Antimicrobial Resistance of Enterococcus Isolates from Poultry Farms in the Republic of Serbia (Autonomous Province of Vojvodina)

Enterococcus species are significant intestinal commensals of animals, including poultry. However, they have emerged as important opportunistic infective agents in both veterinary and human medicine as well as major nosocomial pathogens, owing to their increasing antimicrobial resistance. This research aimed to investigate the prevalence and antimicrobial resistance patterns of Enterococcus spp. isolated from poultry farms in the north of Serbia. A total of 40 samples of overshoes or feces were collected from 40 poultry farms and analyzed for the presence of Enterococcus spp. using PCR or MALDI-TOF mass spectrometry for their identification. The number of isolates was 40 and included 11 isolates from laying hens, 2 isolates from turkeys, 3 from broiler breeders, and 24 from broilers. The Kirby-Bauer disk diffusion method was used to test for antibiotic susceptibility in accordance with the Clinical and Laboratory Standards Institute and EUCAST guidelines. The results showed that Enterococcus faecalis was isolated from 37.5% farms, and E. faecium from 42.5%. E. hirae was identified in 15% of poultry establishments, and E. durans and E. thialandicus on 2.5%. Notably, resistance to erythromycin, streptomycin, fluoroquinolones, and tetracyclines among the frequently used antibiotics was found. Furthermore, 35% of the isolates had multidrug resistance (MDR). In order to prevent the spread of antibiotic resistance in chicken farming and protect the health of the public and animals alike, our findings highlight the critical need for improved surveillance and control measures. To effectively establish a containment strategy for Enterococcus spp. isolated from poultry farms, more research into the processes behind their antibiotic resistance is required.

Antimicrobial resistance among indicator Enterococcus faecium and Escherichia coli in Swedish pig farms

Monitoring the use of antimicrobials and the emergence of resistance in animals and people is important for the control of antimicrobial resistance, and for establishing sustainable and effective disease management practices. In this study, we used Enterococcus spp. and Escherichia coli as indicator species to investigate antimicrobial susceptibility patterns and how these change over time, on ten Swedish pig farms. Indoor environmental sock sampling was performed once a month during the entire production cycle of one batch of pigs on each farm, resulting in 60 samples collected in total. Selective culture for E. coli and Enterococcus spp. resulted in 122 isolates of E. coli, 74 isolates of E. faecium, but no isolates of E. faecalis. Microdilution was used to determine minimum inhibitory concentrations for twelve antimicrobial substances in E. coli and fifteen substances in E. faecium. The overall prevalence of resistance was low. Among the E. coli isolates, the proportions non-wild type (resistant, NWT) isolates were as follows: azithromycin and amikacin 1% (n = 1), trimethoprim and sulfamethoxazole 2% (n = 3), ampicillin 6% (n = 7) and tetracycline 9% (n = 11). Among the E. faecium isolates, the NWT proportions were: teicoplanin, linezolid and gentamicin 1% (n = 1), daptomycin 3% (n = 2), erythromycin 26% (n = 19), tetracycline 27% (n = 20), quinupristin/dalfopristin 58% (n = 42). The resistance patterns differed between the farms, likely due to different antimicrobial use, biosecurity measures and source of the animals. The NWT prevalence among E. coli decreased over time, whereas no similar trend could be observed in E. faecium. The results of the current study illustrate the complex factors affecting the antimicrobial resistance patterns observed on each farm, indicating that specific practices and risk factors have an impact on the prevalence and type of antimicrobial resistance. Further studies of the farm environments in combination with antimicrobial use and other risk factor data are needed to elucidate the multifaceted drivers of antimicrobial resistance development on livestock farms.

Multidrug-resistant Enterococcus faecium strains enter the Norwegian marine environment through treated sewage

This study aimed to understand the antibiotic resistance prevalence among Enterococcus spp. from raw and treated sewage in Bergen city, Norway. In total, 517 Enterococcus spp. isolates were obtained from raw and treated sewage from five sewage treatment plants (STPs) over three sampling occasions, with Enterococcus faecium as the most prevalent (n = 492) species. E. faecium strains (n = 307) obtained from the influent samples, showed the highest resistance against quinupristin/dalfopristin (67.8%). We observed reduced susceptibility to erythromycin (30.6%) and tetracycline (6.2%) in these strains. E. faecium strains (n = 185) obtained from the effluent samples showed highest resistance against quinupristin/dalfopristin (68.1%) and reduced susceptibility to erythromycin (24.9%) and tetracycline (8.6%). We did not detect resistance against last-resort antibiotics, such as linezolid, vancomycin, and tigecycline in any of the strains. Multidrug-resistant (MDR) E. faecium strains were detected in both influent (2.3%) and effluent (2.2%) samples. Whole genome sequencing of the Enterococcus spp. strains (n = 25) showed the presence of several antibiotic resistance genes, conferring resistance against aminoglycosides, tetracyclines, and macrolides, as well as several virulence genes and plasmid replicons. Two sequenced MDR strains from the effluents belonged to the hospital-associated clonal complex 17 and carried multiple virulence genes. Our study demonstrates that clinically relevant MDR Enterococcus spp. strains are entering the marine environment through treated sewage.

Whole-genome long-read sequencing to unveil Enterococcus antimicrobial resistance in dairy cattle farms exposed a widespread occurrence of Enterococcus lactis

