Consequences of revised CLSI and EUCAST guidelines for antibiotic susceptibility patterns of ESBL- and AmpC β-lactamase-producing clinical Enterobacteriaceae isolates

Objectives This study aimed to: (i) analyse the antibiotic susceptibility testing (AST) profiles of extended spectrum β-lactamase (ESBL)- and AmpC β-lactamase-producing clinical Enterobacteriaceae isolates applying EUCAST 2013 AST guidelines; and (ii) evaluate discrepancies in AST profiles according to EUCAST 2010 guidelines, EUCAST 2013 guidelines, CLSI 2009 guidelines and CLSI 2013 guidelines. Methods The 195 ESBL- and/or AmpC β-lactamase-producing Enterobacteriaceae isolates used in this study were systematically characterized by disc diffusion AST interpreted according to the 2013 guidelines of EUCAST and CLSI, the EUCAST 2010 guidelines and the CLSI 2009 guidelines. Results Individual cephalosporin AST patterns according to EUCAST 2013 guidelines were described for individual ESBL and AmpC β-lactamase genotypes. Significant differences in the susceptibility rates of important cephalosporins such as cefepime, ceftazidime and cefotaxime applying EUCAST 2013 and CLSI 2013 AST guidelines were demonstrated for ESBL- and AmpC β-lactamase-producing isolates. Conclusions The confirmation of ESBL and/or AmpC β-lactamase production can support the selection of an adequate antibiotic drug therapy. Despite a harmonized CLSI and EUCAST ‘report as found' strategy for cephalosporins and ESBL-producing isolates, AST interpretation according to the CLSI 2013 and EUCAST 2013 guidelines shows significant differences in susceptibility rates for mainstay cephalosporins such as cefepime, ceftazidime and cefotaxime. Thus, further harmonization of clinical breakpoints is warrante

Effects of clinical breakpoint changes in CLSI guidelines 2010/2011 and EUCAST guidelines 2011 on antibiotic susceptibility test reporting of Gram-negative bacilli

Objectives The aim of this study was to analyse the effects of clinical breakpoint changes in CLSI 2010 and 2011 guidelines and EUCAST 2011 guidelines on antibiotic susceptibility testing (AST) reports. Methods In total, 3713 non-duplicate clinical isolates of Enterobacteriaceae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Acinetobacter baumannii were analysed. Inhibition zone diameters were determined for β-lactams, carbapenems, fluoroquinolones, aminoglycosides and trimethoprim/sulfamethoxazole. CLSI 2009-11 and EUCAST 2011 clinical breakpoints were applied. Results Changes in resistance as defined per the guidelines affected individual species and drug classes differently. The cefepime resistance rate in Escherichia coli and Enterobacter cloacae increased from 2.1% and 1.3% to 8.2% and 6.9%, respectively, applying CLSI 2009-11 versus EUCAST 2011 guidelines. Ertapenem resistance rates in E. cloacae increased from 2.6% with CLSI 2009 to 7.2% for CLSI 2010 and 2011, and to 10.1% when applying EUCAST 2011. Cefepime and meropenem resistance rates in P. aeruginosa increased from 12.2% and 20.6% to 19.8% and 27.7%, respectively, comparing CLSI 2009-11 with EUCAST 2011. Tobramycin and gentamicin resistance rates in A. baumannii increased from 15.9% and 25.4% to 34.9% and 44.4% applying CLSI 2009-11 versus EUCAST 2011. Conclusions Higher resistance rates reported due to breakpoint changes in CLSI and EUCAST guidelines will result in increasing numbers of Gram-negative bacilli reported as multidrug resistant. AST reports classifying amoxicillin/clavulanic acid, cefepime or carbapenem resistance will lead clinicians to use alternative agents. Upon implementation of the EUCAST guidelines, laboratories should be aware of the implications of modified drug susceptibility testing reports on antibiotic prescription policie

Comparison of European Committee on Antimicrobial Susceptibility Testing (EUCAST) and CLSI screening parameters for the detection of extended-spectrum β-lactamase production in clinical Enterobacteriaceae isolates

