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Maxson T, Overholt WA, Chivukula V, Caban-Figueroa V, Kongphet-Tran T, Medina Cordoba LK, Cherney B, Rishishwar L, Conley A, Sue D. Genetic basis of clarithromycin resistance in Bacillus anthracis. Microbiol Spectr 2024; 12:e0418023. [PMID: 38666793 DOI: 10.1128/spectrum.04180-23] [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: 12/11/2023] [Accepted: 03/26/2024] [Indexed: 06/06/2024] Open
Abstract
The high-consequence pathogen Bacillus anthracis causes human anthrax and often results in lethal infections without the rapid administration of effective antimicrobial treatment. Antimicrobial resistance profiling is therefore critical to inform post-exposure prophylaxis and treatment decisions, especially during emergencies such as outbreaks or where intentional release is suspected. Whole-genome sequencing using a rapid long-read sequencer can uncover antimicrobial resistance patterns if genetic markers of resistance are known. To identify genomic markers associated with antimicrobial resistance, we isolated B. anthracis derived from the avirulent Sterne strain with elevated minimal inhibitory concentrations to clarithromycin. Mutants were characterized both phenotypically through broth microdilution susceptibility testing and observations during culturing, as well as genotypically with whole-genome sequencing. We identified two different in-frame insertions in the L22 ribosomal protein-encoding gene rplV, which were subsequently confirmed to be involved in clarithromycin resistance through the reversion of the mutant gene to the parent (drug-susceptible) sequence. Detection of the rplV insertions was possible with rapid long-read sequencing, with a time-to-answer within 3 h. The mutations associated with clarithromycin resistance described here will be used in conjunction with known genetic markers of resistance for other antimicrobials to strengthen the prediction of antimicrobial resistance in B. anthracis.IMPORTANCEThe disease anthrax, caused by the pathogen Bacillus anthracis, is extremely deadly if not treated quickly and appropriately. Clarithromycin is an antibiotic recommended for the treatment and post-exposure prophylaxis of anthrax by the Centers for Disease Control and Prevention; however, little is known about the ability of B. anthracis to develop resistance to clarithromycin or the mechanism of that resistance. The characterization of clarithromycin-resistant isolates presented here provides valuable information for researchers and clinicians in the event of a release of the resistant strain. Additionally, knowledge of the genetic basis of resistance provides a foundation for susceptibility prediction through rapid genome sequencing to inform timely treatment decisions.
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Affiliation(s)
- Tucker Maxson
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Will A Overholt
- Applied Bioinformatics Laboratory (ASRT, Inc.; IHRC, Inc.), Atlanta, Georgia, USA
| | - Vasanta Chivukula
- Applied Bioinformatics Laboratory (ASRT, Inc.; IHRC, Inc.), Atlanta, Georgia, USA
| | | | - Thiphasone Kongphet-Tran
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Luz K Medina Cordoba
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Blake Cherney
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lavanya Rishishwar
- Applied Bioinformatics Laboratory (ASRT, Inc.; IHRC, Inc.), Atlanta, Georgia, USA
| | - Andrew Conley
- Applied Bioinformatics Laboratory (ASRT, Inc.; IHRC, Inc.), Atlanta, Georgia, USA
| | - David Sue
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Archana CA, Sekar YS, Suresh KP, Subramaniam S, Sagar N, Rani S, Anandakumar J, Pandey RK, Barman NN, Patil SS. Investigating the Influence of ANTXR2 Gene Mutations on Protective Antigen Binding for Heightened Anthrax Resistance. Genes (Basel) 2024; 15:426. [PMID: 38674361 PMCID: PMC11049084 DOI: 10.3390/genes15040426] [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: 02/23/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Bacillus anthracis is the bacterium responsible for causing the zoonotic disease called anthrax. The disease presents itself in different forms like gastrointestinal, inhalation, and cutaneous. Bacterial spores are tremendously adaptable, can persist for extended periods and occasionally endanger human health. The Anthrax Toxin Receptor-2 (ANTXR2) gene acts as membrane receptor and facilitates the entry of the anthrax toxin into host cells. Additionally, mutations in the ANTXR2 gene have been linked to various autoimmune diseases, including Hyaline Fibromatosis Syndrome (HFS), Ankylosing Spondylitis (AS), Juvenile Hyaline Fibromatosis (JHF), and Infantile Systemic Hyalinosis (ISH). This study delves into the genetic landscape of ANTXR2, aiming to comprehend its associations with diverse disorders, elucidate the impacts of its mutations, and pinpoint minimal non-pathogenic mutations capable of reducing the binding affinity of the ANTXR2 gene with the protective antigen. Recognizing the pivotal role of single-nucleotide polymorphisms (SNPs) in shaping genetic diversity, we conducted computational analyses to discern highly deleterious and tolerated non-synonymous SNPs (nsSNPs) in the ANTXR2 gene. The Mutpred2 server determined that the Arg465Trp alteration in the ANTXR2 gene leads to altered DNA binding (p = 0.22) with a probability of a deleterious mutation of 0.808; notably, among the identified deleterious SNPs, rs368288611 (Arg465Trp) stands out due to its significant impact on altering the DNA-binding ability of ANTXR2. We propose these SNPs as potential candidates for hypertension linked to the ANTXR2 gene, which is implicated in blood pressure regulation. Noteworthy among the tolerated substitutions is rs200536829 (Ala33Ser), recognized as less pathogenic; this highlights its potential as a valuable biomarker, potentially reducing side effects on the host while also reducing binding with the protective antigen protein. Investigating these SNPs holds the potential to correlate with several autoimmune disorders and mitigate the impact of anthrax disease in humans.
