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•About 5.8% (12/206) of the pigeons carried an ESBL-producing Enterobacterale isolate.•Two pigeons carried a VIM-2-producing Pseudomonas putidaisolate.•Plasmidic transmission of the IncF/F-:A-:B53 plasmid was observed.•Clonal spread of the Escherichia coliST5584 and ST8149 was observed between two farms.

•ESBL-producing E. coliwere detected in 4.5% of stork nestlings.•ESBL-producing E. coliof lineages ST38, ST58, ST155 and ST162 were detected.•IncI1-blaSHV-12/blaCTX-M-1and IncF-blaCTX-M-32/blaSHV-12were found.•Tn21-derivate and new genetic arrangements were detected in IncF plasmids.

•MSSA CC398 can be found in livestock and companion animals.•MSSA CC398 is frequently found in cats (27.3%).•As in humans, the most frequent spa-type in MSSA CC398 from animals is t571.•WGS analyses showed highly similar MSSA CC398 isolates between animals and humans.

•MRSA isolates from retail meat were diverse, comprising 5 sequence types (STs) and 8 spatypes.•A newly described MRSA sequence type (ST4034-t899) was detected in a pork meat sample.•This is the first report of MRSA ST692-t8646 outside the Asian continent.•Specific kinds of meat appear to be a possible source of MRSA, although the risk to humans is hard to define.

The relatedness of the equine-associated Escherichia colistrain ST1250 and its single- and double-locus variants (ST1250-SLV/DLV), obtained from horses in Europe, was studied by comparative genome analysis. A total of 54 isolates of E. coliST1250 and ST1250-SLV/DLV from healthy and hospitalized horses across Europe (Czech Republic [n = 23], The Netherlands [n = 18], Germany [n = 9], Denmark [n = 3], and France [n = 1]) from 2008 to 2017 were subjected to whole-genome sequencing.

Aim:We sought to investigate the genetic epidemiological relatedness of carbapenem-resistant Acinetobacter baumannii(CRAB) strains of a suspected outbreak in a Lebanese tertiary care hospital to implement necessary infection prevention and control measures. Methods:Twenty-eight nonduplicate CRAB isolates detected among hospitalized patients between January 2016 and July 2017 were studied by real-time polymerase chain reaction (PCR), pulsed-field gel electrophoresis and multilocus sequence typing analyses. Results:Twenty-seven isolates harbored blaOXA-23, of which one also carried blaNDM-1. The isolates distributed temporally in two presumably episodes were stratified by pulsed-field gel electrophoresis into many clusters. Although several clones have become endemic in the hospital, we have rapidly implemented appropriate infection prevention and control measures, achieving full eradication from August 2017 to November 2019. Conclusion:We have successfully investigated and controlled a polyclonal outbreak of OXA-23 producing ST2 CRAB.

•Dynamics of the global epidemiology of OXA-48-like-producing K. pneumoniae in Sahloul Hospital in 2012-2014•Successive dominance of two K. pneumoniaelineage OXA-48-type combinations (ST101/OXA-48 and ST147/OXA-204)

•E. coliand K. pneumoniaeisolates were highly susceptible, except to tétracyclines.•The proportion of ESBL phenotype was low (1.3% in E. coli, 0.4% in K. pneumoniae).•Camels are reservoirs of fluoroquinolone resistance, mcr-1and blaESBLgenes.•Various Inc-types plasmids were found, such as IncHI2 carrying blaCTX-M-1and mcr-1.

•Antimicrobial resistance (AMR) is highly worrisome in Lebanese non-clinical settings.•Animals, foodstuffs and the environment are significant reservoirs of AMR in Lebanon.•Multi- and extensively-drug-resistant Gram-negative bacilli are ubiquitous in Lebanon.•Dissemination of resistant clones in the community may have a zoonotic origin.

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•Dissemination of antibiotic resistance genes associated with conjugative plasmids.•Emergence of colistin-resistant carbapenemase-producing Klebsiella pneumoniaein Tunisia.•First molecular characterisation of colistin resistance mechanism in K. pneumoniaein Tunisia.

