Resistome, virulome and mobilome of nasal staphylococci from healthy humans and animalsA One Health approach with public health implications stars

Abstract

Antimicrobial resistance (AMR) and pathogenicity in Staphylococcus constitute one of the major global health challenges that need to be addressed using a holistic “One Health” approach. Nasal Staphylococcus microbiota in healthy hosts and their molecular characterizations could provide relevant information. The inclusion of wild animals has been considered necessary to obtain adequate epidemiological links of Staphylococcus across the “One Health” niches. This thesis determined the diversity and performed the molecular and genomic characterization of Staphylococcus species in the nasal cavities of healthy humans (with or without animal contact) and healthy animals (pigs, dogs, and nestlings of parent white storks that foraged in natural and landfill areas). Of the four hosts studied, nestling storks had the most diverse Staphylococcus species, followed by pigs, whereas healthy humans had the least. Specifically, S. sciuri (85.7%) was the most predominant species in the storks; S. aureus in pigs (64%) and pig farmers (80%); S. pseudintermedius (32.4%) in dogs and S. epidermidis (87.7%) in healthy humans. In relation to methicillin-resistance trait and genetic lineages of coagulase-positive staphylococci, most of the S. aureus from pigs (60%, CC398), pig farmers (70%, CC398) and one from a dog owner (CC5) were MRSA. Whereas all other ones from the four hosts were methicillin-susceptible (MS)-S. aureus (MSSA) and methicillin-susceptible S. pseudintermedius (MSSP), of which the φSa3-carrying MSSA-CC398 was the predominant lineage. Using core-genome single nucleotide polymorphism analyses, transmission of MRSA-CC398 from pig-to-pig farmer, MSSP-ST1115 from dog-to-dog owner and acquisition of human-adapted MSSA-CC398 in nestling storks were confirmed. Moreover, pig-to-pig transmission of S. borealis was also observed. AMR genes to all classes of antibiotics in staphylococci were detected including unusual and critically important ones. It is remarkable the detection of linezolid-resistance in MRSA-CC5 mediated by novel point mutations at G2261A & T1584A in 23S rDNA and in S. epidermidis-ST35 from two dog owners with four mutations in L3 (I188V, G218V, N219I, L220D) and L4 (N158S). Moreover, a plasmid-bound (41.6kb) cfr in S. saprophyticus from a pig and a chromosomally located cfr in S. epidermidis-ST16 from a pig farmer were identified. It is also remarkable the identification of a rare pig-to-pig farmer transmission of ermT-positive MRSA-CC398 as wells as a multidrug-resistant S. lentus strain harbouring both mecA and mecC genes in SCCmec type VI hybrid in nestling stork and the detection of the ermT gene located in the plasmid repUS18 in a pig in a S. borealis strain. Diverse lineages of S. aureus strains from healthy humans who had no animal contact (85%) showed the highest frequency of clinically relevant virulence genes (including lukF/S-PV, tst, eta, etb, etd, sea, seb, sec), followed by strains from nestling storks which carried tst (CC22 and CC30), eta (CC9) and etb (CC45). None of the S. aureus strains from pigs, pig farmers, dogs and dog owners carried these virulence factors. However, all the S. pseudintermedius carried the lukS/F-I, siet, and sient genes. Remarkably, sec- and sel-carrying S. epidermidis-ST595 from a nestling stork was detected. The whole genome sequencing data of 107 strains revealed the presence of multiple plasmids-bound AMR genes, which were predominant in Staphylococcus strains from pigs and pig farmers, but least in nestling storks (p<0.0001). Moreover, transposons-linked AMR genes such as ant9’(Tn554), ermA (Tn554). fexA (Tn554, Tn558), tet(M) (Tn916, Tn925, Tn6006) and dfrK (Tn559) were identified. Complete CRISPR-Cas system was detected in 19.2% of the CoNS strains, of which cas-1, -2 and -9 predominated and especially in 75% of the S. borealis strains. All the S. aureus strains had no CRISPR-Cas. The phylogenetic analysis identified clusters of related S. epidermidis lineages with other countries (SNP <100). This thesis showed the influence of ecological niches on AMR levels and the presence and/ or transmission of various epidemic Staphylococcus species and lineages across healthy humans and animals and their relatedness with international strains. Since MSSA-CC398 was detected in three of the four ecosystems studied, the combination of erythromycin-clindamycin inducible resistance and ermT gene could be useful diagnostic markers of the MSSA-CC398 subclade. Collectively, this report underscores the need to strengthen the genomic epidemiological approach and inclusion of all Staphylococcus species from all hosts (even the healthy ones) to adequately understand the global spread of antimicrobial-resistant strains and track pathogenic ones using the “One Health” model.