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Gutiérrez-Santana JC, Rosas-Espinosa V, Martinez E, Casiano-García E, Coria-Jiménez VR. Metal Nanoparticle-Based Biosensors for the Early Diagnosis of Infectious Diseases Caused by ESKAPE Pathogens in the Fight against the Antimicrobial-Resistance Crisis. BIOSENSORS 2024; 14:339. [PMID: 39056615 PMCID: PMC11274948 DOI: 10.3390/bios14070339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 07/28/2024]
Abstract
The species included in the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and the genus Enterobacter) have a high capacity to develop antimicrobial resistance (AMR), a health problem that is already among the leading causes of death and could kill 10 million people a year by 2050. The generation of new potentially therapeutic molecules has been insufficient to combat the AMR "crisis", and the World Health Organization (WHO) has stated that it will seek to promote the development of rapid diagnostic strategies. The physicochemical properties of metallic nanoparticles (MNPs) have made it possible to design biosensors capable of identifying low concentrations of ESKAPE bacteria in the short term; other systems identify antimicrobial susceptibility, and some have been designed with dual activity in situ (bacterial detection and antimicrobial activity), which suggests that, in the near future, multifunctional biosensors could exist based on MNPs capable of quickly identifying bacterial pathogens in clinical niches might become commercially available. This review focuses on the use of MNP-based systems for the rapid and accurate identification of clinically important bacterial pathogens, exhibiting the necessity for exhaustive research to achieve these objectives. This review focuses on the use of metal nanoparticle-based systems for the rapid and accurate identification of clinically important bacterial pathogens.
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Affiliation(s)
- Juan Carlos Gutiérrez-Santana
- Laboratorio de Bacteriología Experimental, Instituto Nacional de Pediatría, Insurgentes sur 3700-C, Col. Insurgentes Cuicuilco, Coyoacán C.P. 04530, Mexico (V.R.C.-J.)
| | - Viridiana Rosas-Espinosa
- Laboratorio de Bacteriología Experimental, Instituto Nacional de Pediatría, Insurgentes sur 3700-C, Col. Insurgentes Cuicuilco, Coyoacán C.P. 04530, Mexico (V.R.C.-J.)
| | - Evelin Martinez
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Coyoacán C.P. 04960, Mexico;
| | - Esther Casiano-García
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Coyoacán C.P. 04960, Mexico;
| | - Victor Rafael Coria-Jiménez
- Laboratorio de Bacteriología Experimental, Instituto Nacional de Pediatría, Insurgentes sur 3700-C, Col. Insurgentes Cuicuilco, Coyoacán C.P. 04530, Mexico (V.R.C.-J.)
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Epidemiology, Biology, and Impact of Clonal Pseudomonas aeruginosa Infections in Cystic Fibrosis. Clin Microbiol Rev 2018; 31:31/4/e00019-18. [PMID: 30158299 DOI: 10.1128/cmr.00019-18] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chronic lower airway infection with Pseudomonas aeruginosa is a major contributor to morbidity and mortality in individuals suffering from the genetic disease cystic fibrosis (CF). Whereas it was long presumed that each patient independently acquired unique strains of P. aeruginosa present in their living environment, multiple studies have since demonstrated that shared strains of P. aeruginosa exist among individuals with CF. Many of these shared strains, often referred to as clonal or epidemic strains, can be transmitted from one CF individual to another, potentially reaching epidemic status. Numerous epidemic P. aeruginosa strains have been described from different parts of the world and are often associated with an antibiotic-resistant phenotype. Importantly, infection with these strains often portends a worse prognosis than for infection with nonclonal strains, including an increased pulmonary exacerbation rate, exaggerated lung function decline, and progression to end-stage lung disease. This review describes the global epidemiology of clonal P. aeruginosa strains in CF and summarizes the current literature regarding the underlying biology and clinical impact of globally important CF clones. Mechanisms associated with patient-to-patient transmission are discussed, and best-evidence practices to prevent infections are highlighted. Preventing new infections with epidemic P. aeruginosa strains is of paramount importance in mitigating CF disease progression.
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Evaluation of quantitative PCR for early diagnosis of Pseudomonas aeruginosa infection in cystic fibrosis: a prospective cohort study. Clin Microbiol Infect 2016; 23:203-207. [PMID: 27903460 DOI: 10.1016/j.cmi.2016.11.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/31/2016] [Accepted: 11/22/2016] [Indexed: 01/29/2023]
Abstract
OBJECTIVES Early detection of Pseudomonas aeruginosa lung positivity is a key element in cystic fibrosis (CF) management. PCR has increased the accuracy of detection of many microorganisms. Clinical relevance of P. aeruginosa quantitative PCR (qPCR) in this context is unclear. Our aim was to determine P. aeruginosa qPCR sensitivity and specificity, and to assess the possible time saved by qPCR in comparison with standard practice (culture). METHODS A multicentre cohort study was conducted over a 3-year period in 96 patients with CF without chronic P. aeruginosa colonization. Sputum samples were collected at each visit. Conventional culture and two-step qPCR (oprL qPCR and gyrB/ecfX qPCR) were performed for 707 samples. The positivity criteria were based on the qPCR results, defined in a previous study as follow: oprL qPCR positivity alone if bacterial density was <730 CFU/mL or oprL qPCR combined with gyrB/ecfX qPCR if bacterial density was ≥730 CFU/mL. RESULTS During follow up, 36 of the 96 patients with CF were diagnosed on culture as colonized with P. aeruginosa. This two-step qPCR displayed a sensitivity of 94.3% (95% CI 79.7%-98.6%), and a specificity of 86.3% (95% CI 83.4%-88.7%). It enabled P. aeruginosa acquisition to be diagnosed earlier in 20 patients, providing a median detection time gain of 8 months (interquartile range 3.7-17.6) for them. CONCLUSIONS Implementing oprL and gyrB/ecfX qPCR in the management of patients with CF allowed earlier detection of first P. aeruginosa lung positivity than culture alone.
