Exposure assessment of extended-spectrum beta-lactamases/AmpC beta-lactamases-producing Escherichia coli in meat in Denmark

INTRODUCTION Extended-spectrum beta-lactamases (ESBL) and AmpC beta-lactamases (AmpC) are of concern for veterinary and public health because of their ability to cause treatment failure due to antimicrobial resistance in Enterobacteriaceae. The main objective was to assess the relative contribution (RC) of different types of meat to the exposure of consumers to ESBL/AmpC and their potential importance for human infections in Denmark. MATERIAL AND METHODS The prevalence of each genotype of ESBL/AmpC-producing E. coli in imported and nationally produced broiler meat, pork and beef was weighted by the meat consumption patterns. Data originated from the Danish surveillance program for antibiotic use and antibiotic resistance (DANMAP) from 2009 to 2011. DANMAP also provided data about human ESBL/AmpC cases in 2011, which were used to assess a possible genotype overlap. Uncertainty about the occurrence of ESBL/AmpC-producing E. coli in meat was assessed by inspecting beta distributions given the available data of the genotypes in each type of meat. RESULTS AND DISCUSSION Broiler meat represented the largest part (83.8%) of the estimated ESBL/AmpC-contaminated pool of meat compared to pork (12.5%) and beef (3.7%). CMY-2 was the genotype with the highest RC to human exposure (58.3%). However, this genotype is rarely found in human infections in Denmark. CONCLUSION The overlap between ESBL/AmpC genotypes in meat and human E. coli infections was limited. This suggests that meat might constitute a less important source of ESBL/AmpC exposure to humans in Denmark than previously thought - maybe because the use of cephalosporins is restricted in cattle and banned in poultry and pigs. Nonetheless, more detailed surveillance data are required to determine the contribution of meat compared to other sources, such as travelling, pets, water resources, community and hospitals in the pursuit of a full source attribution model.

Risk factors for Clostridium difficile nosocomial diarrhea in patients at the Michael E. Debakey Veterans Affairs Medical Center, Houston, Texas

Background. Clostridium difficile is the leading cause of hospital associated infectious diarrhea and colitis. About 3 million cases of Clostridium difficile diarrhea occur each year with an annual cost of $1 billion. ^ About 20% of patients acquire C. difficile during hospitalization. Infection with Clostridium difficile can result in serious complications, posing a threat to the patient's life. ^ Purpose. The aim of this research was to demonstrate the uniqueness in the characteristics of C. difficile positive nosocomial diarrhea cases compared with C. difficile negative nosocomial diarrhea controls admitted to a local hospital. ^ Methods. One hundred and ninety patients with a positive test and one hundred and ninety with a negative test for Clostridium difficile nosocomial diarrhea, selected from patients tested between January 1, 2002 and December 31, 2003, comprised the study population. Demographic and clinical data were collected from medical records. Logistic regression analyses were conducted to determine the associated odds between selected variables and the outcome of Clostridium difficile nosocomial diarrhea. ^ Results. For the antibiotic classes, cephalosporins (OR, 1.87; CI 95, 1.23 to 2.85), penicillins (OR, 1.57; CI 95, 1.04 to 2.37), fluoroquinolones (OR, 1.65; CI 95, 1.09 to 2.48) and antifungals (OR, 2.17; CI 95, 1.20 to 3.94), were significantly associated with Clostridium difficile nosocomial diarrhea Ceftazidime (OR, 1.95; CI 95, 1.25 to 3.03, p=0.003), gatifloxacin (OR, 1.97; CI 95, 1.31 to 2.97, p=0.001), clindamycin (OR, 3.13; CI 95, 1.99 to 4.93, p<0.001) and vancomycin (OR, 1.77; CI 95, 1.18 to 2.66, p=0.006, were also significantly associated with the disease. Vancomycin was not statistically significant when analyzed in a multivariable model. Other significantly associated drugs were, antacids, laxatives, narcotics and ranitidine. Prolong use of antibiotics and an increased number of comorbid conditions were also associated with C. difficile nosocomial diarrhea. ^ Conclusion. The etiology for C. difficile diarrhea is multifactorial. Exposure to antibiotics and other drugs, prolonged antibiotic usage, the presence and severity of comorbid conditions and prolonged hospital stay were shown to contribute to the development of the disease. It is imperative that any attempt to prevent the disease, or contain its spread, be done on several fronts. ^

The catalytic mechanism of beta-lactamases: NMR titration of an active-site lysine residue of the TEM-1 enzyme.

