The Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in <named-content content-type="genus-species">Acinetobacter baumannii</named-content>: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication

ABSTRACT The emergence of fluoroquinolone resistance in nosocomial pathogens has restricted the clinical efficacy of this antibiotic class. In Acinetobacter baumannii, the majority of clinical isolates now show high-level resistance due to mutations in gyrA (DNA gyrase) and parC (topoisomerase IV [t...

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Autores principales:	Edward Geisinger, Germán Vargas-Cuebas, Nadav J. Mortman, Sapna Syal, Yunfei Dai, Elizabeth L. Wainwright, David Lazinski, Stephen Wood, Zeyu Zhu, Jon Anthony, Tim van Opijnen, Ralph R. Isberg
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	Acinetobacter DNA gyrase fitness fluoroquinolone prophage antibiotic resistance Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/1509ec34b30745a8b0fd843a51447f90
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spelling	oai:doaj.org-article:1509ec34b30745a8b0fd843a51447f902021-11-15T15:55:25ZThe Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in <named-content content-type="genus-species">Acinetobacter baumannii</named-content>: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication10.1128/mBio.01127-192150-7511https://doaj.org/article/1509ec34b30745a8b0fd843a51447f902019-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01127-19https://doaj.org/toc/2150-7511ABSTRACT The emergence of fluoroquinolone resistance in nosocomial pathogens has restricted the clinical efficacy of this antibiotic class. In Acinetobacter baumannii, the majority of clinical isolates now show high-level resistance due to mutations in gyrA (DNA gyrase) and parC (topoisomerase IV [topo IV]). To investigate the molecular basis for fluoroquinolone resistance, an exhaustive mutation analysis was performed in both drug-sensitive and -resistant strains to identify loci that alter ciprofloxacin sensitivity. To this end, parallel fitness tests of over 60,000 unique insertion mutations were performed in strains with various alleles in genes encoding the drug targets. The spectra of mutations that altered drug sensitivity were found to be similar in the drug-sensitive and gyrA parC double-mutant backgrounds, having resistance alleles in both genes. In contrast, the introduction of a single gyrA resistance allele, resulting in preferential poisoning of topo IV by ciprofloxacin, led to extreme alterations in the insertion mutation fitness landscape. The distinguishing feature of preferential topo IV poisoning was enhanced induction of DNA synthesis in the region of two endogenous prophages, with DNA synthesis associated with excision and circularization of the phages. Induction of the selective DNA synthesis in the gyrA background was also linked to heightened prophage gene transcription and enhanced activation of the mutagenic SOS response relative to that observed in either the wild-type (WT) or gyrA parC double mutant. Therefore, the accumulation of mutations that result in the stepwise evolution of high ciprofloxacin resistance is tightly connected to modulation of the SOS response and endogenous prophage DNA synthesis. IMPORTANCE Fluoroquinolones have been extremely successful antibiotics due to their ability to target multiple bacterial enzymes critical to DNA replication, the topoisomerases DNA gyrase and topo IV. Unfortunately, mutations lowering drug affinity for both enzymes are now widespread, rendering these drugs ineffective for many pathogens. To undermine this form of resistance, we examined how bacteria with target alterations differentially cope with fluoroquinolone exposures. We studied this problem in the nosocomial pathogen A. baumannii, which causes drug-resistant life-threatening infections. Employing genome-wide approaches, we uncovered numerous pathways that could be exploited to raise fluoroquinolone sensitivity independently of target alteration. Remarkably, fluoroquinolone targeting of topo IV in specific mutants caused dramatic hyperinduction of prophage replication and enhanced the mutagenic DNA damage response, but these responses were muted in strains with DNA gyrase as the primary target. This work demonstrates that resistance evolution via target modification can profoundly modulate the antibiotic stress response, revealing potential resistance-associated liabilities.Edward GeisingerGermán Vargas-CuebasNadav J. MortmanSapna SyalYunfei DaiElizabeth L. WainwrightDavid LazinskiStephen WoodZeyu ZhuJon AnthonyTim van OpijnenRalph R. IsbergAmerican Society for MicrobiologyarticleAcinetobacterDNA gyrasefitnessfluoroquinoloneprophageantibiotic resistanceMicrobiologyQR1-502ENmBio, Vol 10, Iss 3 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Acinetobacter DNA gyrase fitness fluoroquinolone prophage antibiotic resistance Microbiology QR1-502
spellingShingle	Acinetobacter DNA gyrase fitness fluoroquinolone prophage antibiotic resistance Microbiology QR1-502 Edward Geisinger Germán Vargas-Cuebas Nadav J. Mortman Sapna Syal Yunfei Dai Elizabeth L. Wainwright David Lazinski Stephen Wood Zeyu Zhu Jon Anthony Tim van Opijnen Ralph R. Isberg The Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in <named-content content-type="genus-species">Acinetobacter baumannii</named-content>: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication
description	ABSTRACT The emergence of fluoroquinolone resistance in nosocomial pathogens has restricted the clinical efficacy of this antibiotic class. In Acinetobacter baumannii, the majority of clinical isolates now show high-level resistance due to mutations in gyrA (DNA gyrase) and parC (topoisomerase IV [topo IV]). To investigate the molecular basis for fluoroquinolone resistance, an exhaustive mutation analysis was performed in both drug-sensitive and -resistant strains to identify loci that alter ciprofloxacin sensitivity. To this end, parallel fitness tests of over 60,000 unique insertion mutations were performed in strains with various alleles in genes encoding the drug targets. The spectra of mutations that altered drug sensitivity were found to be similar in the drug-sensitive and gyrA parC double-mutant backgrounds, having resistance alleles in both genes. In contrast, the introduction of a single gyrA resistance allele, resulting in preferential poisoning of topo IV by ciprofloxacin, led to extreme alterations in the insertion mutation fitness landscape. The distinguishing feature of preferential topo IV poisoning was enhanced induction of DNA synthesis in the region of two endogenous prophages, with DNA synthesis associated with excision and circularization of the phages. Induction of the selective DNA synthesis in the gyrA background was also linked to heightened prophage gene transcription and enhanced activation of the mutagenic SOS response relative to that observed in either the wild-type (WT) or gyrA parC double mutant. Therefore, the accumulation of mutations that result in the stepwise evolution of high ciprofloxacin resistance is tightly connected to modulation of the SOS response and endogenous prophage DNA synthesis. IMPORTANCE Fluoroquinolones have been extremely successful antibiotics due to their ability to target multiple bacterial enzymes critical to DNA replication, the topoisomerases DNA gyrase and topo IV. Unfortunately, mutations lowering drug affinity for both enzymes are now widespread, rendering these drugs ineffective for many pathogens. To undermine this form of resistance, we examined how bacteria with target alterations differentially cope with fluoroquinolone exposures. We studied this problem in the nosocomial pathogen A. baumannii, which causes drug-resistant life-threatening infections. Employing genome-wide approaches, we uncovered numerous pathways that could be exploited to raise fluoroquinolone sensitivity independently of target alteration. Remarkably, fluoroquinolone targeting of topo IV in specific mutants caused dramatic hyperinduction of prophage replication and enhanced the mutagenic DNA damage response, but these responses were muted in strains with DNA gyrase as the primary target. This work demonstrates that resistance evolution via target modification can profoundly modulate the antibiotic stress response, revealing potential resistance-associated liabilities.
format	article
author	Edward Geisinger Germán Vargas-Cuebas Nadav J. Mortman Sapna Syal Yunfei Dai Elizabeth L. Wainwright David Lazinski Stephen Wood Zeyu Zhu Jon Anthony Tim van Opijnen Ralph R. Isberg
author_facet	Edward Geisinger Germán Vargas-Cuebas Nadav J. Mortman Sapna Syal Yunfei Dai Elizabeth L. Wainwright David Lazinski Stephen Wood Zeyu Zhu Jon Anthony Tim van Opijnen Ralph R. Isberg
author_sort	Edward Geisinger
title	The Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in <named-content content-type="genus-species">Acinetobacter baumannii</named-content>: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication
title_short	The Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in <named-content content-type="genus-species">Acinetobacter baumannii</named-content>: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication
title_full	The Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in <named-content content-type="genus-species">Acinetobacter baumannii</named-content>: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication
title_fullStr	The Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in <named-content content-type="genus-species">Acinetobacter baumannii</named-content>: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication
title_full_unstemmed	The Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in <named-content content-type="genus-species">Acinetobacter baumannii</named-content>: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication
title_sort	landscape of phenotypic and transcriptional responses to ciprofloxacin in <named-content content-type="genus-species">acinetobacter baumannii</named-content>: acquired resistance alleles modulate drug-induced sos response and prophage replication
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/1509ec34b30745a8b0fd843a51447f90
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The Landscape of Phenotypic and Transcriptional Responses to Ciprofloxacin in <named-content content-type="genus-species">Acinetobacter baumannii</named-content>: Acquired Resistance Alleles Modulate Drug-Induced SOS Response and Prophage Replication

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