1
|
Liu J, Wang Y, Deng X, Zhang M, Sun H, Gao L, Song H, Xin J, Ming R, Yang D, Yang M. Transcription factor NnMYB5 controls petal color by regulating GLUTATHIONE S-TRANSFERASE2 in Nelumbo nucifera. PLANT PHYSIOLOGY 2023; 193:1213-1226. [PMID: 37348874 PMCID: PMC10517185 DOI: 10.1093/plphys/kiad363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/24/2023]
Abstract
Lotus (Nelumbo spp.) is an important aquatic ornamental genus in the family Nelumbonaceae comprising only 2 species: Nelumbo lutea with yellow flowers and Nelumbo nucifera with red or white flowers. The petal color variations between these 2 species have previously been associated with the potential activities of FLAVONOL SYNTHASE (FLS) and MYB5. However, the underlying genetic mechanisms of flower color divergence within the N. nucifera species remain unclear. Here, quantitative trait locus mapping led to the identification of MYB5, a candidate gene controlling petal color in N. nucifera. Genotyping of 213 natural lotus accessions revealed an 80 kb presence/absence variant (PAV) of the NnMYB5 gene that is associated with petal color variation. Transcriptome analysis, dual-luciferase, and yeast 1-hybrid assays showed that NnMYB5 could directly activate the anthocyanin transporter gene GLUTATHIONE S-TRANSFERASE2 (NnGST2). Heterologous expression of NnGST2 in Arabidopsis (Arabidopsis thaliana) and its overexpression in lotus petals induced anthocyanin accumulation. Deletion of the 80 kb PAV within NnMYB5 inactivated NnGST2 expression and blocked anthocyanin accumulation in white N. nucifera petals. In contrast, the anthocyanin deficiency of N. lutea occurred due to pseudogenized NlMYB5 alleles. Our results establish a regulatory link between NnMYB5 and NnGST2 in petal anthocyanin accumulation and demonstrate the independent mechanisms controlling flower coloration in Nelumbo.
Collapse
Affiliation(s)
- Juan Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Yuxin Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- College of Life Science, University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Xianbao Deng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Minghua Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- College of Life Science, University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Heng Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Lei Gao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Heyun Song
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- College of Life Science, University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Jia Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- College of Life Science, University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Dong Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| |
Collapse
|
2
|
Pitcher NJ, Feder A, Bolden N, Zirbes CF, Pamatmat AJ, Boyken L, Hill JJ, Bartels AR, Thurman AL, Reeb VC, Porterfield HS, Moustafa AM, Planet PJ, Fischer AJ. Parallel evolution of linezolid-resistant Staphylococcus aureus in patients with cystic fibrosis. Microbiol Spectr 2023; 11:e0208423. [PMID: 37724867 PMCID: PMC10581212 DOI: 10.1128/spectrum.02084-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/10/2023] [Indexed: 09/21/2023] Open
Abstract
Linezolid is an antibiotic used to treat serious Staphylococcus aureus infections. Resistance to linezolid is considered rare but could emerge with repeated dosing. We recently reported widespread prescription of linezolid for a cohort of patients with cystic fibrosis (CF). The goals of this study were to determine the incidence of linezolid-resistant methicillin-resistant Staphylococcus aureus (MRSA) in CF and identify molecular mechanisms for linezolid resistance. We identified patients who cultured S. aureus resistant to linezolid with minimum inhibitory concentration (MIC) >4 at the University of Iowa CF Center between 2008 and 2018. We obtained isolates from these patients and retested susceptibility to linezolid using broth microdilution. We used whole genome sequencing to perform phylogenetic analysis of linezolid-resistant isolates and examine sequences for mutations or accessory genes that confer linezolid resistance. Between 2008 and 2018, 111 patients received linezolid, and 4 of these patients cultured linezolid-resistant S. aureus. We sequenced 11 resistant and 21 susceptible isolates from these 4 subjects. Phylogenetic analysis indicated that linezolid resistance developed in ST5 or ST105 backgrounds. Three individuals had linezolid-resistant S. aureus with a G2576T mutation in 23S rRNA. One of these subjects additionally had a mutS- mutL- hypermutating S. aureus