Linezolid- and Multidrug-Resistant Enterococci in Raw Commercial Dog Food, Europe, 2019-2020.
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ABSTRACT:
SUBMITTER: Freitas AR
PROVIDER: S-EPMC8314808 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The significant increase of the linezolid-resistant enterococci (LRE) has been observed in Polish hospitals since 2012 and our study aimed at elucidating the possible reasons for this phenomenon. Polish LRE isolates were analysed by multilocus-sequence typing (MLST) and multiple locus variable-number tandem repeat (VNTR) analysis (MLVA), polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP) to establish clonal relatedness and mechanism of linezolid resistance, respectively. Fifty analysed LRE (2008-2015) included mostly Enterococcus faecium (82%) and Enterococcus faecalis (16%). Enterococcus faecium belonged to the hospital-adapted lineages 17/18 and 78, while E. faecalis isolates represented ST6, a hospital-associated type, and ST116, found in both humans and food-production animals. The G2576T 23S rRNA mutation was the most frequent (94%) mechanism of linezolid/tedizolid resistance of LRE. None of the isolates carried the plasmid-associated gene of Cfr methyltransferase, whereas optrA, encoding the ABC-type drug transporter, was identified in two E. faecalis isolates. In these isolates, optrA was located on a plasmid, transferable to both E. faecium and E. faecalis, whose partial (36.3 kb) sequence was 100% identical to the pE394 plasmid, identified previously in China in both clinical and farm animal isolates. The optrA-E. faecium transconjugant displayed a significant growth deficiency, in contrast to the optrA-E. faecalis. Our study indicates the role of mutation acquisition by hospital-adapted clones of enterococci as a major driver of increasing resistance to linezolid and tedizolid. Transferability and apparent lack of a biological cost of resistance suggest that E. faecalis may be a natural reservoir of optrA, an emerging mechanism of oxazolidinone resistance.
| S-EPMC5495842 | biostudies-literature
Project description:BackgroundLinezolid is an alternative treatment option for infections with multidrug-resistant Gram-positive bacteria including vancomycin-resistant enterococci. Some countries report an increasing number of isolates with resistance to linezolid. The recent publication of the Commission for Hospital Hygiene in Germany on enterococci/VRE recommends screening for linezolid-resistant enterococci (LRE). However, a suitable selective medium or a genetic test is not available. Our aim was to establish a selective screening agar for LRE detection and validate its application with a comprehensive collection of clinical LRE and linezolid-susceptible enterococci.MethodsWe decided to combine the selective power of an enterococcal screening agar with a supplementation of linezolid. Several rounds of analyses with reference, control and test strains and under varying linezolid concentrations of a wider and a smaller range were investigated and assessed. The collection of linezolid-resistant enterococcal control strains included isolates with different resistance mechanisms (23S rDNA mutations, cfr(B), optrA, poxtA). Finally, we validated our LRE screening agar with 400 samples sent to our National Reference Centre in 2019.ResultsSeveral rounds of pre-tests and confirmatory analyses favored Enterococcosel® Agar supplemented with a concentration of 2?mg/L linezolid. A 48?h incubation period was essential for accurate identification of LRE strains. Performance of the LRE screening agar revealed a sensitivity of 96.6% and a specificity of 94.4%.ConclusionsHere we describe preparation of a suitable screening agar and a procedure to identify LRE isolates with high accuracy.
| S-EPMC6929501 | biostudies-literature
Project description:The objective of this study was to investigate an apparent increase in linezolid-nonsusceptible staphylococci and enterococci following a laboratory change in antimicrobial susceptibility testing from disk diffusion to an automated susceptibility testing system. Isolates with nonsusceptible results (n = 27) from Vitek2 were subjected to a battery of confirmatory testing which included disk diffusion, Microscan broth microdilution, Clinical and Laboratory Standards Institute (CLSI) reference broth microdilution, gradient diffusion (Etest), 23S rRNA gene sequencing, and cfr PCR. Our results show that there is poor correlation between methods and that only 70 to 75% of isolates were confirmed as linezolid resistant with alternative phenotypic testing methods (disk diffusion, Microscan broth microdilution, CLSI broth microdilution, and Etest). 23S rRNA gene sequencing identified mutations previously associated with linezolid resistance in 16 (59.3%) isolates, and the cfr gene was detected in 3 (11.1%) isolates. Mutations located at positions 2576 and 2534 of the 23S rRNA gene were most common. In addition, two previously undescribed variants (at positions 2083 and 2345 of the 23S rRNA gene) were also identified and may contribute to linezolid resistance.