Enterococcus faecalis (Efs) and Enterococcus faecium (Efm) are major causes of multiresistant healthcare-associated or nosocomial infections. Efm has been traditionally divided into clades A (healthcare associated) and B (community associated) but clade B has been recently reassigned to Enterococcus lactis (Elc). However, identification techniques do not routinely differentiate Elc from Efm. As part of a longitudinal study to investigate the antimicrobial resistance of Enterococcus in dairy cattle, isolates initially identified as Efm were confirmed as Elc after Oxford-Nanopore long-fragment whole-genome sequencing and genome comparisons. An Efm-specific PCR assay was developed and used to identify isolates recovered from animal feces on five farms, resulting in 44 Efs, 23 Efm, and 59 Elc. Resistance, determined by broth microdilution, was more frequent in Efs than in Efm and Elc but all isolates were susceptible to ampicillin, daptomycin, teicoplanin, tigecycline, and vancomycin. Genome sequencing analysis of 32 isolates identified 23 antimicrobial resistance genes (ARGs, mostly plasmid-located) and 2 single nucleotide polymorphisms associated with resistance to 10 antimicrobial classes, showing high concordance with phenotypic resistance. Notably, linezolid resistance in Efm was encoded by the optrA gene, located in plasmids downstream of the fexA gene. Although most Elc lacked virulence factors and genetic determinants of resistance, one isolate carried a plasmid with eight ARGs. This study showed that Elc is more prevalent than Efm in dairy cattle but carries fewer ARGs and virulence genes. However, Elc can carry multi-drug-resistant plasmids like those harbored by Efm and could act as a donor of ARGs for other pathogenic enterococcal species.IMPORTANCEEnterococcus species identification is crucial due to differences in pathogenicity and antibiotic resistance profiles. The failure of traditional methods or whole-genome sequencing-based taxonomic classifiers to distinguish Enterococcus lactis (Elc) from Enterococcus faecium (Efm) results in a biased interpretation of Efm epidemiology. The Efm species-specific real-time PCR assay developed here will help to properly identify Efm (only the formerly known clade A) in future studies. Here, we showed that Elc is prevalent in dairy cattle, and although this species carries fewer genetic determinants of resistance (GDRs) than Enterococcus faecalis (Efs) and Efm, it can carry multi-drug-resistant (MDR) plasmids and could act as a donor of resistance genes for other pathogenic enterococcal species. Although all isolates (Efs, Efm, and Elc) were susceptible to critically or highly important antibiotics like daptomycin, teicoplanin, tigecycline, and vancomycin, the presence of GDRs in MDR-plasmids is a concern since antimicrobials commonly used in livestock could co-select and confer resistance to critically important antimicrobials not used in food-producing animals.

Analysis of Retrospective Laboratory Data on the Burden of Bacterial Pathogens Isolated at the National Veterinary Research Institute Nigeria, 2018-2021

Farm animals harbour bacterial pathogens, which are often viewed as important indicators of animal health and determinants of food safety. To better understand the prevalence and inform treatment, we audited laboratory data at the Bacteriology Laboratory of the NVRI from 2018-2021. Antibiotics were classified into seven basic classes: quinolones, tetracyclines, beta-lactams, aminoglycosides, macrolides, nitrofuran, and cephalosporins. Trends were analysed using a generalised linear model with a log link function for the Poisson distribution, comparing proportions between years with an offset to account for the variability in the total number of organisms per year. Avian (73.18%) samples were higher than any other sample. The major isolates identified were Escherichia. coli, Salmonella spp., Klebsiella spp., Staphylococcus spp., Proteus spp., and Pseudomonas spp. We found that antimicrobial resistance to baseline antibiotics increased over the years. Of particular concern was the increasing resistance of Klebsiella spp. to cephalosporins, an important second-generation antibiotic. This finding underscores the importance of farm animals as reservoirs of pathogens harbouring antimicrobial resistance. Effective biosecurity, surveillance, and frugal use of antibiotics in farms are needed because the health of humans and animals is intricately connected.

Antibiotic Resistance among Gastrointestinal Bacteria in Broilers: A Review Focused on Enterococcus spp. and Escherichia coli

Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. Furthermore, some clonal lineages, such as ST16, ST194, and ST195 in Enterococcus spp. and ST117 in E. coli, have been identified in humans and animals. These data suggest that consuming contaminated animal-source food, direct contact with animals, or environmental exposure can lead to the transmission of antimicrobial-resistant bacteria. Therefore, this review focused on Enterococcus spp. and E. coli from the broiler industry to better understand how antibiotic-resistant strains have emerged, which antibiotic-resistant genes are most common, what clonal lineages are shared between broilers and humans, and their impact through a One Health perspective.

Assessment of antibiotic resistance and biofilm formation of Enterococcus species isolated from different pig farm environments in Poland

BACKGROUND

Enteroccocus spp. are human opportunistic pathogens causing a variety of serious and life-threating infections in humans, including urinary tract infection, endocarditis, skin infection and bacteraemia. Farm animals and direct contact with them are important sources of Enterococcus faecalis (EFA) and Enterococcus faecium (EFM) infections among farmers, veterinarians and individuals working in breeding farms and abattoirs. The spread of antibiotic-resistant strains is one of the most serious public health concerns, as clinicians will be left without therapeutic options for the management of enterococcal infections. The aim of the study was to evaluate the occurrence and antimicrobial susceptibility of EFA and EFM strains isolated from a pig farm environment and to determine the biofilm formation ability of identified Enterococcus spp. strains.

RESULTS

A total numer of 160 enterococcal isolates were obtained from 475 samples collected in total (33.7%). Among them, 110 of genetically different strains were identified and classified into EFA (82; 74.5%) and EFM (28; 25.5%). Genetic similarity analysis revealed the presence of 7 and 1 clusters among the EFA and EFM strains, respectively. The highest percentage of EFA strains (16; 19.5%) was resistant to high concentrations of gentamicin. Among the EFM strains, the most frequent strains were resistant to ampicillin and high concentrations of gentamicin (5 each; 17.9%). Six (7.3%) EFA and 4 (14.3%) EFM strains showed vancomycin resistance (VRE - Vancomycin-Resistant Enterococcus). Linezolid resistance was found in 2 strains of each species. The multiplex PCR analysis was performed to identify the vancomycin resistant enterococci. vanB, vanA and vanD genotypes were detected in 4, 1 and 1 EFA strains, respectively. Four EFA VRE-strains in total, 2 with the vanA and 2 with the vanB genotypes, were identified. The biofilm analysis revealed that all vancomycin-resistant E. faecalis and E. faecium strains demonstrated a higher biofilm-forming capacity, as compared to the susceptible strains. The lowest cell count (5.31 log CFU / cm²) was reisolated from the biofilm produced by the vancomycin-sensitive strain EFM 2. The highest level of re-isolated cells was observed for VRE EFA 25 and VRE EFM 7 strains, for which the number was 7 log CFU / cm² and 6.75 log CFU / cm², respectively.

