Enterococci from Wild Magellanic Penguins (Spheniscus magellanicus) as an Indicator of Marine Ecosystem Health and Human Impact

Abstract

Enterococci are commensals that proliferated as animals crawled ashore hundreds of millions of years ago. They are also leading causes of multidrug-resistant hospital infection. While most studies are driven by clinical interest, comparatively little is known about enterococci in the wild, or the effect of human activity on them. Pharmaceutical pollution and runoff from other human activities are encroaching widely into natural habitats. To assess its reach into remote habitats, we investigated the identity, genetic relatedness, and presence of specific traits among 172 enterococcal isolates from wild Magellanic Penguins. Four enterococcal species, eighteen lineages groups, and different colonization patterns were identified. One E. faecalis lineage, ST475, was isolated from three different penguins, making it of special interest. Its genome was compared to those of other E. faecalis sequence types (ST116 and ST242) recovered from Magellanic Penguins, as well as to an existing phylogeny of E. faecalis isolated from diverse origins over the past 100 years. No penguin-derived E. faecalis strains were closely related to dominant clinical lineages. Most possessed intact CRISPR defenses, few mobile elements, antibiotic resistances limited to those intrinsic to the species, and lacked pathogenic features conveyed by mobile elements. Interestingly, plasmids were identified in penguin isolates that also had been reported in other marine mammals. Enterococci isolated from penguins showed limited anthropogenic impact, indicating that they are likely representative of those naturally circulating in the ecosystem inhabited by the penguins. These findings establish an important baseline for detecting the encroachment of human activity into remote planetary environments. IMPORTANCE Enterococci are host-associated microbes that have an unusually broad range, from the built hospital environment to the guts of insects and other animals in remote locations. Despite their occurrence in the guts of animals for hundreds of millions of years, we know little about the properties that confer this range, or how anthropogenic activities may be introducing new selective forces. Magellanic Penguins live at the periphery of human habitation. It was of interest to examine enterococci from these animals for the presence of antibiotic resistance and other markers reflective of anthropogenic selection. Diverse enterococcal lineages found discount the existence of a single well-adapted intrinsic penguin-specific species. Instead, they appear to be influenced by a carnivorous lifestyle and enterococci present in the coastal sea life consumed. These results indicate that currently, the penguin habitat remains relatively free of pollutants that select for adaptation to human-derived stressors.

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

“…Traits conveying AMR have been shown to be abundant in E. faecalis isolates from migratory wild birds 20 , and we accordingly detected majority of wild bird isolates in the present collection to carry multiple ARGs, unlike what has been found even in domesticated poultry when screening for ARGs in S. aureus isolates 3 . Intriguingly, flightless birds in locations remote from anthropogenic impact carried E. faecalis isolates lacking other but intrinsic ARGs, in agreement with lack of selection driven by human-applied antimicrobials in the population and its environment 58 . Although selective pressure due to direct antibiotic usage in wild birds may be considered limited, many wild bird species dwelling in human-adjacent locations may be influenced by pharmaceutical pollution and other human activity through shared habitats.…”

Genome Mining for Antimicrobial Compounds in Wild Marine Animals-associated Enterococci

“…As expected, these were most common in E. faecium and E. faecalis where they have been most thoroughly studied. Some of these traits are encoded within the core genomes 16,17 . The unique E. faecium harbored efaAfm and acm genes, while all E. faecalis contained several genes associated with adhesion (ace, efaAfs), biofilm production (ebpA, ebpB and ebpC), proteases (gelE and srtA), protection against oxidative stress (tpx), and quorum sensing and sex pheromone (cad, camE, cCF10, cOB1, and fsrB).…”

“…5b) revealed that all E. casseliflavus genomes (n = 3) possessed genes related to low level vancomycin resistance (vanRC and vanXYC), as expected since these are part of the core genome for that species 52 . All E. faecalis genomes (n = 10) contained genes within the core genomes 16 conferring resistance to trimethoprim (dfrE); to macrolide, fluoroquinolone, and rifamycin (efrA and efrB); to pleuromutilin, lincosamide, and streptogramin (lsaA); and have a multidrug and toxic compound extrusion transporter (emeA). On the other hand, the unique E. faecium genome possessed genes related to resistance to aminoglycosides (aac(6')-Ii); to macrolide, lincosamide, streptogramin, tetracycline, oxazolidinone, phenicol, pleuromutilin (eatAv); and to macrolide, lincosamide, streptogramin (msrC).…”

“…Twenty-two enterococci strains previously described 16,77,80 were evaluated in the present study. Table 1).…”

Genome Mining for Antimicrobial Compounds in Wild Marine Animals-Associated Enterococci

“…It was, therefore, of interest to us to explore marine animals from remote habitats for hostassociated microbes that encode novel natural product biosynthetic pathways. Further, we focused on host-associated enterococci, a genus of gut microbes associated with all classes of land animals studied [25], and with animals that have returned to the marine environment [26]. Although most enterococci exist as harmless commensals, some lineages of the species Enterococcus faecalis and Enterococcus faecium have emerged as leading causes of multidrug-resistant hospital infection [25,[27][28][29][30].…”