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Venkataraman P, Nagendra P, Ahlawat N, Brajesh RG, Saini S. Convergent genetic adaptation of Escherichia coli in minimal media leads to pleiotropic divergence. Front Mol Biosci 2024; 11:1286824. [PMID: 38660375 PMCID: PMC11039892 DOI: 10.3389/fmolb.2024.1286824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/15/2024] [Indexed: 04/26/2024] Open
Abstract
Adaptation in an environment can either be beneficial, neutral or disadvantageous in another. To test the genetic basis of pleiotropic behaviour, we evolved six lines of E. coli independently in environments where glucose and galactose were the sole carbon sources, for 300 generations. All six lines in each environment exhibit convergent adaptation in the environment in which they were evolved. However, pleiotropic behaviour was observed in several environmental contexts, including other carbon environments. Genome sequencing reveals that mutations in global regulators rpoB and rpoC cause this pleiotropy. We report three new alleles of the rpoB gene, and one new allele of the rpoC gene. The novel rpoB alleles confer resistance to Rifampicin, and alter motility. Our results show how single nucleotide changes in the process of adaptation in minimal media can lead to wide-scale pleiotropy, resulting in changes in traits that are not under direct selection.
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Affiliation(s)
| | | | | | | | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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Kelly SA, O'Connell NH, Thompson TP, Dillon L, Wu J, Creevey C, Powell J, Gilmore BF, Dunne CP. A novel characterized multi-drug-resistant Pseudocitrobacter sp. isolated from a patient colonized while admitted to a tertiary teaching hospital. J Hosp Infect 2024; 145:193-202. [PMID: 38215945 DOI: 10.1016/j.jhin.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND Reports of nosocomial infections typically describe recognised microorganisms. Here, a novel bacterial species was isolated, based on rectal swab screening for carbapenemases post-admission, then phenotypically and genetically characterized. METHODS Sensititre, Vitek and API kits, MALDI and Illumina MiSeq were employed before profiles and phylogeny were compared with other related species. FINDINGS Determined to be a possible Enterobacterales, the isolate was found to have 99.7% 16s rRNA identity to Pseudocitrobacter corydidari; an Asian cockroach-associated species. Given the highly conserved/low variability of 16S rRNA genes in Enterobacterales, average nucleotide identity (ANI) analysis compared the new isolate's genome with those of 18 Enterobacteriaceae species, including confirmed species of Pseudocitrobacter and unnamed Pseudocitrobacter species in the SILVA database. Of these, Pseudocitrobactercorydidari had the highest ANI at 0.9562. The published genome of the only known isolate of P.corydidari does not include Antimicrobial Resistance Genes (ARGs), with exception of potential drug efflux transporters. In contrast, our clinical isolate bears recognised antimicrobial resistance genes, including Klebsiella pneumoniae carbapenemase. The associated genome suggests resistance to carbapenems, β-lactams, sulfonamides, fluoroquinolones, macrolides, aminoglycosides and cephalosporins. Phenotypic antimicrobial resistance was confirmed. CONCLUSION Evident variations in ARG profiles, human colonization and origin in a clinically relevant niche that is geographically, physically and chemically disparate lend credibility for divergent evolution or, less likely, parallel evolution with P. corydidari. Genome data for this new species have been submitted to GENBANK using the proposed nomenclature Pseudocitrobacter limerickensis. The patient was colonized, rather than infected, and did not require antimicrobial treatment.
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Affiliation(s)
- S A Kelly
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - N H O'Connell
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland; School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity, University of Limerick, Limerick, Ireland
| | - T P Thompson
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - L Dillon
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - J Wu
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - C Creevey
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - J Powell
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland; School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity, University of Limerick, Limerick, Ireland
| | - B F Gilmore
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - C P Dunne
- School of Medicine and Centre for Interventions in Infection, Inflammation, and Immunity, University of Limerick, Limerick, Ireland.
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Knowles B, Bonachela JA, Cieslik N, Della Penna A, Diaz B, Baetge N, Behrenfeld MJ, Naumovitz K, Boss E, Graff JR, Halsey KH, Haramaty L, Karp-Boss L, Bidle KD. Altered growth and death in dilution-based viral predation assays. PLoS One 2023; 18:e0288114. [PMID: 37418487 DOI: 10.1371/journal.pone.0288114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/20/2023] [Indexed: 07/09/2023] Open
Abstract
Viral lysis of phytoplankton is one of the most common forms of death on Earth. Building on an assay used extensively to assess rates of phytoplankton loss to predation by grazers, lysis rates are increasingly quantified through dilution-based techniques. In this approach, dilution of viruses and hosts are expected to reduce infection rates and thus increase host net growth rates (i.e., accumulation rates). The difference between diluted and undiluted host growth rates is interpreted as a measurable proxy for the rate of viral lytic death. These assays are usually conducted in volumes ≥ 1 L. To increase throughput, we implemented a miniaturized, high-throughput, high-replication, flow cytometric microplate dilution assay to measure viral lysis in environmental samples sourced from a suburban pond and the North Atlantic Ocean. The most notable outcome we observed was a decline in phytoplankton densities that was exacerbated by dilution, instead of the increased growth rates expected from lowered virus-phytoplankton encounters. We sought to explain this counterintuitive outcome using theoretical, environmental, and experimental analyses. Our study shows that, while die-offs could be partly explained by a 'plate effect' due to small incubation volumes and cells adhering to walls, the declines in phytoplankton densities are not volume-dependent. Rather, they are driven by many density- and physiology-dependent effects of dilution on predation pressure, nutrient limitation, and growth, all of which violate the original assumptions of dilution assays. As these effects are volume-independent, these processes likely occur in all dilution assays that our analyses show to be remarkably sensitive to dilution-altered phytoplankton growth and insensitive to actual predation pressure. Incorporating altered growth as well as predation, we present a logical framework that categorizes locations by the relative dominance of these mechanisms, with general applicability to dilution-based assays.
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Affiliation(s)
- Ben Knowles
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, California, United States of America
- Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Juan A Bonachela
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Nick Cieslik
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Alice Della Penna
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Ben Diaz
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Nick Baetge
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Micheal J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Karen Naumovitz
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
| | - Jason R Graff
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Kimberly H Halsey
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Liti Haramaty
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, Maine, United States of America
| | - Kay D Bidle
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, United States of America
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