Beta-Lactamases are widespread in the bacterial world, where they are responsible for resistance to penicillins, cephalosporins, and related compounds, currently the most widely used antibacterial agents. Detailed structural and mechanistic understanding of these enzymes can be expected to guide the design of new antibacterial compounds resistant to their action. A number of high-resolution structures are available for class A beta-lactamases, whose catalytic mechanism involves the acylation of a serine residue at the active site. The identity of the general base which participates in the activation of this serine residue during catalysis has been the subject of controversy, both a lysine residue and a glutamic acid residue having been proposed as candidates for this role. We have used the pH dependence of chemical modification of epsilon-amino groups by 2,4,6,-trinitrobenzenesulfonate and the pH dependence of the epsilon-methylene 1H and 13C chemical shifts (in enzyme selectively labeled with [epsilon-13C]lysine) to estimate the pKa of the relevant lysine residue, lysine-73, of TEM-1 beta-lactamase. Both methods show that the pKa of this residue is > 10, making it very unlikely that this residue could act as a proton acceptor in catalysis. An alternative mechanism in which this role is performed by glutamate-166 through an intervening water molecule is described.

Frequência de resistência a múltiplos fármacos em pseudomonas aeroginosa

A multirresistência bacteriana tem crescido significativamente nos últimos anos. Entre os gram negativos a P. aeruginosa demonstra facilidade de desenvolvimento de resistência aos antibióticos. O objetivo deste estudo foi determinar a frequência de resistência a múltiplos fármacos em isolados de Pseudomonas aeruginosa e detectar cepas multirresistentes em um hospital público de Maceió/AL. De forma retrospectiva, descritiva e transversal, entre janeiro de 2012 a dezembro de 2013, iniciou-se uma ampla análise documental dos registros de atendimento no setor de Microbiologia do Hospital Universitário Professor Alberto Antunes (HUPAA/UFAL) para avaliar o material obtido de pacientes que apresentaram cultura positiva para P. aeruginosa. Vários espécimes clínicos foram obtidos e as cepas identificadas fenotipicamente pelo método automatizado Vitek®, bem como as análises do perfil de susceptibilidade aos antimicrobianos, seguindo os critérios adotados pelo National Committee for Clinical and Laboratory Standards (NCCLS). Foram obtidas 78 culturas com isolados positivos para P. aeruginosa, sendo a maioria procedente de pacientes da UTI geral (47,4%), seguida da Clínica cirúrgica (16,7%). Entre as amostras clínicas analisadas, a secreção traqueal foi a de maior incidência com 25,6%, seguida de secreção de ferida (20,5%) e escarro (18%). O composto mais ativo contra a P. aeruginosa foi a Colistina (100,0%). Detectou-se elevada multirresistência de P. aeruginosa aos betalactâmicos, cefalosporinas e carbapenêmicos. Baseando-se nos dados apresentados, torna-se evidente a necessidade de um monitoramento rotineiro do perfil de sensibilidade desta bactéria em ambiente hospitalar, sendo de extrema utilidade para a escolha adequada na terapêutica empírica, proporcionando conhecimento prévio dos antimicrobianos que apresentam boa eficácia diante deste patógeno, favorecendo o uso racional de antimicrobianos. PALAVRAS-CHAVE: Multirresistência; Pseudomonas aeruginosa;Sensibilidade; Antimicrobianos.

A Multiplex Real-Time PCR with High Resolution Melting Analysis for the Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae.