SUMMARYIn 2008, a previously unknown Escherichia coliclonal group, sequence type 131 (ST131), was identified on three continents. Today, ST131 is the predominant E. colilineage among extraintestinal pathogenic E. coli(ExPEC) isolates worldwide. Retrospective studies have suggested that it may originally have risen to prominence as early as 2003. Unlike other classical group B2 ExPEC isolates, ST131 isolates are commonly reported to produce extended-spectrum ß-lactamases, such as CTX-M-15, and almost all are resistant to fluoroquinolones. Moreover, ST131 E. coliisolates are considered to be truly pathogenic, due to the spectrum of infections they cause in both community and hospital settings and the large number of virulence-associated genes they contain. ST131 isolates therefore seem to contradict the widely held view that high levels of antimicrobial resistance are necessarily associated with a fitness cost leading to a decrease in pathogenesis. Six years after the first description of E. coliST131, this review outlines the principal traits of ST131 clonal group isolates, based on the growing body of published data, and highlights what is currently known and what we need to find out to provide public health authorities with better information to help combat ST131.

ABSTRACTIn the community, close contacts between humans and dogs may promote the transfer of extended-spectrum beta-lactamase/plasmidic AmpC cephalosporinase (ESBL/pAmpC) genes. Large-scale prevalence studies on ESBL/pAmpC carriage in dogs are rare, and data on ESBL/pAmpC plasmids are even more limited. Here, a considerable rate of 18.5% ESBL/pAmpC carriers was found among 368 unrelated healthy dogs in Paris, France. This prevalence is much higher than the one found in healthy humans in the same city (6%) but close to that recently reported in dogs in China (24.5%). All isolates were identified as Escherichia coli, except one Salmonella entericaand one Klebsiella pneumoniaeisolate. The sequence type 131 (ST131) clone was rare (2/73 isolates). Interestingly, two plasmids (blaCTX-M-1/IncI1/ST3 and blaCMY-2/IncI1/ST2) were unexpectedly highly predominant, raising the question of their successful spread. Considering that CTX-M-1 was recently found to be equally as abundant as CTX-M-15 in healthy Parisian subjects, the question of dogs being a CTX-M-1 reservoir for humans is open. Such a high prevalence of the blaCMY-2/IncI1/ST2 plasmid may result from the use of cephalexin in veterinary medicine, as previously demonstrated experimentally. In all, our study points out healthy urban dogs as a potential source of ESBL/pAmpC genes that can further disseminate to the human community.

Staphylococcus pseudintermediusis a frequent pathogen in dogs. The emergence of meticillin-resistant S. pseudintermedius(MRSP), which is concomitantly resistant to nearly all veterinary licensed antibiotics used for systemic treatment in dogs, is a major problem for veterinarians. In France, 16.9% (41/243) of the S. pseudintermediuscollected in 2010 were MRSP. They mainly belonged to the multiresistant MLST sequence type ST71, spatype t02, SCCmectype II-III (ST71–t02–II-III) European clone. Moreover, we also report the emergence of multiresistant meticillin-susceptible S. pseudintermediusisolates presenting atypical and/or new spatypes. This study highlights the need for surveillance, optimised treatment guidelines and new therapeutic alternatives.

Coagulase-positive staphylococci (CoPS) are potential causative agents of equine infections, but they are rarely responsible for the death of the animal. In the current study, staphylococci implicated in the death or euthanasia of horses were retrospectively studied in 3,457 necropsies performed over a decade (1995-2006). Morbidity associated with CoPS was 1.7%, representing 60 isolates of CoPS, which were identified as Staphylococcus aureus(59) and Staphylococcus pseudintermedius(1). Coagulase-positive staphylococci (alone or in association with another bacterial species) were associated with the death or euthanasia of 90% of the cases (54/60). Proportions of antibiotic resistance to penicillin G and tetracycline reached 62.7% and 23.7%, respectively. Virulence genes were detected in 91.7% of the strains, with a majority of sehor seienterotoxin genes. Finally, 3 methicillin-resistant Staphylococcus aureus(MRSA) isolates belonging to the t064 spa-type were identified. One strain was isolated in 2003 and might thus be one of the first cases of equine MRSA in France.

