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Samuel L. Direct-from-Blood Detection of Pathogens: a Review of Technology and Challenges. J Clin Microbiol 2023; 61:e0023121. [PMID: 37222587 PMCID: PMC10358183 DOI: 10.1128/jcm.00231-21] [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] [Indexed: 05/25/2023] Open
Abstract
Blood cultures have been the staple of clinical microbiology laboratories for well over half a century, but gaps remain in our ability to identify the causative agent in patients presenting with signs and symptoms of sepsis. Molecular technologies have revolutionized the clinical microbiology laboratory in many areas but have yet to present a viable alternative to blood cultures. There has been a recent surge of interest in utilizing novel approaches to address this challenge. In this minireview, I discuss whether molecular tools will finally give us the answers we need and the practical challenges of incorporating them into the diagnostic algorithm.
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Affiliation(s)
- Linoj Samuel
- Division of Clinical Microbiology, Department of Pathology and Laboratory Medicine, Henry Ford Health, Detroit, Michigan, USA
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Edgar RH, Samson AP, Kowalski RP, Kellum JA, Hempel J, Viator JA, Jhanji V. Differentiating methicillin resistant and susceptible Staphylococcus aureus from ocular infections using photoacoustic labeling. Front Med (Lausanne) 2023; 10:1017192. [PMID: 36910486 PMCID: PMC9995766 DOI: 10.3389/fmed.2023.1017192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction Antibiotic resistance in bacterial species constitutes a growing problem in the clinical management of infections. Not only does it limit therapeutic options, but application of ineffective antibiotics allows resistant species to progress prior to prescribing more effective treatment to patients. Methicillin resistance in Staphylococcus aureus is a major problem in clinical infections as it is the most common hospital acquired infection. Methods We developed a photoacoustic flow cytometer using engineered bacteriophage as probes for rapid determination of methicillin resistance in Staphylococcus aureus with thirteen clinical samples obtained from keratitis patients. This method irradiates cells under flow with 532 nm laser light and selectively generates acoustic waves in labeled bacterial cells, thus enabling detection and enumeration of them. Staphylococcus aureus isolates were classified from culture isolation as either methicillin resistant or susceptible using cefoxitin disk diffusion testing. The photoacoustic method enumerates bacterial cells before and after treatment with antibiotics. Decreasing counts of bacteria after treatment indicate susceptible strains. We quantified the bacterial cells in the treated and untreated samples. Results Using k-means clustering on the data, we achieved 100% concordance with the classification of Staphylococcus aureus resistance using culture. Discussion Photoacoustics can be used to differentiate methicillin resistant and susceptible strains of bacteria from ocular infections. This method may be generalized to other bacterial species using appropriate bacteriophages and testing for resistance using other antibiotics.
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Affiliation(s)
- Robert H Edgar
- Swanson School of Engineering, Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Anie-Pier Samson
- Department of Engineering, Duquesne University, Pittsburgh, PA, United States
| | - Regis P Kowalski
- School of Medicine and Ophthalmology, University of Pittsburgh, Pittsburgh, PA, United States
| | - John A Kellum
- Center for Central Care Nephrology, Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Spectral Medical, Toronto, ON, Canada
| | - John Hempel
- Department of Engineering, Duquesne University, Pittsburgh, PA, United States
| | - John A Viator
- Swanson School of Engineering, Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Engineering, Duquesne University, Pittsburgh, PA, United States
| | - Vishal Jhanji
- School of Medicine and Ophthalmology, University of Pittsburgh, Pittsburgh, PA, United States
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Duan R, Wang P. Rapid and Simple Approaches for Diagnosis of Staphylococcus aureus in Bloodstream Infections. Pol J Microbiol 2022; 71:481-489. [PMID: 36476633 PMCID: PMC9944965 DOI: 10.33073/pjm-2022-050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
Staphylococcus aureus is an important causative pathogen of bloodstream infections. An amplification assay such as real-time PCR is a sensitive, specific technique to detect S. aureus. However, it needs well-trained personnel, and costs are high. A literature review focusing on rapid and simple methods for diagnosing S. aureus was performed. The following methods were included: (a) Hybrisep in situ hybridization test, (b) T2Dx system, (c) BinaxNow Staphylococcus aureus and PBP2a, (d) Gram staining, (e) PNA FISH and QuickFISH, (f) Accelerate PhenoTM system, (g) MALDI-TOF MS, (h) BioFire FilmArray, (i) Xpert MRSA/SA. These rapid and simple methods can rapidly identify S. aureus in positive blood cultures or direct blood samples. Furthermore, BioFire FilmArray and Xpert MRSA/SA identify methicillin-resistant S. aureus (MRSA), and the Accelerate PhenoTM system can also provide antimicrobial susceptibility testing (AST) results. The rapidity and simplicity of results generated by these methods have the potential to improve patient outcomes and aid in the prevention of the emergence and transmission of MRSA.
