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Giulieri SG, Holmes NE, Stinear TP, Howden BP. Use of bacterial whole-genome sequencing to understand and improve the management of invasive Staphylococcus aureus infections. Expert Rev Anti Infect Ther 2016; 14:1023-1036. [PMID: 27626511 DOI: 10.1080/14787210.2016.1233815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Management of invasive Staphylococcus aureus infections is complex. Dramatic improvements in bacterial whole genome sequencing (WGS) offer new opportunities for personalising the treatment of S. aureus infections. Areas covered: We address recent achievements in S. aureus genomics, describe genetic determinants of antibiotic resistance and summarise studies that have defined molecular characteristics associated with risk and outcome of S. aureus invasive infections. Potential clinical use of WGS for resistance prediction, infection outcome stratification and management of persistent /relapsing infections is critically discussed. Expert commentary: WGS is not only providing invaluable information to track the emergence and spread of important S. aureus clones, but also allows rapid determination of resistance genotypes in the clinical environment. An evolving opportunity is to infer clinically important outcomes and optimal therapeutic approaches from widely available S. aureus genome data, with the goal of individualizing management of invasive S. aureus infections.
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Affiliation(s)
- Stefano G Giulieri
- a Microbiological Diagnostic Unit Public Health Laboratory , Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne , Australia.,b Infectious Diseases Service , Department of Medicine, Lausanne University Hospital , Lausanne , Switzerland
| | - Natasha E Holmes
- c Infectious Diseases Department , Austin Health , Heidelberg , Australia
| | - Timothy P Stinear
- d Doherty Applied Microbial Genomics , Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne , Australia.,e Department of Microbiology and Immunology , The University of Melbourne at the Peter Doherty Institute for Infection and Immunity , Melbourne , Australia
| | - Benjamin P Howden
- a Microbiological Diagnostic Unit Public Health Laboratory , Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne , Australia.,c Infectious Diseases Department , Austin Health , Heidelberg , Australia.,e Department of Microbiology and Immunology , The University of Melbourne at the Peter Doherty Institute for Infection and Immunity , Melbourne , Australia
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Morrow BJ, Abbanat D, Baum EZ, Crespo-Carbone SM, Davies TA, He W, Shang W, Queenan AM, Lynch AS. Antistaphylococcal activities of the new fluoroquinolone JNJ-Q2. Antimicrob Agents Chemother 2011; 55:5512-21. [PMID: 21911562 PMCID: PMC3232800 DOI: 10.1128/aac.00470-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 09/02/2011] [Indexed: 11/20/2022] Open
Abstract
The new broad-spectrum fluoroquinolone JNJ-Q2 displays in vitro activity against Gram-negative and Gram-positive organisms, including methicillin-resistant Staphylococcus aureus (MRSA) and ciprofloxacin-resistant MRSA isolates. Tested with isogenic methicillin-susceptible S. aureus (MSSA) and MRSA strains bearing quinolone-resistant target mutations, JNJ-Q2 displayed MICs ≤ 0.12 μg/ml, values 16- to 32-fold lower than those determined for moxifloxacin. Overexpression of the NorA efflux pump did not impact JNJ-Q2 MICs. Inhibition of S. aureus DNA gyrase and DNA topoisomerase IV enzymes demonstrated that JNJ-Q2 was more potent than comparators against wild-type enzymes and enzymes carrying quinolone-resistant amino acid substitutions, and JNJ-Q2 displayed equipotent activity against both enzymes. In serial-passage studies comparing resistance selection in parallel MRSA cultures by ciprofloxacin and JNJ-Q2, ciprofloxacin readily selected for mutants displaying MIC values of 128 to 512 μg/ml, which were observed within 18 to 24 days of passage. In contrast, cultures passaged in the presence of JNJ-Q2 displayed MICs ≤ 1 μg/ml for a minimum of 27 days of serial passage. A mutant displaying a JNJ-Q2 MIC of 4 μg/ml was not observed until after 33 days of passage. Mutant characterization revealed that ciprofloxacin-passaged cultures with MICs of 256 to 512 μg/ml carried only 2 or 3 quinolone resistance-determining region (QRDR) mutations. Cultures passaged with JNJ-Q2 selection for up to 51 days displayed MICs of 1 to 64 μg/ml and carried between 4 and 9 target mutations. Established in vitro biofilms of wild-type or ciprofloxacin-resistant MRSA exposed to JNJ-Q2 displayed greater decreases in bacterial counts (7 days of exposure produced 4.5 to >7 log(10) CFU decreases) than biofilms exposed to ciprofloxacin, moxifloxacin, rifampin, or vancomycin.