that produced five resistant isolates with multiple ribosomal subunit mutations. In one subject, the genetic basis for linezolid resistance was unclear. We conclude that linezolid resistant S. aureus can occur through multiple genetic mechanisms in patients with repeated exposure to this antibiotic. IMPORTANCE Patients with cystic fibrosis have persistent lung infections with Staphylococcus aureus that require extensive antibiotic treatments. Linezolid, an antibiotic given by oral or intravenous route, is prescribed repeatedly for patients whose lung disease has progressed. After treatment with linezolid, S. aureus strains can evolve antibiotic resistance through multiple genetic mechanisms. In addition to a common mutation in the 23S ribosomal RNA known to confer linezolid resistance, S. aureus strains can evolve novel resistance based on a combination of mutations affecting the bacterial ribosome. This combination of mutations was observed in a strain that exhibited hypermutation owing to the loss of the DNA repair genes mutS and mutL. In this cohort of patients with cystic fibrosis, linezolid resistance was transient, possibly due to the growth disadvantage of resistant strains. However, ongoing chronic exposure to linezolid may create optimal conditions for the future emergence of resistance to this critical antibiotic.
Collapse
Affiliation(s)
- Nicholas J. Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Andries Feder
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nicholas Bolden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christian F. Zirbes
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Anthony J. Pamatmat
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Linda Boyken
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, lowa, USA
| | - Jared J. Hill
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Alyssa R. Bartels
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Andrew L. Thurman
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, lowa, USA
| | - Valerie C. Reeb
- State Hygienic Laboratory at the University of Iowa, Coralville, lowa, USA
| | | | - Ahmed M. Moustafa
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paul J. Planet
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Anthony J. Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| |
Collapse
|
3
|
Pitcher NJ, Feder A, Bolden N, Zirbes CF, Pamatmat AJ, Boyken L, Hill JJ, Thurman AL, Reeb VC, Porterfield HS, Moustafa AM, Planet PJ, Fischer AJ. Parallel Evolution of Linezolid Resistant Staphylococcus aureus in Patients with Cystic Fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539145. [PMID: 37205485 PMCID: PMC10187253 DOI: 10.1101/2023.05.02.539145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Background Linezolid is an antibiotic used to treat serious Staphylococcus aureus infections. Resistance to linezolid is considered rare but could emerge with repeated dosing. We recently reported widespread prescription of linezolid for a cohort of patients with cystic fibrosis (CF). Objectives The goals of this study were to determine the incidence of linezolid resistance in CF and identify molecular mechanisms for linezolid resistance. Methods We identified patients with S. aureus resistant to linezolid (MIC > 4) at the University of Iowa CF Center between 2008 and 2018. We obtained isolates from these patients and retested susceptibility to linezolid using broth microdilution. We used whole genome sequencing to perform phylogenetic analysis of linezolid resistant isolates and examine sequences for mutations or accessory genes that confer linezolid resistance. Main Results Between 2008 and 2018, 111 patients received linezolid and 4 of these patients cultured linezolid resistant S. aureus . We sequenced 11 resistant and 21 susceptible isolates from these 4 subjects. Phylogenetic analysis indicated that linezolid resistance developed in ST5 or ST105 backgrounds. Three individuals had linezolid resistant S. aureus with a G2576T mutation in 23S rRNA. One of these subjects additionally had a mutS - mutL - hypermutating S. aureus that produced 5 resistant isolates with multiple ribosomal subunit mutations. In one subject, the genetic basis for linezolid resistance was unclear. Conclusions Linezolid resistance evolved in 4 of 111 patients in this study. Linezolid resistance occurred by multiple genetic mechanisms. All resistant strains developed in ST5 or ST105 MRSA backgrounds. Key Point Linezolid resistance arises through multiple genetic mechanisms and could be facilitated by mutator phenotypes. Linezolid resistance was transient, possibly due to growth disadvantage.