| S-EPMC4844726 | biostudies-literature
Project description:BackgroundBrazil is a low- to medium-income country and has the second largest pet food market in the world with 8% of world pet food consumption. The lowest-income social class spends around 17% of their domestic budget on pet food and other items related to pets. Consumers are frequently misled by advertising as there is no precise information about the main sources of protein, carbohydrates and fat in the labels, and the Brazilian pet food industry can legally claim that their products contain certain items like salmon or beef even if they use just a flavoring compound.MethodsThe stable isotope methodology compares the stable isotope ratios of carbon (13C/12C) and nitrogen (15N/14N) between source and product. The 13C/12C ratio of a specific product (e.g., dog food) reveals the proportions of C4 (maize) and C3 (soybean, rice and wheat) plants in that product and the 15N/14N ratio reveals the proportion of the compounds derived from animals. With this isotopic data, we used MixSIAR, a Bayesian stable isotope-mixing model, to estimate the proportion of maize, grains, poultry and beef in dog food.ResultsThe δ13C values of dry dog food ranged from -24.2‰ to -12.8‰, with an average (± standard-deviation) of -17.1‰ ± 2.8‰. The δ13C values of wet pet food ranged from -25.4‰ to -16.9‰, with an average (± standard-deviation) of -21.2‰ ± 2.4‰, which was significantly lower (p < 0.01). The δ15N values of the dry and wet food ranged from 1.7‰ to 4.2‰, and from 0.5‰ to 5.5‰, respectively. The average δ15N values of dry food (2.9‰ ± 0.5‰) was not higher than the wet food (2.6‰ ± 1.3‰) (p > 0.01). The output of the MixSIAR showed a low proportion of bovine products in dry dog food samples. On the other hand, poultry was obviously the dominant ingredient present in most of the samples. Maize was the second dominant ingredient. Wet and dry dog food showed similar isotopic analysis results. The only difference was a lower proportion of maize and higher proportion of grains in wet dog food.DiscussionThe main finding is that dog food in Brazil is mostly made of approximately 60% (ranging from 32% to 86%) animal-based and 40% (ranging from 14% to 67%) plant-based products. Poultry and maize are the main ingredients. Poultry is added as a by-product or meal, which avoids competition between dogs and humans for meat products, while they can compete for maize. On the other hand, a large proportion of plant-based products in dog food decreases the energy and environmental footprint, since plant-based food products tend to be less harmful compared to animal-based products. Labels can mislead consumers by showing pictures of items that are not necessarily part of the product composition and by not showing the detailed information on the proportion of each ingredient. This information would allow customers to make their own choices considering their pet's nutrition, the competition between animals and humans for resources and environmental sustainability.
| S-EPMC6387582 | biostudies-literature
Project description:BackgroundLinezolid is a critically important antibiotic used to treat human infections caused by MRSA and VRE. While linezolid is not licensed for food-producing animals, linezolid-resistant (LR) isolates have been reported in European countries, including Belgium.ObjectivesTo: (i) assess LR occurrence in staphylococci and enterococci isolated from different Belgian food-producing animals in 2019 through selective monitoring; and (ii) investigate the genomes and relatedness of these isolates.MethodsFaecal samples (n = 1325) and nasal swab samples (n = 148) were analysed with a protocol designed to select LR bacteria, including a 44-48 h incubation period. The presence of LR chromosomal mutations, transferable LR genes and their genetic organizations and other resistance genes, as well as LR isolate relatedness (from this study and the NCBI database) were assessed through WGS.ResultsThe LR rate differed widely between animal host species, with the highest rates occurring in nasal samples from pigs and sows (25.7% and 20.5%, respectively) and faecal samples from veal calves (16.4%). WGS results showed that LR determinants are present in a large diversity of isolates circulating in the agricultural sector, with some isolates closely related to human isolates, posing a human health risk.ConclusionsLR dedicated monitoring with WGS analysis could help to better understand the spread of LR. Cross-selection of LR transferable genes through other antibiotic use should be considered in future action plans aimed at combatting antimicrobial resistance and in future objectives for the rational use of antibiotics in a One Health perspective.
