Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance.

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.

F74 plasmids are major vectors of virulence genes in bovine NTEC2.

Necrotoxigenic Escherichia coli 2 (NTEC2) are defined as E. coli producing the toxin known as cytotoxic necrotizing factor 2 (CNF2), a potent toxin primarily found in bovine but also in humans. NTEC2 are mostly associated with bovine, and cnf2 is known to be carried by pVir-like plasmids. In this study, we looked for NTEC2 in a collection of E. coli collected between 2011 and 2018 in French bovine. Thirty-two isolates, collected from both sick (n = 19) and healthy (n = 13) animals, were identified and characterized using whole-genome sequencing. One F74 plasmid of this bacterial collection was long-read sequenced: its size was 138 121 bp and it carried the cnf2, F17cA-eG, cdtB, iutA, iucC and ompP virulence factors (VFs), but no resistance gene. A large variety of genetic backgrounds was observed, but all cnf2-carrying plasmids belonged to the IncF family, and most of them (78·1%) were of the F74 group. Similar F74 plasmids were also reported from bovine in the United Kingdom and the United States, as identified in the publically available databases. Consequently, these F74 plasmids, which are widely disseminated among E. coli from cattle in the French territory, are vectors of virulence determinants that largely went unnoticed until now.

OASIS evaluation of the French surveillance network for antimicrobial resistance in diseased animals (RESAPATH): success factors underpinning a well-performing voluntary system.

Antimicrobial resistance is a One Health issue requiring the development of surveillance systems in the human, environmental and animal sectors. In the European Economic Area, the surveillance of antimicrobial resistance in zoonotic pathogens and indicator bacteria in healthy food-producing animals is required legally, while countries are also expected to extend their surveillance to diseased animals in the frame of national action plans. In this context, evaluating existing antimicrobial resistance surveillance systems in animal health is important to improve systems in place, but also to help other countries learn from these experiences, understand success factors and anticipate challenges. With this aim, the French surveillance network for antimicrobial resistance in bacteria from diseased animals (RESAPATH) was evaluated using the Outil d'Analyse des Systèmes d'Information en Santé (OASIS) assessment tool. Key performance factors included (i) a strong and inclusive central institutional organisation defining clear and well-accepted surveillance objectives, scope and procedures, (ii) strong skills in epidemiology and microbiology and (iii) a win-win approach enabling the voluntary participation of 71 field laboratories and where free annual proficiency testing plays a pivotal role. The main area for improvement of RESAPATH was its time-consuming data management system.

Overall changes in the transcriptome of Escherichia coli O26:H11 induced by a subinhibitory concentration of ciprofloxacin.

AIMS: The goal was to explore the effects of subinhibitory concentration (SIC) (0·5 MIC = 20 µg l-1 ) of ciprofloxacin on the transcriptome of enterohaemorrhagic Escherichia coli O26:H11 isolate by 60 minutes of exposure. MATERIALS AND RESULTS: We used a combination of comparative genomic and transcriptomic (RNAseq) analyses. The whole genome of the E. coli O26:H11 #30934 strain of bovine origin was sequenced and assembled. This genome was next used as reference for the differential gene expression analysis. A whole-genome-based analysis of 36 publicly available E. coli O26:H11 genomes was performed to define the core and the accessory transcriptome of E. coli O26:H11. Using RNAseq and RT-qPCR analysis we observed overexpression of the SOS response and of T3SS effectors, together with the inhibition of specific motility-associated genes. Among the large set of transposases present, only three were activated, suggesting moderate transposition of genes with low doses of ciprofloxacin. Our results illustrated that transcriptional repressors, such as the CopG family protein, belonging to the core genome of E. coli O26:H11, are altered in response to fluoroquinolone exposure. The gene ontology enrichment analysis showed SIC of ciprofloxacin induced binding functions and catalytic activities, including mostly transferase and hydrolase proteins. The amino acid pathways involved in metabolic processes were significantly enhanced after the treatment. CONCLUSIONS: Although the core genome of E. coli O26:H11 constituted only 54·5% of the whole genome, we demonstrated that most differentially expressed genes were associated with the core genome of E. coli O26:H11, and that effects on the mobile genetic element, phage, and plasmid-related genes were rare. SIGNIFICANCE AND IMPACT OF THE STUDY: For the first time the effect of low dose of ciprofloxacin on the core transcriptome of E. coli O26:H11 was described. The effects on the main biological functions and protein classes including transcriptional regulators were illustrated.

