Common transcriptomic changes in the adaptation of Salmonella enterica Typhimurium to biocides and antibiotics

Objectives: Concern about developing co-resistance to biocides and antibiotics exists. These antimicrobials are frequently used, in combination or sequentially, to treat infections or to prevent the growth of Salmonella species on surfaces. Available data about the effect of biocide (triclosan, TRI; chlorhexidine, CHX, benzalkonium chloride, BKC and sodium hypochlorite, SHC) and antibiotic (ampicillin, AMP, ciprofloxacin, CIP, and ceftazidima, CAZ) on the cell stasis are scarce and disperse. We analysed the effect of acquiring biocide resistance on the susceptibility to a wide range of antimicrobials. Fitness costs and global transcriptomics for selected mutants and natural isolates with diverse biocide phenotype were also studied. Methods: Fourteen mutants of different biocide susceptibility phenotype (4 TRIR/BZCR/CHXR, 1 TRIR/BZCR, 4 TRIHS/BKCR/CHXR, 2 BKCR, 2 TRIHS and 1 TRIHS/CHXHS) obtained after exposure of SL1344 strain to TRI, BZC, CHX AMP and CIP or without previous exposure to any compound were analysed for antimicrobial susceptibility by E-test and phenotype microarrays for 240 compounds (PM11-PM20, Biolog, Hayward, California, USA). The growth kinetics of 7 selected biocide mutants TRIRBKCRCHXR (NE/TRI1, NE/CHX100), BKCR (CIP/TRI1, TRI/BKC100), TRIHSBKCRCHXR (NE/BKC100), TRISCHXS (CIP/CHX64) and TRIHS (CHX/AMP4), and the parental SL1344 strain was measured in fresh LB broth culture (approximately 104 CFU/ml) every 10 min for 24 h in Bioscreen C (optical density at 600 nm). Transcriptomic profile of representative mutants and natural isolates of Salmonella using a custom expression microarray was analysed. Results: Striking changes in the antibiotic susceptibility after exposure to biocides were usually accompanied of a fitness cost (up to 52%). For most mutants decreased susceptibility to a wide range of antimicrobials (mostly to protein synthesis inhibitors excepting aminoglycosides) and toxic cations, and increased susceptibility to ß-lactams, cationic compounds acting in the membrane (poli-L-lysine, polymixin B, colistin) or toxic anions was observed. Comparative transcriptomic analysis showed that similar changes related to stress and virulence response occurred in both in vitro-selected biocide mutants and natural isolates showing reduced biocide susceptibility. Such changes included overexpression of efflux pumps, ribosomal proteins and transcription-related genes, cold-shock response and metabolic enzymes such as the phosphotransferase system. The efflux pump sugE, the putative cobalt-precorrin-6A synthase, and the pyruvate kinase were expressed at higher levels in mutants as well as in natural isolates. Moreover, all but one ribosomal protein (L21) overexpressed in wild-type strains were also identified for mutants (8 versus 25). In natural isolates more metabolism-related genes were overexpressed (16 versus 8). Conclusions: This study highlights the wide range of multiple pathways employed by Salmonella to counteract the action of biocides. Phenotypic and transcriptomic changes reveal that global stress response, metabolic changes and alterations in the membrane permeability. Triggering these responses impose a severe fitness cost that may reduce the chances for spread of biocide resistant mutants.