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Fitzpatrick KJ, Rohlf HJ, Sutherland TD, Koo KM, Beckett S, Okelo WO, Keyburn AL, Morgan BS, Drigo B, Trau M, Donner E, Djordjevic SP, De Barro PJ. Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains. ACS Sens 2021; 6:4283-4296. [PMID: 34874700 DOI: 10.1021/acssensors.1c01973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The spread of antimicrobial resistance (AMR) is a rapidly growing threat to humankind on both regional and global scales. As countries worldwide prepare to embrace a One Health approach to AMR management, which is one that recognizes the interconnectivity between human, animal, and environmental health, increasing attention is being paid to identifying and monitoring key contributing factors and critical control points. Presently, AMR sensing technologies have significantly progressed phenotypic antimicrobial susceptibility testing (AST) and genotypic antimicrobial resistance gene (ARG) detection in human healthcare. For effective AMR management, an evolution of innovative sensing technologies is needed for tackling the unique challenges of interconnected AMR across various and different health domains. This review comprehensively discusses the modern state-of-play for innovative commercial and emerging AMR sensing technologies, including sequencing, microfluidic, and miniaturized point-of-need platforms. With a unique view toward the future of One Health, we also provide our perspectives and outlook on the constantly changing landscape of AMR sensing technologies beyond the human health domain.
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Affiliation(s)
- Kira J. Fitzpatrick
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
| | - Hayden J. Rohlf
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
| | - Tara D. Sutherland
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Kevin M. Koo
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, Queensland 4029, Australia
| | - Sam Beckett
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Walter O. Okelo
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Anthony L. Keyburn
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, Victoria 3220, Australia
| | - Branwen S. Morgan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, South Australia 5095, Australia
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia 5095, Australia
| | - Steven P. Djordjevic
- Ithree Institute, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Paul J. De Barro
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health & Biosecurity, EcoSciences Precinct, Brisbane, Queensland 4001, Australia
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Fidalgo B, Rubio E, Pastor V, Parera M, Ballesté-Delpierre C, Fernández MJ, Chasco GC, Vergara A, Zboromyrska Y, Aylagas C, Salvador P, Fernández A, Valls ME, Alvarez Martinez MJ, Mira A, Marcos MA, Vila J, Martinez MJ, Casals-Pascual C. Improved diagnosis of gastrointestinal infections using a semi-automated multiplex real-time PCR for detection of enteropathogens. J Med Microbiol 2021; 70. [PMID: 34516365 DOI: 10.1099/jmm.0.001367] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Introduction. The identification of enteropathogens is critical for the clinical management of patients with suspected gastrointestinal infection. The FLOW multiplex PCR system (FMPS) is a semi-automated platform (FLOW System, Roche) for multiplex real-time PCR analysis.Hypothesis/Gap Statement. FMPS has greater sensitivity for the detection of enteric pathogens than standard methods such as culture, biochemical identification, immunochromatography or microscopic examination.Aim.The diagnostic performance of the FMPS was evaluated and compared to that of traditional microbiological procedures.Methodology. A total of 10 659 samples were collected and analysed over a period of 7 years. From 2013 to 2018 (every July to September), samples were processed using standard microbiological culture methods. In 2019, the FMPS was implemented using real-time PCR to detect the following enteropathogens: Shigella spp., Salmonella spp., Campylobacter spp., Giardia intestinalis, Entamoeba histolytica, Blastocystis hominis, Cryptosporidum spp., Dientamoeba fragilis, adenovirus, norovirus and rotavirus. Standard microbiological culture methods (2013-2018) included stool culture, microscopy and immunochromatography.Results. A total of 1078 stool samples were analysed prospectively using the FMPS from July to September (2019): bacterial, parasitic and viral pathogens were identified in 15.3, 9.71 and 5.29 % of cases, respectively. During the same period of 6 years (2013-2018), the proportion of positive identifications using standard microbiological methods from 2013 to 2018 was significantly lower. A major significant recovery improvement was observed for all bacteria species tested: Shigella spp./enteroinvasive Escherichia coli (EIEC) (P <0.05), Salmonella spp. (P <0.05) and Campylobacter spp. (P <0.05). Marked differences were also observed for the parasites G. intestinalis, Cryptosporidium spp. and D. fragilis.Conclusion. These results support the value of multiplex real-time PCR analysis for the detection of enteric pathogens in laboratory diagnosis with outstanding performance in identifying labile micro-organisms. The identification of unsuspected micro-organisms for less specific clinical presentations may also impact on clinical practice and help optimize patient management.