Antimicrobial resistance patterns of bacteria isolated from dogs with otitis.

Antimicrobial-resistant bacteria in dogs can be transmitted to humans and close contact between dogs and people might foster dissemination of resistance determinants. The aim of our study was to describe the antimicrobial resistance (AMR) pattern of the major causative agents of canine otitis - one of the most common diseases in dogs - isolated in France. Data collected between 2012 and 2016 by the French national surveillance network for AMR, referred to as RESAPATH, were analysed. Resistance trends were investigated using non-linear analysis (generalised additive models). A total of 7021 antibiograms were analysed. The four major causative agents of canine otitis in France were coagulase-positive staphylococci, Pseudomonas aeruginosa, Proteus mirabilis and streptococci. Since 2013, resistance to fluoroquinolones has been on the decrease in both P. aeruginosa and Staphylococcus pseudintermedius isolates. For P. aeruginosa, 19.4% of isolates were resistant to both enrofloxacin and gentamicin. The levels of multidrug resistance (acquired resistance to at least one antibiotic in three or more antibiotic classes) ranged between 11.9% for P. mirabilis and 16.0% for S. pseudintermedius. These results are essential to guide prudent use of antibiotics in veterinary medicine. They will also help in designing efficient control strategies and in measuring their effectiveness.

Antimicrobial resistance trends in Escherichia coli isolated from diseased food-producing animals in France: A 14-year period time-series study.

Antimicrobial resistance (AMR) among bacteria isolated from food-producing animals is a growing concern with implications for public health. AMR surveillance is essential to identify resistance trends and help in the design of effective and efficient control strategies. The aim of the study was to describe the antimicrobial susceptibility of pathogenic Escherichia coli isolated from three livestock productions in France (cattle, swine and poultry). The trend in resistance to the most commonly prescribed antibiotics in animal health was analysed as follows: amoxicillin (penicillin), spectinomycin or streptomycin (aminoglycoside), tetracycline and trimethoprim-sulfamethoxazole/Enrofloxacin and ceftiofur were also taken into account as members of critically important antimicrobial families in human and veterinary medicine, that is fluoroquinolones and third-generation cephalosporins, respectively. Data collected between 2002 and 2015 by the French national surveillance network of AMR referred to as RESAPATH were analysed. Resistance trends were investigated using non-linear analysis (generalized additive models) applied to time-series stratified by livestock production and antibiotic. Irrespective of the species and the antibiotic considered, resistance signals over time showed no significant annual cycle. Resistance to third-generation cephalosporins emerged during the period of the study, with a peak at 22% [20.5; 24.0] in poultry in 2010, decreasing afterwards, while it remained consistently below 10% for the other species. The proportion of resistance to fluoroquinolones was broadly similar between species and remained under 30%, with a slight decreasing trend after 2009. Resistances to tetracycline and amoxicillin remained high, between 90% and 40% over time in cattle and swine. After 2010, there was a decrease in resistance to these antibiotics for all species, especially to tetracycline for poultry with a drop from 84% in 2009 to 43% in 2015. These results contribute to risk assessment and constitute objective evidence on which to evaluate the efficacy of control measures implemented to limit AMR occurrence.

Extended-spectrum ß-lactamase/AmpC- and carbapenemase-producing Enterobacteriaceae in animals: a threat for humans?

There has been a great and long-term concern that extended-spectrum ß-lactamase (ESBL)/AmpC- and carbapenemase-producing Enterobacteriaceae occurring in animals may constitute a public-health issue. A large number of factors with complex interrelations contribute to the spread of those bacteria among animals and humans. ESBL/AmpC- or carbapenemase-encoding genes are most often located on mobile genetic elements favouring their dissemination. Some shared reservoirs of ESBL/AmpC or carbapenemase genes, plasmids or clones have been identified and suggest cross-transmissions. Even though exposure to animals is regarded as a risk factor, evidence for a direct transfer of ESBL/AmpC-producing bacteria from animals to humans through close contacts is limited. Nonetheless, the size of the commensal ESBL/AmpC reservoir in non-human sources is dramatically rising. This may constitute an indirect risk to public health by increasing the gene pool from which pathogenic bacteria can pick up ESBL/AmpC/carbapenemase genes. The extent to which food contributes to potential transmission of ESBL/AmpC producers to humans is also not well established. Overall, events leading to the occurrence of ESBL/AmpC- and carbapenemase-encoding genes in animals seem very much multifactorial. The impact of animal reservoirs on human health still remains debatable and unclear; nonetheless, there are some examples of direct links that have been identified.