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Affiliation(s)
- Chamalapura Ashwathama Archana
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | - Yamini Sri Sekar
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | - Kuralayanapalya Puttahonnappa Suresh
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | | | - Ningegowda Sagar
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | - Swati Rani
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | - Jayashree Anandakumar
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
| | - Rajan Kumar Pandey
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Solna, Sweden;
| | - Nagendra Nath Barman
- College of Veterinary Science, Assam Agricultural University (AAU), Guwahati 781022, India;
| | - Sharanagouda S. Patil
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Bengaluru 560064, India; (C.A.A.); (Y.S.S.); (N.S.); (S.R.); (J.A.); (S.S.P.)
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3
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Squire S, Sebghati S, Hammond MC. Cytoplasmic Accumulation and Permeability of Antibiotics in Gram Positive and Gram Negative Bacteria Visualized in Real-Time via a Fluorogenic Tagging Strategy. ACS Chem Biol 2024; 19:3-8. [PMID: 38096425 PMCID: PMC10805102 DOI: 10.1021/acschembio.3c00510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 01/23/2024]
Abstract
In this study, we describe the first real-time live cell assay for compound accumulation and permeability in both Gram positive and Gram negative bacteria. The assay utilizes a novel fluorogenic tagging strategy that permits direct visualization of compound accumulation dynamics in the cytoplasm of live cells, unobscured by washing or other processing steps. Quantitative differences could be reproducibly measured by flow cytometry at compound concentrations below the limit of detection for MS-based approaches. We establish the fluorogenic assay in E. coli and B. subtilis and compare the intracellular accumulation of two antibiotics, ciprofloxacin and ampicillin, with related pharmacophores in these bacteria.
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Affiliation(s)
- Scott
O. Squire
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Sepehr Sebghati
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Ming C. Hammond
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
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4
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Luo ZX, Li Y, Liu MF, Zhao R. Ciprofloxacin enhances the biofilm formation of Staphylococcus aureus via an agrC-dependent mechanism. Front Microbiol 2023; 14:1328947. [PMID: 38179460 PMCID: PMC10764545 DOI: 10.3389/fmicb.2023.1328947] [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: 10/27/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Staphylococcus aureus readily forms biofilms on host tissues and medical devices, enabling its persistence in chronic infections and resistance to antibiotic therapy. The accessory gene regulator (Agr) quorum sensing system plays a key role in regulating S. aureus biofilm formation. This study reveals the widely used fluoroquinolone antibiotic, ciprofloxacin, strongly stimulates biofilm formation in methicillin-resistant S. aureus, methicillin-sensitive S. aureus, and clinical isolates with diverse genetic backgrounds. Crystal violet staining indicated that ciprofloxacin induced a remarkable 12.46- to 15.19-fold increase in biofilm biomass. Confocal laser scanning microscopy revealed that ciprofloxacin induced denser biofilms. Phenotypic assays suggest that ciprofloxacin may enhance polysaccharide intercellular adhesin production, inhibit autolysis, and reduce proteolysis during the biofilm development, thus promoting initial adhesion and enhancing biofilm stability. Mechanistically, ciprofloxacin significantly alters the expression of various biofilm-related genes (icaA, icaD, fnbA, fnbB, eap, emp) and regulators (agrA, saeR). Gene knockout experiments revealed that deletion of agrC, rather than saeRS, abolishes the ciprofloxacin-induced enhancement of biofilm formation, underscoring the key role of agrC. Thermal shift assays showed ciprofloxacin binds purified AgrC protein, thereby inhibiting the Agr system. Molecular docking results further support the potential interaction between ciprofloxacin and AgrC. In summary, subinhibitory concentrations of ciprofloxacin stimulate S. aureus biofilm formation via an agrC-dependent pathway. This inductive effect may facilitate local infection establishment and bacterial persistence, ultimately leading to therapeutic failure.
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Affiliation(s)
- Zhao-xia Luo
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, China
- School of Public Health, Nanchang University, Nanchang, China
| | - Yuting Li
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, China
- School of Public Health, Nanchang University, Nanchang, China
| | - Mei-fang Liu
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Rui Zhao
- Department of Clinical Laboratory, Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, China
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5
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Shariati A, Arshadi M, Khosrojerdi MA, Abedinzadeh M, Ganjalishahi M, Maleki A, Heidary M, Khoshnood S. The resistance mechanisms of bacteria against ciprofloxacin and new approaches for enhancing the efficacy of this antibiotic. Front Public Health 2022; 10:1025633. [PMID: 36620240 PMCID: PMC9815622 DOI: 10.3389/fpubh.2022.1025633] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
For around three decades, the fluoroquinolone (FQ) antibiotic ciprofloxacin has been used to treat a range of diseases, including chronic otorrhea, endocarditis, lower respiratory tract, gastrointestinal, skin and soft tissue, and urinary tract infections. Ciprofloxacin's main mode of action is to stop DNA replication by blocking the A subunit of DNA gyrase and having an extra impact on the substances in cell walls. Available in intravenous and oral formulations, ciprofloxacin reaches therapeutic concentrations in the majority of tissues and bodily fluids with a low possibility for side effects. Despite the outstanding qualities of this antibiotic, Salmonella typhi, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa have all shown an increase in ciprofloxacin resistance over time. The rise of infections that are resistant to ciprofloxacin shows that new pharmacological synergisms and derivatives are required. To this end, ciprofloxacin may be more effective against the biofilm community of microorganisms and multi-drug resistant isolates when combined with a variety of antibacterial agents, such as antibiotics from various classes, nanoparticles, natural products, bacteriophages, and photodynamic therapy. This review focuses on the resistance mechanisms of bacteria against ciprofloxacin and new approaches for enhancing its efficacy.
