The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee.

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.

Cloning and occurrence of czrC, a gene conferring cadmium and zinc resistance in methicillin-resistant Staphylococcus aureus CC398 isolates.

We recently reported a phenotypic association between reduced susceptibility to zinc and methicillin resistance in Staphylococcus aureus CC398 isolates from Danish swine (F. M. Aarestrup, L. M. Cavaco, and H. Hasman, Vet. Microbiol. 142:455-457, 2009). The aim of this study was to identify the genetic determinant causing zinc resistance in CC398 and examine its prevalence in isolates of animal and human origin. Based on the sequence of the staphylococcal cassette chromosome mec (SCCmec) element from methicillin-resistant S. aureus (MRSA) CC398 strain SO385, a putative metal resistance gene was identified in strain 171 and cloned in S. aureus RN4220. Furthermore, 81 MRSA and 48 methicillin-susceptible S. aureus (MSSA) strains, isolated from pigs (31 and 28) and from humans (50 and 20) in Denmark, were tested for susceptibility to zinc chloride and for the presence of a putative resistance determinant, czrC, by PCR. The cloning of czrC confirmed that the zinc chloride and cadmium acetate MICs for isogenic constructs carrying this gene were increased compared to those for S. aureus RN4220. No difference in susceptibility to sodium arsenate, copper sulfate, or silver nitrate was observed. Seventy-four percent (n = 23) of the animal isolates and 48% (n = 24) of the human MRSA isolates of CC398 were resistant to zinc chloride and positive for czrC. All 48 MSSA strains from both human and pig origins were found to be susceptible to zinc chloride and negative for czrC. Our findings showed that czrC is encoding zinc and cadmium resistance in CC398 MRSA isolates, and that it is widespread both in humans and animals. Thus, resistance to heavy metals such as zinc and cadmium may play a role in the coselection of methicillin resistance in S. aureus.

Antimicrobial-resistant faecal Escherichia coli in wild mammals in central Europe: multiresistant Escherichia coli producing extended-spectrum beta-lactamases in wild boars.

AIMS: To determine the presence of antibiotic-resistant faecal Escherichia coli in populations of wild mammals in the Czech Republic and Slovakia. METHODS AND RESULTS: Rectal swabs or faeces collected during 2006-2008 from wild mammals were spread on MacConkey agar and MacConkey agar containing 2 mg l(-1) of cefotaxime. From plates with positive growth, one isolate was recovered and identified as E. coli. Susceptibility to 12 antibiotics was tested using the disk diffusion method. Resistance genes, class 1 and 2 integrons and gene cassettes were detected in resistant isolates by polymerase chain reaction (PCR). Extended-spectrum beta-lactamases (ESBL) were further characterized by DNA sequencing, macrorestriction profiling and determination of plasmid sizes. Plasmid DNA was subjected to EcoRV digestion, transferability by conjugation and incompatibility grouping by multiplex PCR. The prevalence of resistant isolates was 2% in small terrestrial mammals (rodents and insectivores, n(E. coli) = 242), 12% in wild ruminants and foxes (n(E. coli) = 42), while no resistant isolates were detected in brown bears (n(E. coli) = 16). In wild boars (Sus scrofa) (n(E. coli) = 290), the prevalence of resistant isolates was 6%. Class 1 and 2 integrons with various gene cassettes were recorded in resistant isolates. From wild boars, five (2%, n(rectal smears) = 293) multiresistant isolates producing ESBL were recovered: one isolate with bla(CTX-M-1) + bla(TEM-1), three with bla(CTX-M-1) and one with bla(TEM-52b). The bla(CTX-M-1) genes were carried on approx. 90 kb IncI1 conjugative plasmids. CONCLUSIONS: Antibiotic-resistant E. coli occurred in populations of wild mammals in various prevalences. SIGNIFICANCE AND IMPACT OF THE STUDY: Wild mammals are reservoirs of antibiotic-resistant E. coli including ESBL-producing strains which were found in wild boars.

A classification system for plasmids from enterococci and other Gram-positive bacteria.