A simplified method of performance indicators development for epidemiological surveillance networks--application to the RESAPATH surveillance network.

BACKGROUND: Develop and calculate performance indicators allows to continuously follow the operation of an epidemiological surveillance network. This is an internal evaluation method, implemented by the coordinators in collaboration with all the actors of the network. Its purpose is to detect weak points in order to optimize management. A method for the development of performance indicators of epidemiological surveillance networks was developed in 2004 and was applied to several networks. Its implementation requires a thorough description of the network environment and all its activities to define priority indicators. Since this method is considered to be complex, our objective consisted in developing a simplified approach and applying it to an epidemiological surveillance network. METHODS: We applied the initial method to a theoretical network model to obtain a list of generic indicators that can be adapted to any surveillance network. RESULTS: We obtained a list of 25 generic performance indicators, intended to be reformulated and described according to the specificities of each network. It was used to develop performance indicators for RESAPATH, an epidemiological surveillance network of antimicrobial resistance in pathogenic bacteria of animal origin in France. CONCLUSION: This application allowed us to validate the simplified method, its value in terms of practical implementation, and its level of user acceptance. Its ease of use and speed of application compared to the initial method argue in favor of its use on broader scale.

Identifying antimicrobial multiresistance patterns of Escherichia coli sampled from diarrhoeic calves by cluster analysis techniques: a way to guide research on multiresistance mechanisms.

Multiresistance is a critical issue. This study points out the usefulness of cluster analysis techniques to describe concisely the antimicrobial susceptibility patterns of bacterial isolates in a way that could effectively help in generating hypotheses on multiresistance mechanisms. Data were selected from the French antimicrobial resistance survey network on veterinary pathogens (Resapath). They were related to 1545 Escherichia coli isolates, which were isolated from faecal samples of diarrhoeic calves in France between 2002 and 2006. Ten clusters of isolates displaying similar features in terms of resistance profile to 13 relevant antimicrobials were computed. The presence of two to ten simultaneous resistances was detected in nine out of the ten clusters. Looking at potential mechanistic interpretations, results may suggest genetic links between some resistance mechanisms, but this should be confirmed by molecular investigation of the corresponding isolates. Looking at therapeutical potential implications, the high level of resistance and multiresistance to several antimicrobials observed in E. coli makes a critical reassessment of empiric oral antimicrobial therapy in calves highly desirable.

Study of hypothalamic leptin receptor expression in low-birth-weight piglets and effects of leptin supplementation on neonatal growth and development.

Low birth weight resulting from intrauterine growth retardation (IUGR) is a risk factor for further development of metabolic diseases. The pig appears to reproduce nearly all of the phenotypic pathological consequences of human IUGR and is likely to be more relevant than rodents in studies of neonatal development. In the present work, we characterized the model of low-birth-weight piglets with particular attention to the hypothalamic leptin-sensitive system, and we tested whether postnatal leptin supplementation can reverse the precocious signs of adverse metabolic programming. Our results demonstrated that 1) IUGR piglets present altered postnatal growth and increased adiposity; 2) IUGR piglets exhibit abnormal hypothalamic distribution of leptin receptors that may be linked to further disturbance in food-intake behavior; and 3) postnatal leptin administration can partially reverse the IUGR phenotype by correcting growth rate, body composition, and development of several organs involved in metabolic regulation. We conclude that IUGR may be characterized by altered leptin receptor distribution within the hypothalamic structures involved in metabolic regulation and that leptin supplementation can partially reverse the IUGR phenotype. These results open interesting therapeutic perspectives in physiopathology for the correction of defects observed in IUGR.

Characterization of inducible stx2-positive Escherichia coli O157:H7/H7- strains isolated from cattle in France.