Resistance to antibiotics used against Neisseria gonorrhoeae infections is a major public health concern. Antimicrobial resistance (AMR) testing relies on time-consuming culture-based methods. Development of rapid molecular tests for detecting AMR determinants could provide valuable tools for surveillance, epidemiological studies and to inform individual case management. We developed a fast (<1.5 hrs) SYBR-green based real-time PCR method with high resolution melting (HRM) analysis. One triplex and three duplex reactions included two sequences for N. gonorrhoeae identification and seven determinants of resistance to extended-spectrum cephalosporins (ESCs), azithromycin, ciprofloxacin, and spectinomycin. The method was validated by testing 39 previously fully-characterized N. gonorrhoeae strains, 19 commensal Neisseria spp., and an additional panel of 193 gonococcal isolates. Results were compared with culture-based AMR determination. The assay correctly identified N. gonorrhoeae and the presence or absence of the seven AMR determinants. There was some cross-reactivity with non-gonococcal Neisseria species and the detection limit was 10(3)-10(4) gDNA copies/reaction. Overall, the platform accurately detected resistance to ciprofloxacin (sensitivity and specificity, 100%), ceftriaxone (sensitivity 100%, specificity 90%), cefixime (sensitivity 92%, specificity 94%), azithromycin and spectinomycin (both sensitivity and specificity, 100%). In conclusion, our methodology accurately detects mutations generating resistance to antibiotics used to treat gonorrhea. Low assay sensitivity prevents direct diagnostic testing of clinical specimens but this method can be used to screen collections of gonococcal isolates for AMR more quickly than with current culture-based AMR testing.

Cefepime versus cefpirome: The importance of creatinine clearance

Standard dosage recommendations for beta-lactam antibiotics can result in very low drug levels in intensive care (IC) patients without renal dysfunction. We compared the pharmacokinetics of two fourth-generation cephalosporins, cefepime and cefpirome, and examined the relationship of drug clearance (CL) to creatinine clearance (CLCR). Two separate but similar pharmacokinetic studies (which used 2 g twice daily for each antibiotic) were conducted. Blood was sampled after an initial and a subsequent antibiotic dose. Drug plasma concentrations were measured, and pharmacokinetic analyses were conducted and compared. The pharmacokinetics of cefepime and cefpirome are similar in IC patients. Any differences in drug CL can largely be attributed to differences in CLCR. Despite normal plasma creatinine concentrations, 54% of patients' antibiotic concentrations were less than the minimum inhibitory concentration (MIC) (4 mg/L) for >20% of the dosing interval. Thirty-four percent of patients had CLCR >144 mL/min (20% higher than the expected maximum of 120 mL/min). Only CLCR was an independent predictor of antibiotic CL. Time above MIC was predicted only by CLCR. Some IC patients have a very large CLCR which results in very low levels of studied antibiotics. Either shortening the dosage interval or using continuous infusions would prevent low levels and keep troughs above the MIC for longer periods. In view of the lack of bedside measurement of cephalosporin levels, we suggest that more frequent use be made of CLCR to allow prediction of small concentrations clinically.

Australian and New Zealand practice in intensive care (ANZPIC II: The spectrum of practice in the diagnosis and management of pneumonia in patients requiring mechanical ventilation