AbstractThe goal of this study was to estimate the distribution of pathogens, as well as their antimicrobial resistance pattern, in cows affected by clinical or subclinical mastitis in the Rhône-Alpes region of France. A total of 1770 samples were taken between January 2007 and March 2008, leading to the identification of 1631 bacterial isolates. Streptococcus uberis(22.1%), Escherichia coli(16%), and coagulase-positive staphylococci (15.8%) were identified as the major causative agents of clinical mastitis, whereas coagulase-positive staphylococci (30.2%), coagulase-negative staphylococci (13.7%), and Streptococcus dysgalactiae(9.3%) were predominantly implicated in subclinical mastitis. Yet, in both types of mastitis, about 20% of all cases were due to a large number of different bacterial species that were isolated at a low frequency (<5%), which cannot be considered as minor (e.g., Klebsiellaspp.) or noncontagious (e.g., Corynebacteriumspp.). The overall proportion of antibiotic resistance was low, except for penicillin G in staphylococci, as well as for macrolides and tetracycline in streptococci. Yet, these resistance proportions were much lower than those reported in human medicine. Besides providing up-to-date information on mastitis in France, this survey also indicates the prudent use of antibiotics by veterinarians. As a result, this study suggests that the risk of transmission of resistant bacteria from milk or milk products to human is very limited, even in case of consumption of raw milk. However, it also confirms the fact that attention must be maintained to avoid any emergence of such resistant bacteria.

Feces from 2,255 cattle (calves, young beef cattle, and culled cows) were collected at slaughter from nine departments across France. Campylobacterwas recovered from 16.5% of the 2,255 samples (C. jejunifrom 12.8% and C. colifrom 3.7%), predominantly from calves. Antimicrobial resistance to six antibiotics of medical and/or veterinary interest was tested with the Etest. Resistance to tetracycline was found in most isolates (52.8% of C. jejuniisolates and 88.1% of C. coliisolates) in contrast to low but consistent resistance to ampicillin and erythromycin. Only two C. coliisolates were resistant to gentamicin. Multiple resistance was frequently detected in C. jejuniand C. coliisolates, and 0.8% (3 of 372) of the isolates were resistant to five of the six antimicrobials. An upward trend in the resistance to quinolones and fluoroquinolones in C. jejunifrom calves was found; resistance to nalidixic acid reached 70.4% in 2006 and fluoroquinolone resistance increased from 29.7 to 70.4% during 2002 through 2006. All data were analyzed in parallel using clinical breakpoints or epidemiological cutoff values, and the results overlapped largely, except those for gentamicin. This 5-year survey (2002 through 2006) gives the first overview of the prevalence and antimicrobial resistance of C. jejuniand C. coliin cattle in France and documents to what extent cattle may contribute to the environmental reservoir of Campylobacterin France in the context of recurrent reports on links between human campylobacterioses and livestock. The results underline a notable increase in the resistance to fluoroquinolones in C. jejunifrom cattle that may be of significant importance for public health.

AbstractWe report here the results of the survey of antimicrobial resistance in 148 serotype Typhimurium strains isolated from cattle in France from 2002 to 2007 and displaying more than two antimicrobial resistances. Salmonella entericaserotype Typhimurium of definitive phage type 104 strains that are commonly resistant to ampicillin–amoxicillin, chloramphenicol–florfenicol, streptomycin–spectinomycin, sulfonamides, and tetracycline (ACSSuT phenotype) harbored resistance genes clustered on a complex class 1 integron In104 of the Salmonellagenomic island 1 (SGI1). In our isolates, the most common antimicrobial resistance pattern was ACSSuT (77.7%) or ACSSuT combined to additional resistances. SGI1 was detected in 143 strains and constituted thus the main structure involved in resistance to antimicrobials in these strains. In spite of the high recombination potential of In104, SGI1 variability was quite limited among these strains since only two SGI1 variants, SGI1-B and SGI1-C, were identified. One hundred and thirty-eight out of the 143 SGI1-positive isolates belonged to the DT104 complex. Pulsed-field gel electrophoresis profile A was the most prevalent in 135 SGI1-positive isolates, confirming the diffusion of the DT104 clone. However, changes in phages susceptibility have occurred in three serotype Typhimurium strains of phage type DT12, as they displayed the same pulsed-field gel electrophoresis profile as the SGI1-positive serotype Typhimurium DT104. No variant harboring an additional resistance gene was identified, but the risk of recombination between SGI1 and any other mobile structure carrying other antimicrobial resistance genes is still an issue in serotype Typhimurium.

