique-related complications (surgical site occurrences). RESULTS: One hundred and forty-three patients were randomized and finally 116 were analyzed (64 in the intervention arm and 52 in the control arm). Groups were homogeneous. Mean [SD] age, 65 [18] years; 86 (60.6%) were women. The cumulative TSIH incidence was lower in the intervention group although the differences did not reach statistical significance, assessed either radiologically (16 [25.4%] vs 17 [31.5%], p = 0.538) or clinically (9 [16.1%] vs 9 [20], p = 0.613). No differences in surgical site infection, hematoma or seroma were detected. Mean follow-up was 670 days (range 223-1294). CONCLUSION: Our results show that, when properly assessed, the overall TSIH incidence is extremely high. Although polypropylene onlay mesh placement is safe, it does not appear to be effective in reducing the TSIH incidence rate. Radiological evaluation may be more accurate. TRIAL REGISTRATION: ClinicalTrials.org NCT03495557. Date of registration: April 12, 2018.

Early Management of Severe Biliary Infection in the Era of the Tokyo Guidelines.

Sepsis of biliary origin is increasing worldwide and has become one of the leading causes of emergency department admissions. The presence of multi-resistant bacteria (MRB) is increasing, and mortality rates may reach 20%. This review focuses on the changes induced by the Tokyo guidelines and new concepts related to the early treatment of severe biliary disease. If cholecystitis or cholangitis is suspected, ultrasound is the imaging test of choice. Appropriate empirical antibiotic treatment should be initiated promptly, and selection should be performed while bearing in mind the severity and risk factors for MRB. In acute cholecystitis, laparoscopic cholecystectomy is the main therapeutic intervention. In patients not suitable for surgery, percutaneous cholecystostomy is a valid alternative for controlling the infection. Treatment of severe acute cholangitis is based on endoscopic or transhepatic bile duct drainage and antibiotic therapy. Endoscopic ultrasound and other new endoscopic techniques have been added to the arsenal as novel alternatives in high-risk patients. However, biliary infections remain serious conditions that can lead to sepsis and death. The introduction of internationally accepted guidelines, based on clinical presentation, laboratory tests, and imaging, provides a framework for their rapid diagnosis and treatment. Prompt assessment of patient severity, timely initiation of antimicrobials, and early control of the source of infection are essential to reduce morbidity and mortality rates.

Reducing the duration of antibiotic therapy in surgical patients through a specific nationwide antimicrobial stewardship program. A prospective, interventional cohort study.

BACKGROUND: Guidelines recommend 5-7 days of antibiotic treatment in patients with surgical infection and adequate source control. This nationwide stewardship intervention aimed to reduce the duration of treatments in surgical patients to <7 days. METHODS: Prospective cohort study evaluating surgical patients receiving antibiotics ≥7 days in 32 hospitals. Indication for treatment, quality of source control, type of recommendations issued, and adherence to the recommendations were analysed. Temporal trends in the percentages of patients with treatment >7 days were evaluated using a linear regression model and Pearson's correlation coefficients. RESULTS: A total of 32 499 patients were included. Of these, 13.7% had treatments ≥7 days. In all, 3912 stewardship interventions were performed, primarily in general surgery (90.7%) and urology (8.1%). The main types of infection were intra-abdominal (73.4%), skin/soft tissues (9.8%) and urinary (9.2%). The septic focus was considered controlled in 59.9% of cases. Out of 5458 antibiotic prescriptions, the most frequently analysed drugs were piperacillin/tazobactam (21.7%), metronidazole (11.2%), amoxicillin/clavulanate (10.3%), meropenem (10.7%), ceftriaxone (9.3%) and ciprofloxacin (6.7%). The main recommendations issued were: treatment discontinuation (35.0%), maintenance (40.0%) or de-escalation (15.5%), and the overall adherence rate was 91.5%. With adequate source control, the most frequent recommendation was to terminate treatment (51.2%). Throughout the study period, a significant decrease in the percentage of prolonged treatments was observed (Pc=-0.69;P < 0.001). CONCLUSIONS: This stewardship programme reduced the duration of treatments in surgical departments. Preference was given to general surgery services, intra-abdominal infection, and beta-lactam antibiotics, including carbapenems. Adherence to the issued recommendations was high.