Objectives To compare the performance of European Committee on Antimicrobial Susceptibility Testing (EUCAST) and CLSI breakpoints following their revision in 2010, for the detection of extended-spectrum β-lactamase (ESBL) production in Enterobacteriaceae. Methods 236 well-characterized clinical isolates (including 118 ESBL producers) were investigated by antibiotic disc testing with cefpodoxime, ceftriaxone, cefepime, cefotaxime EUCAST (5 μg/disc), ceftazidime EUCAST (10 μg/disc), cefotaxime CLSI (30 μg/disc) and ceftazidime CLSI (30 μg/disc) with the Kirby-Bauer method. Additionally, synergy phenomena were recorded between amoxicillin/clavulanic acid discs (20/10 μg/disc) and cefepime (30 μg/disc), EUCAST cefotaxime (5 μg/disc), EUCAST ceftazidime (10 μg/disc), CLSI cefotaxime (30 μg/disc) and CLSI ceftazidime [30 μg/disc; disc approximation method (DAM)]. Results Overall sensitivity of the cefotaxime EUCAST non-susceptible breakpoint equalled sensitivity of the cefotaxime CLSI ESBL screening breakpoint (99.2%). With the ceftazidime EUCAST non-susceptible breakpoint, 27/118 ESBL-producing isolates were not detected, whereas the ceftazidime CLSI ESBL screening breakpoint missed 41/118 ESBL-producing isolates. For cefpodoxime the resistant EUCAST breakpoint showed higher sensitivity for ESBL detection compared with the CLSI ESBL screening breakpoint/disc content (100% versus 98.3%, respectively). Sensitivities of ceftazidime and cefotaxime DAM with CLSI or EUCAST disc contents were comparable (sensitivities ranging from 84.7% to 89.8%). DAM with cefepime displayed the highest overall sensitivity (96.6%). In AmpC-producing isolates, synergy of amoxicillin/clavulanic acid with cefepime showed sensitivity and specificity for ESBL detection of 100% and 97.4%, respectively. Conclusions EUCAST non-susceptible breakpoints for ceftazidime and cefpodoxime detect more ESBL-producing Enterobacteriaceae isolates compared with corresponding CLSI ESBL screening breakpoints. Implementation of the cefepime DAM can facilitate ESBL screening, especially in strains producing an AmpC β-lactamase since the test shows high sensitivity and specificit

Evaluation of the AID ESBL line probe assay for rapid detection of extended-spectrum β-lactamase (ESBL) and KPC carbapenemase genes in Enterobacteriaceae

Objectives This study aimed at evaluating the AID ESBL line probe assay for the detection of extended-spectrum β-lactamase (ESBL) and KPC carbapenemase genes in Enterobacteriaceae. Methods The AID ESBL line probe assay was verified for accuracy of its probes using PCR products from clinical ESBL Enterobacteriaceae strains harbouring TEM, SHV and CTX-M ESBL genes and KPC genes and mutant fusion PCR products generated from Enterobacteriaceae strains containing wild-type (wt) TEM and wt SHV. Sensitivity and specificity was determined testing a set of 424 clinical Enterobacteriaceae strains (including 170 strains negative for TEM, SHV, CTX-M and KPC to evaluate the possibility of false positive signals). Results The line probe assay was shown to detect with 100% accuracy ESBL genes for which oligonucleotide probes are present in the assay. Testing a set of 424 clinical Enterobacteriaceae strains showed 100% sensitivity and specificity for the detection and differentiation of TEM, SHV and CTX-M ESBL genes present in that group. In addition, the line probe assay detected KPC genes accurately. Conclusions The AID ESBL line probe assay is an accurate and easy-to-use test for the detection of ESBL and KPC genes, which can readily be implemented in the diagnostic laborator

Acquisition of clarithromycin resistance mutations in the 23S rRNA gene of Mycobacterium abscessus in the presence of inducible erm(41)