A classification system for plasmids isolated from enterococci and other Gram-positive bacteria was developed based on 111 published plasmid sequences from enterococci and other Gram-positive bacteria; mostly staphylococci. Based on PCR amplification of conserved areas of the replication initiating genes (rep), alignment of these sequences and using a cutoff value of 80% identity on both protein and DNA level, 19 replicon families (rep-families) were defined together with several unique sequences. The prevalence of these rep-families was tested on 79 enterococcal isolates from a collection of isolates of animal and human origin. Difference in prevalence of the designed rep-families were detected with rep(9) being most prevalent in Enterococcus faecalis and rep(2) in Enterococcus faecium. In 33% of the tested E. faecium and 32% of the tested E. faecalis no positive amplicons were detected. Furthermore, conjugation experiments were performed obtaining 30 transconjugants when selecting for antimicrobial resistance. Among them 19 gave no positive amplicons indicating presence of rep-families not tested for in this experimental setup.

Modelling conjugation with stochastic differential equations.

Conjugation is an important mechanism involved in the transfer of resistance between bacteria. In this article a stochastic differential equation based model consisting of a continuous time state equation and a discrete time measurement equation is introduced to model growth and conjugation of two Enterococcus faecium strains in a rich exhaustible media. The model contains a new expression for a substrate dependent conjugation rate. A maximum likelihood based method is used to estimate the model parameters. Different models including different noise structure for the system and observations are compared using a likelihood-ratio test and Akaike's information criterion. Experiments indicating conjugation on the agar plates selecting for transconjugants motivates the introduction of an extended model, for which conjugation on the agar plate is described in the measurement equation. This model is compared to the model without plate conjugation. The modelling approach described in this article can be applied generally when modelling dynamical systems.

Heterogeneity among methicillin-resistant Staphylococcus aureus from Italian pig finishing holdings.

A survey for methicillin-resistant Staphylococcus aureus (MRSA) in finishing pig holdings was carried out in Italy in 2008. MRSA isolates were characterised by spa-, MLST-, SCCmec- and antimicrobial susceptibility typing. A prevalence of 38% (45/118, 95% CI 29.4-46.9%) positive holdings was observed. Eleven different spa-types were found among 102 MRSA isolates, clustering in lineages associated with farm animals (ST398, ST9, ST(CC)97 in 36 holdings) and humans (ST1, 7 holdings). Nine (7.6%) holdings were positive for two, three or four different and unrelated spa-types in various combinations. ST398 was the most prevalent lineage (33 positive holdings). The most prevalent spa-type was t899 (ST398), detected in 22 positive holdings. Three novel spa-types (t4794 of ST9; t4795 of ST97; t4838 of ST398) were detected. Ten holdings were positive for spa-type t1730, that proved to be a new single-locus variant of ST97, within the CC97 (ST1476). The most prevalent SCCmec was Type V (79 isolates), while Type IVb was found in 10 isolates. None of the isolates was positive for Panton-Valentine Leukocidin, while most of the t127 and t1730 isolates, one t4794, one t4795, and one t2922 were positive for LukE-LukD genes. All 64 antimicrobial susceptibility tested isolates were resistant to tetracyclines, with high resistance rates to trimethoprim (68.8%), erythromycin (60.9%), and ciprofloxacin (35.4%). All t127, ST1 isolates were resistant to tetracycline-ciprofloxacin-erythromycin. This survey provides the first report of MRSA ST1 and ST(CC)97 among pigs and the first report of MRSA ST9 from pigs in Europe. The presence of human-associated CA-MRSA (t127, ST1, SCCmec type V) in 6% holdings surveyed can represent an additional MRSA reservoir for infections in humans.

Spa type distribution in Staphylococcus aureus originating from pigs, cattle and poultry.

