Use of microbiological and patient data for choice of empirical antibiotic therapy in acute cholangitis.
ABSTRACT: BACKGROUND:Ineffective antibiotic therapy increases mortality of acute cholangitis. The choice of antibiotics should reflect local resistance patterns and avoid the overuse of broad-spectrum agents. In this study, we analysed how results of bile and blood cultures and patient data can be used for selection of empirical antibiotic therapy in acute cholangits. METHODS:Pathogen frequencies and susceptibility rates were determined in 423 positive bile duct cultures and 197 corresponding blood cultures obtained from 348 consecutive patients with acute cholangitis. Patient data were retrieved from the medical records. Associations of patient and microbiological data were assessed using the Chi-2 test and multivariate binary logistic regression. RESULTS:In bile cultures, enterobacterales and enterococci were isolated with equal frequencies of approximately 30% whereas in blood cultures, enterobacterales predominated (56% compared to 21% enterococci). Antibiotic resistance rates of enterobacterales were?>?20% for fluorochinolones, cephalosporines and acylureidopenicillins but not for carbapenems (
Project description:<h4>Background</h4>Acute cholangitis (AC) requires the immediate initiation of antibiotic therapy in addition to treatment for biliary obstruction. Against a background of an increasing prevalence of multi-drug resistant (MDR) bacteria, the risk factors for the failure of empiric therapy must be defined.<h4>Methods</h4>Using a pathogen-based approach, 1764 isolates from positive bile duct cultures were retrospectively analyzed to characterize the respective pathogen spectra in two German tertiary centers. Using a patient-based approach, the clinical and laboratory data for 83 patients with AC were assessed to identify risk factors for AC with pathogens resistant to the applied empiric therapy.<h4>Results</h4>Bile cultures were predominantly polymicrobial, and empiric antibiotic therapies did not cover the full biliary pathogen spectrum in 78% of cases. MDR bacteria were isolated from the bile of 24/83 (29%) patients. The univariate risk factors for biliary MDR bacteria were male sex, nosocomial AC, prior antibiotic exposure and prior biliary stenting, of which biliary stenting was the only independent risk factor according to multivariate analysis (OR = 3.8; 95% CI 1.3-11.0, P = 0.013). Although there were no significant differences in survival or hospital stay in AC patients with and without detected biliary MDR pathogens, the former more often had a concomitant bloodstream infection (58% vs. 24%; P = 0.019), including those involving MDR pathogens or fungi (21% vs. 2%; P = 0.007).<h4>Conclusion</h4>Patients with biliary stents who develop AC should receive empiric therapy covering enterococci and extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae. These patients are at an increased risk for bloodstream infections by MDR pathogens or fungi.
Project description:<h4>Background</h4>Intraoperative cultures are commonly sent in complicated appendicitis. Culture-guided antibiotics used to prevent postoperative infectious complications are debated. In this study, we describe the microbial overlap between intraoperative and abscess cultures, and antibiotic resistance patterns.<h4>Method</h4>A local register of a children's hospital treating children 0-15 years old with appendicitis between 2006 and 2013 was used to find cases with intraoperative cultures, and cultures from drained or aspirated postoperative intraabdominal abscesses. Culture results, administered antibiotics, their nominal coverage of the identified microorganisms, and rationales given for changes in antibiotic regimens were collected from electronic medical records.<h4>Results</h4>In 25 of 35 patients who met inclusion criteria, there was no overlap between the intraoperative and abscess cultures. In 33 of 35 patients, all identified intraoperative organisms were covered with postoperative antibiotics. In 14 patients, organisms in the abscess culture were not covered by administered antibiotics. Enterococci not found in the intraoperative culture were found in 12 of 35 abscesses. We found no difference in the antibiotic coverage between rationales given for antibiotic changes.<h4>Conclusion</h4>The overlap between intraoperative cultures and cultures from subsequent abscesses was small. Lack of antibiotic coverage of intraoperative cultures was not an important factor in abscess formation.