ABSTRACTStreptococcus uberisis an environmental pathogen commonly causing bovine mastitis, an infection that is generally treated with penicillin G. No field case of true penicillin-resistant S. uberis(MIC > 16 mg/liter) has been described yet, but isolates presenting decreased susceptibility (MIC of 0.25 to 0.5 mg/liter) to this drug are regularly reported to our laboratory. In this study, we demonstrated that S. uberiscan readily develop penicillin resistance in laboratory-evolved mutants. The molecular mechanism of resistance (acquisition of mutations in penicillin-binding protein 1A [PBP1A], PBP2B, and PBP2X) was generally similar to that of all other penicillin-resistant streptococci described so far. In addition, it was also specific to S. uberisin that independent resistant mutants carried a unique set of seven consensus mutations, of which only one (Q554E in PBP2X) was commonly found in other streptococci. In parallel, independent isolates from bovine mastitis with different geographical origins (France, Holland, and Switzerland) and presenting a decreased susceptibility to penicillin were characterized. No mosaic PBPs were detected, but they all presented mutations identical to the one found in the laboratory-evolved mutants. This indicates that penicillin resistance development in S. uberismight follow a stringent pathway that would explain, in addition to the ecological niche of this pathogen, why naturally occurring resistances are still rare. In addition, this study shows that there is a reservoir of mutated PBPs in animals, which might be exchanged with other streptococci, such as Streptococcus agalactiae, that could potentially be transmitted to humans.

ABSTRACTDrinking water has rarely been recognized as a source of antimicrobial resistance for humans, and only in low-income countries. Here, a sequence type 48 Escherichia coliisolate carrying the blaCTX-M-1IncI1/ST3 plasmid was recovered from drinking water in France. This plasmid was similar to other blaCTX-M-1IncI1/ST3 plasmids found previously in animals and humans. Our findings highlight the possible human transfer of extended-spectrum β-lactamase (ESBL) genes through drinking water in high-income countries.

AbstractThe goal of this study was to assess the presence of enterococci species presenting van-mediated glycopeptide resistance in French cattle. Fecal samples were collected from healthy and sick animals, and enterococci were screened for vancomycin resistance. Vancomycin resistance was principally encountered in Enterococcus gallinarumand Enterococcus casseliflavusstrains. However, glycopeptide resistance was detected in three different species of enterococci (E. faecalis, E. faecium, and E. casseliflavus). Molecular characterization of the genetic support proved that they all presented the prototypic VanA element. Interestingly, the E. casseliflavusstrain displayed a remarkable VanB phenotype/vanA-vanCgenotype. Transferability, associated resistances, and factors of vanAcotransfer were sought. This study proved that acquired vanAgenes can still be detected in food-producing animals more than a decade after the avoparcin ban. Indeed, calves, which are recurrently exposed to antibiotics in France, may allow the re-emergence of glycopeptide resistance through coselection factors, and this might potentially be concerning for human health.

Prion-related protein (PrP) is a glycosylphosphatidylinositol-linked cell-surface protein expressed by a wide variety of cells, including those of the nervous system and the immune system. Several functions of normal cellular PrP (PrPc) have been proposed that may be associated with the capacity of this protein to bind copper. In the present study, we describe the generation of a panel of monoclonal antibodies raised to copper-refolded PrP, which may be used to analyse the normal and disease-associated forms of this protein. The anti-PrP monoclonal antibodies were reactive by Western blot and ELISA with recombinant murine PrPc refolded in the presence or absence of either copper or manganese, and with the disease-susceptible allelic form V136R154Q171 ('VRQ'; where single-letter amino-acid notation has been used) and disease-resistant allelic form A136R154R171 ('ARR') of recombinant ovine PrPc. FACS analysis of lymphoid cells using these monoclonal antibodies showed that wild-type non-activated mouse lymphocytes expressed little, if any, PrPc. These monoclonal antibodies were shown to react with the unglycosylated and monoglycosylated forms of PrPSc (abnormal disease-specific conformation of PrP) in prion-infected tissue samples from all of the different species tested by Western blot. In addition, this analysis allowed one to make a distinction between bovine spongiform encephalopathy ('BSE') and scrapie PrPSc isolates from experimentally infected sheep on the basis of their different electrophoretic mobilities.

Until now, there has been no indication that the evolutionary dynamics of Escherichia coliST131 may reflect independent and host-specific adaptation of this lineage outside humans. In contrast, the limited number of ST131 reports in animals supported the common view that it rather reflects a spillover of the human sector.