CONCLUSIONS

The irrational use of antibiotics in agriculture and veterinary practice is considered to be one of the key reasons for the rapid spread of antibiotic resistance among microorganisms. Owing to the fact that piggery environment can be a reservoir of antimicrobial resistance and transmission route of antimicrobial resistance genes from commensal zoonotic bacteria to clinical strains, it is of a great importance to public health to monitor trends in this biological phenomenon.

Determination of Epidemiological Cutoff Values for Antimicrobial Resistance of Enterococcus cecorum

Enterococcus cecorum, a commensal Gram-positive bacterium of the chicken gut, has emerged as a worldwide cause of lameness in poultry, particularly in fast-growing broilers. It is responsible for osteomyelitis, spondylitis, and femoral head necrosis, causing animal suffering, mortality, and antimicrobial use. Research on the antimicrobial resistance of E. cecorum clinical isolates in France is scarce, and epidemiological cutoff (ECOFF) values are unknown. To determine tentative ECOFF (COWT) values for E. cecorum and to investigate the antimicrobial resistance patterns of isolates from mainly French broilers, we tested the susceptibility of a collection of commensal and clinical isolates (n = 208) to 29 antimicrobials by the disc diffusion (DD) method. We also determined the MICs of 23 antimicrobials by the broth microdilution method. To detect chromosomal mutations conferring antimicrobial resistance, we investigated the genomes of 118 E. cecorum isolates obtained mainly from infectious sites and described previously in the literature. We determined the COWT values for more than 20 antimicrobials and identified two chromosomal mutations explaining fluoroquinolone resistance. The DD method appears better suited for detecting E. cecorum antimicrobial resistance. Although tetracycline and erythromycin resistances were persistent in clinical and nonclinical isolates, we found little or no resistance to medically important antimicrobials.

An in-house 45-plex array for the detection of antimicrobial resistance genes in Gram-positive bacteria

Identifying antimicrobial resistance (AMR) genes and determining their occurrence in Gram-positive bacteria provide useful data to understand how resistance can be acquired and maintained in these bacteria. We describe an in-house bead array targeting AMR genes of Gram-positive bacteria and allowing their rapid detection all at once at a reduced cost. A total of 41 AMR probes were designed to target genes frequently associated with resistance to tetracycline, macrolides, lincosamides, streptogramins, pleuromutilins, phenicols, glycopeptides, aminoglycosides, diaminopyrimidines, oxazolidinones and particularly shared among Enterococcus and Staphylococcus spp. A collection of 124 enterococci and 62 staphylococci isolated from healthy livestock animals through the official Belgian AMR monitoring (2018-2020) was studied with this array from which a subsample was further investigated by whole-genome sequencing. The array detected AMR genes associated with phenotypic resistance for 93.0% and 89.2% of the individual resistant phenotypes in enterococci and staphylococci, respectively. Although linezolid is not used in veterinary medicine, linezolid-resistant isolates were detected. These were characterized by the presence of optrA and poxtA, providing cross-resistance to other antibiotics. Rarer, vancomycin resistance was conferred by the vanA or by the vanL cluster. Numerous resistance genes circulating among Enterococcus and Staphylococcus spp. were detected by this array allowing rapid screening of a large strain collection at an affordable cost. Our data stress the importance of interpreting AMR with caution and the complementarity of both phenotyping and genotyping methods. This array is now available to assess other One-Health AMR reservoirs.

Molecular Detection of Some Vancomycin and Virulence Factor Genes in Enterococcus faecium

Multidrug-resistant (MDR) and pathogenic E. faecium is a crisis in healthcare settings. This survey aimed at antibiotic susceptibility profiling and virulence determinants of E. faecium. This study pooled 100 fecal E. faecium isolates identified by phenotypic and molecular tests. Antibiotic susceptibility and ampicillin MIC were determined according to clinical and laboratory standards institute (CLSI) 2017. Moreover, biofilm formation was assayed by a microtiter tissue plate assay. Virulence genes pattern was performed by polymerase chain reaction (PCR) method. Among 460 fecal samples, 100 isolates of E. faecium were identified, among which the highest resistance was related to penicillin (81%), cephalothin (78%), cefazolin (76%), tetracycline and cefepime (69%). In contrast, 83% of them were susceptible to vancomycin. Moreover, four vancomycin-resistant isolates had vancomycin MIC>32µg/mL, and 11 isolates had MIC>8µg/mL. Of 32 ampicillin-resistant isolates, 18 (56%) produced strong biofilm, and 14 isolates (44%) produced moderate biofilm. Among 17 vancomycin-resistant E. faecium (VREfa), 15 (88.23%) isolates produced strong biofilms, and two of them produced moderate-level biofilms, which was significantly higher than susceptible isolates (p=0.0144). The vanA (vancomycin MIC: 16-64µg/mL) and vanB (vancomycin MIC: 8-64µg/mL) genes were detected in twelve and five isolates, respectively. The rate of adhesin genes ace, esp and ebp included 68%, 97% and 82%, respectively. All the VREfa harbored the ace, esp and ebp genes. The antibiotic resistance rate of E. faecium was low. Biofilm formation was significantly different between VREfa and vancomycin-susceptible isolates but not between k9ampicillin-resistant and ampicillin-susceptible isolates. All the VREfa harbored the ace, esp and ebp genes. The virulence adhesin genes were not significantly associated with biofilm formation. Further studies are essential to appreciate better the relation between biofilm formation, drug non-susceptibility and adhesin genes. Keywords: E. faecium, antibiotic resistance, biofilm formation, virulence genes

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Enterococcus faecalis in poultry

Enterococcus faecalis (E. faecalis) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for poultry in a previous scientific opinion. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9 and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR E. faecalis can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (33-66% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2 and 4 (Categories A, B and D; 0-5%, 5-10% and 1-10% probability of meeting the criteria, respectively) and the AHAW Panel is uncertain whether it meets the criteria in Sections 3 and 5 (Categories C and E, 33-66% and 33-66% probability of meeting the criteria, respectively). The animal species to be listed for AMR E. faecalis according to Article 8 criteria are mostly birds of the orders Galliformes and Anseriformes, but also mammals and reptiles can serve as reservoirs.