Project description:NG-Test CTX-M MULTI and NG-Test Carba 5 (NG Biotech) are two rapid <i>in vitro</i> immunochromatographic assays that are widely used for the detection of the most common extended spectrum beta-lactamases (ESBL) and carbapenemases in Enterobacterales. ESBL and carbapenemases are leading causes of morbidity and mortality worldwide and their rapid detection from positive blood cultures is crucial for early initiation of effective antimicrobial therapy in bloodstream infections (BSI) involving antibiotic-resistant organisms. In this study, we developed a rapid workflow for positive blood cultures for direct identification of Enterobacterales by MALDI-TOF mass-spectrometry, followed by detection of ESBL and carbapenemases using NG-Test CTX-M MULTI and NG-Test Carba 5 (NG Biotech). The workflow was evaluated using Enterobacterales isolates (<i>n</i> = 114), primarily Klebsiella species (<i>n</i> = 50) and Escherichia coli (<i>n</i> = 40). Compared to the standard testing approach in our institution using BD Phoenix, our new testing approach demonstrates 100% sensitivity and specificity for organism identification and detection of ESBL and carbapenemases. Implementation of a rapid workflow in diagnostic microbiology laboratories will enable more effective antimicrobial management of patients with BSI due to ESBL- and carbapenemase-producing Enterobacterales. <b>IMPORTANCE</b> The incidence of bloodstream infections (BSI) with extended spectrum beta-lactamase (ESBL) producing and carbapenemase producing Enterobacterales (CPE) is increasing at an alarming rate, for which only limited therapeutic options remain available. Rapid identification of these bacteria along with their antibiotic resistance mechanisms in positive blood cultures with Gram-negative bacteria will allow for early initiation of effective therapy and limit the overuse of broad-spectrum antibiotics in BSI (1). In this study we evaluated a combined approach of testing positive blood cultures directly, using MALDI-TOF MS followed by rapid immunochromatographic tests, for the detection of ESBLs and CPEs. Our approach demonstrates 100% sensitivity and specificity for the identification of Enterobacterales and detection of ESBLs and CPEs in positive blood culture with a turnaround time (TAT) of ≤60 min compared to a TAT of 48 h required by conventional culture and susceptibility testing methods.
Project description:<h4>Background</h4>The optimal antibiotic therapy duration for cholangitis is unclear. Guideline recommendations vary between 4 and 14 days after biliary drainage. Clinical observations and some evidence however suggest that shorter antibiotic therapy may be sufficient.<h4>Objective</h4>To compare the effectiveness and safety of short-course therapy of ≤ 3 days with long-course therapy of ≥ 4 days after biliary drainage in cholangitis patients.<h4>Methods</h4>We searched the databases PubMed, EMBASE, Cochrane Library, and trial registers for literature up to August 5, 2020. RCTs and observational studies including case series reporting on antibiotic therapy duration for acute cholangitis were eligible for inclusion. Two reviewers independently evaluated study eligibility, extracted data, assessed risk of bias and quality of evidence. A meta-analysis was planned if the included studies were comparable with regard to important study characteristics. Primary outcomes included recurrent cholangitis, subsequent other infection, and mortality.<h4>Results</h4>We included eight studies with 938 cholangitis patients. Four observational studies enrolled patients treated for ≤ 3 days. Recurrent cholangitis occurred in 0-26.8% of patients treated with short-course therapy, which did not differ from long-course therapy (range 0-21.1%). Subsequent other infection and mortality rates were also comparable. Quality of available evidence was very low.<h4>Conclusion</h4>There is no high-quality evidence available to draw a strong conclusion, but heterogeneous observational studies suggest that antibiotic therapy of ≤ 3 days is sufficient in cholangitis patients with common bile duct stones.