This study of ventilated patients investigated current clinical practice in 476 episodes of pneumonia (48% community-acquired pneumonia, 24% hospital-acquired pneumonia, 28% ventilator-associated pneumonia) using a prospective survey in 14 intensive care units (ICUs) within Australia and New Zealand. Diagnostic methods and confidence, disease severity, microbiology and antibiotic use were assessed. All pneumonia types had similar mortality (community-acquired pneumonia 33%, hospital-acquired pneumonia 37% and ventilator-associated pneumonia 24%, P = 0.15) with no inter-hospital differences (P = 0.08-0.91). Bronchoscopy was performed in 26%, its use predicted by admission hospital (one tertiary: OR 9.98, CI 95% 5.11-19.49, P < 0.001; one regional: OR 629, CI 95% 3.24-12.20, P < 0.001), clinical signs of consolidation (OR 3.72, CI 95% 2.09-662, P < 0.001) and diagnostic confidence (OR 2.19, CI 95% 1.29-3.72, P = 0.004). Bronchoscopy did not predict outcome (P = 0.11) or appropriate antibiotic selection (P = 0.69). Inappropriate antibiotic prescription was similar for all pneumonia types (11-13%, P = 0.12) and hospitals (0-16%, P = 0.25). Blood cultures were taken in 51% of cases. For community-acquired pneumonia, 70% received a third generation cephalosporin and 65% a macrolide. Third generation cephalosporins were less frequently used for mild infections (OR 0.38, CI 95% 0.16-0.90, P = 0.03), hospital-acquired pneumonia (OR 0.40, CI 95% 0.23-0.72, P < 0.01), ventilator-associated pneumonia (OR 0.04, CI 95% 0.02-0.13, P < 0.001), suspected aspiration (OR 0.20, CI 95% 0.04-0.92, P = 0.04), in one regional (OR 0.26, CI 95% 0.07-0.97, P = 0.05) and one tertiary hospital (OR 0.14, CI 95% 0.03-0.73, P = 0.02) but were more commonly used in older patients (OR 1.02, CI 95% 1.01-1.03, P = 0.01). There is practice variability in bronchoscopy and antibiotic use for pneumonia in Australian and New Zealand ICUs without significant impact on patient outcome, as the prevalence of inappropriate antibiotic prescription is low. There are opportunities for improving microbiological diagnostic work-up for isolation of aetiological pathogens.

Long-term persistence of multi-drug-resistant Salmonella enterica serovar Newport in two dairy herds

Objective - To evaluate the association between maintaining joint hospital and maternity pens;and persistence of multi-drug-resistant (MDR) Salmonella enterica serovar Newport on 2 dairy farms. Design - Observational study. Sample Population - Feces and environmental samples from 2 dairy herds. Procedure - Herds were monitored for fecal shedding of S enterica Newport after outbreaks of clinical disease. Fecal and environmental samples were collected approximately monthly from pens housing sick cows and calving cows and from pens containing lactating cows. Cattle shedding the organism were tested serially on subsequent visits to determine carrier status. One farm was resampled after initiation of interventional procedures, including separation of hospital and maternity pens. Isolates were characterized via serotyping, determination of antimicrobial resistance phenotype, detection of the CMY-2 gene, and DNA fingerprinting. Results - The prevalence (32.4% and 33.3% on farms A and B, respectively) of isolating Salmonella from samples from joint hospital-maternity pens was significantly higher than the prevalence in samples from pens housing preparturient cows (0.8%, both farms) and postparturient cows on Farm B (8.8%). Multi-drug-resistant Salmonella Newport was isolated in high numbers from bedding material, feed refusals, lagoon slurry, and milk filters. One cow excreted the organism for 190 days. Interventional procedures yielded significant reductions in the prevalences of isolating the organism from fecal and environmental samples. Most isolates were of the C2 serogroup and were resistant to third-generation cephalosporins. Conclusions and Clinical Relevance - Management practices may be effective at reducing the persistence of MDR Salmonella spp in dairy herds, thus mitigating animal and public health risk.