Methicillin-resistant S. aureus (MRSA) of clonal complex 398 (CC398) is emerging globally among production animals such as cattle, pigs and poultry as well as among humans. However, little is known about the prevalence of CC398 among methicillin sensitive S. aureus (MSSA) or the relative clonal distribution of S. aureus isolated from these three animal reservoirs. To study this, we have analyzed a random sample of S. aureus consisting of 296 epidemiologically unrelated isolates from infections and colonisation of pigs, cattle and poultry. These were examined and compared by spa and multi-locus sequence typing (MLST) and the result was compared to the most common spa types found among human blood isolates. Little overlap in spa types was seen between isolates from the three animal reservoirs or between animals and humans. Most of the porcine isolates had the spa types t034 (CC398), t1333 (CC30) and t337 (CC9), while the bovine isolates mainly had spa types t518 (CC50), t524 (CC97) and t529 (CC151). None of these spa types are common among human blood isolates in Denmark. Surprisingly, almost all of the poultry isolates (96%) belonged to CC5 (spa types t002 and t306), which is also known to be commonly found among human blood isolates and subsequent pulsed-field gel electrophoresis (PFGE) analysis identified indistinguishable PFGE patterns among a poultry isolate and selected human isolates. In conclusion, strains of MSSA CC398 were commonly present in pigs but not present at all in the other reservoirs tested.

qnrD, a novel gene conferring transferable quinolone resistance in Salmonella enterica serovar Kentucky and Bovismorbificans strains of human origin.

In a previous study, four Salmonella isolates from humans in the Henan province of China showed reduced susceptibility to ciprofloxacin (MIC, 0.125 to 0.25 microg/ml) but were susceptible to nalidixic acid (MIC, 4 to 8 microg/ml). All isolates were negative for known qnr genes (A, B, and S), aac(6')Ib-cr, and mutations in gyrA and parC. Plasmid DNA was extracted from all four isolates and transformed into Escherichia coli TG1 and DH10B cells by electroporation, and transformants were selected on 0.06 microg/ml ciprofloxacin containing brain heart infusion agar plates. Resistance to ciprofloxacin could be transferred by electroporation, and a similar 4,270-bp plasmid was found in all transformants. By sequence analysis, the plasmid was found to carry an open reading frame that had similarities to other qnr genes and that encoded a 214-amino-acid pentapeptide repeat protein. This gene, designated qnrD, showed 48% similarity to qnrA1, 61% similarity to qnrB1, and 41% similarity to qnrS1. Further subcloning of the qnrD coding region into the constitutively expressed tetA gene of vector pBR322 showed that the gene conferred an increase in the MIC of ciprofloxacin by a factor of 32 (from an MIC of 0.002 to an MIC of 0.06 microg/ml). For comparison, qnrA1 and qnrS1 were also subcloned into pBR322 and transformed into DH10B cells, conferring MICs of 0.125 and 0.5 microg/ml, respectively. A phylogenetic analysis of all known qnr sequences was performed and showed that qnrD was more closely related to the qnrB variants but formed an independent cluster. To our knowledge, this is the first description of this qnrD gene.

Molecular characterisation of multidrug-resistant Salmonella enterica serovar Typhimurium isolates from Gomel region, Belarus.

This study describes the characterisation by pulsed-field gel electrophoresis (PFGE), multilocus variable number tandem repeat analysis (MLVA) typing and antimicrobial resistance profiles of 35 Salmonella enterica serovar Typhimurium isolates, mostly from infections in children who acquired an infection outside hospitals in the Gomel region of Belarus. Thirty-one isolates were highly similar according to PFGE and MLVA typing, were multidrug-resistant, including resistance to ceftiofur, and harboured the bla(CTX-M-5) gene. These results indicate that a common source may have been responsible for most of the infections.

Epidemiology and etiology of catheter-related nosocomial infections in a Turkish hospital.