Collapse
Affiliation(s)
- Nicholas J. Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Andries Feder
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Nicholas Bolden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Christian F. Zirbes
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Anthony J. Pamatmat
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Linda Boyken
- Pathology. University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Jared J. Hill
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Andrew L. Thurman
- Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Valérie C. Reeb
- State Hygienic Laboratory at the University of Iowa, Coralville, IA 52241
| | - Harry S. Porterfield
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Ahmed M. Moustafa
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul J. Planet
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Anthony J. Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| |
Collapse
|
4
|
Bianco CM, Moustafa AM, O’Brien K, Martin MA, Read TD, Kreiswirth BN, Planet PJ. Pre-epidemic evolution of the MRSA USA300 clade and a molecular key for classification. Front Cell Infect Microbiol 2023; 13:1081070. [PMID: 36761897 PMCID: PMC9902376 DOI: 10.3389/fcimb.2023.1081070] [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: 10/26/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction USA300 has remained the dominant community and healthcare associated methicillin-resistant Staphylococcus aureus (MRSA) clone in the United States and in northern South America for at least the past 20 years. In this time, it has experienced epidemic spread in both of these locations. However, its pre-epidemic evolutionary history and origins are incompletely understood. Large sequencing databases, such as NCBI, PATRIC, and Staphopia, contain clues to the early evolution of USA300 in the form of sequenced genomes of USA300 isolates that are representative of lineages that diverged prior to the establishment of the South American epidemic (SAE) clade and North American epidemic (NAE) clade. In addition, historical isolates collected prior to the emergence of epidemics can help reconstruct early events in the history of this lineage. Methods Here, we take advantage of the accrued, publicly available data, as well as two newly sequenced pre-epidemic historical isolates from 1996, and a very early diverging ACME-negative NAE genome, to understand the pre-epidemic evolution of USA300. We use database mining techniques to emphasize genomes similar to pre-epidemic isolates, with the goal of reconstructing the early molecular evolution of the USA300 lineage. Results Phylogenetic analysis with these genomes confirms that the NAE and SAE USA300 lineages diverged from a most recent common ancestor around 1970 with high confidence, and it also pinpoints the independent acquisition events of the of the ACME and COMER loci with greater precision than in previous studies. We provide evidence for a North American origin of the USA300 lineage and identify multiple introductions of USA300 into South and North America. Notably, we describe a third major USA300 clade (the pre-epidemic branching clade; PEB1) consisting of both MSSA and MRSA isolates circulating around the world that diverged from the USA300 lineage prior to the establishment of the South and North American epidemics. We present a detailed analysis of specific sequence characteristics of each of the major clades, and present diagnostic positions that can be used to classify new genomes.