Beta-lactam allergy in adults with cystic fibrosis

Background: Allergic reactions to one or more beta-lactam antibiotic can pose a management problem in patients with cystic fibrosis (CF), and may limit antibiotic choice. Method: The aim of this study was to assess the prevalence of allergy to anti-pseudomonal beta-lactam antibiotics in an adult CF centre and to assess variables, which may contribute to the development of allergic reactions. A questionnaire-based interview and a review of medical records were performed. Results: Of the 150 patients, 54 (36%) had allergic reactions to one or more beta-lactam antibiotics and 20 (19%) had allergic reactions to multiple beta-lactam antibiotics. The proportion of patients allergic to specific beta-lactam antibiotics varied from 10% to 26%. Rates of reactions were highest for penicillins and cephalosporins, intermediate for carbepenems and lowest for aztreonam. Of all reactions, 40% occurred within 24 h of the commencement of an individual antibiotic course. Patients with one or more beta-lactam allergic reactions had received greater cumulative exposure (p < 0.0001), were older (p=0.016) and had lower lung function (p=0.037) than patients without a history of beta-lactam allergy. Cystic Fibrosis transmembrane regulator (CFTR) status, gender, peripheral blood eosinophil count and total IgE concentrations were not different in patients with allergic reactions. Conclusions: This study demonstrates that the prevalence of allergic reactions to beta-lactam antibiotics is high in adults with CF. Increasing age; cumulative exposure and decreasing FEV1 were associated with the development of allergy. (C) 2006 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

Neonatal enteral feeding tubes as loci for colonisation by members of the Enterobacteriaceae

Background The objective of this study was to determine whether neonatal nasogastric enteral feeding tubes are colonised by the opportunistic pathogen Cronobacter spp. (Enterobacter sakazakii) and other Enterobacteriaceae, and whether their presence was influenced by the feeding regime. Methods One hundred and twenty-nine tubes were collected from two neonatal intensive care units (NICU). A questionnaire on feeding regime was completed with each sample. Enterobacteriaceae present in the tubes were identified using conventional and molecular methods, and their antibiograms determined. Results The neonates were fed breast milk (16%), fortified breast milk (28%), ready to feed formula (20%), reconstituted powdered infant formula (PIF, 6%), or a mixture of these (21%). Eight percent of tubes were received from neonates who were 'nil by mouth'. Organisms were isolated from 76% of enteral feeding tubes as a biofilm (up to 107 cfu/tube from neonates fed fortified breast milk and reconstituted PIF) and in the residual lumen liquid (up to 107 Enterobacteriaceae cfu/ml, average volume 250 µl). The most common isolates were Enterobacter cancerogenus (41%), Serratia marcescens (36%), E. hormaechei (33%), Escherichia coli (29%), Klebsiella pneumoniae (25%), Raoultella terrigena (10%), and S. liquefaciens (12%). Other organisms isolated included C. sakazakii (2%),Yersinia enterocolitica (1%),Citrobacter freundii (1%), E. vulneris (1%), Pseudomonas fluorescens (1%), and P. luteola (1%). The enteral feeding tubes were in place between < 6 h (22%) to > 48 h (13%). All the S. marcescens isolates from the enteral feeding tubes were resistant to amoxicillin and co-amoxiclav. Of additional importance was that a quarter of E. hormaechei isolates were resistant to the 3rd generation cephalosporins ceftazidime and cefotaxime. During the period of the study, K. pneumoniae and S. marcescens caused infections in the two NICUs. Conclusion This study shows that neonatal enteral feeding tubes, irrespective of feeding regime, act as loci for the bacterial attachment and multiplication of numerous opportunistic pathogens within the Enterobacteriaceae family. Subsequently, these organisms will enter the stomach as a bolus with each feed. Therefore, enteral feeding tubes are an important risk factor to consider with respect to neonatal infections.

Studies on the mode of action and beta-lactamase inhibitory properties of novel oxapenem compounds