Antimicrobial resistance in Enterococcus faecium and Enterococcus faecalis isolates of swine origin from eighteen provinces in China

Enterococcus faecium and E. faecalis are important human pathogens and also served as sentinel organisms for monitoring systems of antimicrobial resistance in both animals and humans. In this study, 106 E. faecium and 56 E. faecalis isolates were collected from 61 pig farms in 18 proveinces of China. Antimicrobial susceptibility was determined for 9 clinically important antibiotics and 3 antimicrobial growth promoters. The Enterococcus isolates showed high prevalence of resistance to medically important antibiotics, such as ampicillin (50.9% for E. faecium and 19.6% for E. faecalis), chloramphenicol (24.5% for E. faecium and 41.1% for E. faecalis), erythromycin (83.0% for E. faecium and 91.1% for E. faecalis), tetracycline (79.2% for E. faecium and 100% for E. faecalis), quinupristin/dalfopristin (26.4% for E. faecium) and ciprofloxacin (73.6% for E. faecium and 66.1% for E. faecalis). Resistance to tigecycline, linezolid and vancomycin was very rare. The resistance status of three representative in-feed antibiotics bacitracin, nosiheptide and enramycin was firstly investigated with Enterococcus as indicator bacteria. The Enterococcus isolates showed extremely high frequency of bacitracin resistance (96.7% for E. faecium and 87.8% for E. faecalis), while no nosiheptide and enramycin resistance was observed. Pulsed-field gel electrophoresis (PFGE) analysis showed that a majority of E. faecium and E. faecalis strains showed unrelated profiles, indicating high heterogeneity among the Enterococcus isolates. Our study provided basic data on the antimicrobial resistance of E. faecium and E. faecalis isolates.

Linezolid-resistant (Tn6246::fexB-poxtA) Enterococcus faecium strains colonizing humans and bovines on different continents: similarity without epidemiological link

OBJECTIVES

poxtA is the most recently described gene conferring acquired resistance to linezolid, a relevant antibiotic for treating enterococcal infections. We retrospectively screened for poxtA in diverse enterococci and aimed to characterize its genetic/genomic contexts.

METHODS

poxtA was screened by PCR in 812 enterococci from 458 samples (hospitals/healthy humans/wastewater/animals/retail food) obtained in Portugal/Angola/Tunisia (1996-2019). Antimicrobial susceptibility testing was performed for 13 antibiotics (EUCAST/CLSI). poxtA stability (∼500 generations), transfer (filter mating), clonality (SmaI-PFGE) and location (S1-PFGE/hybridization) were tested. WGS (Illumina-HiSeq) was performed for clonal representatives.

RESULTS

poxtA was detected in Enterococcus faecium from six samples (1.3%): a healthy human (rectal swab) in Porto, Portugal (ST32/2001); four farm cows (milk) in Mateur, Tunisia (ST1058/2015); and a hospitalized patient (faeces) in Matosinhos, Portugal (ST1058/2015). All expressed resistance to linezolid (MIC = 8 mg/L), chloramphenicol, tetracycline and erythromycin, with variable resistance to ciprofloxacin and streptomycin. ST1058-poxtA-carrying isolates from Tunisia and Portugal differed by two SNPs and had similar plasmid content. poxtA, located in an IS1216-flanked Tn6246-like element, co-hybridized with fexB on one or more plasmids per isolate (one to three plasmids of 30-100 kb), was stable after several generations and transferred only from ST1058. ST1058 strains carried resistance/virulence genes (Efmqnr/acm) possibly induced under selective quinolone treatment.

CONCLUSIONS

poxtA has been circulating in Portugal since at least 2001, corresponding to the oldest description worldwide to date. We also extend the reservoir of poxtA to bovines. The similar linezolid-resistant poxtA-carrying strains colonizing humans and livestock on different continents, and without a noticeable relationship, suggests a recent transmission event or convergent evolution of E. faecium populations in different hosts and geographic regions.

A Conjugative MDR pMG1-Like Plasmid Carrying the lsa(E) Gene of Enterococcus faecium With Potential Transmission to Staphylococcus aureus

lsa(E) is a pleuromutilin, lincosamide, and streptogramin A (PLSA phenotype) resistance gene that was first described in S. aureus and was thought to have been transferred from Enterococcus sp. This study aimed to elucidate the prevalence of the lsa(E) gene among E. faecium isolates at a tertiary teaching hospital and to evaluate the transferability of the lsa(E) gene from E. faecium to S. aureus in vitro. A total of 96 E. faecium strains isolated from one hospital in Beijing in 2013 were analysed for quinupristin-dalfopristin (QDA) resistance genes, and multilocus sequence typing (MLST) was performed. The transferability of QDA resistance between ten E. faecium strains and four S. aureus strains was determined by filter mating. Genome sequencing of the transconjugant was performed. A total of 46 E. faecium isolates (46/96, 47.92%) tested positive for lsa(E), while two isolates (2/96, 2.08%) tested positive for lsa(A). Thirty-six lsa(E)-positive strains (36/46, 78.3%) belonged to ST78. Among 40 mating tests, lsa(E) was successfully transferred through one conjugation at a frequency of 1.125 × 10^-7 transconjugants per donor. The QDA resistance of the transconjugant N7435-R3645 was expressed at a higher level (MIC = 16 mg/L) than that of the parent S. aureus strain (MIC = 0.38 mg/L). Next-generation sequencing (NGS) analysis of the transconjugant N7435-R3645 showed that the complete sequence of the lsa(E)-carrying plasmid pN7435-R3645 had a size of 92,396 bp and a G + C content of 33% (accession no. MT022086). The genetic map of pN7435-R3645 had high nucleotide similarity and shared the main open reading frame (ORF) features with two plasmids: E. faecium pMG1 (AB206333.1) and E. faecium LS170308 (CP025078.1). The rep gene of pN7435-R3645 showed 100% identity with that of pMG1, although it did not belong to the rep1-19 family but instead a unique rep family. Multiple antibiotic resistance genes, including lsa(E), aadE and lnu(B), erm(B), ant6-Ia, and lnu(B), were present on the plasmid. In conclusion, an lsa(E)-carrying plasmid that can be transferred by conjugation from E. faecium to S. aureus in vitro was identified. This multidrug resistance (MDR) pMG1-like plasmid may act as a vector in the dissemination of antimicrobial resistance among species.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