Objectives Antibiotic therapy of pulmonary Mycobacterium abscessus infection is based on a combination treatment including clarithromycin. Recent data demonstrated that M. abscessus may carry a chromosomal, inducible erm gene coding for the ribosomal methylase Erm(41). The purpose of this study was to investigate whether in patients with chronic M. abscessus infection undergoing clarithromycin therapy, M. abscessus acquires clarithromycin resistance mutations in the rrl gene in addition to the presence of an inducible Erm(41) methylase. Methods We determined clarithromycin MICs, erm(41) and rrl sequences for 29 clinical M. abscessus subsp. abscessus isolates of five different patients. The isolates were obtained between 2007 and 2011 covering a longitudinal observation period of 2-4 years for the individual patients. Results In three out of five patients with an initial rrl wild-type isolate, follow-up isolates demonstrated acquisition of resistance mutations in the rrl gene in addition to the presence of an inducible Erm methylase. Conclusions Our results show that in M. abscessus, clarithromycin resistance mutations in the 23S rRNA peptidyltransferase region provide an additional selective advantage independent of a functional erm(41) gen

Listeriosis Caused by Persistence of Listeria monocytogenes Serotype 4b Sequence Type 6 in Cheese Production Environment

A nationwide outbreak of human listeriosis in Switzerland was traced to persisting environmental contamination of a cheese dairy with Listeria monocytogenes serotype 4b, sequence type 6, cluster type 7488. Whole-genome sequencing was used to match clinical isolates to a cheese sample and to samples from numerous sites within the production environment. Listeriosis is a potentially lethal infection, and the elderly population, pregnant women, and immunocompromised persons at particular risk (1). Foods, in particular ready-to-eat foodstuffs, including meat, fish, dairy products, fruits, and vegetables, represent the major vehicle for sporadic cases and outbreaks of listeriosis (2). Listeria monocytogenes serotype 4b sequence type 6 (ST6) has emerged since 1990 as a hypervirulent clone that is associated with particularly worse outcome for case-patients who have Listeria meningitis and therefore poses a particular threat to consumer health (3,4). L. monocytogenes ST6 is increasingly associated with outbreaks, including an outbreak linked to frozen vegetables in 5 countries in Europe during 2015–2018 (5), an outbreak associated with contaminated meat pâté in Switzerland during 2016 (6), and the largest listeriosis outbreak globally, which occurred in South Africa during 2017–2018 (7,8). More recently, the largest outbreak of listeriosis in Europe in the past 25 years was reported in Germany and was traced back to blood sausages contaminated with L. monocytogenes ST6 belonging to a particular clone referred to as Epsilon1a (9). Human listeriosis is a reportable disease in Switzerland. All cases of culture- or PCR-confirmed human listeriosis are reported to the Swiss Federal Office of Public Health (SFOPH). Diagnostic laboratories and regional (cantonal) laboratories forward isolates to the Swiss National Reference Centre for Enteropathogenic Bacteria and Listeria for strain characterization, ensuring early recognition of Listeria clusters among food isolates or human cases. We report an outbreak of listeriosis associated with cheese contaminated with L. monocytogenes 4b ST6 in Switzerland

Aminoglycoside-modifying enzymes determine the innate susceptibility to aminoglycoside antibiotics in rapidly growing mycobacteria

