The emergence of methicillin-resistant Staphylococcus aureus (MRSA) poses an important threat in human and animal health. In this study, we ask whether resistance and virulence genes in S. aureus are homogeneously distributed or constrained by different animal hosts. We carried out whole genome sequencing of 114 S. aureus isolates from ten species of animals sampled from four New England states (USA) in 2017–2019. The majority of the isolates came from cats, cows and dogs. The maximum likelihood phylogenetic tree based on the alignment of 89,143 single nucleotide polymorphisms of 1173 core genes reveal 31 sequence types (STs). The most common STs were ST5, ST8, ST30, ST133 and ST2187. Every genome carried at least eight acquired resistance genes. Genes related to resistance found in all genomes included norA (fluoroquinolone), arlRS (fluoroquinolone), lmrS (multidrug), tet(38) (tetracycline) and mepAR (multidrug and tigecycline resistance). The most common superantigen genes were tsst-1, sea and sec. Acquired antibiotic resistance (n = 10) and superantigen (n = 9) genes of S. aureus were widely shared between S. aureus lineages and between strains from different animal hosts. These analyses provide insights for considering bacterial gene sharing when developing strategies to combat the emergence of high-risk clones in animals.

Campylobacter jejuni is likely the most common bacterial cause of gastroenteritis worldwide, responsible for millions of cases of inflammatory diarrhea characterized by severe abdominal cramps and blood in the stool. Further, C. jejuni infections are associated with post-infection sequelae in developed countries and malnutrition and growth-stunting in low- and middle-income countries. Despite the increasing prevalence of the disease, campylobacteriosis, and the recognition that this pathogen is a serious health threat, our understanding of C. jejuni pathogenesis remains incomplete. In this review, we focus on the Campylobacter secretion systems proposed to contribute to host-cell interactions and survival in the host. Moreover, we have applied a genomics approach to defining the structural and mechanistic features of C. jejuni type III, IV, and VI secretion systems. Special attention is focused on the flagellar type III secretion system and the prediction of putative effectors, given that the proteins exported via this system are essential for host cell invasion and the inflammatory response. We conclude that C. jejuni does not possess a type IV secretion system and relies on the type III and type VI secretion systems to establish a niche and potentiate disease.

Staphylococcus pseudintermedius is a major bacterial colonizer and opportunistic pathogen in dogs. Methicillin-resistant S. pseudintermedius (MRSP) continues to emerge as a significant challenge to maintaining canine health. We sought to determine the phylogenetic relationships of S. pseudintermedius across five states in the New England region of the United States and place them in a global context. The New England dataset consisted of 125 previously published S. pseudintermedius genomes supplemented with 45 newly sequenced isolates. The core genome phylogenetic tree revealed many deep branching lineages consisting of 142 multi-locus sequence types (STs). In silico detection of the mecA gene revealed 40 MRSP and 130 methicillin-susceptible S. pseudintermedius (MSSP) isolates. MRSP were derived from five structural types of SCCmec, the mobile genetic element that carries the mecA gene conferring methicillin resistance. Although many genomes were MSSP, they nevertheless harbored genes conferring resistance to many other antibiotic classes, including aminoglycosides, macrolides, tetracyclines and penams. We compared the New England genomes to 297 previously published genomes sampled from five other states in the United States and 13 other countries. Despite the prevalence of the clonally expanding ST71 found worldwide and in other parts of the United States, we did not detect it in New England. We next sought to interrogate the combined New England and global datasets for the presence of coincident gene pairs linked to antibiotic resistance. Analysis revealed a large co-circulating accessory gene cluster, which included mecA as well as eight other resistance genes [aac (6′)-Ie-aph (2″)-Ia, aad (6), aph (3′)-IIIa, sat4, ermB, cat, blaZ, and tetM]. Furthermore, MRSP isolates carried significantly more accessory genes than their MSSP counterparts. Our results provide important insights to the evolution and geographic spread of high-risk clones that can threaten the health of our canine companions.

Strombidium rassoulzadegani is a planktonic ciliate that retains chloroplasts from its food and uses them to obtain a nutritional supplement from photosynthesis. Unlike most members of the Oligotrichia, it is not difficult to grow in culture and thus it can serve as an experimental model for this kind of mixotrophy. We report here on its distribution, seasonal pattern of occurrence in the western North Atlantic, and on experiments to elucidate patterns of encystment and excystment, preferred food algae, and heterotrophic growth. Among ten different microalgae, including members of the Dinophyceae, Chlorophyceae, Haptophyceae, Cryptophyceae, and Bacillariophyceae, only four could support growth for more than 1 week, and only the chlorophyte Tetraselmis chui (PLY 429) could consistently support sustained growth in the dark. Of the four algae that supported growth, three also resulted in longer survival when the ciliate was subsequently starved in the light, compared to the dark, suggesting that all of them provided some photosynthetic benefit to the ciliate. The dinoflagellate Prorocentrum minimum (JA) supported similar survival in the light and dark and likely does not undergo chloroplast retention in the ciliate.