From the Farms to the Dining Table: The Distribution and Molecular Characteristics of Antibiotic-Resistant Enterococcus spp. in Intensive Pig Farming in South Africa

Foodborne pathogens, including antibiotic-resistant species, constitute a severe menace to food safety globally, especially food animals. Identifying points of concern that need immediate mitigation measures to prevent these bacteria from reaching households requires a broad understanding of these pathogens’ spread along the food production chain. We investigated the distribution, antibiotic susceptibility, molecular characterization and clonality of Enterococcus spp. in an intensive pig production continuum in South Africa, using the farm-to-fork approach. Enterococcus spp. were isolated from 452 samples obtained along the pig farm-to-fork continuum (farm, transport, abattoir, and retail meat) using the IDEXX Enterolert^®/Quanti-Tray^® 2000 system. Pure colonies were obtained on selective media and confirmed by real-time PCR, targeting genus- and species-specific genes. The susceptibility to antibiotics was determined by the Kirby–Bauer disk diffusion method against 16 antibiotics recommended by the WHO-AGISAR using EUCAST guidelines. Selected antibiotic resistance and virulence genes were detected by real-time PCR. Clonal relatedness between isolates across the continuum was evaluated by REP-PCR. A total of 284 isolates, consisting of 79.2% E. faecalis, 6.7% E. faecium, 2.5% E. casseliflavus, 0.4% E. gallinarum, and 11.2% other Enterococcus spp., were collected along the farm-to-fork continuum. The isolates were most resistant to sulfamethoxazole-trimethoprim (78.8%) and least resistant to levofloxacin (5.6%). No resistance was observed to vancomycin, teicoplanin, tigecycline and linezolid. E. faecium displayed 44.4% resistance to quinupristin-dalfopristin. Also, 78% of the isolates were multidrug-resistant. Phenotypic resistance to tetracycline, aminoglycosides, and macrolides was corroborated by the presence of the tetM, aph(3′)-IIIa, and ermB genes in 99.1%, 96.1%, and 88.3% of the isolates, respectively. The most detected virulence gene was gelE. Clonality revealed that E. faecalis isolates belonged to diverse clones along the continuum with major REP-types, mainly isolates from the same sampling source but different sampling rounds (on the farm). E. faecium isolates revealed a less diverse profile. The results suggest that intensive pig farming could serve as a reservoir of antibiotic-resistant bacteria that could be transmitted to occupationally exposed workers via direct contact with animals or consumers through animal products/food. This highlights the need for more robust guidelines for antibiotic use in intensive farming practices and the necessity of including Enterococcus spp. as an indicator in antibiotic resistance surveillance systems in food animals.

Molecular characteristics of optrA-carrying Enterococcus faecalis from chicken meat in South Korea

The purpose of this study was to identify the genetic environment of optrA gene in linezolid (LZD)-resistant Enterococcus faecalis from chicken meat and to describe the probable mechanism of dissemination of the optrA gene through plasmid or chromosomal integration. Whole genome sequencing and analysis revealed that all 3 E. faecalis isolates confirmed as LZD- and chloramphenicol-resistant carried fexA adjacent to the optrA gene as well as a variety of resistance genes for macrolides, tetracyclines, and aminoglycosides, simultaneously. But, the other genes conferring LZD resistance, cfr and poxtA, were not detected in those strains. Two isolates harboring the optrA gene in their chromosomal DNA showed >99% similarity in arrangement to the transposon Tn6674 and the transposase genes, tnpA, tnpB, and tnpC and were located in the first open reading frame for transposase. One isolate harboring an optrA-carrying plasmid also showed >99% similarity with the previously reported pE439 plasmid but had 2 amino acid changes (Thr96Lys and Tyr160Asp) and a higher minimum inhibitory concentration against LZD of 16 mg/L than that of pE439 (8 mg/L). Mobile genetic elements such as transposons or plasmids flanking the optrA gene conduct a crucial role in the dissemination of antimicrobial resistance genes. Further investigations are required to identify the way by which optrA is integrated into chromosomal DNA and plasmids.

Resistance patterns to C and D antibiotic categories for veterinary use of Campylobacter spp., Escherichia coli and Enterococcus spp. commensal isolates from laying hen farms in Spain during 2018

Antimicrobial Resistance (AMR) is a global threat for human and animal health. Few studies have been carried out on laying hens. The aim of this work was to evaluate the antimicrobial susceptibility of commensal Campylobacter spp., E. coli, and Enterococcus spp. isolates in Spanish laying hens in 2018. Samples were collected from 39 laying hen farms. The microorganisms of interest were isolated and confirmed by PCR. The Minimum Inhibitory Concentration (MIC) to antimicrobials of C and D categories were determined. 195 E. coli, 195 Enterococcus spp. and 25 Campylobacter spp. isolates were obtained. E. coli isolates showed high resistance to D category antimicrobials (sulfamethoxazole 76.41 %, tetracycline 62.05 %, trimethoprim 50.77 %, ampicillin 30.77 %) and lower resistance to C category (azithromycin 30.26 %, gentamicin 12.31 %, chloramphenicol 4.62 %). A 10.26 % of E. coli isolates were susceptible to all antimicrobials tested, Multi Drug Resistance (MDR) to 3 antimicrobial families was found in 23.08 % of the isolates and 13.85 % were MDR to 4 families, being Erythromycin-Sulfamethoxazole-Tetracycline the most common resistance profile (10.77 %). Enterococcus spp. showed very high resistance to D category tetracycline (78.47 %) and C category erythromycin (76.42 %). The 11.79 % of Enterococcus spp. isolates were susceptible to all antimicrobials and 53.33 % were resistant to 2 families, being Erythromycin-Tetracycline the most common AMR profile (51.79 %). Regarding Campylobacter spp., resistance to tetracycline (48 %) was higher than resistance to C category antimicrobials (erythromycin 28 %, streptomycin 24 %, gentamicin 16 %). There was a 52 % sensitivity to all tested antimicrobials and 24 % showed MDR to aminoglycosides, macrolides and tetracyclines (Gentamicin-Streptomycin-Erythromycin-Tetracycline MDR profile). Novel data on AMR in laying hen commensal isolates in Spain was provided. High resistance to several antimicrobials was found, especially to key drugs for the treatment of zoonosis, which represents a public health risk. Better surveillance and careful regulation of antimicrobial use is required in laying hen production.