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Affiliation(s)
- Aref Shariati
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein, Iran
| | - Maniya Arshadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Mostafa Abedinzadeh
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mahsa Ganjalishahi
- Student Research Committee, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Abbas Maleki
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran,Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran,*Correspondence: Mohsen Heidary
| | - Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran,Student Research Committee, Ilam University of Medical Sciences, Ilam, Iran,Saeed Khoshnood
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6
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Maxson T, Kongphet-Tran T, Mongkolrattanothai T, Travis T, Hendricks K, Parker C, McLaughlin HP, Bugrysheva J, Ambrosio F, Michel P, Cherney B, Lascols C, Sue D. Systematic Review of In Vitro Antimicrobial Susceptibility Testing for Bacillus anthracis, 1947-2019. Clin Infect Dis 2022; 75:S373-S378. [PMID: 36251548 PMCID: PMC9649422 DOI: 10.1093/cid/ciac520] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Indexed: 11/05/2022] Open
Abstract
Bacillus anthracis, the causative agent of anthrax, is a high-consequence bacterial pathogen that occurs naturally in many parts of the world and is considered an agent of biowarfare or bioterrorism. Understanding antimicrobial susceptibility profiles of B. anthracis isolates is foundational to treating naturally occurring outbreaks and to public health preparedness in the event of an intentional release. In this systematic review, we searched the peer-reviewed literature for all publications detailing antimicrobial susceptibility testing of B. anthracis. Within the set of discovered articles, we collated a subset of publications detailing susceptibility testing that followed standardized protocols for Food and Drug Administration-approved, commercially available antimicrobials. We analyzed the findings from the discovered articles, including the reported minimal inhibitory concentrations. Across the literature, most B. anthracis isolates were reported as susceptible to current first-line antimicrobials recommended for postexposure prophylaxis and treatment. The data presented for potential alternative antimicrobials will be of use if significant resistance to first-line antimicrobials arises, the strain is bioengineered, or first-line antimicrobials are not tolerated or available.
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Affiliation(s)
- Tucker Maxson
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thiphasone Kongphet-Tran
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thitipong Mongkolrattanothai
- Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tatiana Travis
- Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katherine Hendricks
- Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Corinne Parker
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heather P McLaughlin
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Julia Bugrysheva
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Frank Ambrosio
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Pierre Michel
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Blake Cherney
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christine Lascols
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - David Sue
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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7
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Artificial Selection for Pathogenicity Mutations in Staphylococcus aureus Identifies Novel Factors Relevant to Chronic Infection. Infect Immun 2019; 87:IAI.00884-18. [PMID: 30642903 DOI: 10.1128/iai.00884-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Adaptation of Staphylococcus aureus to host microenvironments during chronic infection involves spontaneous mutations, yet changes underlying adaptive phenotypes remain incompletely explored. Here, we employed artificial selection and whole-genome sequencing to better characterize spontaneous chromosomal mutations that alter two pathogenicity phenotypes relevant to chronic infection in S. aureus: intracellular invasiveness and intracellular cytotoxicity. We identified 23 genes whose alteration coincided with enhanced virulence, 11 that were previously known and 12 (52%) that had no previously described role in S. aureus pathogenicity. Using precision genome editing, transposon mutants, and gene complementation, we empirically assessed the contributions of individual genes to the two virulence phenotypes. We functionally validated 14 of 21 genes tested as measurably influencing invasion and/or cytotoxicity, including 8 newly implicated by this study. We identified inactivating mutations (murA, ndhC, and a hypothetical membrane protein) and gain-of-function mutations (aroE Thr182Ile, yhcF Thr74Ile, and Asp486Glu in a hypothetical peptidase) in previously unrecognized S. aureus virulence genes that enhance pathogenesis when introduced into a clean genetic background, as well as a novel activating mutation in the known virulence regulator gene saeS (Ala106Thr). Investigation of potentially epistatic interactions identified a tufA mutation (Ala271Val) that enhances virulence only in the context of purine operon repressor gene (purR) inactivation. This project reveals a functionally diverse range of genes affected by gain- or loss-of-function mutations that contribute to S. aureus adaptive virulence phenotypes. More generally, the work establishes artificial selection as a means to determine the genetic mechanisms underlying complex bacterial phenotypes relevant to adaptation during infection.
