Dataset Information

Faecal carriage of enterococci harbouring oxazolidinone resistance genes among healthy humans in the community in Switzerland.

ABSTRACT:

Objectives

This study aimed to investigate the faecal carriage of enterococci harbouring oxazolidinone resistance genes among healthy humans in Switzerland and to genetically characterize the isolates.

Methods

A total of 399 stool samples from healthy individuals employed in different food-processing plants were cultured on a selective medium containing 10 mg/L florfenicol. Resulting enterococci were screened by PCR for the presence of cfr, optrA and poxtA. A hybrid approach combining short-read and long-read WGS was used to analyse the genetic context of the cfr, optrA and poxtA genes.

Results

Enterococcus faecalis (n = 6), Enterococcus faecium (n = 6), Enterococcus gallinarum (n = 1) and Enterococcus hirae (n = 2) were detected in 15/399 (3.8%) of the faecal samples. They carried cfr + poxtA, optrA, optrA + poxtA or poxtA. Four E. faecalis harbouring optrA and one E. faecium carrying poxtA were resistant to linezolid (8 mg/L). In most optrA-positive isolates, the genetic environments of optrA were highly variable, but often resembled previously described platforms. In most poxtA-positive isolates, the poxtA gene was flanked on both sides by IS1216E elements and located on medium-sized plasmids.

Conclusions

Faecal carriage of Enterococcus spp. harbouring cfr, optrA and poxtA in healthy humans associated with the food-production industry demonstrates the possibility of spread of oxazolidinone resistance genes into the community. Given the importance of linezolid as a last-resort antibiotic for the treatment of serious infections caused by Gram-positive pathogens, the detection of the oxazolidinone resistance determinants in enterococci from healthy humans is of concern for public health.

SUBMITTER: Nuesch-Inderbinen M

PROVIDER: S-EPMC9525073 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Publications

Faecal carriage of enterococci harbouring oxazolidinone resistance genes among healthy humans in the community in Switzerland.

Nüesch-Inderbinen Magdalena M Biggel Michael M Zurfluh Katrin K Treier Andrea A Stephan Roger R

The Journal of antimicrobial chemotherapy 20220901 10

<h4>Objectives</h4>This study aimed to investigate the faecal carriage of enterococci harbouring oxazolidinone resistance genes among healthy humans in Switzerland and to genetically characterize the isolates.<h4>Methods</h4>A total of 399 stool samples from healthy individuals employed in different food-processing plants were cultured on a selective medium containing 10 mg/L florfenicol. Resulting enterococci were screened by PCR for the presence of cfr, optrA and poxtA. A hybrid approach combi ...[more]

PMID: 35971252

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Project description:BackgroundLinezolid is a critically important oxazolidinone antibiotic used in human medicine. Although linezolid is not licensed for use in food-producing animals, the use of florfenicol in veterinary medicine co-selects for oxazolidinone resistance genes.ObjectiveThis study aimed to assess the occurrence of cfr, optrA, and poxtA in florfenicol-resistant isolates from beef cattle and veal calves from different herds in Switzerland.MethodsA total of 618 cecal samples taken from beef cattle and veal calves at slaughter originating from 199 herds were cultured after an enrichment step on a selective medium containing 10 mg/L florfenicol. Isolates were screened by PCR for cfr, optrA, and poxtA which are genes known to confer resistance to oxazolidinones and phenicols. One isolate per PCR-positive species and herd was selected for antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS).ResultsOverall, 105 florfenicol-resistant isolates were obtained from 99 (16%) of the samples, corresponding to 4% of the beef cattle herds and 24% of the veal calf herds. Screening by PCR revealed the presence of optrA in 95 (90%) and poxtA in 22 (21%) of the isolates. None of the isolates contained cfr. Isolates included for AST and WGS analysis were Enterococcus (E.) faecalis (n = 14), E. faecium (n = 12), E. dispar (n = 1), E. durans (n = 2), E. gallinarum (n = 1), Vagococcus (V.) lutrae (n = 2), Aerococcus (A.) urinaeequi (n = 1), and Companilactobacillus (C.) farciminis (n = 1). Thirteen isolates exhibited phenotypic linezolid resistance. Three novel OptrA variants were identified. Multilocus sequence typing identified four E. faecium ST18 belonging to hospital-associated clade A1. There was a difference in the replicon profile among optrA- and poxtA-harboring plasmids, with rep9 (RepA_N) plasmids dominating in optrA-harboring E. faecalis and rep2 (Inc18) and rep29 (Rep_3) plasmids in poxtA-carrying E. faecium.ConclusionBeef cattle and veal calves are reservoirs for enterococci with acquired linezolid resistance genes optrA and poxtA. The presence of E. faecium ST18 highlights the zoonotic potential of some bovine isolates. The dispersal of clinically relevant oxazolidinone resistance genes throughout a wide variety of species including Enterococcus spp., V. lutrae, A. urinaeequi, and the probiotic C. farciminis in food-producing animals is a public health concern.

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.

Dataset Information

Faecal carriage of enterococci harbouring oxazolidinone resistance genes among healthy humans in the community in Switzerland.

Objectives

Methods

Results

Conclusions

Publications

Faecal carriage of enterococci harbouring oxazolidinone resistance genes among healthy humans in the community in Switzerland.

Similar Datasets

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