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Project description:A 1-year 11-month intact female Alaskan Malamute fed a raw food diet was referred to the Queen Mother Hospital for Animals for further investigation of hyporexia and increased hepatobiliary enzyme activities. Clinicopathological and imaging findings were consistent with cholangiohepatitis, with coccidial zoites identified on bile cytology. Polymerase chain reaction and amplicon sequencing from the bile identified Hammondia heydorni, a Sarcocytid coccidial protozoa with an obligate 2-host life cycle. The dog was treated with clindamycin, marbofloxacin, ursodeoxycholic acid (UDCA) and S-adenosylmethionine/silybin with complete clinical and biochemical resolution documented after 6 weeks. Infection with Hammondia spp. should be considered in patients receiving raw food diets in which coccidial zoites are identified in the bile, but the pathogenic potential of this organism is unknown and the possibility of its presence as a commensal cannot be discounted.
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Project description:In order to identify mechanisms of drug resistance to HER2-targeted therapy, we performed cDNA microarray analysis on drug naiive BT474 and drug resistant BT474 cells treated with lapatinib for 0, 10, and 20 hrs.
2020-04-14 | GSE136304 | GEO
Project description:As at 27 January 2020, 42 novel coronavirus (2019-nCoV) cases were confirmed outside China. We estimate the risk of case importation to Europe from affected areas in China via air travel. We consider travel restrictions in place, three reported cases in France, one in Germany. Estimated risk in Europe remains high. The United Kingdom, Germany and France are at highest risk. Importation from Beijing and Shanghai would lead to higher and widespread risk for Europe.
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Project description:Clustered, regularly interspaced short palindromic repeats (CRISPR) provide bacteria and archaea with sequence-specific, acquired defense against plasmids and phage. Because mobile elements constitute up to 25% of the genome of multidrug-resistant (MDR) enterococci, it was of interest to examine the codistribution of CRISPR and acquired antibiotic resistance in enterococcal lineages. A database was built from 16 Enterococcus faecalis draft genome sequences to identify commonalities and polymorphisms in the location and content of CRISPR loci. With this data set, we were able to detect identities between CRISPR spacers and sequences from mobile elements, including pheromone-responsive plasmids and phage, suggesting that CRISPR regulates the flux of these elements through the E. faecalis species. Based on conserved locations of CRISPR and CRISPR-cas loci and the discovery of a new CRISPR locus with associated functional genes, CRISPR3-cas, we screened additional E. faecalis strains for CRISPR content, including isolates predating the use of antibiotics. We found a highly significant inverse correlation between the presence of a CRISPR-cas locus and acquired antibiotic resistance in E. faecalis, and examination of an additional eight E. faecium genomes yielded similar results for that species. A mechanism for CRISPR-cas loss in E. faecalis was identified. The inverse relationship between CRISPR-cas and antibiotic resistance suggests that antibiotic use inadvertently selects for enterococcal strains with compromised genome defense.
| S-EPMC2975353 | biostudies-literature
Project description:Linezolid was approved in 2000 for treatment of gram-positive coccal infections. We performed a case-control study during a hospital outbreak of linezolid-resistant enterococci (LRE) infections, comparing cases of LRE infection (cases) with linezolid-sensitive enterococci infections (controls). Nasal and perirectal swab samples were obtained from all patients in a 1-day point-prevalence survey. We examined antimicrobial drug use and calculated the defined daily dose of linezolid per 1,000 patient-days. Fifteen LRE cases were identified (13 Enterococcus faecalis and 2 E. faecium); 7 were vancomycin-resistant. Compared with controls, case-patients had increased in-hospital mortality rates and lengths of stay. Multivariate analysis identified independent predictors of LRE infection: prior cultures positive for methicillin-resistant Staphylococcus aureus (adjusted odds ratio [AOR] 27), hospitalization duration before index culture (AOR 1.1 per day), and duration of preceding linezolid therapy (AOR 1.1 per day). Linezolid exposure and patient-to-patient transmission appear to be responsible for LRE infections, an important emeraina hospital problem.
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