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Affiliation(s)
- Brian J Morrow
- Johnson & Johnson Pharmaceutical Research and Development, LLC, Raritan, New Jersey 08869, USA.
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Vernet G. Genomics of Infectious Diseases and Private Industry. GENETICS AND EVOLUTION OF INFECTIOUS DISEASE 2011. [PMCID: PMC7149633 DOI: 10.1016/b978-0-12-384890-1.00019-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Beaume M, Hernandez D, Francois P, Schrenzel J. New approaches for functional genomic studies in staphylococci. Int J Med Microbiol 2009; 300:88-97. [PMID: 20005775 DOI: 10.1016/j.ijmm.2009.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Functional transcriptomics studies have resulted in interesting insights into Staphylococcus aureus diversity and pathogenicity. Here we review the principles, advantages and disadvantages of recent technical developments in the field of transcriptomics and their potential impact on S. aureus research.
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Affiliation(s)
- Marie Beaume
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals (HUG), CH-1211 Geneva 14, Switzerland
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Townsend MB, Smagala JA, Dawson ED, Deyde V, Gubareva L, Klimov AI, Kuchta RD, Rowlen KL. Detection of adamantane-resistant influenza on a microarray. J Clin Virol 2008; 42:117-23. [PMID: 18299250 DOI: 10.1016/j.jcv.2007.12.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 11/30/2007] [Accepted: 12/27/2007] [Indexed: 11/28/2022]
Abstract
BACKGROUND Influenza A has the ability to rapidly mutate and become resistant to the commonly prescribed influenza therapeutics, thereby complicating treatment decisions. OBJECTIVE To design a cost-effective low-density microarray for use in detection of influenza resistance to the adamantanes. STUDY DESIGN We have taken advantage of functional genomics and microarray technology to design a DNA microarray that can detect the two most common mutations in the M2 protein associated with adamantane resistance, V27A and S31N. RESULTS In a blind study of 22 influenza isolates, the antiviral resistance-chip (AVR-Chip) had a success rate of 95% for detecting these mutations. Microarray data from a larger set of samples were further analyzed using an artificial neural network and resulted in a correct identification rate of 94% for influenza virus samples that had V27A and S31N mutations. CONCLUSIONS The AVR-Chip provided a method for rapidly screening influenza viruses for adamantane sensitivity, and the general approach could be easily extended to detect resistance to other chemotherapeutics.
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Affiliation(s)
- Michael B Townsend
- Department of Chemistry and Biochemistry, The University of Colorado at Boulder, UCB #215, Boulder, CO 80309, USA
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Characterization of new staphylococcal cassette chromosome mec (SCCmec) and topoisomerase genes in fluoroquinolone- and methicillin-resistant Staphylococcus pseudintermedius. J Clin Microbiol 2008; 46:1818-23. [PMID: 18305127 DOI: 10.1128/jcm.02255-07] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluoroquinolone- and methicillin-resistant Staphylococcus pseudintermedius isolates harbor two new staphylococcal cassette chromosome mec (SCCmec) elements that belong to class A, allotype 3 (SCCmec II-III), and to the new allotype 5 (SCCmec VII). Analysis of the complete nucleotide sequences of the topoisomerase loci gyrB/gyrA and grlB/grlA revealed mutations involved in fluoroquinolone resistance.
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Strommenger B, Schmidt C, Werner G, Roessle-Lorch B, Bachmann TT, Witte W. DNA microarray for the detection of therapeutically relevant antibiotic resistance determinants in clinical isolates of Staphylococcus aureus. Mol Cell Probes 2007; 21:161-70. [PMID: 17123780 DOI: 10.1016/j.mcp.2006.10.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Revised: 10/07/2006] [Accepted: 10/12/2006] [Indexed: 11/20/2022]
Abstract
An oligonucleotide microarray was constructed for the rapid and sensitive molecular detection of antibiotic resistance determinants in Staphylococcus aureus. The array is equipped with oligonucleotide capture probes for the detection of 10 clinically and therapeutically relevant antibiotic resistance genes and -mutations (mecA, aacA-aphD, tetK, tetM, vat(A), vat(B), vat(C), erm(A), erm(C), grlA-mutation) as well as several control probes. A microarray concept was established including multiplexed PCR amplification, DNA labeling, hybridization and data processing. This concept was applied to clinical Staphylococcus aureus isolates and results were concordant with those from standard genotypic and phenotypic resistance testing. Our microarray concept offers rapid and accurate identification of antibiotic resistance profiles. It is easily expandable and thus can be adapted to changing clinical and epidemiological requirements in clinical diagnosis as well as in epidemiological studies.