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8
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Gargis AS, McLaughlin HP, Conley AB, Lascols C, Michel PA, Gee JE, Marston CK, Kolton CB, Rodriguez-R LM, Hoffmaster AR, Weigel LM, Sue D. Analysis of Whole-Genome Sequences for the Prediction of Penicillin Resistance and β-Lactamase Activity in Bacillus anthracis. mSystems 2018; 3:e00154-18. [PMID: 30574557 PMCID: PMC6290263 DOI: 10.1128/msystems.00154-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/14/2018] [Indexed: 12/01/2022] Open
Abstract
Penicillin (PEN) is a low-cost option for anthrax treatment, but naturally occurring resistance has been reported. β-Lactamase expression (bla1, bla2) in Bacillus anthracis is regulated by a sigma factor (SigP) and its cognate anti-sigma factor (RsiP). Mutations leading to truncation of RsiP were previously described as a basis for PEN resistance. Here, we analyze whole-genome sequencing (WGS) data and compare the chromosomal sigP-bla1 regions from 374 B. anthracis strains to determine the frequency of mutations, identify mutations associated with PEN resistance, and evaluate the usefulness of WGS for predicting PEN resistance. Few (3.5%) strains contained at least 1 of 11 different mutations in sigP, rsiP, or bla1. Nine of these mutations have not been previously associated with PEN resistance. Four strains showed PEN resistance (PEN-R) by conventional broth microdilution, including 1 strain with a novel frameshift in rsiP. One strain that carries the same rsiP frameshift mutation as that found previously in a PEN-R strain showed a PEN-susceptible (PEN-S) phenotype and exhibited decreased bla1 and bla2 transcription. An unexpectedly small colony size, a reduced growth rate, and undetectable β-lactamase activity levels (culture supernatant and cell lysate) were observed in this PEN-S strain. Sequence analysis revealed mutations in genes associated with growth defects that may contribute to this phenotype. While B. anthracis rsiP mutations cannot be exclusively used to predict resistance, four of the five strains with rsiP mutations were PEN-R. Therefore, the B. anthracis sigP-bla1 region is a useful locus for WGS-based PEN resistance prediction, but phenotypic testing remains essential. IMPORTANCE Determination of antimicrobial susceptibility of B. anthracis is essential for the appropriate distribution of antimicrobial agents for postexposure prophylaxis (PEP) and treatment of anthrax. Analysis of WGS data allows for the rapid detection of mutations in antimicrobial resistance (AMR) genes in an isolate, but the presence of a mutation in an AMR gene does not always accurately predict resistance. As mutations in the anti-sigma factor RsiP have been previously associated with high-level penicillin resistance in a limited number of strains, we investigated WGS assemblies from 374 strains to determine the frequency of mutations and performed functional antimicrobial susceptibility testing. Of the five strains that contained mutations in rsiP, only four were PEN-R by functional antimicrobial susceptibility testing. We conclude that while sequence analysis of this region is useful for AMR prediction in B. anthracis, genetic analysis should not be used exclusively and phenotypic susceptibility testing remains essential.
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Affiliation(s)
- A. S. Gargis
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - H. P. McLaughlin
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - A. B. Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
| | - C. Lascols
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - P. A. Michel
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J. E. Gee
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - C. K. Marston
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - C. B. Kolton
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - L. M. Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - A. R. Hoffmaster
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - L. M. Weigel
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - D. Sue
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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9
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Hassan KA, Fagerlund A, Elbourne LDH, Vörös A, Kroeger JK, Simm R, Tourasse NJ, Finke S, Henderson PJF, Økstad OA, Paulsen IT, Kolstø AB. The putative drug efflux systems of the Bacillus cereus group. PLoS One 2017; 12:e0176188. [PMID: 28472044 PMCID: PMC5417439 DOI: 10.1371/journal.pone.0176188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 04/06/2017] [Indexed: 12/19/2022] Open
Abstract
The Bacillus cereus group of bacteria includes seven closely related species, three of which, B. anthracis, B. cereus and B. thuringiensis, are pathogens of humans, animals and/or insects. Preliminary investigations into the transport capabilities of different bacterial lineages suggested that genes encoding putative efflux systems were unusually abundant in the B. cereus group compared to other bacteria. To explore the drug efflux potential of the B. cereus group all putative efflux systems were identified in the genomes of prototypical strains of B. cereus, B. anthracis and B. thuringiensis using our Transporter Automated Annotation Pipeline. More than 90 putative drug efflux systems were found within each of these strains, accounting for up to 2.7% of their protein coding potential. Comparative analyses demonstrated that the efflux systems are highly conserved between these species; 70-80% of the putative efflux pumps were shared between all three strains studied. Furthermore, 82% of the putative efflux system proteins encoded by the prototypical B. cereus strain ATCC 14579 (type strain) were found to be conserved in at least 80% of 169 B. cereus group strains that have high quality genome sequences available. However, only a handful of these efflux pumps have been functionally characterized. Deletion of individual efflux pump genes from B. cereus typically had little impact to drug resistance phenotypes or the general fitness of the strains, possibly because of the large numbers of alternative efflux systems that may have overlapping substrate specificities. Therefore, to gain insight into the possible transport functions of efflux systems in B. cereus, we undertook large-scale qRT-PCR analyses of efflux pump gene expression following drug shocks and other stress treatments. Clustering of gene expression changes identified several groups of similarly regulated systems that may have overlapping drug resistance functions. In this article we review current knowledge of the small molecule efflux pumps encoded by the B. cereus group and suggest the likely functions of numerous uncharacterised pumps.