Surgical Infection Reduction Program of the Observatory of Surgical Infection (PRIQ-O): Delphi prioritization and consensus document on recommendations for the prevention of surgical site infection.

Surgical site infection is the most frequent and avoidable complication of surgery, but clinical guidelines for its prevention are insufficiently followed. We present the results of a Delphi consensus carried out by a panel of experts from 17 Scientific Societies with a critical review of the scientific evidence and international guidelines, to select the measures with the highest degree of evidence and facilitate their implementation. Forty measures were reviewed and 53 recommendations were issued. Ten main measures were prioritized for inclusion in prevention bundles: preoperative shower; correct surgical hand hygiene; no hair removal from the surgical field or removal with electric razors; adequate systemic antibiotic prophylaxis; use of minimally invasive approaches; skin decontamination with alcoholic solutions; maintenance of normothermia; plastic wound protectors-retractors; intraoperative glove change; and change of surgical and auxiliary material before wound closure.

Leveraging a nationwide infection surveillance program to implement a colorectal surgical site infection reduction bundle: a pragmatic, prospective, and multicenter cohort study.

BACKGROUND: Bundled interventions usually reduce surgical site infection (SSI) when implemented at single hospitals, but the feasibility of their implementation at the nationwide level and their clinical results are not well established. MATERIALS AND METHODS: Pragmatic interventional study to analyze the implementation and outcomes of a colorectal surgery care bundle within a nationwide quality improvement program. The bundle consisted of antibiotic prophylaxis, oral antibiotic prophylaxis (OAP), mechanical bowel preparation, laparoscopy, normothermia, and a wound retractor. Control group (CG) and Intervention group (IG) were compared. Overall SSI, superficial (S-SSI), deep (D-SSI), and organ/space (O/S-SSI) rates were analyzed. Secondary endpoints included microbiology, 30-day mortality, and length of hospital stay. RESULTS: A total of 37 849 procedures were included, 19 655 in the CG and 18 194 in the IG. In all, 5462 SSIs (14.43%) were detected: 1767 S-SSI (4.67%), 847 D-SSI (2.24%), and 2838 O/S-SSI (7.5%). Overall SSI fell from 18.38% (CG) to 10.17% (IG), odds ratio (OR) of 0.503 [0.473-0.524]. O/S-SSI rates were 9.15% (CG) and 5.72% (IG), OR of 0.602 [0.556-0.652]. The overall SSI rate was 16.71% when no measure was applied and 6.23% when all six were used. Bundle implementation reduced the probability of overall SSI (OR: 0.331; CI 95 : 0.242-0.453), and also O/S-SSI rate (OR: 0.643; CI 95 : 0.416-0.919). In the univariate analysis, all measures except normothermia were associated with a reduction in overall SSI, while only laparoscopy, OAP, and mechanical bowel preparation were related to a decrease in O/S-SSI. Laparoscopy, wound retractor, and OAP decreased overall SSI and O/S-SSI in the multivariate analysis. CONCLUSIONS: In this cohort study, the application of a specific care bundle within a nationwide nosocomial infection surveillance system proved feasible and resulted in a significant reduction in overall and O/S-SSI rates in the elective colon and rectal surgery. The OR for SSI fell between 1.5 and 3 times after the implementation of the bundle.

What have we learned from the surveys of the AEC, AECP and the Observatory of Infection in Surgery? Compliance with postoperative infection prevention measures and comparison with the AEC recommendations.

Before planning improvement strategies, it is crucial to know the degree of implementation of preventative measures for postoperative infection. The aggregated results of 3 surveys carried out by the Observatory of Infection in Surgery to members of 11 associations of surgeons and perioperative nurses are presented. The questions were aimed to determine the knowledge of the scientific evidence, personal beliefs and the actual use of the main measures. Of 2295 respondents, 45.1% did not receive feedback on the infection rate of their unit. Insufficient knowledge of some of the main prevention recommendations and some disturbing rates of use were observed. The preferred strategies to improve compliance with preventive guidelines and their degree of implementation were investigated. A gap between scientific evidence and clinical practice in the prevention of infection in different surgical specialties was confirmed.

A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R.

Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics experiments have become increasingly popular because of the wide range of metabolites that can be analyzed and the possibility to measure novel compounds. LC-MS instrumentation and analysis conditions can differ substantially among laboratories and experiments, thus resulting in non-standardized datasets demanding customized annotation workflows. We present an ecosystem of R packages, centered around the MetaboCoreUtils, MetaboAnnotation and CompoundDb packages that together provide a modular infrastructure for the annotation of untargeted metabolomics data. Initial annotation can be performed based on MS1 properties such as m/z and retention times, followed by an MS2-based annotation in which experimental fragment spectra are compared against a reference library. Such reference databases can be created and managed with the CompoundDb package. The ecosystem supports data from a variety of formats, including, but not limited to, MSP, MGF, mzML, mzXML, netCDF as well as MassBank text files and SQL databases. Through its highly customizable functionality, the presented infrastructure allows to build reproducible annotation workflows tailored for and adapted to most untargeted LC-MS-based datasets. All core functionality, which supports base R data types, is exported, also facilitating its re-use in other R packages. Finally, all packages are thoroughly unit-tested and documented and are available on GitHub and through Bioconductor.

An interventional nationwide surveillance program lowers postoperative infection rates in elective colorectal surgery. A cohort study (2008-2019).

BACKGROUND: Colorectal surgery is associated with the highest rate of surgical site infection (SSI). This study analyses the effectiveness of an interventional surveillance program on SSI rates after elective colorectal surgery. MATERIAL AND METHODS: Cohort study showing temporal trends of SSI rates and Standardized Infection Ratio (SIR) in elective colorectal surgery over a 12-year period. Prospectively collected data of a national SSI surveillance program was analysed and the effect of specific interventions was evaluated. Patient and procedure characteristics, as well as SIR and SSI rates were stratified by risk categories and type of SSI analysed using stepwise multivariate logistic regression models. RESULTS: In a cohort of 42,330 operations, overall cumulative SSI incidence was 16.31%, and organ-space SSI (O/S-SSI) was 8.59%. There was a 61.63% relative decrease in SSI rates (rho = -0.95804). The intervention which achieved the greatest SSI reduction was a bundle of 6 measures. SSI in pre-bundle period was 19.73% vs. 11.10% in post-bundle period (OR 1.969; IC 95% 1.860-2.085; p < 0.0001). O/S-SSI were 9.08% vs. 6.06%, respectively (OR 1.547; IC 95% 1.433-1.670; p < 0.0001). Median length of stay was 7 days, with a significant decrease over the studied period (rho = -0.98414). Mortality of the series was 1.08%, ranging from 0.35% to 2.0%, but a highly significant decrease was observed (rho = -0.67133). CONCLUSIONS: Detailed analysis of risk factors and postoperative infection in colorectal surgery allows strategies for reducing SSI incidence to be designed. An interventional surveillance program has been effective in decreasing SIR and SSI rates.

Oral Antibiotic Prophylaxis Lowers Surgical Site Infection in Elective Colorectal Surgery: Results of a Pragmatic Cohort Study in Catalonia.

BACKGROUND: The role of oral antibiotic prophylaxis (OAP) and mechanical bowel preparation (MBP) in the prevention of surgical site infection (SSI) after colorectal surgery is still controversial. The aim of this study was to analyze the effect of a bundle including both measures in a National Infection Surveillance Network in Catalonia. METHODS: Pragmatic cohort study to assess the effect of OAP and MBP in reducing SSI rate in 65 hospitals, comparing baseline phase (BP: 2007-2015) with implementation phase (IP: 2016-2019). To compare the results, a logistic regression model was established. RESULTS: Out of 34,421 colorectal operations, 5180 had SSIs (15.05%). Overall SSI rate decreased from 18.81% to 11.10% in BP and IP, respectively (OR 0.539, CI95 0.507-0.573, p < 0.0001). Information about bundle implementation was complete in 61.7% of cases. In a univariate analysis, OAP and MBP were independent factors in decreasing overall SSI, with OR 0.555, CI95 0.483-0.638, and OR 0.686, CI95 0.589-0.798, respectively; and similarly, organ/space SSI (O/S-SSI) (OR 0.592, CI95 0.494-0.710, and OR 0.771, CI95 0.630-0.944, respectively). However, only OAP retained its protective effect at both levels at multivariate analyses. CONCLUSIONS: oral antibiotic prophylaxis decreased the rates of SSI and O/S-SSI in a large series of elective colorectal surgery.