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Affiliation(s)
- Birgit Strommenger
- Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855 Wernigerode, Germany.
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Francois P, Hernandez D, Schrenzel J. Genome content determination in methicillin-resistant Staphylococcus aureus. Future Microbiol 2007; 2:187-98. [PMID: 17661655 DOI: 10.2217/17460913.2.2.187] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Staphylococcus aureus is a major pathogen responsible for both nosocomial and community-acquired infections. While the first S. aureus isolates displaying resistance to methicillin were reported in the early 1960s, endemic strains of methicillin-resistant S. aureus (MRSA) carrying multiple resistance determinants only became a worldwide nosocomial problem in the early 1980s, carrying a threefold attributable cost and a threefold excess length of hospital stay when compared with methicillin-susceptible S. aureus bacteremia. Recent efforts in the field of high-throughput sequencing resulted in the release of several MRSA genome sequences enabling the development of massively parallel tools to study clinical isolates of MRSA at the organism scale. Microarrays covering whole genomes and high-throughput sequencing devices are the two main techniques currently utilizable for whole-genome characterization. These tools not only provide information for the development of genotyping assays but also allow evaluation of potential virulence of the strains, by enumerating genetic-encoded resistance markers and toxin content. This appears particularly attractive for understanding the epidemiology of MRSA and the relationship between genome content on one side and virulence potential or epidemicity on the other side. In addition, sequence information is mandatory for the development of molecular tests allowing the rapid identification, genotyping and characterization of clinical isolates.
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Affiliation(s)
- Patrice Francois
- Service of Infectious Diseases, Genomic Research Laboratory, Department of Internal Medicine, Geneva 14, Switzerland.
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Francois P, Charbonnier Y, Jacquet J, Utinger D, Bento M, Lew D, Kresbach GM, Ehrat M, Schlegel W, Schrenzel J. Rapid bacterial identification using evanescent-waveguide oligonucleotide microarray classification. J Microbiol Methods 2006; 65:390-403. [PMID: 16216356 DOI: 10.1016/j.mimet.2005.08.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Revised: 08/16/2005] [Accepted: 08/17/2005] [Indexed: 11/18/2022]
Abstract
Bacterial identification relies primarily on culture-based methodologies and requires 48-72 h to deliver results. We developed and used i) a bioinformatics strategy to select oligonucleotide signature probes, ii) a rapid procedure for RNA labelling and hybridization, iii) an evanescent-waveguide oligoarray with exquisite signal/noise performance, and iv) informatics methods for microarray data analysis. Unique 19-mer signature oligonucleotides were selected in the 5'-end of 16s rDNA genes of human pathogenic bacteria. Oligonucleotides spotted onto a Ta(2)O(5)-coated microarray surface were incubated with chemically labelled total bacterial RNA. Rapid hybridization and stringent washings were performed before scanning and analyzing the slide. In the present paper, the eight most abundant bacterial pathogens representing >54% of positive blood cultures were selected. Hierarchical clustering analysis of hybridization data revealed characteristic patterns, even for closely related species. We then evaluated artificial intelligence-based approaches that outperformed conventional threshold-based identification schemes on cognate probes. At this stage, the complete procedure applied to spiked blood cultures was completed in less than 6 h. In conclusion, when coupled to optimal signal detection strategy, microarrays provide bacterial identification within a few hours post-sampling, allowing targeted antimicrobial prescription.
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Affiliation(s)
- Patrice Francois
- University Hospitals of Geneva, Genomic Research Laboratory, Service of Infectious Diseases, Switzerland.
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Vernet G, Tran N. The DNA-Chip technology as a new molecular tool for the detection of HBV mutants. J Clin Virol 2006; 34 Suppl 1:S49-53. [PMID: 16461224 DOI: 10.1016/s1386-6532(05)80010-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Genetic variability of the Hepatitis B virus (HBV) strongly impacts the natural history of infection and the efficiency of diagnosis, vaccination and treatment. A genotypc assay able to provide genetic information on all HBV genes would be a very important tool for clinicians and epidemiologists. The DNA-Chip technology has proved to be powerful and convenient for the diagnosis of infectious diseases due to bacteria and viruses. We have designed a genotyping assay based on polymerase chain reaction and DNA-Chip for HBV Starting from a unique specimen, analysis of polymorphisms at 150 positions along the genome and 383 mutations is possible as well as the determination of the genotype. Preliminary experiments with plasmas from infected patients show that results obtained with this reagent are strongly correlated with those obtained with sequencing.
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Affiliation(s)
- Guy Vernet
- Advanced Technology Unit, R&D department, bioMérieux, 69280, Marcy-l'Etoile, France.
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