Four novel oxapenem compounds were evaluated for their ß-lactamase inhibitory and antibacterial properties. Two (AM-112 and AM-113) displayed intrinsic antibacterial activity with MICs of between 2 to 16µg/ml and 0.5-2µg/ml against Escherichia coli and methicillin-sensitive and -resistant Staphylococcus aureus, respectively. The isomers of these compounds, AM-115 and AM-114 did not display significant antibacterial activity. Combination of the oxapenems with ceftazidime afforded protection against ß-lactamase-producing strains, including hyperproducers of class C enzymes and extended-spectrum ß-lactamase enzymes. A fixed 4µg/ml concentration of AM-112 protected a panel of eight cephalosporins against hydrolysis by class A and class C ß-lactamase producers. In vivo studies confirmed the protective effect of AM-112 for ceftazidime against ß-lactamase producing S. aureus, Enterobacter cloacae and E. coli strains in a murine intraperitoneal infection model. Each of the oxapenems inhibited class A, class C and class D ß-lactamases isolated from whole cells and purified by isoelectric focusing. AM-114 and AM-115 were as effective as clavulanic acid against class A enzymes. AM-112 and AM-113 were less potent against these enzymes. Class C and class D enzymes proved very susceptible to inhibition by the oxapenems. Molecular modelling of the oxapenems in the active site of the class A. TEM-1 and class C P99 enzymes identified a number of potential sites of interaction. The modelling suggested that Ser-130 in TEM-1 and Tyr-150 in P99 were likely candidates for cross-linking of the inhibitor, leading to inhibition of the enzyme. Morphology studies indicated that sub-inhibitory concentrations of the oxapenems caused the formation of round-shaped cells in E. coli DC0, indicating inhibition of penicillin-binding protein 2 (PBP2). The PBP affinity profile of AM-112 was examined in isolated cell membranes of E. coli DC0, S. aureus NCTC 6571, Enterococcus faecalis SFZ and E. faecalis ATCC 29213, in competition with a radiolabelled penicillin. PBP2 was identified as the primary target for AM-112 in E. coli DC0. Studies on S. aureus NCTC 6571 failed to identify a binding target. AM-112 bound to all the PBPs of both E. faecalis strains, and a concentration of 10µg/ml inhibited all the PBPs except PBP3.

High-performance liquid chromatography and pharmacokinetics of some antibiotics

The principles of High Performance Liquid Chromatography (HPLC) and pharmacokinetics were applied to the use of several clinically-important drugs at the East Birmingham Hospital. Amongst these was gentamicin, which was investigated over a two-year period by a multi-disciplinary team. It was found that there was considerable intra- and inter-patient variation that had not previously been reported and the causes and consequences of such variation were considered. A detailed evaluation of available pharmacokinetic techniques was undertaken and 1- and 2-compartment models were optimised with regard to sampling procedures, analytical error and model-error. The implications for control of therapy are discussed and an improved sampling regime is proposed for routine usage. Similar techniques were applied to trimethoprim, assayed by HPLC, in patients with normal renal function and investigations were also commenced into the penetration of drug into peritoneal dialysate. Novel assay techniques were also developed for a range of drugs including 4-aminopyridine, chloramphenicol, metronidazole and a series of penicillins and cephalosporins. Stability studies on cysteamine, reaction-rate studies on creatinine-picrate and structure-activity relationships in HPLC of aminopyridines are also reported.

Post-cesarean Section Peritonitis at a Referral Hospital in Rwanda: Factors Associated with Maternal Morbidity and Mortality

Background: Post-cesarean section peritonitis is the leading cause of maternal morbidity and mortality at the main referral hospital in Rwanda. Published data on the management of post-cesarean section peritonitis is limited. This study examined predictors of maternal morbidity and mortality for post-cesarean peritonitis.

Methods: We performed a prospective observational cohort study at the University Teaching Hospital Kigali (CHUK) from January 1 until December 31 2015, followed by a retrospective chart review of all subjects with post-cesarean section peritonitis admitted to CHUK from January 1 until December 31, 2014. All patients admitted with the diagnosis of post-cesarean section peritonitis undergoing exploratory laparotomy at CHUK were enrolled. Patients were followed to either discharge or death. Study variables included baseline demographic/clinical characteristics, admission physical exam, intraoperative findings, and management. Data were analyzed using STATA version 14.

Results: Of the 167 patients enrolled, 81 survived without requiring hysterectomy (49%), 49 survived requiring hysterectomy (29%), and 36 died (22%). In the multivariate analysis, severe sepsis was the most significant predictor of mortality (RR=4.0 [2.2-7.7]) and uterine necrosis was the most significant predictor of hysterectomy (RR=6.3 [1.6-25.2]). There were high rates of antimicrobial resistance (AMR) among the bacterial isolates cultured from intra-abdominal pus, with 52% of bacteria resistant to third-generation cephalosporins.