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Affiliation(s)
- Karl A. Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
- School of BioMedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Annette Fagerlund
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Liam D. H. Elbourne
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Aniko Vörös
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Jasmin K. Kroeger
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Institut für Pharmazeutische Biologie und Biotechnologie, Albert-Ludwigs Universität, Freiburg, Germany
| | - Roger Simm
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Nicolas J. Tourasse
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Sarah Finke
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Peter J. F. Henderson
- School of BioMedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Ole Andreas Økstad
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
- * E-mail: (ABK); (ITP)
| | - Anne-Brit Kolstø
- Laboratory for Microbial Dynamics (LaMDa), Section for Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway
- * E-mail: (ABK); (ITP)
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10
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Jaing CJ, McLoughlin KS, Thissen JB, Zemla A, Gardner SN, Vergez LM, Bourguet F, Mabery S, Fofanov VY, Koshinsky H, Jackson PJ. Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing. PLoS One 2016; 11:e0163458. [PMID: 27668749 PMCID: PMC5036845 DOI: 10.1371/journal.pone.0163458] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/08/2016] [Indexed: 11/19/2022] Open
Abstract
Francisella tularensis is classified as a Class A bioterrorism agent by the U.S. government due to its high virulence and the ease with which it can be spread as an aerosol. It is a facultative intracellular pathogen and the causative agent of tularemia. Ciprofloxacin (Cipro) is a broad spectrum antibiotic effective against Gram-positive and Gram-negative bacteria. Increased Cipro resistance in pathogenic microbes is of serious concern when considering options for medical treatment of bacterial infections. Identification of genes and loci that are associated with Ciprofloxacin resistance will help advance the understanding of resistance mechanisms and may, in the future, provide better treatment options for patients. It may also provide information for development of assays that can rapidly identify Cipro-resistant isolates of this pathogen. In this study, we selected a large number of F. tularensis live vaccine strain (LVS) isolates that survived in progressively higher Ciprofloxacin concentrations, screened the isolates using a whole genome F. tularensis LVS tiling microarray and Illumina sequencing, and identified both known and novel mutations associated with resistance. Genes containing mutations encode DNA gyrase subunit A, a hypothetical protein, an asparagine synthase, a sugar transamine/perosamine synthetase and others. Structural modeling performed on these proteins provides insights into the potential function of these proteins and how they might contribute to Cipro resistance mechanisms.
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Affiliation(s)
- Crystal J. Jaing
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
- * E-mail:
| | - Kevin S. McLoughlin
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - James B. Thissen
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Adam Zemla
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Shea N. Gardner
- Computations Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Lisa M. Vergez
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Feliza Bourguet
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | - Shalini Mabery
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
| | | | | | - Paul J. Jackson
- Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America
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11
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McGann P, Bunin JL, Snesrud E, Singh S, Maybank R, Ong AC, Kwak YI, Seronello S, Clifford RJ, Hinkle M, Yamada S, Barnhill J, Lesho E. Real time application of whole genome sequencing for outbreak investigation - What is an achievable turnaround time? Diagn Microbiol Infect Dis 2016; 85:277-282. [PMID: 27185645 DOI: 10.1016/j.diagmicrobio.2016.04.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/30/2016] [Accepted: 04/27/2016] [Indexed: 12/20/2022]
Abstract
Whole genome sequencing (WGS) is increasingly employed in clinical settings, though few assessments of turnaround times (TAT) have been performed in real-time. In this study, WGS was used to investigate an unfolding outbreak of vancomycin resistant Enterococcus faecium (VRE) among 3 patients in the ICU of a tertiary care hospital. Including overnight culturing, a TAT of just 48.5 h for a comprehensive report was achievable using an Illumina Miseq benchtop sequencer. WGS revealed that isolates from patient 2 and 3 differed from that of patient 1 by a single nucleotide polymorphism (SNP), indicating nosocomial transmission. However, the unparalleled resolution provided by WGS suggested that nosocomial transmission involved two separate events from patient 1 to patient 2 and 3, and not a linear transmission suspected by the time line. Rapid TAT's are achievable using WGS in the clinical setting and can provide an unprecedented level of resolution for outbreak investigations.
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Affiliation(s)
- Patrick McGann
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - Jessica L Bunin
- Department of Critical Care, Tripler Army Medical Center, Honolulu, HI, USA
| | - Erik Snesrud
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Seema Singh
- Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA
| | - Rosslyn Maybank
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ana C Ong
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Yoon I Kwak
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Scott Seronello
- Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA
| | - Robert J Clifford
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mary Hinkle
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Stephen Yamada
- Infectious Diseases Service, Tripler Army Medical Center, Honolulu, HI, USA
| | - Jason Barnhill
- Department of Pathology, Tripler Army Medical Center, Honolulu, HI, USA
| | - Emil Lesho
- Multidrug-resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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12
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Bertelli C, Greub G. Rapid bacterial genome sequencing: methods and applications in clinical microbiology. Clin Microbiol Infect 2013; 19:803-13. [DOI: 10.1111/1469-0691.12217] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/02/2013] [Accepted: 03/07/2013] [Indexed: 02/01/2023]
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13
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Systems-level antimicrobial drug and drug synergy discovery. Nat Chem Biol 2013; 9:222-31. [PMID: 23508188 DOI: 10.1038/nchembio.1205] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/07/2013] [Indexed: 01/01/2023]
Abstract
Here, we review the 'target-centric' genomic strategy to antimicrobial discovery and share our perspective on identification, validation and prioritization of potential antimicrobial drug targets in the context of emerging chemical biology, genomics and phenotypic screening strategies. We propose that coupling the dual processes of antimicrobial small-molecule screening and target identification in a whole-cell context is essential to empirically annotate 'druggable' targets and advance early stage antimicrobial discovery. We also advocate a systems-level approach to annotating synthetic-lethal genetic interactions comprehensively within yeast and bacteria models. The resulting genetic interaction networks provide a landscape to rationally predict and exploit drug synergy between cognate inhibitors. We posit that synergistic combination agents provide an important and largely unexploited strategy to 'repurpose' existing chemical space and simultaneously address issues of potency, spectrum, toxicity and drug resistance in early stages of antimicrobial drug discovery.