In this study a total of 219 patients who developed nosocomial infections and were treated in Sisli Etfal Training and Research Hospital between January 2001 and March 2003 were evaluated retrospectively. In all, 337 bacterial strains were isolated in these patients. The aim of our study was to assess the causative agents of catheter-related nosocomial infections, the distribution rate of causative agents due to hospital units, infection sites and catheter types, and determine the risk factors which facilitate such nosocomial infections. The most frequently isolated causative agents in catheter infections were Pseudomonas spp. (17%), Klebsiella spp. (16%), E. coli (13%), Acinetobacter spp. (12%), Coagulase Negative Staphylococci (CNS) (11%) and Methicillin-Resistant S. aureus (MRSA) (9%). In 136 (59%) patients infections were due to urinary catheterization and in 52 patients (23%) due to tracheal aspiration catheters. Of the 229 catheters applied, the polymicrobial infection rate was found to be 24% (55 patients). Multiple drug resistant strains were more frequently isolated in Intensive Care Units (ICU). It was emphasized that as ICUs are important risk factors for the development of catheter infections, the resistance patterns of the isolated microorganisms from the unit should be taken into consideration for the selection of appropriate antibiotics. We also conclude that it is important to avoid unnecessary catheterization and that preventive measures should be properly applied.

Acute renal failure: a common manifestation of leptospirosis.

Leptospirosis is an infectious disease caused by pathogenic leptospires and may vary in degree from an asymptomatic infection to severe and fatal illness. Sixteen patients (all males; aged 40+/-17 years) with leptospirosis were admitted to Sisli Etfal Training and Research Hospital between July 1998 and August 2003 and were retrospectively reviewed. Age, gender, occupation, clinical presentation, laboratory features, seasonal distribution of the disease, diagnostical approach, and prognostic factors were evaluated. Eleven patients were cured with no complication; four patients died of hepatic and/or renal failure. Eight patients presented with acute renal failure; seven of them needed dialytic support. One patient developed chronic renal failure and had to undergo regular hemodialysis. All deceased patients (aged 61+/-7 years) were anuric at admission and their serum bilirubin changed between 39-44 mg/dL (mean 41.3+/-2.2 mg/dL). Cured patients ranged in age from 14-62 years (34+/-14 years) and their serum bilirubin levels ranged from 9-35 mg/dL (23.1+/-11.4 mg/dL). Crystalline penicillin G 12 million U/day was administered to all patients. Six patients also received hepatic coma treatment. This study emphasizes that leptospirosis presenting with renal failure is a severe disease, and mortality is frequently related to delays in diagnosis due to lack of clinical understanding. The association of acute renal failure and jaundice should lead the clinician to suspect leptospirosis. We concluded that old age, oliguria/anuria, high serum bilirubin levels (>36 mg/dL), and high serum potassium levels might be risk factors that increase mortality in leptospirosis.

Members of the genera Paenibacillus and Rhodococcus harbor genes homologous to enterococcal glycopeptide resistance genes vanA and vanB.

Genes homologous to enterococcal glycopeptide resistance genes vanA and vanB were found in glycopeptide-resistant Paenibacillus and Rhodococcus strains from soil. The putative D-Ala:D-Lac ligase genes in Paenibacillus thiaminolyticus PT-2B1 and Paenibacillus apiarius PA-B2B were closely related to vanA (92 and 87%) and flanked by genes homologous to vanH and vanX in vanA operons.

DNA microarray analysis of fim mutations in Escherichia coli.

Bacterial adhesion is often mediated by complex polymeric surface structures referred to as fimbriae. Type 1 fimbriae of Escherichia coli represent the archetypical and best characterised fimbrial system. These adhesive organelles mediate binding to D-mannose and are directly associated with virulence in the urinary tract. A typical type 1 fimbriated bacterium has up to 500 fimbriae on its surface, with each fimbria consisting of approximately 1000 individual subunits. This equates to approximately 8% of the total cellular protein and is potentially a significant resource drain for the cell. Here we have used DNA microarray analysis to examine the molecular events involved in response to fimbrial gene expression in E. coli K-12. Observed differential expression levels of the fim genes were in good agreement with our current knowledge of the stoichiometry of type 1 fimbriae. Changes in fim expression correlated directly with alterations in colony morphology. Deletion of the entire fim gene cluster resulted in the converse expression of another surface protein Antigen 43 (Ag43). Specific deletion of the fimH gene did not affect expression of other fim genes or Ag43, but did dramatically reduce the number of fimbriae expressed on the cell surface. The use of high-resolution oligonucleotide arrays for defining points of transcription initiation and termination is also demonstrated.