Conclusions: Post-cesarean section peritonitis carries a high mortality rate in Rwanda. It is also associated with a high rate of hysterectomy. Understanding the disease process and identifying factors associated with outcomes can help guide management during admission.

Antimicrobial susceptibility of Pseudomonas aeruginosa isolated from cystic fibrosis patients through Northern Europe

Pseudomonas aeruginosa is a major cause of morbidity and mortality in cystic fibrosis patients. This study compares the antimicrobial susceptibility of 153 P. aeruginosa isolates from the United Kingdom (UK) (n=58), Belgium (n=44), and Germany (n=51) collected from 120 patients during routine visits over the 2006-2012 period. MICs were measured by broth microdilution. Genes encoding extended spectrum β-lactamases (ESBL), metallo-β-lactamases and carbapenemases were detected by PCR. Pulsed Field Gel Electrophoresis and Multi-Locus Sequence Typing were performed on isolates resistant to ≥ 3 antibiotic classes among penicillins/cephalosporins, carbapenems, fluoroquinolones, aminoglycosides, polymyxins. Based on EUCAST/CLSI breakpoints, susceptibility was ≤ 30%/≤ 40% (penicillins, ceftazidime, amikacin, ciprofloxacin), 44-48%/48-63% (carbapenems), 72%/72% (tobramycin), and 92%/78% (colistin) independently of patient's age. Sixty percent of strains were multidrug resistant (MDR; European Centre for Disease prevention and Control criteria). Genes encoding ESBL (most prevalent BEL, PER, GES, VEB, CTX-M, TEM, SHV, and OXA), metallo β-lactamases (VIM, IMP, NDM), or carbapenemases (OXA-48, KPC) were not detected. The Liverpool Epidemic Strain (LES) was prevalent in UK isolates only (75% of MDR isolates). Four MDR ST958 isolates were found spread over the three countries. The other MDR clones were evidenced in ≤ 3 isolates and localized in a single country. A new sequence type (ST2254) was discovered in one MDR isolate in Germany. Clonal and non-clonal isolates with different susceptibility profiles were found in 21 patients. Thus, resistance and MDR are highly prevalent in routine isolates from 3 countries, with carbapenem (meropenem), tobramycin and colistin remaining the most active drugs.

Molecular characterization of extended-spectrum cephalosporin-resistance in Escherichia coli in pigs on-farm and from clinical cases throughout Quebec, Canada during 16 years