Association of florfenicol residues with the abundance of oxazolidinone resistance genes in livestock manures

Livestock and poultry manures are major reservoirs of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). Linezolid is a clinical medicine for humans and has never been approved for use in livestock. Interestingly, three linezolid resistance genes (cfr, optrA, and poxtA) have been detected in bacteria of animal origin, arousing public concern. This study investigated the abundance of three ARGs, cfr, optrA, and poxtA, in manures from 157 large-scale farms in China using real-time quantitative polymerase chain reaction. The residual concentrations of linezolid, florfenicol, tiamulin, and valnemulin were determined using ultra-high performance liquid chromatography-tandem mass spectrometry. A total of 140 livestock farms were tested positive for ARGs, and the positive detection rate was 89.17 %. OptrA was the most commonly detected ARG. The diversity and abundance of ARGs were significantly higher in poultry and swine manure than in bovine manure. Redundancy analysis presented a strong association between florfenicol and all the three ARGs targeted in the study, and tiamulin showed a significant correlation with optrA. Our results indicated that the residual concentration of florfenicol had a major effect on the distribution of the three ARGs in livestock manures, and extensive use of florfenicol may lead to the production of linezolid resistance genes.

Characteristics of linezolid-resistant Enterococcus faecalis isolates from broiler breeder farms

Linezolid is an oxazolidinone class antibiotic used for treatment infections caused by various multidrug-resistant gram-positive pathogens including enterococci. However, recently, linezolid-resistant isolates in animals are considered as a human health hazard. In a broiler operation system, antimicrobial resistance can be transferred to the environment and commercial broiler via the fecal-oral route. Therefore, this study was conducted to investigate the prevalence and characteristics of linezolid-resistant Enterococcus faecalis (E. faecalis) from broiler parent stock in a broiler operation system. Among 297 E. faecalis isolates from 85 flocks in 8 broiler breeder farms, the prevalence of chloramphenicol- and linezolid-resistant isolates was 0 to 12.1% and 0 to 8.0%, respectively; however, there were no significant differences between farms. Therefore, a total of 14 (4.7%) chloramphenicol- and/or linezolid-resistant E. faecalis showed resistance to 7 or more antimicrobial classes. The drug-resistance gene optrA, which can confer resistance to linezolid, tedizolid, and phenicols, was found in 8 (2.69%) isolates, and 7 (2.36%) of the 8 optrA-positive isolates co-carried the phenicol exporter gene fexA. However, E. faecalis isolates from 3 of 8 broiler breeder farms only carried the optrA and/or fexA genes. As linezolid is one of the last antimicrobial treatments of choice for multidrug-resistant gram-positive pathogens including E. faecalis, the presence of antibiotic-resistant E. faecalis in broiler breeder farms should be monitored to prevent the introduction of linezolid-resistant strains to the food chain.

Detection of vancomycin-resistant enterococci in samples from broiler flocks and houses in Turkey

Vancomycin-resistant enterococcus (VRE) is a global threat to public health. Knowledge about the occurrence of vanA-carrying enterococci in broiler and environmental samples is important as antibiotic resistance can be transferred to human bacteria. The aim of this study was to investigate the presence of VRE in broiler cloacal and environmental (house) samples and to genotype the isolates. In this study, 350 swabs were collected from broiler farms. All samples were plated onto enterococcus selective agar containing 6 mg/L vancomycin and 64 mg/L ceftazidime. Minimum inhibitory concentration (MIC) values were determined for vancomycin and teicoplanin. Vancomycin-resistant Enterococcus faecium (VREfm) was isolated from 6 out of 300 (2%) broiler cloacal samples and 13 out of 50 (26%) house samples. All E. faecium isolates had vanA genes. All VREfm isolates (19 isolates) were confirmed to be 95% similar to each other. In conclusion, although 20 years have passed since the ban on avoparcin in Turkey, the present study shows that VREfm isolates are still present in broiler production and especially in broiler houses, and most importantly, a major VREfm clone was isolated from broiler cloacal and house samples.

Antimicrobial Resistance, Virulence Genes, and Biofilm Formation Capacity Among Enterococcus species From Yaks in Aba Tibetan Autonomous Prefecture, China

Yaks provide necessities such as meat and milk for Tibetans living at high altitudes on and around the Qinghai-Tibetan Plateau. Enterococci are ubiquitous members of the animal gut microbiota that can cause biofilm-associated opportunistic infections. Meanwhile, multidrug-resistant Enterococcus also poses a serious threat to public health. This study aims to characterize antibiotic resistance, virulence genes, and biofilm formation of enterococci from yaks. From April 2018 to July 2019, we collected 395 fecal samples of yaks in Aba Tibetan Autonomous Prefecture, China. Enterococci isolated from the samples were identified and classified according to the 16S rDNA sequence. The antibiotic resistance of each isolate was detected according to the Kirby-Bauer disk diffusion method, and antibiotic resistance genes were detected by polymerase chain reaction (PCR) and sequencing. Enterococcal biofilms were assessed using standard procedures. Different virulence genes were detected by PCR and sequencing. In total, 381 enterococci strains were recovered, with Enterococcus faecalis (41.99%) and Enterococcus faecium (37.80%) being the predominant species. Many isolates were multidrug- resistant (60.37%) and showed a high resistance rate to rifampicin (64.30%) and tetracycline (61.54%). We also detected various antimicrobial resistance (AMR) genes in the tested strains. The E. faecalis strains had higher frequency of biofilm formation and virulence genes than other enterococcal species. This is the first report that shows yaks are repositories for drug-resistant enterococci with virulent determinants and biofilms that may spread into humans and to environment. This study also provides useful data suggesting that enterococci may pose a potential health risk to yaks. Therefore, active surveillance of AMR and pathogenesis in enterococci from yaks is urgently warranted.