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14
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Yuan Y, Peng Q, Gao M. Characteristics of a broad lytic spectrum endolysin from phage BtCS33 of Bacillus thuringiensis. BMC Microbiol 2012; 12:297. [PMID: 23249212 PMCID: PMC3534610 DOI: 10.1186/1471-2180-12-297] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 12/10/2012] [Indexed: 12/19/2022] Open
Abstract
Background Endolysins produced by bacteriophages lyse bacteria, and are thus considered a novel type of antimicrobial agent. Several endolysins from Bacillus phages or prophages have previously been characterized and used to target Bacillus strains that cause disease in animals and humans. B. thuringiensis phage BtCS33 is a Siphoviridae family phage and its genome has been sequenced and analyzed. In the BtCS33 genome, orf18 was found to encode an endolysin protein (PlyBt33). Results Bioinformatic analyses showed that endolysin PlyBt33 was composed of two functional domains, the N-terminal catalytic domain and the C-terminal cell wall binding domain. In this study, the entire endolysin PlyBt33, and both the N- and C-termini,were expressed in Escherichia coli and then purified. The lytic activities of PlyBt33 and its N-terminus were tested on bacteria. Both regions exhibited lytic activity, although PlyBt33 showed a higher lytic activity than the N-terminus. PlyBt33 exhibited activity against all Bacillus strains tested from five different species, but was not active against Gram-negative bacteria. Optimal conditions for PlyBt33 reactivity were pH 9.0 and 50°C. PlyBt33 showed high thermostability, with 40% of initial activity remaining following 1 h of treatment at 60°C. The C-terminus of PlyBt33 bound to B. thuringiensis strain HD-73 and Bacillus subtilis strain 168. This cell wall binding domain might be novel, as its amino acid sequence showed little similarity to previously reported endolysins. Conclusions PlyBt33 showed potential as a novel antimicrobial agent at a relatively high temperature and had a broad lytic spectrum within the Bacillus genus. The C-terminus of PlyBt33 might be a novel kind of cell wall binding domain.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR, China.
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15
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Coonrod EM, Durtschi JD, Margraf RL, Voelkerding KV. Developing genome and exome sequencing for candidate gene identification in inherited disorders: an integrated technical and bioinformatics approach. Arch Pathol Lab Med 2012; 137:415-33. [PMID: 22770468 DOI: 10.5858/arpa.2012-0107-ra] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Advances in sequencing technology with the commercialization of next-generation sequencing (NGS) has substantially increased the feasibility of sequencing human genomes and exomes. Next-generation sequencing has been successfully applied to the discovery of disease-causing genes in rare, inherited disorders. By necessity, the advent of NGS has fostered the concurrent development of bioinformatics approaches to expeditiously analyze the large data sets generated. Next-generation sequencing has been used for important discoveries in the research setting and is now being implemented into the clinical diagnostic arena. OBJECTIVE To review the current literature on technical and bioinformatics approaches for exome and genome sequencing and highlight examples of successful disease gene discovery in inherited disorders. To discuss the challenges for implementing NGS in the clinical research and diagnostic arenas. DATA SOURCES Literature review and authors' experience. CONCLUSIONS Next-generation sequencing approaches are powerful and require an investment in infrastructure and personnel expertise for effective use; however, the potential for improvement of patient care through faster and more accurate molecular diagnoses is high.
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Affiliation(s)
- Emily M Coonrod
- Research and Development, ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA
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16
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Párraga-Niño N, Colomé-Calls N, Canals F, Querol E, Ferrer-Navarro M. A comprehensive proteome of Mycoplasma genitalium. J Proteome Res 2012; 11:3305-16. [PMID: 22582988 DOI: 10.1021/pr300084c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycoplasma genitalium is a human pathogen associated with several sexually transmitted diseases. Proteomic technologies, along with other methods for global gene expression analysis, play a key role in understanding the mechanisms of bacterial pathogenesis and physiology. The proteome of M. genitalium, model of a minimal cell, has been extended using a combination of different proteomic approaches and technologies. The total proteome of this microorganism has been analyzed using gel-based and gel-free approaches, achieving the identification of 85.3% of the predicted ORFs. In addition, a comprehensive analysis of membrane subproteome has been performed. For this purpose, the TX-114 soluble fraction has been analyzed as well as the surface proteins, using cell-surface protein labeling with CyDye. Finally, the serological response of M. genitalium-infected patients and healthy donors has been analyzed to identify proteins that trigger immunological response. Here, we present the most extensive M. genitalium proteome analysis (85.3% of predicted ORFs), a comprehensive M. genitalium membrane analysis, and a study of the human serological response to M. genitalium.