AIMS: To quantify the variability of the Shiga toxin 2 (Stx2) production by a panel of stx2-positive Escherichia coli O157:H7/H7- isolates from healthy cattle before and after induction with enrofloxacin. METHODS AND RESULTS: ProSpecT ELISA was used to quantify the Stx2 production by stx2-positive E. coli O157:H7/H7- isolates in native conditions (basal level) or after induction with enrofloxacin. Whereas only 15.2% of the E. coli O157:H7/H7- strains studied displayed significant amounts of detectable Stx2 without induction, most of them were shown to be inducible, and at various levels, in presence of subinhibitory concentrations of enrofloxacin. CONCLUSIONS: We demonstrated the capability of a highly elevated proportion of stx2-positive, but constitutively Stx2-negative, E. coli O157:H7/H7- isolates from healthy cattle to produce significant levels of Shiga toxin Stx2 in presence of subtherapeutic concentrations of enrofloxacin, an antibiotic of the fluoroquinolones family only licensed for veterinary use. SIGNIFICANCE AND IMPACT OF THE STUDY: This study documents the risk that bovine-associated Shiga toxin producing E. coli isolates may become more frequently pathogenic to humans as a side-effect of the increasing use of veterinary fluoroquinolones in the oral treatment of food animals like cattle or poultry.

Estimates of the prevalence of transmissible spongiform encephalopathies in sheep and goats in France in 2002.

An active surveillance programme for transmissible spongiform encephalopathies (TSES) in sheep and goats was implemented in France in 2002 at abattoirs and rendering plants. The analysis of the results of this programme highlighted three biases: a potentially non-random sampling scheme in both rendering plants and abattoirs, a heterogeneous geographical sampling ratio, and the use of two diagnostic tests of unequal sensitivity. Simulations were run to estimate the prevalence of TSES by taking these biases into account. A comparison of the prevalence of TSES calculated from the raw data with the simulation results showed that the effects of non-random sampling were minor in comparison with the effects of the heterogeneous geographical sampling ratio and the use of two diagnostic tests.

Abnormal prion protein in genetically resistant sheep from a scrapie-infected flock.

The central molecular event in transmissible spongiform encephalopathies, such as scrapie in sheep, is the accumulation in tissues of an abnormal isoform of the cellular prion protein. A previous investigation of 26 sheep showed that the accumulation of PrP(res) in brain correlated more with the prnp genotype than with the severity of the clinical disease. Here, the ability of a sandwich ELISA to detect PrP(res) distribution in the brain was demonstrated. Immunohistochemistry also strongly supported the hypothesis that the dorsal motor nucleus of the vagus nerve is the possible entry site in the brain for the scrapie agent. Remarkably, three asymptomatic (or possibly asymptomatic for scrapie) sheep carrying an allele known to be associated with clinical scrapie resistance (ARR), which were negative for the detection of PrP(res) by Western blotting and immunohistochemistry, were positive for the presence of PrP(res) by ELISA, raising the possibility of carriers resistant to the disease and possibly contributing to the persistence of scrapie in certain flocks.

Atypical scrapie cases in Germany and France are identified by discrepant reaction patterns in BSE rapid tests.

The intensified surveillance of scrapie in small ruminants in the European Union (EU) has resulted in a substantial increase of the number of diagnosed cases. Four rapid tests which have passed the EU evaluation for BSE testing of cattle are also recommended currently and used for the testing of small ruminants by the EU authorities. These tests include an indirect ELISA (cELISA), a colorimetric sandwich ELISA (sELISA I), a chemiluminescent sandwich ELISA (sELISA II), and a Western blot (WB). To this point, the majority of samples have been screened by using either sELISA I (predominantly in Germany) or WB (predominantly in France). In this study, it is shown that a number of the German and French scrapie cases show inconsistent results using rapid and confirmatory test methods. Forty-eight German sheep, 209 French sheep and 19 French goat transmissible spongiform encephalopathy (TSE) cases were tested. All cases were recognised by the sELISA I and either one of the confirmatory methods (scrapie-associated fibrils (SAF)-immunoblot or immunohistochemistry). Surprisingly, three rapid tests failed to detect a significant number of scrapie cases (29 in France and 24 in Germany). The possible reasons for these inconsistent reaction patterns of scrapie cases are discussed. Similar discrepancies have not been observed during rapid testing of cattle for BSE, the disease for which all diagnostic methods applied have been evaluated.