Antigen 43 from Escherichia coli induces inter- and intraspecies cell aggregation and changes in colony morphology of Pseudomonas fluorescens.

Antigen 43 (Ag43) is a surface-displayed autotransporter protein of Escherichia coli. By virtue of its self-association characteristics, this protein is able to mediate autoaggregation and flocculation of E. coli cells in static cultures. Additionally, surface display of Ag43 is associated with a distinct frizzy colony morphology in E. coli. Here we show that Ag43 can be expressed in a functional form on the surface of the environmentally important Pseudomonas fluorescens strain SBW25 with ensuing cell aggregation and frizzy colony types. Using green fluorescence protein-tagged cells, we demonstrate that Ag43 can be used as a tool to provide interspecies cell aggregation between E. coli and P. fluorescens. Furthermore, Ag43 expression enhances biofilm formation in P. fluorescens to glass surfaces. The versatility of this protein was also reflected in Ag43 surface display in a variety of other gram-negative bacteria. Display of heterologous Ag43 in selected bacteria might offer opportunities for rational design of multispecies consortia where the concerted action of several bacterial species is required, e.g., waste treatment and degradation of pollutants.

Expression and purification of the mannose recognition domain of the FimH adhesin.

Type 1 fimbriae have been shown to be specifically required for Escherichia coli colonisation and pathogenesis of the urinary tract. These structural organelles mediate specific adhesion to alpha-D-mannosides by virtue of the FimH adhesin. FimH is a two-domain protein in which the N-terminal domain contains the receptor-binding site and the C-terminal domain is required for organelle integration. To date, FimH has only been isolated as a complex with the system-specific chaperone FimC. Here we report that a functional form of the FimH receptor-binding domain can be readily isolated and characterised by replacing the C-terminal domain with a histidine tag.

Antigen 43 and type 1 fimbriae determine colony morphology of Escherichia coli K-12.

Colony morphology has been used as an important identification and characterization criterion in bacteriology for many decades. However, the molecular mechanisms underlying the appearance of different colony types have been given little attention. The synthesis of O antigen is defunct in Escherichia coli K-12, and colonies should accordingly only appear to be rough. However, previous reports have noted the presence of different interchangeable colony morphology types. In this study we have addressed the influence of two phase-variable surface structures, antigen 43 and type 1 fimbriae, on colony morphology. Due to differential expression of these structures, four different colony phenotypes could be distinguished. By creating and studying defined mutants of the respective loci, i.e. , flu and fim, we conclude that the presence or absence of the corresponding gene products on the cells correlates with the observed colony morphology forms. Interestingly, the habitat specificity of bacteria under static liquid conditions seems to correlate with the colony phenotypes.

Antigen-43-mediated autoaggregation of Escherichia coli is blocked by fimbriation.

Antigen 43 (Ag43), the product of the flu gene, is a surface-displayed autotransporter protein of Escherichia coli. Ag43 is responsible for the autoaggregation and flocculation of static liquid cultures of many E. coli strains. The expression of Ag43 has been reported to be phase variable and controlled by the product of the oxyR gene. Type 1 fimbriae are thin adhesive thread-like surface organelles responsible for bacterial receptor recognition and tissue colonization. Like that of Ag43, the expression of type 1 fimbriae is phase variable. Interestingly, previous results have suggested that the expression of type 1 fimbriae and the expression of Ag43 are mutually exclusive. In the present report, we show, by use of well-defined mutants, that fimbriation abolishes Ag43-mediated autoaggregation but does not affect Ag43 expression. Autoaggregation is shown to require an intercellular Ag43-Ag43 interaction, and the physical presence of fimbriae on the cells seems to abrogate this interaction. The Ag43 or OxyR status does not appear to influence fimbria expression, and our results suggest that the expression of Ag43 and the expression of fimbriae are independent processes.