Collapse
Affiliation(s)
- Colleen M. Bianco
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Ahmed M. Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kelsey O’Brien
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michael A. Martin
- Division of Infectious Diseases & Department of Human Genetics Emory University School of Medicine, Atlanta, GA, United States
| | - Timothy D. Read
- Division of Infectious Diseases & Department of Human Genetics Emory University School of Medicine, Atlanta, GA, United States
| | - Barry N. Kreiswirth
- Center for Discovery & Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Paul J. Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA, United States,American Museum of Natural History, New York, NY, United States,*Correspondence: Paul J. Planet,
| |
Collapse
|
5
|
Copper Resistance Promotes Fitness of Methicillin-Resistant Staphylococcus aureus during Urinary Tract Infection. mBio 2021; 12:e0203821. [PMID: 34488457 PMCID: PMC8546587 DOI: 10.1128/mbio.02038-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Urinary tract infection (UTI) is one of the most common infectious conditions affecting people in the United States and around the world. Our knowledge of the host-pathogen interaction during UTI caused by Gram-positive bacterial uropathogens is limited compared to that for Gram-negative pathogens. Here, we investigated whether copper and the primary copper-containing protein, ceruloplasmin, are mobilized to urine during naturally occurring UTI caused by Gram-positive uropathogens in patients. Next, we probed the role of copper resistance in the fitness of methicillin-resistant Staphylococcus aureus (MRSA) during experimental UTI in a murine model. Our findings demonstrate that urinary copper and ceruloplasmin content are elevated during UTI caused by Enterococcus faecalis, S. aureus, S. epidermidis, and S. saprophyticus. MRSA strains successfully colonize the urinary tract of female CBA mice with selective induction of inflammation in the kidneys but not the bladder. MRSA mutants lacking CopL, a copper-binding cell surface lipoprotein, and the ACME genomic region containing copL, exhibit decreased fitness in the mouse urinary tract compared to parental strains. Copper sensitivity assays, cell-associated copper and iron content, and bioavailability of iron during copper stress demonstrate that homeostasis of copper and iron is interlinked in S. aureus. Importantly, relative fitness of the MRSA mutant lacking the ACME region is further decreased in mice that receive supplemental copper compared to the parental strain. In summary, copper is mobilized to the urinary tract during UTI caused by Gram-positive pathogens, and copper resistance is a fitness factor for MRSA during UTI. IMPORTANCE Urinary tract infection (UTI) is an extremely common infectious condition affecting people throughout the world. Increasing antibiotic resistance in pathogens causing UTI threatens our ability to continue to treat patients in the clinics. Better understanding of the host-pathogen interface is critical for development of novel interventional strategies. Here, we sought to elucidate the role of copper in host-Staphylococcus aureus interaction during UTI. Our results reveal that copper is mobilized to the urine as a host response in patients with UTI. Our findings from the murine model of UTI demonstrate that copper resistance is involved in the fitness of methicillin-resistant S. aureus (MRSA) during interaction with the host. We also establish a critical link between adaptation to copper stress and iron homeostasis in S. aureus.
Collapse
|
6
|
Moustafa AM, Planet PJ. Emerging SARS-CoV-2 Diversity Revealed by Rapid Whole-Genome Sequence Typing. Genome Biol Evol 2021; 13:evab197. [PMID: 34432021 PMCID: PMC8449825 DOI: 10.1093/gbe/evab197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 12/14/2022] Open
Abstract
Discrete classification of SARS-CoV-2 viral genotypes can identify emerging strains and detect geographic spread, viral diversity, and transmission events. We developed a tool (GNU-based Virus IDentification [GNUVID]) that integrates whole-genome multilocus sequence typing and a supervised machine learning random forest-based classifier. We used GNUVID to assign sequence type (ST) profiles to all high-quality genomes available from GISAID. STs were clustered into clonal complexes (CCs) and then used to train a machine learning classifier. We used this tool to detect potential introduction and exportation events and to estimate effective viral diversity across locations and over time in 16 US states. GNUVID is a highly scalable tool for viral genotype classification (https://github.com/ahmedmagds/GNUVID) that can quickly classify hundreds of thousands of genomes in a way that is consistent with phylogeny. Our genotyping ST/CC analysis uncovered dynamic local changes in ST/CC prevalence and diversity with multiple replacement events in different states, an average of 20.6 putative introductions and 7.5 exportations for each state over the time period analyzed. We introduce the use of effective diversity metrics (Hill numbers) that can be used to estimate the impact of interventions (e.g., travel restrictions, vaccine uptake, mask mandates) on the variation in circulating viruses. Our classification tool uncovered multiple introduction and exportation events, as well as waves of expansion and replacement of SARS-CoV-2 genotypes in different states. GNUVID classification lends itself to measures of ecological diversity, and, with systematic genomic sampling, it could be used to track circulating viral diversity and identify emerging clones and hotspots.
