Dataset Information

Coexistence of the Oxazolidinone Resistance-Associated Genes cfr and optrA in Enterococcus faecalis From a Healthy Piglet in Brazil.

ABSTRACT: Oxazolidinones are one of the most important antimicrobials potentially active against glycopeptide- and ?-lactam-resistant Gram-positive pathogens. Linezolid-the first oxazolidinone to be approved for clinical use in 2000 by the US Food and Drug Administration-and the newer molecule in the class, tedizolid, inhibit protein synthesis by suppressing the formation of the 70S ribosomal complex in bacteria. Over the past two decades, transferable oxazolidinone resistance genes, in particular cfr and optrA, have been identified in Firmicutes isolated from healthcare-related infections, livestock, and the environment. Our goals in this study were to investigate the genetic contexts and the transferability of the cfr and optrA genes and examine genomic features, such as antimicrobial resistance genes, plasmid incompatibility types, and CRISPR-Cas defenses of a linezolid-resistant Enterococcus faecalis isolated in feces from a healthy pig during an antimicrobial surveillance program for animal production in Brazil. The cfr gene was found to be integrated into a transposon-like structure of 7,759 nt flanked by IS1216E and capable of excising and circularizing, distinguishing it from known genetic contexts for cfr in Enterococcus spp., while optrA was inserted into an Inc18 broad host-range plasmid of >58 kb. Conjugal transfer of cfr and optrA was shown by filter mating. The coexistence of cfr and optrA in an E. faecalis isolated from a healthy nursery pig highlights the need for monitoring the use of antibiotics in the Brazilian swine production system for controlling spread and proliferation of antibiotic resistance.

SUBMITTER: Almeida LM

PROVIDER: S-EPMC7546817 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Coexistence of the Oxazolidinone Resistance-Associated Genes cfr and optrA in Enterococcus faecalis From a Healthy Piglet in Brazil.

Almeida Lara M LM Gaca Anthony A Bispo Paulo M PM Lebreton François F Saavedra Jose T JT Silva Rafael A RA Basílio-Júnior Irinaldo D ID Zorzi Felipe M FM Filsner Pedro H PH Moreno Andrea M AM Gilmore Michael S MS

Frontiers in public health 20200924

Oxazolidinones are one of the most important antimicrobials potentially active against glycopeptide- and β-lactam-resistant Gram-positive pathogens. Linezolid-the first oxazolidinone to be approved for clinical use in 2000 by the US Food and Drug Administration-and the newer molecule in the class, tedizolid, inhibit protein synthesis by suppressing the formation of the 70S ribosomal complex in bacteria. Over the past two decades, transferable oxazolidinone resistance genes, in particular cfr< ...[more]

PMID: 33102417

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Project description:Abstract Background Oxazolidinones are relatively novel antibiotics used exclusively in human medicine as last resort drugs for resistant pathogens like MRSA, vancomycin-resistant enterococci and penicillin-resistant Streptococcus pneumoniae. However, in the last two decades, oxazolidinone resistance genes cfr and optrA have been sporadically reported worldwide in Staphylococcus spp. of livestock origin.1 These genes can be chromosomal, but they are often transferable through mobile genetic elements, especially plasmids.2 In Italy, they have been recently detected in enterococci of swine origin.3 Objectives To uncover the presence of cfr and optrA genes in methicillin-resistant CoNS (MRCoNS) originating from swine nasal swabs sampled in a high farm-density area of northwestern Italy. Healthy pigs were sampled from three productive stages (finishing, weaners and sows). After isolating pure cultures, selected staphylococci (n = 27), resulted methicillin-resistant from previous mecA identification, were phenotypically tested through Kirby–Bauer disc diffusion method for the antibiotics clindamycin, doxycycline, erythromycin, enrofloxacin, florfenicol, gentamicin, linezolid, tetracycline, tiamulin and trimethoprim/sulfamethoxazole (EUCAST v.11.0 guidelines for linezolid disc, CLSI VET08 for the other antibiotics). MIC through Etest (Liofilchem®, Roseto degli Abbruzzi, Teramo, Italy) was used for the antibiotic ceftaroline. Results All the chosen MRCoNS were MDR (MDR CoNS), as they were phenotypically resistant to more than three antibiotic classes. No strain was positive for ceftaroline resistance. Since linezolid resistance was recovered in six samples, we decided to perform PCR for the cfr gene (746 bp), which was detected in Staphylococcus sciuri from a piglet (GenBank accession number OL412394), and optrA (1395 bp), which was recovered in Staphylococcus pasteuri from a finisher, S. sciuri from a sow and Staphylococcus cohnii from a weaner (GenBank accession numbers OM165030, OM165031 and OM165032). Sanger sequencing confirmed PCR result for cfr, with 100% identity with the cfr gene detected from a clinical Italian isolate of MRSA (MH746818), and for optrA gene, which had 100% identity with the optrA previously found in a swine Italian Enterococcus faecium strain (MT723958). As far as we know, this is the first time that a cfr gene has been detected in S. sciuri from a nasal sample of animal origin in Italy. Furthermore, optrA was never detected in S. pasteuri and S. cohnii strains. Conclusions These results are relevant from a One Health perspective, as they underline the need for oxazolidinone resistance monitoring, not only in human medicine, but also at farm level. In this way, it will be easier to prevent the dissemination of this resistance to human community and hospitals, where oxazolidinones are considered last-resort antibiotics. Furthermore, they remind the importance of surveillance of antibiotic usage in pigs, as cfr and optrA resistance in staphylococci can be elicited using certain antibiotics, like phenicols, due to cross-resistance to this antibiotic class.

