1
|
Fitzgerald BA, Wadud A, Slimak Z, Slonczewski JL. Enterococcus faecalis OG1RF Evolution at Low pH Selects Fusidate-Sensitive Mutants in Elongation Factor G and at High pH Selects Defects in Phosphate Transport. Appl Environ Microbiol 2023; 89:e0046623. [PMID: 37272807 PMCID: PMC10304957 DOI: 10.1128/aem.00466-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023] Open
Abstract
Enterococcus bacteria inhabit human and soil environments that show a wide range of pH values. Strains include commensals as well as antibiotic-resistant pathogens. We investigated the adaptation to pH stress in E. faecalis OG1RF by conducting experimental evolution under acidic (pH 4.8), neutral pH (pH 7.0), and basic (pH 9.0) conditions. A serial planktonic culture was performed for 500 generations and in a high-pH biofilm culture for 4 serial bead transfers. Nearly all of the mutations led to nonsynonomous codons, indicating adaptive selection. All of the acid-adapted clones from the planktonic culture showed a mutation in fusA (encoding elongation factor G). The acid-adapted fusA mutants had a trade-off of decreased resistance to fusidic acid (fusidate). All of the base-adapted clones from the planktonic cultures as well as some from the biofilm-adapted cultures showed mutations that affected the Pst phosphate ABC transporter (pstA, pstB, pstB2, pstC) and pyrR (pyrimidine biosynthesis regulator/uracil phosphoribosyltransferase). The biofilm cultures produced small-size colonies on brain heart infusion agar. These variants each contained a single mutation in pstB2, pstC, or pyrR. The pst and pyrR mutants outgrew the ancestral strain at pH 9.2, with a trade-off of lower growth at pH 4.8. Additional genes that had a mutation in multiple clones that evolved at high pH (but not at low pH) include opp1BCDF (oligopeptide ABC transporter), ccpA (catabolite control protein A), and ftsZ (septation protein). Overall, the experimental evolution of E. faecalis showed a strong pH dependence, favoring the fusidate-sensitive elongation factor G modification at low pH and the loss of phosphate transport genes at high pH. IMPORTANCE E. faecalis bacteria are found in dental biofilms, where they experience low pH as a result of fermentative metabolism. Thus, the effect of pH on antibiotic resistance has clinical importance. The loss of fusidate resistance is notable for OG1RF strains in which fusidate resistance is assumed to be a stable genetic marker. In endodontal infections, enterococci can resist calcium hydroxide therapy that generates extremely high pH values. In other environments, such as the soil and plant rhizosphere, enterococci experience acidification that is associated with climate change. Thus, the pH modulation of natural selection in enterococci is important for human health as well as for understanding soil environments.
Collapse
Affiliation(s)
| | - Ayman Wadud
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | - Zachary Slimak
- Department of Biology, Kenyon College, Gambier, Ohio, USA
| | | |
Collapse
|
2
|
Bohm RP, Breed MW, Cohen JK, Haertel AJ, Halliday LC, Kramer JA, Lieberman MT, Rice KA, Roberts JA, Russell-Logrigue KE, Salyards GW, Scorpio DG, Weese JS. Formal Comment on "Mitigation of endemic GI-tract pathogen-mediated inflammation through development of multimodal treatment regimen and its impact on SIV acquisition in rhesus macaques" by Bochart et al. (2021). PLoS Pathog 2022; 18:e1010831. [PMID: 36166449 PMCID: PMC9514602 DOI: 10.1371/journal.ppat.1010831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 08/22/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rudolf P. Bohm
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America
| | - Matthew W. Breed
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Bethesda, Maryland, United States of America
- * E-mail:
| | - Joyce K. Cohen
- The Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Andrew J. Haertel
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Lisa C. Halliday
- Biologic Resources Laboratory, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Joshua A. Kramer
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Bethesda, Maryland, United States of America
| | - Mia T. Lieberman
- Harvard Center for Comparative Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kelly A. Rice
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jeffery A. Roberts
- California National Primate Research Center, University of California Davis, Davis, California, United States of America
| | - Kasi E. Russell-Logrigue
- Tulane National Primate Research Center, Tulane University, Covington, Louisiana, United States of America
| | - Gregory W. Salyards
- Division of Veterinary Resources, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Diana G. Scorpio
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - J. Scott Weese
- Ontario Veterinary College, University of Guelph, Guelph, Canada
| |
Collapse
|
3
|
Chilambi GS, Nordstrom HR, Evans DR, Kowalski RP, Dhaliwal DK, Jhanji V, Shanks RMQ, Van Tyne D. Genomic and phenotypic diversity of Enterococcus faecalis isolated from endophthalmitis. PLoS One 2021; 16:e0250084. [PMID: 33852628 PMCID: PMC8046195 DOI: 10.1371/journal.pone.0250084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/30/2021] [Indexed: 11/30/2022] Open
Abstract
Enterococcus faecalis are hospital-associated opportunistic pathogens and also causative agents of post-operative endophthalmitis. Patients with enterococcal endophthalmitis often have poor visual outcomes, despite appropriate antibiotic therapy. Here we investigated the genomic and phenotypic characteristics of E. faecalis isolates collected from 13 patients treated at the University of Pittsburgh Medical Center Eye Center over 19 years. Comparative genomic analysis indicated that patients were infected with E. faecalis belonging to diverse multi-locus sequence types (STs) and resembled E. faecalis sampled from clinical, commensal, and environmental sources. We identified known E. faecalis virulence factors and antibiotic resistance genes in each genome, including genes conferring resistance to aminoglycosides, erythromycin, and tetracyclines. We assessed all isolates for their cytolysin production, biofilm formation, and antibiotic susceptibility, and observed phenotypic differences between isolates. Fluoroquinolone and cephalosporin susceptibilities were particularly variable between isolates, as were biofilm formation and cytolysin production. In addition, we found evidence of E. faecalis adaptation during recurrent endophthalmitis by identifying genetic variants that arose in sequential isolates sampled over eight months from the same patient. We identified a mutation in the DNA mismatch repair gene mutS that was associated with an increased rate of spontaneous mutation in the final isolate from the patient. Overall this study documents the genomic and phenotypic variability among E. faecalis causing endophthalmitis, as well as possible adaptive mechanisms underlying bacterial persistence during recurrent ocular infection.
Collapse
Affiliation(s)
- Gayatri Shankar Chilambi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Hayley R. Nordstrom
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Daniel R. Evans
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Regis P. Kowalski
- The Charles T. Campbell Ophthalmic Microbiology Laboratory, UPMC Eye Center, Ophthalmology and Visual Sciences Research Center, The Eye and Ear Institute, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Deepinder K. Dhaliwal
- The Charles T. Campbell Ophthalmic Microbiology Laboratory, UPMC Eye Center, Ophthalmology and Visual Sciences Research Center, The Eye and Ear Institute, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Vishal Jhanji
- The Charles T. Campbell Ophthalmic Microbiology Laboratory, UPMC Eye Center, Ophthalmology and Visual Sciences Research Center, The Eye and Ear Institute, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Robert M. Q. Shanks
- The Charles T. Campbell Ophthalmic Microbiology Laboratory, UPMC Eye Center, Ophthalmology and Visual Sciences Research Center, The Eye and Ear Institute, Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|