The prion protein (PrP) from sheep was produced in large quantities of entire protein in Escherichia coliafter fusion with a carboxy‐terminal hexahistidine sequence. In contrast, amino‐terminal fusion with glutathione S‐transferase (GST) revealed a high susceptibility toward cleavage of the protein. Both recombinant proteins were recognised, at variable levels, in Western blots using a panel of antibodies against the 40–56, 89–104, 98–113 and 112–115 sequences of the prion protein, similarly to the abnormal prion protein extracted from scrapie‐infected sheep. Interestingly, monoclonal antibody 3F4 was found to react with these three proteins in Western blot.

ABSTRACTIt 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.

TEM-52 extended-spectrum β-lactamases (ESBLs) have been detected in members of the Enterobacteriaceae isolated from human and non-human reservoirs, mainly in European countries. Here we report the first draft genome of a multidrug-resistant TEM-52b-positive Escherichia coliisolated from a companion animal in France.

The emergence of Enterobacteriaceae isolates resistant to the last-resort antibiotic fosfomycin outside of Asia is a public-health issue. Here we report the draft genome of an Escherichia coliisolate presenting both an extended-spectrum β-lactamase (ESBL) and the fosA3gene in a healthy cow in Brazil.

AbstractEnrofloxacin-resistant mutants of Stx2-producing Escherichia coliO157:H7 from cattle were selected. Mutants produced threefold higher Stx2 levels than native strains after induction with enrofloxacin. Mutants were also inducible using hundredfold higher enrofloxacin concentrations than the ones used for native strains. These results suggest that Escherichia coliO157:H7 from cattle may become more frequently pathogenic to humans as a side effect of the increasing use of veterinary fluoroquinolones.

Colistin is used in Brazil for the treatment of food-producing animals. The colistin resistance gene mcr-1has already been reported from chicken and swine in this country. Here we report the draft genome of an Escherichia coliisolate presenting both an extended-spectrum β-lactamase (ESBL) gene and the mcr-1gene in a healthy cow in Brazil.

Escherichia coli, the main host of the CTX-M-15 extended-spectrum β-lactamase (ESBL) enzyme, is widely distributed and exchanged between the environment, animals and humans. Therefore, identification of blaCTX-M-15-positive lineages in food has a significant impact on public health. In this regard, until the end of 1990s, ESBL-producing isolates were mainly associated with hospital-acquired infections, with a predominance of SHV- and TEM-type enzymes. In recent years, a new trend has been observed among ESBL-producers, where most isolates now harbour CTX-M-type, being further isolated from community-acquired infections. Nowadays, CTX-M-15 has been recognised as the most important ESBL variant, invading virtually all human and animal compartments, leading to a global pandemic. Thus, whilst the rapid emergence and dissemination of CTX-M-15 among E. coliisolates has generated a large genetic reservoir from which other members of the Enterobacteriaceae family can easily acquire this resistance gene, there are an increasing number of new reservoirs and transmission mechanisms that must be investigated. In this study, we present the draft genome sequence of a CTX-M-15-producing E. coliST345 isolated from commercial chicken meat in Brazil. This draft genome can be used as a reference sequence for comparative analysis among CTX-M-15-producers.

Colistin has become a last-resort antibiotic for the treatment of infections caused by highly drug-resistant Gram-negative bacteria. Moreover, it has been widely used in the livestock sector.

Bivalves are filter-feeding animals and markers of bacterial pollution. We report a massive spread of blaCTX-M-15through dominant Escherichia coliand Klebsiella pneumoniaelineages and/or plasmid subtypes (F31:A4:B1) as well as the presence of OXA-23-producing Acinetobacter baumanniisequence type 2 (ST2) in seafood, highlighting a direct risk for the consumer.

The prion protein (PrP) from sheep was produced in large quantities of entire protein in Escherichia coli after fusion with a carboxy-terminal hexahistidine sequence. In contrast, amino-terminal fusion with glutathione S-transferase (GST) revealed a high susceptibility toward cleavage of the protein. Both recombinant proteins were recognised, at variable levels, in Western blots using a panel of antibodies against the 40–56, 89–104, 98–113 and 112–115 sequences of the prion protein, similarly to the abnormal prion protein extracted from scrapie-infected sheep. Interestingly, monoclonal antibody 3F4 was found to react with these three proteins in Western blot.