Insights Into the Evolution of Staphylococcus aureus Daptomycin Resistance From an in vitro Bioreactor Model
The extensive use of daptomycin for treating complex methicillin-resistant Staphylococcus aureus infections has led to the emergence of daptomycin-resistant strains. Although genomic studies have identified mutations associated with daptomycin resistance, they have not necessarily provided insight i...
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doaj-09973eeaad49448cacd81a19a98301602020-11-24T23:32:10ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-02-011010.3389/fmicb.2019.00345415675Insights Into the Evolution of Staphylococcus aureus Daptomycin Resistance From an in vitro Bioreactor ModelErica Lasek-Nesselquist0Jackson Lu1Ryan Schneider2Zhuo Ma3Vincenzo Russo4Smruti Mishra5Manjunath P. Pai6Janice D. Pata7Janice D. Pata8Kathleen A. McDonough9Kathleen A. McDonough10Meenakshi Malik11Wadsworth Center, New York State Department of Health, Albany, NY, United StatesAlbany College of Pharmacy and Health Sciences, Albany, NY, United StatesDepartment of Biomedical Sciences, University at Albany, School of Public Health, Albany, NY, United StatesAlbany College of Pharmacy and Health Sciences, Albany, NY, United StatesAlbany College of Pharmacy and Health Sciences, Albany, NY, United StatesAlbany College of Pharmacy and Health Sciences, Albany, NY, United StatesDepartment of Clinical Pharmacy, University of Michigan, Ann Arbor, MI, United StatesWadsworth Center, New York State Department of Health, Albany, NY, United StatesDepartment of Biomedical Sciences, University at Albany, School of Public Health, Albany, NY, United StatesWadsworth Center, New York State Department of Health, Albany, NY, United StatesDepartment of Biomedical Sciences, University at Albany, School of Public Health, Albany, NY, United StatesAlbany College of Pharmacy and Health Sciences, Albany, NY, United StatesThe extensive use of daptomycin for treating complex methicillin-resistant Staphylococcus aureus infections has led to the emergence of daptomycin-resistant strains. Although genomic studies have identified mutations associated with daptomycin resistance, they have not necessarily provided insight into the evolution and hierarchy of genetic changes that confer resistance, particularly as antibiotic concentrations are increased. Additionally, plate-dependent in vitro analyses that passage bacteria in the presence of antibiotics can induce selective pressures unrelated to antibiotic exposure. We established a continuous culture bioreactor model that exposes S. aureus strain N315 to increasing concentrations of daptomycin without the confounding effects of nutritional depletion to further understand the evolution of drug resistance and validate the bioreactor as a method that produces clinically relevant results. Samples were collected every 24 h for a period of 14 days and minimum inhibitory concentrations were determined to monitor the acquisition of daptomycin resistance. The collected samples were then subjected to whole genome sequencing. The development of daptomycin resistance in N315 was associated with previously identified mutations in genes coding for proteins that alter cell membrane charge and composition. Although genes involved in metabolic functions were also targets of mutation, the common route to resistance relied on a combination of mutations at a few key loci. Tracking the frequency of each mutation throughout the experiment revealed that mutations need not arise progressively in response to increasing antibiotic concentrations and that most mutations were present at low levels within populations earlier than would be recorded based on single-nucleotide polymorphism (SNP) filtering criteria. In contrast, a serial-passaged population showed only one mutation in a gene associated with resistance and provided limited detail on the changes that occur upon exposure to higher drug dosages. To conclude, this study demonstrates the successful in vitro modeling of antibiotic resistance in a bioreactor and highlights the evolutionary paths associated with the acquisition of daptomycin non-susceptibility.https://www.frontiersin.org/article/10.3389/fmicb.2019.00345/fullStaphylococcus aureusbioreactor culturedaptomycinwhole-genome sequencing analysisevolution of resistance |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Erica Lasek-Nesselquist Jackson Lu Ryan Schneider Zhuo Ma Vincenzo Russo Smruti Mishra Manjunath P. Pai Janice D. Pata Janice D. Pata Kathleen A. McDonough Kathleen A. McDonough Meenakshi Malik |