Project description:The aim of this study was to investigate the transferability of acquired linezolid resistance genes and associated mobile genetic elements in an Enterococcus faecalis isolate QZ076, cocarrying optrA, cfr, cfr(D), and poxtA2 genes. MICs were determined by broth microdilution. Whole-genome sequencing (WGS) was performed using the Illumina and Nanopore platforms. The transfer of linezolid resistance genes was investigated by conjugation, using E. faecalis JH2-2 and clinical methicillin-resistant Staphylococcus aureus (MRSA) 109 as recipients. E. faecalis QZ076 harbors four plasmids, designated pQZ076-1 to pQZ076-4, with optrA located in the chromosomal DNA. The gene cfr was located on a novel pseudocompound transposon, designated Tn7515, integrated into the 65,961-bp pCF10-like pheromone-responsive conjugative plasmid pQZ076-1. Tn7515 generated 8-bp direct target duplications (5'-GATACGTA-3'). The genes cfr(D) and poxtA2 were colocated on the 16,397-bp mobilizable broad-host-range Inc18 plasmid pQZ076-4. The cfr-carrying plasmid pQZ076-1 could transfer from E. faecalis QZ076 to E. faecalis JH2-2, along with the cfr(D)- and poxtA2-cocarrying plasmid pQZ076-4, conferring the corresponding resistant phenotype to the recipient. Moreover, pQZ076-4 could also transfer to MRSA 109. To the best of our knowledge, this study presented the first report of four acquired linezolid resistance genes [optrA, cfr, cfr(D), and poxtA2] being simultaneously present in the same E. faecalis isolate. The location of the cfr gene on a pseudocompound transposon in a pheromone-responsive conjugative plasmid will accelerate its rapid dissemination. In addition, the cfr-carrying pheromone-responsive conjugative plasmid in E. faecalis was also able to mobilize the interspecies transfer of the cfr(D)- and poxtA2-cocarrying plasmid between enterococci and staphylococci. IMPORTANCE In this study, the simultaneous occurrence of four acquired oxazolidinone resistance genes [optrA, cfr, cfr(D), and poxtA2] was identified in an E. faecalis isolate of chicken origin. The association of the cfr gene with a novel pseudocompound transposon Tn7515 integrated into a pCF10-like pheromone-responsive conjugative plasmid will accelerate its dissemination. Moreover, the location of the resistance genes cfr(D) and poxtA2 on a mobilizable broad-host-range Inc18 family plasmid represents the basis for their intra- and interspecies dissemination with the aid of a conjugative plasmid and further accelerates the spreading of acquired oxazolidinone resistance genes, such as cfr, cfr(D), and poxtA2, among Gram-positive pathogens.

Dataset Information

Coexistence of the Oxazolidinone Resistance-Associated Genes cfr and optrA in Enterococcus faecalis From a Healthy Piglet in Brazil.

Publications

Coexistence of the Oxazolidinone Resistance-Associated Genes <i>cfr</i> and <i>optrA</i> in <i>Enterococcus faecalis</i> From a Healthy Piglet in Brazil.

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