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Affiliation(s)
- Noemí Párraga-Niño
- Institut de Biotecnologia i de Biomedicina (IBB) and Dpt Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona (UAB), E-08193 Cerdanyola del Vallès (Barcelona), Spain
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17
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Simm R, Vörös A, Ekman JV, Sødring M, Nes I, Kroeger JK, Saidijam M, Bettaney KE, Henderson PJF, Salkinoja-Salonen M, Kolstø AB. BC4707 is a major facilitator superfamily multidrug resistance transport protein from Bacillus cereus implicated in fluoroquinolone tolerance. PLoS One 2012; 7:e36720. [PMID: 22615800 PMCID: PMC3353944 DOI: 10.1371/journal.pone.0036720] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 04/12/2012] [Indexed: 01/03/2023] Open
Abstract
Transcriptional profiling highlighted a subset of genes encoding putative multidrug transporters in the pathogen Bacillus cereus that were up-regulated during stress produced by bile salts. One of these multidrug transporters (BC4707) was selected for investigation. Functional characterization of the BC4707 protein in Escherichia coli revealed a role in the energized efflux of xenobiotics. Phenotypic analyses after inactivation of the gene bc4707 in Bacillus cereus ATCC14579 suggested a more specific, but modest role in the efflux of norfloxacin. In addition to this, transcriptional analyses showed that BC4707 is also expressed during growth of B. cereus under non-stressful conditions where it may have a role in the normal physiology of the bacteria. Altogether, the results indicate that bc4707, which is part of the core genome of the B. cereus group of bacteria, encodes a multidrug resistance efflux protein that is likely involved in maintaining intracellular homeostasis during growth of the bacteria.
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Affiliation(s)
- Roger Simm
- Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Aniko Vörös
- Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Jaakko V. Ekman
- Department of Biosciences, Biocenter 1, University of Helsinki, Helsinki, Finland
| | - Marianne Sødring
- Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Ingerid Nes
- Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Jasmin K. Kroeger
- Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
| | - Massoud Saidijam
- Astbury Centre for Structural Molecular Biology, Institute of Membrane and Systems Biology, University of Leeds, Leeds, United Kingdom
- School of Medicine, Hamedan University of Medical Sciences, Hamedan, Iran
| | - Kim E. Bettaney
- Astbury Centre for Structural Molecular Biology, Institute of Membrane and Systems Biology, University of Leeds, Leeds, United Kingdom
| | - Peter J. F. Henderson
- Astbury Centre for Structural Molecular Biology, Institute of Membrane and Systems Biology, University of Leeds, Leeds, United Kingdom
| | | | - Anne-Brit Kolstø
- Laboratory for Microbial Dynamics, Department of Pharmaceutical Biosciences, School of Pharmacy, University of Oslo, Oslo, Norway
- * E-mail:
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18
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Abstract
The serendipitous discovery of penicillin inspired intensive research into how small molecules affect basic cellular processes and their potential to treat disease. Biochemical and genetic approaches have been fundamental for clarifying small-molecule modes of action. Genomic technologies have permitted the use of chemical-genetic strategies that comprehensively study compound-target relationships in the context of a living cell, providing a systems biology view of both the cellular targets and the interdependent networks that respond to chemical stress. These studies highlight the fact that in vitro determinations of mechanism rarely translate into a complete understanding of drug behavior in the cell. Here, we review key discoveries that gave rise to the field of chemical genetics, with particular attention to chemical-genetic strategies developed for bakers' yeast, their extension to clinically relevant microbial pathogens, and the potential of these approaches to affect antimicrobial drug discovery.
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19
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Schmidt A, Beck M, Malmström J, Lam H, Claassen M, Campbell D, Aebersold R. Absolute quantification of microbial proteomes at different states by directed mass spectrometry. Mol Syst Biol 2011; 7:510. [PMID: 21772258 PMCID: PMC3159967 DOI: 10.1038/msb.2011.37] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 05/18/2011] [Indexed: 11/17/2022] Open
Abstract
Over the past decade, liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has evolved into the main proteome discovery technology. Up to several thousand proteins can now be reliably identified from a sample and the relative abundance of the identified proteins can be determined across samples. However, the remeasurement of substantially similar proteomes, for example those generated by perturbation experiments in systems biology, at high reproducibility and throughput remains challenging. Here, we apply a directed MS strategy to detect and quantify sets of pre-determined peptides in tryptic digests of cells of the human pathogen Leptospira interrogans at 25 different states. We show that in a single LC-MS/MS experiment around 5000 peptides, covering 1680 L. interrogans proteins, can be consistently detected and their absolute expression levels estimated, revealing new insights about the proteome changes involved in pathogenic progression and antibiotic defense of L. interrogans. This is the first study that describes the absolute quantitative behavior of any proteome over multiple states, and represents the most comprehensive proteome abundance pattern comparison for any organism to date.