Project description:Ceftriaxone resistance in the Enterobacterales is typically the result of production of ESBLs or AmpC β-lactamases. The genes encoding these enzymes are often co-located with other antibiotic resistance genes leading to resistance to aminoglycosides, quinolones and trimethoprim/sulfamethoxazole. Carbapenems are stable to ESBLs and AmpC giving them reliable <i>in vitro</i> activity against producers of these β-lactamases. In contrast, piperacillin/tazobactam and amoxicillin/clavulanate are compromised by co-production of OXA-1, which is not inhibited by tazobactam or clavulanate. These <i>in vitro</i> findings provide an explanation for the MERINO trial outcomes, where 3.7% (7/191) randomized to meropenem died compared with 12.3% (23/187) randomized to piperacillin/tazobactam as definitive treatment of bloodstream infection due to ceftriaxone-resistant organisms. No randomized trials have yet put cefepime and carbapenems head to head, but some observational studies have shown worse outcomes with cefepime. We argue that carbapenems are the antibiotics of choice for ceftriaxone-resistant Enterobacterales.
Project description:Due to the importance of a rapid determination of patients infected by multidrug resistant bacteria, we evaluated two rapid diagnostic tests for the detection of third-generation cephalosporins (3GC)-resistant Enterobacterales directly from positive blood cultures within 1 h: BL-REDTM (electrochemical method) and ?-LACTATM test (chromogenic method). A panel of 150 clinical strains characterized for their resistance profiles (e.g., penicillinases, extended-spectrum beta-lactamases (ESBLs), overproduction of cephalosporinase, carbapenemases, impermeability) was tested. Approximately 100 CFU of each isolate was spiked into sterile blood culture bottles and incubated in a BD BACTECTM FX automated system (Becton Dickinson, USA). Positive blood cultures were examined to parallel testing using the BL-REDTM and ?-LACTATM tests and conventional susceptibility method (disc diffusion following EUCAST recommendations). For all phenotypes combined, the sensitivity, specificity, positive predictive value, and negative predictive value in the detection of 3GC resistance were, respectively (i) with BL-REDTM: 45.7, 100, 100, and 54.2% and (ii) with ?-LACTATM test: 52.2, 100, 100, and 56.9%. The positivity of tests allows to adapt antibiotic treatment whereas the negative result requires other tests. Moreover, these tests detect most Ambler class A-producing Enterobacterales (KPC, ESBL, extended-spectrum OXY) with sensitivities and specificities of 87.5 and 99% for BL-REDTM, respectively and both 100% for ?-LACTATM test (47/47 isolates). These two rapid tests failed to detect AmpC overexpressed (sensitivities of 2.7% for BL-REDTM and 0% for ?-LACTATM test) and Ambler class B-producing Enterobacterales (sensitivities of 40% for both tests) notably strains without ESBLs associated (sensitivities of 0% for both tests). BL-REDTM and ?-LACTATM tests are easy-to-use and mainly attractive when a positive result is obtained notably to detect most of the Ambler class A-producing Enterobacterales in <1 h after the positivity of the blood culture, allowing a rapid adaptation of the antibiotic therapy in patients.
Project description:<h4>Background</h4>Patients hospitalized with coronavirus disease 2019 (COVID-19) are at increased risk of health care-associated infections (HAIs), especially with prolonged hospital stays. We sought to identify incidence, antimicrobial susceptibilities, and outcomes associated with bacterial/fungal secondary infections in a large cohort of patients with COVID-19.<h4>Methods</h4>We evaluated adult patients diagnosed with COVID-19 between 2 March and 31 May 2020 and hospitalized >24 hours. Data extracted from medical records included diagnoses, vital signs, laboratory results, microbiological data, and antibiotic use. Microbiologically confirmed bacterial and fungal pathogens from clinical cultures were evaluated to characterize community- and health care-associated infections, including describing temporal changes in predominant organisms on presentation and throughout hospitalization. Univariable and multivariable logistic regression analyses were performed to investigate risk factors for HAIs.<h4>Results</h4>A total of 3028 patients were included and accounted for 899 positive clinical cultures. Overall, 516 (17%) patients with positive cultures met criteria for infection. Community-associated coinfections were identified in 183 (6%) patients, whereas HAIs occurred in 350 (12%) patients. Fifty-seven percent of HAIs were caused by gram-negative bacteria and 19% by fungi. Antibiotic resistance increased with longer hospital stays, with incremental increases in the proportion of vancomycin resistance among enterococci and ceftriaxone and carbapenem resistance among Enterobacterales. Intensive care unit stay, invasive mechanical ventilation, and steroids were associated with HAIs.<h4>Conclusions</h4>HAIs occur in a small proportion of patients hospitalized with COVID-19 and are most often caused by gram-negative and fungal pathogens. Antibiotic resistance is more prevalent with prolonged hospital stays. Antimicrobial stewardship is imperative in this population to minimize unnecessary broad-spectrum antibiotic use.