Collapse
Affiliation(s)
- Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Pennsylvania, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| |
Collapse
|
7
|
Miller JJ, Shah IT, Hatten J, Barekatain Y, Mueller EA, Moustafa AM, Edwards RL, Dowd CS, Planet PJ, Muller FL, Jez JM, Odom John AR. Structure-guided microbial targeting of antistaphylococcal prodrugs. eLife 2021; 10:66657. [PMID: 34279224 PMCID: PMC8318587 DOI: 10.7554/elife.66657] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/16/2021] [Indexed: 01/07/2023] Open
Abstract
Carboxy ester prodrugs are widely employed to increase oral absorption and potency of phosphonate antibiotics. Prodrugging can mask problematic chemical features that prevent cellular uptake and may enable tissue-specific compound delivery. However, many carboxy ester promoieties are rapidly hydrolyzed by serum esterases, limiting their therapeutic potential. While carboxy ester-based prodrug targeting is feasible, it has seen limited use in microbes as microbial esterase-specific promoieties have not been described. Here we identify the bacterial esterases, GloB and FrmB, that activate carboxy ester prodrugs in Staphylococcus aureus. Additionally, we determine the substrate specificities for FrmB and GloB and demonstrate the structural basis of these preferences. Finally, we establish the carboxy ester substrate specificities of human and mouse sera, ultimately identifying several promoieties likely to be serum esterase-resistant and microbially labile. These studies will enable structure-guided design of antistaphylococcal promoieties and expand the range of molecules to target staphylococcal pathogens.
Collapse
Affiliation(s)
- Justin J Miller
- Department of Pediatrics, Washington University School of Medicine, St. Louis, United States.,Department of Biology, Washington University in St. Louis, St. Louis, United States
| | - Ishaan T Shah
- Department of Pediatrics, Washington University School of Medicine, St. Louis, United States
| | - Jayda Hatten
- Department of Pediatrics, Washington University School of Medicine, St. Louis, United States
| | - Yasaman Barekatain
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Elizabeth A Mueller
- Department of Biology, Washington University in St. Louis, St. Louis, United States
| | - Ahmed M Moustafa
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, United States
| | - Rachel L Edwards
- Department of Pediatrics, Washington University School of Medicine, St. Louis, United States
| | - Cynthia S Dowd
- Department of Chemistry, The George Washington University, Washington, United States
| | - Paul J Planet
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, United States
| | - Florian L Muller
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Joseph M Jez
- Department of Biology, Washington University in St. Louis, St. Louis, United States
| | - Audrey R Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, United States.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, United States
| |
Collapse
|
8
|
Viana AS, Nunes Botelho AM, Moustafa AM, Boge CL, Pires Ferreira AL, da Silva Carvalho MC, Guimarães MA, Costa BDSS, de Mattos MC, Maciel SP, Echevarria-Lima J, Narechania A, O’Brien K, Ryan C, Gerber JS, Carvalho BTF, Figueiredo AMS, Planet PJ. Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus Associated with Bacteremia and Monocyte Evasion, Rio de Janeiro, Brazil. Emerg Infect Dis 2021; 27:2825-2835. [PMID: 34670645 PMCID: PMC8544994 DOI: 10.3201/eid2711.210097] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We typed 600 methicillin-resistant Staphylococcus aureus (MRSA) isolates collected in 51 hospitals in the Rio de Janeiro, Brazil, metropolitan area during 2014-2017. We found that multiple new clonal complex (CC) 5 sequence types had replaced previously dominant MRSA lineages in hospitals. Whole-genome analysis of 208 isolates revealed an emerging sublineage of multidrug-resistant MRSA, sequence type 105, staphylococcal cassette chromosome mec II, spa t002, which we designated the Rio de Janeiro (RdJ) clone. Using molecular clock analysis, we hypothesized that this lineage began to expand in the Rio de Janeiro metropolitan area in 2009. Multivariate analysis supported an association between bloodstream infections and the CC5 lineage that includes the RdJ clone. Compared with other closely related isolates, representative isolates of the RdJ clone more effectively evaded immune function related to monocytic cells, as evidenced by decreased phagocytosis rate and increased numbers of viable unphagocytosed (free) bacteria after in vitro exposure to monocytes.
