Identification and characterization of differentially expressed genes in Caenorhabditis elegans in response to pathogenic and nonpathogenic Stenotrophomonas maltophilia

Stenotrophomonas maltophilia is an emerging nosocomial pathogen that causes infection in immunocompromised patients. S. maltophilia isolates are genetically diverse, contain diverse virulence factors, and are variably pathogenic within several host species. Members of the Stenotrophomonas genus are part of the native microbiome of C. elegans, being found in greater relative abundance within the worm than its environment, suggesting that these bacteria accumulate within C. elegans. Thus, study of the C. elegans-Stenotrophomonas interaction is of both medical and ecological significance. To identify host defense mechanisms, we analyzed the C. elegans transcriptomic response to Escherichia coli OP50 or S. maltophilia strains of varying pathogenicity: K279a, an avirulent clinical isolate, JCMS, a virulent strain isolated in association with nematodes near Manhattan, KS, and JV3, an even more virulent environmental isolate. The goal of this study was to compare host responses to both pathogenic and nonpathogenic S. maltophilia and identify common and strain-specific genetic responses. Wild-type, synchronized, larval stage 4 (L4) C. elegans were transferred to treatment bacteria (S. maltophilia K279a, JCMS, or JV3) or E. coli OP50. After 12 hours of exposure to treatment bacteria at 25° C, bulk RNA was extracted. Three biological replicates were collected for each treatment, and two technical replicates were sequenced for each biological replicate.