Project description:<h4>Objectives</h4>To estimate the incidence and epidemiology of catheter-related bloodstream infections (CRBSIs) on a national scale by using prospective epidemiological data from the Swiss <i>Antibiotic Resistance Surveillance System</i> (ANRESIS).<h4>Design</h4>Observational study.<h4>Setting</h4>National surveillance from 2008 to 2015 of acute hospitals in Switzerland.<h4>Participants</h4>We included acute Swiss hospitals that sent blood cultures and catheter tip culture results on a regular basis during the entire study period to the ANRESIS database.<h4>Outcome measure</h4>A catheter-related bloodstream infection (termed 'modified CRBSI', mCRBSI) was defined as isolating the same microorganism with identical antibiogram from ?1?blood cultures (performed ±7 days around the catheter removal) as the one recovered from the catheter tip. Incidence rates of mCRBSI were calculated per 1000 admissions.<h4>Results</h4>From 2008 to 2015, the mCRBSI incidence rate decreased from 0.83 to 0.58 episodes/1000 admissions (-6% per year, p<0.001). Coagulase-negative staphylococci, <i>Staphylococcus aureus</i> and fungi all exhibited decreasing trends, while rates of enterococci and Gram-negative bacteria remained stable.<h4>Conclusions</h4>The overall incidence of mCRBSI in Switzerland is decreasing; however, the incidence of mCRBSI due to Enterococci and Gram-negative micro-organisms did not change over time. These pathogens may grow in importance in catheter-related infections, which would have clinical implications for the choice of empirical treatment.
Project description:Antibiotic resistance poses a major threat to public health. More effective ways of the antibiotic prescription are needed to delay the spread of antibiotic resistance. Employment of sequencing technologies coupled with the use of trained neural network algorithms for genotype-to-phenotype prediction will reduce the time needed for antibiotic susceptibility profile identification from days to hours. In this work, we have sequenced and phenotypically characterized 171 clinical isolates of <i>Escherichia coli </i>and <i>Klebsiella pneumoniae</i> from Norway and India. Based on the data, we have created neural networks to predict susceptibility for ampicillin, 3rd generation cephalosporins and carbapenems. All networks were trained on unassembled data, enabling prediction within minutes after the sequencing information becomes available. Moreover, they can be used both on Illumina and MinION generated data and do not require high genome coverage for phenotype prediction. We cross-checked our networks with previously published algorithms for genotype-to-phenotype prediction and their corresponding datasets. Besides, we also created an ensemble of networks trained on different datasets, which improved the cross-dataset prediction compared to a single network. Additionally, we have used data from direct sequencing of spiked blood cultures and found that AMR-Diag networks, coupled with MinION sequencing, can predict bacterial species, resistome, and phenotype as fast as 1-8 h from the sequencing start. To our knowledge, this is the first study for genotype-to-phenotype prediction: (1) employing a neural network method; (2) using data from more than one sequencing platform; and (3) utilizing sequence data from spiked blood cultures.
Project description:Antimicrobial agents should be administered to all patients with suspected acute cholangitis as a priority as soon as possible. Bile cultures should be performed at the earliest opportunity. The important factors which should be considered in selecting antimicrobial therapy include the agent's activity against potentially infecting bacteria, the severity of the cholangitis, the presence or absence of renal and hepatic diseases, the patient's recent history of antimicrobial therapy, and any recent culture results, if available. Biliary penetration of the microbial agents should also be considered in the selection of antimicrobials, but activity against the infecting isolates is of greatest importance. If the causative organisms are identified, empirically chosen antimicrobial drugs should be replaced by narrower-spectrum antimicrobial agents, the most appropriate for the species and the site of the infection.