Rapid Identification of Mycoplasma bovis Strains from Bovine Bronchoalveolar Lavage Fluid with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry after Enrichment Procedure

Mycoplasma bovis is a leading cause of pneumonia in modern calf rearing. Fast identification is essential to ensure appropriate antimicrobial therapy. Therefore, the objective of this study was to develop a protocol to identify M. bovis from bronchoalveolar lavage fluid (BALf) with matrix-assisted laser desorption ionization-time of flight mass spectrometry MALDI-TOF MS and to determine the diagnostic accuracy in comparison with other techniques. BALf was obtained from 104 cattle, and the presence of M. bovis was determined in the following three ways: (i) rapid identification of M. bovis with MALDI-TOF MS (RIMM) (BALf was enriched and after 24, 48, and 72 h of incubation and was analyzed using MALDI-TOF MS), (ii) triplex real-time PCR for M. bovis, Mycoplasma bovirhinis, and Mycoplasma dispar, and (iii) 10-day incubation on selective-indicative agar. The diagnostic accuracy of the three tests was determined with Bayesian latent class modeling (BLCM). After 24 h of enrichment, M. bovis was identified with MALDI-TOF MS in 3 out of 104 BALf samples. After 48 and 72 h of enrichment, 32/104 and 38/100 samples, respectively, were M. bovis positive. Lipase-positive Mycoplasma-like colonies were seen in 28 of 104 samples. Real-time PCR resulted in 28/104 positive and 12/104 doubtful results for M. bovis The BLCM showed a sensitivity (Se) and specificity (Sp) of 86.6% (95% credible interval [CI], 69.4% to 97.6%) and 86.4% (CI, 76.1 to 93.8) for RIMM. For real-time PCR, Se was 94.8% (CI, 89.9 to 97.9) and Sp was 88.9% (CI, 78.0 to 97.4). For selective-indicative agar, Se and Sp were 70.5% (CI, 52.1 to 87.1) and 93.9% (CI, 85.9 to 98.4), respectively. These results suggest that rapid identification of M. bovis with MALDI-TOF MS after an enrichment procedure is a promising test for routine diagnostics in veterinary laboratories.

Draft Genome Sequences of Three Enterococcus casseliflavus Strains Isolated from the Urine of Healthy Bovine Heifers (Gyr Breed)

Enterococcus casseliflavus is a commensal bacterium present in the intestinal microbiota of different animals. Previous studies have found that strains isolated from livestock are often resistant to many different antibiotics. Here, we present three E. casseliflavus strains, UFMG-H7, UFMG-H8, and UFMG-H9, isolated from urine collected from healthy dairy heifers in Brazil.

Enterococcus casseliflavus is a commensal bacterium present in the intestinal microbiota of different animals. Previous studies have found that strains isolated from livestock are often resistant to many different antibiotics. Here, we present three E. casseliflavus strains, UFMG-H7, UFMG-H8, and UFMG-H9, isolated from urine collected from healthy dairy heifers in Brazil.

Antibiotic Resistance and Virulence Traits in Vancomycin-Resistant Enterococci (VRE) and Extended-Spectrum β-Lactamase/AmpC-producing (ESBL/AmpC) Enterobacteriaceae from Humans and Pets

BACKGROUND

We investigated the virulence factors, genes, antibiotic resistance patterns, and genotypes (VRE and ESBL/AmpC) production in Enterococci and Enterobacteriaceae strains isolated from fecal samples of humans, dogs, and cats.

METHODS

A total of 100 fecal samples from 50 humans, 25 dogs, and 25 cats were used in the study. MICs of nine antimicrobials were determined using the broth microdilution method. Polymerase chain reaction was used for the detection of genes responsible for antibiotic resistance (VRE and ESBL/AmpC) and virulence genes both in Enterococcus species, such as cytolysin (cylA, cylB, cylM), aggregation substance (agg), gelatinase (gelE), enterococcal surface protein (esp), cell wall adhesins (efaAfs and efaAfm), and in Enterobacteriaceae, such as cytolysin (hemolysin) and gelatinase production (afa, cdt, cnf1, hlyA, iutA, papC, sfa).

RESULTS

Enterococcus faecium was the most prevalent species in humans and cats, whereas Enterococcus faecalis was the species isolated in the remaining samples. A total of 200 Enterobacteriaceae strains were also detected, mainly from humans, and Escherichia coli was the most frequently isolated species in all types of samples. In the Enterococcus spp, the highest percentages of resistance for ampicillin, amoxicillin/clavulanate, erythromycin, tetracycline, ciprofloxacin, teicoplanin, and vancomycin were detected in cat isolates (41.6%, 52.8%, 38.9%, 23.6%, 62.5%, 20.8%, and 23.6% respectively), and in E. coli, a higher rate of resistance to cefotaxime and ceftazidime emerged in cat and dog samples, if compared with humans (75.4% and 66.0%, 80.0% and 71.4%, and 32.0% and 27.2%, respectively). Regarding the total number of enterococci, 5% and 3.4% of the strains were vancomycin and teicoplanin resistant, and the vancomycin resistance (van A) gene has been detected in all samples by PCR amplification. All the Enterobacteriaceae strains were confirmed as ESBL producers by PCR and sequencing, and the most frequent ESBL genes in E.coli strains from humans and pet samples were blaCTX-M-1 and blaCTX-M-15.

CONCLUSIONS

Our results provide evidence that one or more virulence factors were present in both genera, underlining again the ability of pet strains to act as pathogens.

Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes

Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we lack a comprehensive analysis of human and animal optrA-LREfs strains. To assess if optrA is dispersed in isolates with varied genetic backgrounds or with common genetic features, we investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and optrA-containing platforms of 27 publicly available optrA-positive E. faecalis genomes from different hosts in seven countries. At the genome-level analysis, an in-house database with 64 virulence genes was tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera from Firmicutes. Phylogenies of core and accessory genomes were not congruent, and at least PAI-associated and prophage genes contribute to such differences. Epidemiologically unrelated clones (ST21, ST476-like and ST489) obtained from human clinical and animal hosts in different continents over eight years (2010–2017) could be phylogenetically related (3–126 SNPs difference). optrA was located on the chromosome within a Tn6674-like element (n=10) or on medium-size plasmids (30–60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of optrA was generally identical in chromosomal (Tn6674) or plasmid (impB-fexA-optrA) backbones. Tn6674 was always inserted into the same ∆radC integration site and embedded in a 32 kb chromosomal platform common to strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012–2017. This platform is conserved among hundreds of E. faecalis genomes and proposed as a chromosomal hotspot for optrA integration. The finding of optrA in strains sharing common adaptive features and genetic backgrounds across different hosts and countries suggests the occurrence of common and independent genetic events occurring in distant regions and might explain the easy de novo generation of optrA-positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious impact on the efficacy of linezolid for the treatment of Gram-positive infections.

Urinary TMAO Levels Are Associated with the Taxonomic Composition of the Gut Microbiota and with the Choline TMA-Lyase Gene (cutC) Harbored by Enterobacteriaceae

Gut microbiota metabolization of dietary choline may promote atherosclerosis through trimethylamine (TMA), which is rapidly absorbed and converted in the liver to proatherogenic trimethylamine-N-oxide (TMAO). The aim of this study was to verify whether TMAO urinary levels may be associated with the fecal relative abundance of specific bacterial taxa and the bacterial choline TMA-lyase gene cutC. The analysis of sequences available in GenBank grouped the cutC gene into two main clusters, cut-Dd and cut-Kp. A quantitative real-time polymerase chain reaction (qPCR) protocol was developed to quantify cutC and was used with DNA isolated from three fecal samples collected weekly over the course of three consecutive weeks from 16 healthy adults. The same DNA was used for 16S rRNA gene profiling. Concomitantly, urine was used to quantify TMAO by ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS). All samples were positive for cutC and TMAO. Correlation analysis showed that the cut-Kp gene cluster was significantly associated with Enterobacteriaceae. Linear mixed models revealed that urinary TMAO levels may be predicted by fecal cut-Kp and by 23 operational taxonomic units (OTUs). Most of the OTUs significantly associated with TMAO were also significantly associated with cut-Kp, confirming the possible relationship between these two factors. In conclusion, this preliminary method-development study suggests the existence of a relationship between TMAO excreted in urine, specific fecal bacterial OTUs, and a cutC subgroup ascribable to the choline-TMA conversion enzymes of Enterobacteriaceae.

New antimicrobial susceptibility data from monitoring of Mycoplasma bovis isolated in Europe

Mycoplasma bovis is an important respiratory pathogen of cattle across Europe and is included in the MycoPath pan-European antimicrobial susceptibility monitoring programme. M. bovis strains (232) were isolated from cattle, not recently treated with antimicrobials, at diverse geographical locations in France, Great Britain, Hungary, Italy and Spain during 2014 to 2016. Only one isolate per farm and per outbreak was retained. For each isolate, the MICs of ten antimicrobials were determined in a central laboratory using a broth microdilution method with modified Eaton's medium and incubation at 35 °C ± 1 °C for 24 ± 6 h. MIC₅₀/MIC₉₀ (mg/L) values for the 232 strains were: danofloxacin 0.25/1; enrofloxacin 0.5/8; marbofloxacin 1/4; gamithromycin >64/>64; spiramycin 8/16; tilmicosin >64/>64; tulathromycin >64/>64; tylosin 64/>64; florfenicol 4/8; oxytetracycline 8/32. Minor between-country differences in the MIC₉₀ values were observed for the fluoroquinolones, spiramycin and oxytetracycline, whilst the MIC values for the other compounds were similar. Spain and Italy had the higher MIC₉₀ values for the fluoroquinolones. Compared with the 2010-2012 study (156 isolates) results are similar, with an overall MIC₅₀ increase of at most one doubling dilution for enrofloxacin, spiramycin, tylosin, florfenicol and oxytetracycline. In contrast, the MIC₉₀ value for oxytetracycline decreased from >64 to 32 mg/L. Standardized laboratory methods and interpretive criteria for MIC testing of veterinary mycoplasmas are clearly needed; there are currently no clinical breakpoints available to facilitate data interpretation and correlation of MICs with in vivo efficacy.

Genomic, Antimicrobial Resistance, and Public Health Insights into Enterococcus spp. from Australian Chickens

Due to Australia's management of antimicrobial use in poultry, particularly the discontinued use of avoparcin for nearly 20 years, it is hypothesized that vancomycin-resistant enterococci associated with human disease are not derived from poultry isolates. This study evaluated antimicrobial resistance (AMR) of five enterococcal species isolated from Australian meat chickens, genomic features of Enterococcus faecium and Enterococcus faecalis, and the phylogenetic relationship of the poultry-derived E. faecium with isolates from human sepsis cases. All enterococcal isolates from chicken ceca were subjected to antimicrobial susceptibility testing. E. faecium and E. faecalis underwent whole-genome sequencing. E. faecium was compared at the core genome level to a collection of human isolates (n = 677) obtained from cases of sepsis over a 2-year period spanning 2015 to 2016. Overall, 205 enterococci were isolated consisting of five different species. E. faecium was the most frequently isolated species (37.6%), followed by E. durans (29.7%), E. faecalis (20%), E. hirae (12.2%), and E. gallinarum (0.5%). All isolates were susceptible to vancomycin and gentamicin, while one isolate was linezolid resistant (MIC 16 mg/liter). Core genome analysis of the E. faecium demonstrated two clades consisting predominantly of human or chicken isolates in each clade, with minimal overlap. Principal component analysis for total gene content revealed three clusters comprised of vanA-positive, vanB-positive, and both vanA- and vanB-negative E. faecium populations. The results of this study provide strong evidence that Australian chicken E. faecium isolates are unlikely to be precursor strains to the currently circulating vancomycin-resistant strains being isolated in Australian hospitals.