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Affiliation(s)
- Alexander Schmidt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
- Biozentrum, University of Basel, Basel, Switzerland
| | - Martin Beck
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Johan Malmström
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- BiognoSYS AG, c/o IMSB ETH Zurich, Zurich, Switzerland
| | - Henry Lam
- Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Hong Kong, China
| | - Manfred Claassen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | | | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland
- Department of Science, University of Zurich, Zurich, Switzerland
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20
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Cash P. Investigating pathogen biology at the level of the proteome. Proteomics 2011; 11:3190-202. [DOI: 10.1002/pmic.201100029] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 04/04/2011] [Accepted: 04/19/2011] [Indexed: 11/12/2022]
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21
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Camilli R, Bonnal RJP, Del Grosso M, Iacono M, Corti G, Rizzi E, Marchetti M, Mulas L, Iannelli F, Superti F, Oggioni MR, De Bellis G, Pantosti A. Complete genome sequence of a serotype 11A, ST62 Streptococcus pneumoniae invasive isolate. BMC Microbiol 2011; 11:25. [PMID: 21284853 PMCID: PMC3055811 DOI: 10.1186/1471-2180-11-25] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 02/01/2011] [Indexed: 11/13/2022] Open
Abstract
Background Streptococcus pneumoniae is an important human pathogen representing a major cause of morbidity and mortality worldwide. We sequenced the genome of a serotype 11A, ST62 S. pneumoniae invasive isolate (AP200), that was erythromycin-resistant due to the presence of the erm(TR) determinant, and carried out analysis of the genome organization and comparison with other pneumococcal genomes. Results The genome sequence of S. pneumoniae AP200 is 2,130,580 base pair in length. The genome carries 2216 coding sequences (CDS), 56 tRNA, and 12 rRNA genes. Of the CDSs, 72.9% have a predicted biological known function. AP200 contains the pilus islet 2 and, although its phenotype corresponds to serotype 11A, it contains an 11D capsular locus. Chromosomal rearrangements resulting from a large inversion across the replication axis, and horizontal gene transfer events were observed. The chromosomal inversion is likely implicated in the rebalance of the chromosomal architecture affected by the insertions of two large exogenous elements, the erm(TR)-carrying Tn1806 and a functional prophage designated ϕSpn_200. Tn1806 is 52,457 bp in size and comprises 49 ORFs. Comparative analysis of Tn1806 revealed the presence of a similar genetic element or part of it in related species such as Streptococcus pyogenes and also in the anaerobic species Finegoldia magna, Anaerococcus prevotii and Clostridium difficile. The genome of ϕSpn_200 is 35,989 bp in size and is organized in 47 ORFs grouped into five functional modules. Prophages similar to ϕSpn_200 were found in pneumococci and in other streptococcal species, showing a high degree of exchange of functional modules. ϕSpn_200 viral particles have morphologic characteristics typical of the Siphoviridae family and are capable of infecting a pneumococcal recipient strain. Conclusions The sequence of S. pneumoniae AP200 chromosome revealed a dynamic genome, characterized by chromosomal rearrangements and horizontal gene transfers. The overall diversity of AP200 is driven mainly by the presence of the exogenous elements Tn1806 and ϕSpn_200 that show large gene exchanges with other genetic elements of different bacterial species. These genetic elements likely provide AP200 with additional genes, such as those conferring antibiotic-resistance, promoting its adaptation to the environment.
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Affiliation(s)
- Romina Camilli
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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22
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Chen PE, Willner KM, Butani A, Dorsey S, George M, Stewart A, Lentz SM, Cook CE, Akmal A, Price LB, Keim PS, Mateczun A, Brahmbhatt TN, Bishop-Lilly KA, Zwick ME, Read TD, Sozhamannan S. Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing. PLoS One 2010; 5:e12397. [PMID: 20811637 PMCID: PMC2928293 DOI: 10.1371/journal.pone.0012397] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 07/27/2010] [Indexed: 12/26/2022] Open
Abstract
Background The anthrax letter attacks of 2001 highlighted the need for rapid identification of biothreat agents not only for epidemiological surveillance of the intentional outbreak but also for implementing appropriate countermeasures, such as antibiotic treatment, in a timely manner to prevent further casualties. It is clear from the 2001 cases that survival may be markedly improved by administration of antimicrobial therapy during the early symptomatic phase of the illness; i.e., within 3 days of appearance of symptoms. Microbiological detection methods are feasible only for organisms that can be cultured in vitro and cannot detect all genetic modifications with the exception of antibiotic resistance. Currently available immuno or nucleic acid-based rapid detection assays utilize known, organism-specific proteins or genomic DNA signatures respectively. Hence, these assays lack the ability to detect novel natural variations or intentional genetic modifications that circumvent the targets of the detection assays or in the case of a biological attack using an antibiotic resistant or virulence enhanced Bacillus anthracis, to advise on therapeutic treatments. Methodology/Principal Findings We show here that the Roche 454-based pyrosequencing can generate whole genome draft sequences of deep and broad enough coverage of a bacterial genome in less than 24 hours. Furthermore, using the unfinished draft sequences, we demonstrate that unbiased identification of known as well as heretofore-unreported genetic modifications that include indels and single nucleotide polymorphisms conferring antibiotic and phage resistances is feasible within the next 12 hours. Conclusions/Significance Second generation sequencing technologies have paved the way for sequence-based rapid identification of both known and previously undocumented genetic modifications in cultured, conventional and newly emerging biothreat agents. Our findings have significant implications in the context of whole genome sequencing-based routine clinical diagnostics as well as epidemiological surveillance of natural disease outbreaks caused by bacterial and viral agents.
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Affiliation(s)
- Peter E. Chen
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Kristin M. Willner
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Amy Butani
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Shakia Dorsey
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Matroner George
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Andrew Stewart
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Shannon M. Lentz
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Christopher E. Cook
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Arya Akmal
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Lance B. Price
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Paul S. Keim
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Northern Arizona University, Flagstaff, Arizona, Unites States of America
| | - Alfred Mateczun
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Trupti N. Brahmbhatt
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Kimberly A. Bishop-Lilly
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Timothy D. Read
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Shanmuga Sozhamannan
- Naval Medical Research Center, Biological Defense Research Directorate, Silver Spring, Maryland, United States of America
- * E-mail:
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