spellingShingle |
Erica Lasek-Nesselquist Jackson Lu Ryan Schneider Zhuo Ma Vincenzo Russo Smruti Mishra Manjunath P. Pai Janice D. Pata Janice D. Pata Kathleen A. McDonough Kathleen A. McDonough Meenakshi Malik Insights Into the Evolution of Staphylococcus aureus Daptomycin Resistance From an in vitro Bioreactor Model Frontiers in Microbiology Staphylococcus aureus bioreactor culture daptomycin whole-genome sequencing analysis evolution of resistance |
author_facet |
Erica Lasek-Nesselquist Jackson Lu Ryan Schneider Zhuo Ma Vincenzo Russo Smruti Mishra Manjunath P. Pai Janice D. Pata Janice D. Pata Kathleen A. McDonough Kathleen A. McDonough Meenakshi Malik |
author_sort |
Erica Lasek-Nesselquist |
title |
Insights Into the Evolution of Staphylococcus aureus Daptomycin Resistance From an in vitro Bioreactor Model |
title_short |
Insights Into the Evolution of Staphylococcus aureus Daptomycin Resistance From an in vitro Bioreactor Model |
title_full |
Insights Into the Evolution of Staphylococcus aureus Daptomycin Resistance From an in vitro Bioreactor Model |
title_fullStr |
Insights Into the Evolution of Staphylococcus aureus Daptomycin Resistance From an in vitro Bioreactor Model |
title_full_unstemmed |
Insights Into the Evolution of Staphylococcus aureus Daptomycin Resistance From an in vitro Bioreactor Model |
title_sort |
insights into the evolution of staphylococcus aureus daptomycin resistance from an in vitro bioreactor model |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2019-02-01 |
description |
The extensive use of daptomycin for treating complex methicillin-resistant Staphylococcus aureus infections has led to the emergence of daptomycin-resistant strains. Although genomic studies have identified mutations associated with daptomycin resistance, they have not necessarily provided insight into the evolution and hierarchy of genetic changes that confer resistance, particularly as antibiotic concentrations are increased. Additionally, plate-dependent in vitro analyses that passage bacteria in the presence of antibiotics can induce selective pressures unrelated to antibiotic exposure. We established a continuous culture bioreactor model that exposes S. aureus strain N315 to increasing concentrations of daptomycin without the confounding effects of nutritional depletion to further understand the evolution of drug resistance and validate the bioreactor as a method that produces clinically relevant results. Samples were collected every 24 h for a period of 14 days and minimum inhibitory concentrations were determined to monitor the acquisition of daptomycin resistance. The collected samples were then subjected to whole genome sequencing. The development of daptomycin resistance in N315 was associated with previously identified mutations in genes coding for proteins that alter cell membrane charge and composition. Although genes involved in metabolic functions were also targets of mutation, the common route to resistance relied on a combination of mutations at a few key loci. Tracking the frequency of each mutation throughout the experiment revealed that mutations need not arise progressively in response to increasing antibiotic concentrations and that most mutations were present at low levels within populations earlier than would be recorded based on single-nucleotide polymorphism (SNP) filtering criteria. In contrast, a serial-passaged population showed only one mutation in a gene associated with resistance and provided limited detail on the changes that occur upon exposure to higher drug dosages. To conclude, this study demonstrates the successful in vitro modeling of antibiotic resistance in a bioreactor and highlights the evolutionary paths associated with the acquisition of daptomycin non-susceptibility. |
topic |
Staphylococcus aureus bioreactor culture daptomycin whole-genome sequencing analysis evolution of resistance |
url |
https://www.frontiersin.org/article/10.3389/fmicb.2019.00345/full |
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