Le développement de la multirésistance chez Escherichia coli est un problème important en médecine animale et humaine. En outre, l’émergence et la diffusion des déterminants de résistance aux céphalosporines à larges spectres de troisième génération (ESCs) parmi les isolats, incluant des céphalosporines essentielles en médecine humaine (ex. ceftriaxone et ceftiofur), est un problème majeur de santé publique. Cette thèse visait trois objectifs. D’abord étudier la dynamique de la résistance aux antimicrobiens (AMR) ainsi que la virulence et les profils génétiques de la AMR des E. coli isolées de porcs recevant une nourriture post-sevrage supplémentée avec de la chlortétracycline et de la pénicilline G, et, accessoirement, évaluer les effets d'additifs alimentaires sur cette dynamique en prenant pour exemple d'étude un minéral argileux, la clinoptilolite, étant donné son possible lien avec le gène blaCMY-2 qui confère la résistance au ceftiofur. L'objectif suivant était d'investiguer les mécanismes menant à une augmentation de la prévalence du gène blaCMY-2 chez les porcs qui reçoivent de la nourriture médicamentée et qui n'ont pas été exposés au ceftiofur Ici encore,nous avons examiné les effets d’un supplément alimentaire avec un minéral argileux sur ce phénomène. Enfin, notre dernier objectif était d’étudier, dans le temps, les génotypes des isolats cliniques d'E. coli résistant au ceftiofur, isolés de porcs malades au Québec à partir du moment où la résistance au ceftiofur a été rapportée, soit de 1997 jusqu'à 2012. Dans l'étude initiale, la prévalence de la résistance à 10 agents antimicrobiens, incluant le ceftiofur, s’accroît avec le temps chez les E.coli isolées de porcelets sevrés. Une augmentation tardive de la fréquence du gène blaCMY-2, encodant pour la résistance au ceftiofur, et la présence des gènes de virulence iucD et tsh a été observée chez les isolats. La nourriture supplémentée avec de la clinoptilolite a été associée à une augmentation rapide mais, par la suite, à une diminution de la fréquence des gènes blaCMY-2 dans les isolats. En parallèle, une augmentation tardive dans la fréquence des gènes blaCMY-2 et des gènes de virulence iucD et tsh a été observée dans les isolats des porcs contrôles, étant significativement plus élevé que dans les porcs ayant reçu l'additif au jour 28. La diversité, au sein des E. coli positives pour blaCMY-2 , a été observée au regard des profils AMR. Certaines lignées clonales d'E.coli sont devenues prédominantes avec le temps. La lignée clonale du phylotype A prédominait dans le groupe supplémenté, alors que les lignées clonales du phylotype B1, qui possèdent souvent le gène de virulence iucD associé aux ExPEC, prédominaient dans le groupe contrôle. Les plasmides d'incompatibilité (Inc) des groupes, I1, A/C, et ColE, porteurs de blaCMY-2, ont été observés dans les transformants. Parmi les souches cliniques d'E.coli ESC-résistantes, isolées de porcs malades au Québec de 1997 à 2012, blaCMY-2 était le gène codant pour une β-lactamase le plus fréquemment détecté; suivi par blaTEM et blaCTX-M,. De plus, les analyses clonales montrent une grande diversité génétique. Par contre, des isolats d'E. coli avec des profils PFGE identiques ont été retrouvés dans de multiples fermes la même année mais aussi dans des années différentes. La résistance à la gentamicine, kanamycine, chloramphenicol, et la fréquence de blaTEM et de IncA/C diminuent significativement au cour de la période étudiée, alors que la fréquence de IncI1 et de la multirésistance à sept catégories d'agents antimicrobiens augmente significativement avec le temps. L'émergence d'isolats d'E. coli positifs pour blaCTX-M, une β-lactamase à large spectre et produisant des ESBL, a été observée en 2011 et 2012 à partir de lignées clonales distinctes et chez de nombreuses fermes. Ces résultats, mis ensemble, apportent des précisions sur la dissémination de la résistance au ceftiofur dans les E. coli isolées de porcs. Au sein des échantillons prélevés chez les porcs sevrés recevant l'alimentation médicamentée sur une ferme, et pour laquelle une augmentation de la résistance au ceftiofur a été observée, les données révèlent que les souches d'E. coli positives pour blaCMY-2 et résistantes aux ESCs appartenaient à plusieurs lignées clonales différentes arborant divers profils AMR. Le gène blaCMY-2 se répand à la fois horizontalement et clonalement chez ces E. coli. L'ajout de clinoptilotite à la nourriture et le temps après le sevrage influencent la clonalité et la prévalence du gène blaCMY-2 dans les E. coli. Durant les 16 années d'étude, plusieurs lignées clonales différentes ont été observées parmi les souches d'E. coli résistantes au ceftiofur isolées de porc malades de fermes québécoises, bien qu’aucune lignée n'était persistante ou prédominante pendant l'étude. Les résultats suggèrent aussi que le gène blaCMY-2 s'est répandu à la fois horizontalement et clonalement au sein des fermes. De plus, blaCMY-2 est le gène majeur des β-lactamases chez ces isolats. À partir de 2011, nous rapportons l'émergence du gène blaCTX-M dans des lignées génétiques distinctes.