Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a ...subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST).
The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic–phenotypic concordance from WGS data should be changed to epidemiological cut-off values in order to improve differentiation of wild-type from non-wild-type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretive criteria for WGS-based predictive AST. Only data sets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. To facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical laboratories remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on previous culture because analysis directly on specimens remains challenging.
For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.
Plasmid-acquired carbapenemases in Enterobacteriaceae, which were first discovered in Europe in the 1990s, are now increasingly being identified at an alarming rate. Although their hydrolysis ...spectrum may vary, they hydrolyse most β-lactams, including carbapenems. They are mostly of the KPC, VIM, NDM and OXA-48 types. Their prevalence in Europe as reported in 2011 varies significantly from high (Greece and Italy) to low (Nordic countries). The types of carbapenemase vary among countries, partially depending on the cultural/population exchange relationship between the European countries and the possible reservoirs of each carbapenemase. Carbapenemase producers are mainly identified among Klebsiella pneumoniae and Escherichia coli, and still mostly in hospital settings and rarely in the community. Although important nosocomial outbreaks with carbapenemase-producing Enterobacteriaceae have been extensively reported, many new cases are still related to importation from a foreign country. Rapid identification of colonized or infected patients and screening of carriers is possible, and will probably be effective for prevention of a scenario of endemicity, as now reported for extended-spectrum β-lactamase (mainly CTX-M) producers in all European countries.
Escherichia coli is one of the most-studied microorganisms worldwide but its characteristics are continually changing. Extraintestinal E. coli infections, such as urinary tract infections and ...neonatal sepsis, represent a huge public health problem. They are caused mainly by specialized extraintestinal pathogenic E. coli (ExPEC) strains that can innocuously colonize human hosts but can also cause disease upon entering a normally sterile body site. The virulence capability of such strains is determined by a combination of distinctive accessory traits, called virulence factors, in conjunction with their distinctive phylogenetic background. It is conceivable that by developing interventions against the most successful ExPEC lineages or their key virulence/colonization factors the associated burden of disease and health care costs could foreseeably be reduced in the future. On the other hand, one important problem worldwide is the increase of antimicrobial resistance shown by bacteria. As underscored in the last WHO global report, within a wide range of infectious agents including E. coli, antimicrobial resistance has reached an extremely worrisome situation that ‘threatens the achievements of modern medicine’. In the present review, an update of the knowledge about the pathogenicity, antimicrobial resistance and clinical aspects of this ‘old friend’ was presented.
New knowledgements about pathogenesis, antimicrobial resistance and clinical aspects of Escherichia coli.
Graphical Abstract Figure.
New knowledgements about pathogenesis, antimicrobial resistance and clinical aspects of Escherichia coli.
Minor extended-spectrum β-lactamases Naas, T.; Poirel, L.; Nordmann, P.
Clinical microbiology and infection,
January 2008, 2008-Jan, 2008-01-00, 20080101, Letnik:
14
Journal Article
Recenzirano
Odprti dostop
Extended-spectrum β-lactamases (ESBLs) are usually plasmid-mediated enzymes that confer resistance to a broad range of β-lactams. Initially, resistance to third-generation cephalosporins in ...Gram-negative rods was mainly due to the dissemination of TEM- and SHV-type ESBLs, which are point mutants of the classic TEM and SHV enzymes with extended substrate specificity. During the last ten years, CTX-M-type ESBLs have become increasingly predominant, but less frequent class A β-lactamases have also been described, including SFO, BES, BEL, TLA, GES, PER and VEB types. While several of these latter are rarely identified, or are very localised, others are becoming locally prevalent, or are increasingly isolated worldwide. In addition, mutations can extend the spectrum of some OXA-type β-lactamases to include expanded-spectrum cephalosporins, and several of these enzymes are considered to be ESBLs.
Multidrug-resistant and New Delhi metallo-β-lactamase I (NDM-I) -producing Acinetobacter baumannii are increasingly reported. A collection of five NDM-I-positive A. baumannii isolates recovered in ...four European countries were analysed. Genotyping was performed by pulsed-field gel electrophoresis, multiplex PCR sequence typing, Diversilab and multilocus sequence typing. Three distinct sequence types were identified. All isolates harboured a chromosomally located blaNDM-1. gene within a Tn/25-like transposon. One isolate co-expressed another unrelated carbapenemase OXA-23. This report constitutes the first epidemiological study of NDM-I-producing A. baumannii from four countries.
In this work, a numerical analysis based on CFD method is carried out to examine an unsteady laminar flow of Newtonian fluids in a two-dimensional simulation of a mixer, which is composed of two rods ...inside a moving cylindrical tank. Three stirring protocols are considered: Non-modulated “NM”, Continuously modulated “CM” and non-continuously modulated “ALT” by using the dynamic mesh technique and user defined functions “UDF’s” for the velocity profiles. The chaotic advection is obtained by temporal modulation of the rotational velocity of the cylinder and the rods to enhance the mixing of the fluid for very low Reynolds number. For this purpose, we applied the Poincaré map as a reliable mathematic tool to check mixing quality by tracking particles inside the fluid domain. Additionally, we investigated the evolution of local flow proprieties such as rotation rate, deformation rate and elongation rate at different time periods in order to see the effect of temporal modulation on the fluid kinematics. Among the considered protocols, the results of the mentioned simulation showed that it is possible to obtain a chaotic advection only for non-continuously modulated protocol which enhance mixing fluid efficiency.
Abstract
Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, and detection of antimicrobial resistance ...(AMR). Numerous published methods and protocols exist, but a lack of harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital for global genomic diagnostics and surveillance. As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436
Escherichia coli
were compared to their AMR phenotypes, with the latter used as gold-standard. The pipelines exploited previously known genotype–phenotype associations. No significant differences in software performance were observed. As a consequence, efforts to harmonise AMR predictions from sequence data should focus on: (1) establishing universal minimum to assess performance thresholds (e.g. a control isolate panel, minimum sensitivity/specificity thresholds); (2) standardising AMR gene identifiers in reference databases and gene nomenclature; (3) producing consistent genotype/phenotype correlations. The study also revealed limitations of in-silico technology on detecting resistance to certain antimicrobials due to lack of specific fine-tuning options in bioinformatics tool or a lack of representation of resistance mechanisms in reference databases. Lastly, we noted user friendliness of tools was also an important consideration. Therefore, our recommendations are timely for widespread standardisation of bioinformatics for genomic diagnostics and surveillance globally.
Genes encoding extended-spectrum β-lactamases (ESBLs) have been reported in a variety of Gram-negative species, mostly in Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii. They ...are mostly either TEM or SHV derivatives, CTX-M-like enzymes—now emerging worldwide—or, less frequently, VEB, GES, and PER ESBLs. The mechanisms responsible for their acquisition are very diverse, and mostly are related to insertion sequences (ISs), transposons, class 1 integrons, and also sul1-type integrons containing the ISCR1 element. This diversity of genetic vehicles at the origin of these mobilisation/acquisition processes enhances the spread of ESBLs.
OXA-535 is a chromosome-encoded carbapenemase of
JAB-1 that shares only 91.3% amino acid sequence identity with OXA-48. Catalytic efficiencies are similar to those of OXA-48 for most β-lactams, ...except for ertapenem, where a 2,000-fold-higher efficiency was observed with OXA-535. OXA-535 and OXA-436, a plasmid-encoded variant of OXA-535 differing by three amino acids, form a novel cluster of distantly related OXA-48-like carbapenemases. Comparison of
and
genetic environments suggests that an IS
may be responsible for
gene mobilization from the chromosome of
spp. to plasmids.
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