Nasotracheal enterococcal carriage and resistomes: detection of optrA-, poxtA- and cfrD-carrying strains in migratory birds, livestock, pets, and in-contact humans in Spain

Abstract

This study determined the carriage rates and antimicrobial resistance (AMR) genes of enterococci from nasotracheal samples of three healthy animal species and in-contact humans. Nasal samples were collected from 27 dog-owning households (34 dogs, 41 humans) and 4 pig-farms (40 pigs, 10 pig-farmers), and they were processed for enterococci recovery (MALDI-TOF–MS identification). Also, a collection of 144 enterococci previously recovered of tracheal/nasal samples from 87 white stork nestlings were characterized. The AMR phenotypes were determined in all enterococci and AMR genes were studied by PCR/sequencing. MultiLocus-Sequence-Typing was performed for selected isolates. About 72.5% and 60% of the pigs and pig-farmers, and 29.4% and 4.9%, of healthy dogs and owners were enterococci nasal carriers, respectively. In storks, 43.5% of tracheal and 69.2% of nasal samples had enterococci carriages. Enterococci carrying multidrug-resistance phenotype was identified in 72.5%/40.0%/50.0%/23.5%/1.1% of pigs/pig-farmers/dogs/dogs’ owners/storks, respectively. Of special relevance was the detection of linezolid-resistant enterococci (LRE) in (a) 33.3% of pigs (E. faecalis-carrying optrA and/or cfrD of ST59, ST330 or ST474 lineages; E. casseliflavus-carrying optrA and cfrD); (b) 10% of pig farmers (E. faecalis-ST330-carrying optrA); (c) 2.9% of dogs (E. faecalis-ST585-carrying optrA); and (d) 1.7% of storks (E. faecium-ST1736-carrying poxtA). The fexA gene was found in all optrA-positive E. faecalis and E. casseliflavus isolates, while fexB was detected in the poxtA-positive E. faecium isolate. The enterococci diversity and AMR rates from the four hosts reflect differences in antimicrobial selection pressure. The detection of LRE carrying acquired and transferable genes in all the hosts emphasizes the need to monitor LRE using a One-Health approach.

Staphylococcus aureus Carriage in the Nasotracheal Cavities of White Stork Nestlings (Ciconia ciconia) in Spain: Genetic Diversity, Resistomes and Virulence Factors

“…In relation to the foraging habits of the parents of the storks, 35.0% and 37.5% nasal S. aureus carriage was found in stork nestlings whose parents foraged in natural habitats and landfills, respectively. Moreover, 7.1% and 16.3% tracheal carriage was found in stork nestlings fed natural habitat and landfill foraged food, respectively (Supplementary Table S1) [18]. All these 67 S. aureus strains were further characterized in the present study.…”

“…Storks in colonies 1 and 2 were located in natural habitats in open woodland devoted to extensive livestock grazing where storks forage, while those in colonies 3 and 4 are located on or close to landfills and the adults forage in landfills. These samples were processed for the recovery of the bacterial community diversities, which included S. aureus [18]. Potential S. aureus colonies (up to 6 per sample) were randomly selected based on colour, size and/or hemolysis.…”

“…The strains were identified by matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF; Bruker Daltonics, Bremen, Germany) using the standard extraction protocol recommended by Bruker Daltonics as previously described [19]. The strains identified as S. aureus (n = 67) were obtained from 29 of the 137 samples (21.2%) of 27 of the 87 storks (31%) analysed in a previous study [18]. Specifically, the prevalence of S. aureus carriage was higher in the nasal than in the tracheal cavities (36.5% and 11.9%, respectively), as indicated in the previous study [18].…”

“…The strains identified as S. aureus (n = 67) were obtained from 29 of the 137 samples (21.2%) of 27 of the 87 storks (31%) analysed in a previous study [18]. Specifically, the prevalence of S. aureus carriage was higher in the nasal than in the tracheal cavities (36.5% and 11.9%, respectively), as indicated in the previous study [18]. In relation to the foraging habits of the parents of the storks, 35.0% and 37.5% nasal S. aureus carriage was found in stork nestlings whose parents foraged in natural habitats and landfills, respectively.…”

“…In a previous study, the nasotracheal microbiota of white stork nestlings of parents foraging in different habitats was analysed, obtaining over 800 bacteria isolates of different genera and species, including different staphylococcal species [18]. The present study is focused on characterizing the collection of S. aureus isolates obtained in that study, determining genetic lineage diversities, antimicrobial resistance mechanisms, immune evasion cluster (IEC) types and virulence factors of these isolates.…”