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Affiliation(s)
- Berta Fidalgo
- Department of Microbiology, Hospital Clinic, Barcelona, Spain
| | - Elisa Rubio
- Department of Microbiology, Hospital Clinic, Barcelona, Spain
| | - Victor Pastor
- Molecular Biology Core, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Marta Parera
- Molecular Biology Core, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Clara Ballesté-Delpierre
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | | | | | - Andrea Vergara
- Department of Microbiology, Hospital Clinic, Barcelona, Spain.,Molecular Biology Core, Hospital Clinic of Barcelona, Barcelona, Spain
| | | | | | - Pilar Salvador
- Department of Microbiology, Hospital Clinic, Barcelona, Spain
| | - Adán Fernández
- Department of Microbiology, Hospital Clinic, Barcelona, Spain
| | - M Eugenia Valls
- Department of Microbiology, Hospital Clinic, Barcelona, Spain
| | | | - Aurea Mira
- Biomedical Diagnostic Centre (CDB), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | | | - Jordi Vila
- Department of Microbiology, Hospital Clinic, Barcelona, Spain
| | - Miguel J Martinez
- Department of Microbiology, Hospital Clinic, Barcelona, Spain.,Barcelona Institute for Global Health (ISGlobal), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Climent Casals-Pascual
- Department of Microbiology, Hospital Clinic, Barcelona, Spain.,Barcelona Institute for Global Health (ISGlobal), Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
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Mizusawa M, Carroll KC. Novel strategies for rapid identification and susceptibility testing of MRSA. Expert Rev Anti Infect Ther 2020; 18:759-778. [PMID: 32329637 DOI: 10.1080/14787210.2020.1760842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs. Rapid diagnosis of MRSA infections has been associated with positive impact on clinical outcomes. AREAS COVERED We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review describes screening and diagnostic test methods for MRSA and their analytical performances with a focus on rapid molecular-based assays including those that are on the horizon. Future novel technologies will allow more rapid detection of phenotypic resistance. In the case of whole-genome sequencing, detection of mutations may predict resistance, transmission, and virulence. EXPERT OPINION Currently there are many diagnostic options for the detection of MRSA in surveillance and clinical samples. In general, these are highly accurate and have resulted in improvements in targeted management and reduction in hospital or intensive care unit length of stay for both MSSA and MRSA. Impact on mortality has been variable. Promising novel technologies will not only accurately identify pathogens and detect their resistance markers but will allow discovery of virulence determinants that might further affect patient management.
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Affiliation(s)
- Masako Mizusawa
- Section of Infectious Diseases, Department of Internal Medicine, University of Missouri , Kansas, MO, USA
| | - Karen C Carroll
- Department of Pathology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine , Baltimore, MD, USA
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Marco F. Molecular methods for septicemia diagnosis. Enferm Infecc Microbiol Clin 2017; 35:586-592. [PMID: 28427796 DOI: 10.1016/j.eimc.2017.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 12/12/2022]
Abstract
Septicemia remains a major cause of hospital mortality. Blood culture remains the best approach to identify the etiological microorganisms when a bloodstream infection is suspected but it takes long time because it relies on bacterial or fungal growth. The introduction in clinical microbiology laboratories of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry technology, DNA hybridization, microarrays or rapid PCR-based test significantly reduce the time to results. Tests for direct detection in whole blood samples are highly desirable because of their potential to identify bloodstream pathogens without waiting for blood cultures to become positive. Nonetheless, limitations of current molecular diagnostic methods are substantial. This article reviews these new molecular approaches (LightCycler SeptiFast, Magicplex sepsis real time, Septitest, VYOO, PCR/ESI-MS analysis, T2Candida).
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Affiliation(s)
- Francesc Marco
- Servicio de Microbiología, Centro de Diagnóstico Biomédico, Hospital Clínic, Barcelona, España; ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, España.
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Rapid detection of Staphylococcus aureus by loop-mediated isothermal amplification. Appl Biochem Biotechnol 2014; 175:882-91. [PMID: 25349088 DOI: 10.1007/s12010-014-1328-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 10/15/2014] [Indexed: 01/15/2023]
Abstract
Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), is a major bacterial pathogen associated with nosocomial and community-acquired S. aureus infections all over the world. A rapid detection assay for staphylococcal gene of nuc and mecA is needed. In this study, a rapid identification assay based on the loop-mediated isothermal amplification (LAMP) method was established. PCR and LAMP assays were used to detect Staphylococcus aureus and other related species for nuc and mecA. With optimization of the primers and reaction temperature, the LAMP successfully amplified the genes under isothermal conditions at 62 °C within 60 min, of which the results were identical with those of the conventional PCR methods. The detection limits of the LAMP for nuc and mecA were 1.47 and 14.7 pg/μl DNA per tube, respectively, by naked eye inspections, while the detection limits of the PCR for nuc and mecA were 14.7 pg/μl and 147 pg/μl DNA, respectively. Finally, The LAMP method was then applied to clinical blood plaque samples. The LAMP and PCR demonstrated identical results for the plaque samples with the culture assay. Together, the LAMP offers an alternative detection assay for nuc and mecA with a great advantage of the sensitivity and rapidity.
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