Targeted surveillance to assess the prevalence of BSE in high-risk populations in western France and the associated risk factors.

A pilot study was set up for the first time in France in August 2000, to obtain more precise estimates on the BSE epidemic in France. Three categories of cattle at risk of BSE (found dead on-farm, euthanased and emergency slaughtered) were sampled exhaustively from August 7 to December 22, 2000, in the three regions assumed to be the most affected with BSE in France (Basse-Normandie, Bretagne and Pays de la Loire). The samples were checked by using Prionics tests, and positive samples were confirmed by Western blot or immunohistochemistry. The overall prevalence of positive cattle was 0.16 per cent. Multifactorial logistic regression showed that there was a significantly higher prevalence among cattle from the birth cohorts July 1993 to June 1994 and July 1994 to June 1995, than among those born before July 1993, and among the categories 'euthanased' and 'emergency slaughtered' than among the category 'dead on-farm, and a higher prevalence in the regions Pays de la Loire and Bretagne than in Basse-Normandie. No significant differences in the prevalence of BSE were observed between dairy, beef suckler and mixed herds.

Protease-resistant prion protein in brain and lymphoid organs of sheep within a naturally scrapie-infected flock.

The hallmark of transmissible spongiform encephalopathies (TSE), such as scrapie in sheep, is the accumulation in tissues of an insoluble and protease resistant form (PrPres) of the cellular prion protein. In this study, we evaluated whether the diversity in both the clinical pattern and the PrP genotypes of scrapied sheep from the same flock was connected with different levels and/or glycoform patterns of the PrPres in the brain and lymphoid organs of the animals. Whereas the PrPres levels in spleen, lymph nodes and tonsils from sheep of different PrP genotypes and clinical status appeared comparable, they were highly variable in brain, particularly in the brain stem and the cerebellum. PrPres was only detected in sheep bearing at least one VRQ allele, including three asymptomatic sheep and the highest PrPres load was found in the cerebellum of VRQ/VRQ animals. All together, levels of PrPres in brain did not necessarily correlate with the severity of the clinical disease but might depend on the PrP genotype of the animals. Different brain regions from a given sheep displayed a similar glycopattern of PrPres, whereas the apparent molecular sizes of the unglycosylated and diglycosylated forms of the protein differed between brain and lymphoid tissues. We did not find any notifiable differences in the glycopattern of PrPres in brain from sheep of different PrP genotypes or different clinical status and this PrPres glycotype was also similar to that found in brain from four cattle BSE.

Comparison of French natural scrapie isolates with bovine spongiform encephalopathy and experimental scrapie infected sheep.

We compared the glycoform pattern of the abnormal prion protein (PrP(Sc)) detected by immunoblotting in 21 sheep with natural scrapie, from 21 different outbreaks identified in France since 1996, with a bovine spongiform encephalopathy (BSE)-infected sheep. All the natural scrapie isolates had a higher molecular mass of the unglycosylated PrP(Sc) than in BSE-infected sheep. In the latter case, this molecular mass appeared identical to that found in the CH 1641 experimental scrapie strain (type C pattern), whereas in natural scrapie cases it was similar to that found in the SSBP/1 experimental scrapie strains. These results suggest that all French natural scrapie isolates studied so far would belong, as SSBP/1, to the group of scrapie cases with type A electrophoretic pattern.

Similar signature of the prion protein in natural sheep scrapie and bovine spongiform encephalopathy-linked diseases.

It has been suggested that specific molecular features could characterize the protease-resistant prion protein (PrP res) detected in animal species as well as in humans infected by the infectious agent strain that causes bovine spongiform encephalopathy (BSE). Studies of glycoform patterns in such diseases in French cattle and cheetahs, as well as in mice infected by isolates from both species, revealed this characteristic molecular signature. Similar studies of 42 French isolates of natural scrapie, from 21 different flocks in different regions of France, however, showed levels of the three glycoforms comparable to those found in BSE-linked diseases. Moreover, the apparent molecular size of the unglycosylated form was also indistinguishable among all different sheep isolates, as well as isolates from BSE in cattle. Overall results suggest that scrapie cases with features similar to those of BSE could be found more frequently in sheep than previously described.