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Affiliation(s)
- Rui Duan
- Department of Laboratory Medicine and Blood Transfusion, The First People’s Hospital of Jingmen, Jingmen, Hubei Province, China
| | - Pei Wang
- Department of Laboratory Medicine and Blood Transfusion, The First People’s Hospital of Jingmen, Jingmen, Hubei Province, China, E-mail:
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Combining T2Bacteria and T2Candida Panels for Diagnosing Intra-Abdominal Infections: A Prospective Multicenter Study. J Fungi (Basel) 2022; 8:jof8080832. [PMID: 36012820 PMCID: PMC9409936 DOI: 10.3390/jof8080832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
The T2Bacteria panel is a direct-from-blood assay that delivers rapid results, targeting E. coli, S. aureus, K. pneumoniae, A. baumanii, P. aeruginosa, and E. faecium (ESKAPE pathogens). In this study, T2Bacteria and T2Candida (targeting C. albicans/C. tropicalis, C. glabrata/C. krusei, and C. parapsilosis) were evaluated in parallel with blood cultures in 101 consecutive surgical patients with suspected intra-abdominal infection admitted to the intensive care unit or high dependency unit. Fifteen patients had bacteremia, with T2Bacteria correctly identifying all on-panel (n = 8) pathogens. T2Bacteria was positive in 19 additional patients, 11 of whom had supportive cultures from other normally sterile sites (newly inserted drains, perioperative cultures or blood cultures) within seven days. Six of these eleven patients (55%) received broad-spectrum antibiotics at the sampling time. T2Candida identified the two cases of blood-culture-positive candidemia and was positive in seven additional patients, three of whom were confirmed to have intra-abdominal candidiasis. Of four patients with concurrent T2Bacteria and T2Candida positivity, only one patient had positive blood cultures (candidemia), while three out of four patients had supporting microbiological evidence of a mixed infection. T2Bacteria and T2Candida were fast and accurate in diagnosing on-panel bloodstream infections, and T2Bacteria was able to detect culture-negative intra-abdominal infections.
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Abstract
The World Health Organization describes antimicrobial resistance as one of the biggest threats to global health, food security, and development with indiscriminate use of antimicrobials globally driving the emergence of multidrug-resistant bacteria, resistant to 60% of antimicrobials in some countries. Infections with multidrug-resistant organisms (MDROs) have increased in recent decades in patients with cirrhosis, who are frequently prescribed antibiotics, regularly undergo invasive procedures such as large volume paracentesis, and have recurrent hospitalizations, posing a particular risk in this already immunocompromised cohort of patients. In this review, we explore mechanisms underlying this vulnerability to MDRO infection; the effect of bacterial infections on disease course in cirrhosis; prevalence of MDROs in patients with cirrhosis; outcomes following MDRO infection; fungal infections; antibiotics and their efficacy; and management of MDRO infections in terms of detection, antimicrobial and nonantimicrobial treatments, prophylaxis, antibiotic stewardship, the gut microbiome, and technological interventions.
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Affiliation(s)
- Charles E Gallaher
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, London, United Kingdom
| | - Debbie L Shawcross
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, London, United Kingdom.,Institute of Liver Studies, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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Paggi R, Cenci E, De Socio GV, Belati A, Marini D, Gili A, Camilloni B, Mencacci A. Accuracy and Impact on Patient Management of New Tools for Diagnosis of Sepsis: Experience with the T2 Magnetic Resonance Bacteria Panel. Pathogens 2021; 10:pathogens10091132. [PMID: 34578164 PMCID: PMC8465567 DOI: 10.3390/pathogens10091132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022] Open
Abstract
The rapid and accurate identification of pathogens responsible for sepsis is essential for prompt and effective antimicrobial therapy. Molecular technologies have been developed to detect the most common causative agents, with high sensitivity and short time to result (TTR). T2 Bacteria Panel (T2), based on a combination of PCR and T2 magnetic resonance, can identify directly in blood samples Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterococcus faecium, and Acinetobacter baumannii pathogens. This study evaluates the role of T2 in the diagnosis of sepsis and its impact on patient management, specifically in terms of TTR and the switch from empirical to directed therapy, comparing results of blood culture (BC) and T2 assay in 82 patients with sepsis. T2 significantly improved the detection of the causative agents of sepsis. For pathogens included in the panel, T2 sensitivity was 100% (95% CI 86.3–100.0), significantly higher than that of BC (54.8%, 95% CI 36.0–72.7). The TTR (median, IQR) of positive T2 (3.66 h, 3.59–4.31) was significantly shorter than that of the positive BC (37.58 h, 20.10–47.32). A significant reduction in the duration of empiric therapy and an increase in the percentage of patients with switched therapy was observed in patients with a positive T2 result. In conclusion, T2 can shorten and improve the etiological diagnosis of sepsis with a positive impact on patient management.
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Affiliation(s)
- Riccardo Paggi
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
| | - Elio Cenci
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
| | | | - Alessandra Belati
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
| | - Daniele Marini
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
| | - Alessio Gili
- Public Health Section, Department of Experimental Medicine, University of Perugia, Piazza Lucio Severi 1, 06132 Perugia, Italy;
| | - Barbara Camilloni
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
| | - Antonella Mencacci
- Medical Microbiology Section, Department of Medicine, University of Perugia, Polo Unico Sant’Andrea delle Fratte, 06132 Perugia, Italy; (R.P.); (E.C.); (A.B.); (D.M.); (B.C.)
- Correspondence:
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