Collapse
Affiliation(s)
| | | | | | - Craig L.K. Boge
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Adriana Lucia Pires Ferreira
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Maria Cícera da Silva Carvalho
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Márcia Aparecida Guimarães
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | | | - Marcos Corrêa de Mattos
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Sabrina Pires Maciel
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Juliana Echevarria-Lima
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Apurva Narechania
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Kelsey O’Brien
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Chanelle Ryan
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Jeffrey S. Gerber
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Bernadete Teixeira Ferreira Carvalho
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | | | | |
Collapse
|
9
|
Moustafa AM, Planet PJ. Emerging SARS-CoV-2 diversity revealed by rapid whole genome sequence typing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33398274 PMCID: PMC7781309 DOI: 10.1101/2020.12.28.424582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background Discrete classification of SARS-CoV-2 viral genotypes can identify emerging strains and detect geographic spread, viral diversity, and transmission events. Methods We developed a tool (GNUVID) that integrates whole genome multilocus sequence typing and a supervised machine learning random forest-based classifier. We used GNUVID to assign sequence type (ST) profiles to each of 69,686 SARS-CoV-2 complete, high-quality genomes available from GISAID as of October 20th 2020. STs were then clustered into clonal complexes (CCs), and then used to train a machine learning classifier. We used this tool to detect potential introduction and exportation events, and to estimate effective viral diversity across locations and over time in 16 US states. Results GNUVID is a scalable tool for viral genotype classification (available at https://github.com/ahmedmagds/GNUVID) that can be used to quickly process tens of thousands of genomes. Our genotyping ST/CC analysis uncovered dynamic local changes in ST/CC prevalence and diversity with multiple replacement events in different states. We detected an average of 20.6 putative introductions and 7.5 exportations for each state. Effective viral diversity dropped in all states as shelter-in-place travel-restrictions went into effect and increased as restrictions were lifted. Interestingly, our analysis showed correlation between effective diversity and the date that state-wide mask mandates were imposed. Conclusions Our classification tool uncovered multiple introduction and exportation events, as well as waves of expansion and replacement of SARS-CoV-2 genotypes in different states. Combined with future genomic sampling the GNUVID system could be used to track circulating viral diversity and identify emerging clones and hotspots.
Collapse
Affiliation(s)
- Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| |
Collapse
|
10
|
Moustafa AM, Lal A, Planet PJ. Comparative genomics in infectious disease. Curr Opin Microbiol 2020; 53:61-70. [PMID: 32248056 DOI: 10.1016/j.mib.2020.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 02/07/2023]
Abstract
With more than one million bacterial genome sequences uploaded to public databases in the last 25 years, genomics has become a powerful tool for studying bacterial biology. Here, we review recent approaches that leverage large numbers of whole genome sequences to decipher the spread and pathogenesis of bacterial infectious diseases.
Collapse
Affiliation(s)
- Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Arnav Lal
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA.
| |
Collapse
|
11
|
Abstract
To understand diversity in enormous collections of genome sequences, we need computationally scalable tools that can quickly contextualize individual genomes based on their similarities and identify features of each genome that make them unique. We present WhatsGNU, a tool based on exact match proteomic compression that, in seconds, classifies any new genome and provides a detailed report of protein alleles that may have novel functional differences. We use this technique to characterize the total allelic diversity (panallelome) of Salmonella enterica, Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Staphylococcus aureus. It could be extended to others. WhatsGNU is available from https://github.com/ahmedmagds/WhatsGNU.
Collapse
Affiliation(s)
- Ahmed M. Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Paul J. Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024 USA
| |
Collapse
|