Objectives Infections caused by the rapidly growing mycobacterium (RGM) Mycobacterium abscessus are notoriously difficult to treat due to the innate resistance of M. abscessus to most clinically available antimicrobials. Aminoglycoside antibiotics (AGA) are a cornerstone of antimicrobial chemotherapy against M. abscessus infections, although little is known about intrinsic drug resistance mechanisms. We investigated the role of chromosomally encoded putative aminoglycoside-modifying enzymes (AME) in AGA susceptibility in M. abscessus. Methods Clinical isolates of M. abscessus were tested for susceptibility to a series of AGA with different substituents at positions 2′, 3′ and 4′ of ring 1 in MIC assays. Cell-free extracts of M. abscessus type strain ATCC 19977 and Mycobacterium smegmatis strains SZ380 [aac(2′)-Id+], EP10 [aac(2′)-Id−] and SZ461 [aac(2′)-Id+, rrs A1408G] were investigated for AGA acetylation activity using thin-layer chromatography (TLC). Cell-free ribosome translation assays were performed to directly study drug-target interaction. Results Cell-free translation assays demonstrated that ribosomes of M. abscessus and M. smegmatis show comparable susceptibility to all tested AGA. MIC assays for M. abscessus and M. smegmatis, however, consistently showed the lowest MIC values for 2′-hydroxy-AGA as compared with 2′-amino-AGA, indicating that an aminoglycoside-2′-acetyltransferase, Aac(2′), contributes to innate AGA susceptibility. TLC experiments confirmed enzymatic activity consistent with Aac(2′). Using M. smegmatis as a model for RGM, acetyltransferase activity was shown to be up-regulated in response to AGA-induced inhibition of protein synthesis. Conclusions Our findings point to AME as important determinants of AGA susceptibility in M. abscessu

Comparison of static immersion and intravenous injection systems for exposure of zebrafish embryos to the natural pathogen Edwardsiella tarda

<p>Abstract</p> <p>Background</p> <p>The zebrafish embryo is an important <it>in vivo </it>model to study the host innate immune response towards microbial infection. In most zebrafish infectious disease models, infection is achieved by micro-injection of bacteria into the embryo. Alternatively, <it>Edwardsiella tarda</it>, a natural fish pathogen, has been used to treat embryos by static immersion. In this study we used transcriptome profiling and quantitative RT-PCR to analyze the immune response induced by <it>E. tarda </it>immersion and injection.</p> <p>Results</p> <p>Mortality rates after static immersion of embryos in <it>E. tarda </it>suspension varied between 25-75%, while intravenous injection of bacteria resulted in 100% mortality. Quantitative RT-PCR analysis on the level of single embryos showed that expression of the proinflammatory marker genes <it>il1b </it>and <it>mmp9 </it>was induced only in some embryos that were exposed to <it>E. tarda </it>in the immersion system, whereas intravenous injection of <it>E. tarda </it>led to <it>il1b </it>and <it>mmp9 </it>induction in all embryos. In addition, microarray expression profiles of embryos subjected to immersion or injection showed little overlap. <it>E. tarda</it>-injected embryos displayed strong induction of inflammatory and defense genes and of regulatory genes of the immune response. <it>E. tarda</it>-immersed embryos showed transient induction of the cytochrome P450 gene <it>cyp1a</it>. This gene was also induced after immersion in <it>Escherichia coli </it>and <it>Pseudomonas aeruginosa </it>suspensions, but, in contrast, was not induced upon intravenous <it>E. tarda </it>injection. One of the rare common responses in the immersion and injection systems was induction of <it>irg1l</it>, a homolog of a murine immunoresponsive gene of unknown function.</p> <p>Conclusions</p> <p>Based on the differences in mortality rates between experiments and gene expression profiles of individual embryos we conclude that zebrafish embryos cannot be reproducibly infected by exposure to <it>E. tarda </it>in the immersion system. Induction of <it>il1b </it>and <it>mmp9 </it>was consistently observed in embryos that had been systemically infected by intravenous injection, while the early transcriptional induction of <it>cyp1a </it>and <it>irg1l </it>in the immersion system may reflect an epithelial or other tissue response towards cell membrane or other molecules that are shed or released by bacteria. Our microarray expression data provide a useful reference for future analysis of signal transduction pathways underlying the systemic innate immune response versus those underlying responses to external bacteria and secreted virulence factors and toxins.</p

Broad-Range 16S rRNA Gene Polymerase Chain Reaction for Diagnosis of Culture-Negative Bacterial Infections

This study defines the role of 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) for diagnosis of culture-negative bacterial infections. Our data show that 16S rRNA PCR is particularly valuable for identification of pathogens in patients pretreated with antibiotic