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Diribe O, Fitzpatrick N, Sawyer J, La Ragione R, North S. A Rapid and Simple Loop-Mediated Isothermal Amplification Assay for the Detection of Pseudomonas aeruginosa From Equine Genital Swabs. J Equine Vet Sci 2015. [DOI: 10.1016/j.jevs.2015.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Rashno Taee S, Khansarinejad B, Abtahi H, Najafimosleh M, Ghaznavi-Rad E. Detection of algD, oprL and exoA Genes by New Specific Primers as an Efficient, Rapid and Accurate Procedure for Direct Diagnosis of Pseudomonas aeruginosa Strains in Clinical Samples. Jundishapur J Microbiol 2014; 7:e13583. [PMID: 25632330 PMCID: PMC4295320 DOI: 10.5812/jjm.13583] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 09/22/2013] [Accepted: 01/22/2014] [Indexed: 11/25/2022] Open
Abstract
Background: Pseudomonas aeruginosa is an opportunistic pathogen that infects patients with cystic fibrosis, burning wounds, ophthalmic traumas and immunodeficiency. Objectives: The aim of the present study was to compare the efficiency of newly designed primer sets with some previously published primers for PCR detection of exoA, oprL and algD genes from P. aeruginosa. Materials and Methods: A total of 150 clinical specimens were inoculated into the routine and selective culture media for P. aeruginosa isolation. Specific primers were designed by bioinformatics analysis for detection of the virulence genes determinants, exoA, oprL and algD. The sequences of these three genes were obtained from NCBI and multiple alignments were performed to find the conserved sequences of each gene to design the primers. Multiple alignment and primer design steps were carried out by the AlleleID software, version 7.0. Results: Microbiological culture methods resulted 70 P. aeruginosa strains isolated from 70 of the 150 clinical specimens. The results of the PCR assay using the newly designed exoA, oprL and algD primer sets were positive in 68, 70 and 69 clinical samples which represent 97.2%, 100% and 98% sensitivity for each primer set, respectively. The PCR results using previously published exoA, oprL and algD primer sets were positive only in 57, 49 and 28 specimens that correspond to 81.5%, 70% and 40% sensitivity, respectively. Conclusions: The results of the present study showed that in comparison with previously published primer sets, P. aeruginosa infection can be diagnosed with higher sensitivity and specificity by the conventional PCR assay using the newly designed primers. It was also shown that the results of the PCR assay on clinical samples of severe infections became positive much earlier than the results of conventional culture method.
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Affiliation(s)
- Sedighe Rashno Taee
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran
| | - Behzad Khansarinejad
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran
| | - Hamid Abtahi
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran
| | - Mohammad Najafimosleh
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, IR Iran
| | - Ehsanollah Ghaznavi-Rad
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran
- Molecular Research Center, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran
- Corresponding author: Ehsanollah Ghaznavi-Rad, Department of Medical Microbiology, Faculty of Medicine, Arak University of Medical Sciences, Arak, IR Iran. Tel: +98-8634173526, Fax: +98-8634173526, E-mail:
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Ma L, Chung WK. Quantitative analysis of copy number variants based on real-time LightCycler PCR. CURRENT PROTOCOLS IN HUMAN GENETICS 2014; 80:7.21.1-7.21.8. [PMID: 24510682 PMCID: PMC3949243 DOI: 10.1002/0471142905.hg0721s80] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Quantitative real-time PCR is PCR visualized in real time by the use of fluorescent or intercalating dyes, which are employed to measure gene expression or gene quantification including contiguous gene deletions or duplications. A simple method is described here to quantify DNA copy number from human samples.
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Affiliation(s)
- Lijiang Ma
- Department of Pediatrics, Columbia University, New York, New York
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University, New York, New York,Department of Medicine, Columbia University, New York, New York
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Le Gall F, Le Berre R, Rosec S, Hardy J, Gouriou S, Boisramé-Gastrin S, Vallet S, Rault G, Payan C, Héry-Arnaud G. Proposal of a quantitative PCR-based protocol for an optimal Pseudomonas aeruginosa detection in patients with cystic fibrosis. BMC Microbiol 2013; 13:143. [PMID: 24088260 PMCID: PMC3691768 DOI: 10.1186/1471-2180-13-143] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 06/13/2013] [Indexed: 12/04/2022] Open
Abstract
Background The lung of patients with cystic fibrosis (CF) is particularly sensitive to Pseudomonas aeruginosa. This bacterium plays an important role in the poor outcome of CF patients. During the disease progress, first acquisition of P. aeruginosa is the key-step in the management of CF patients. Quantitative PCR (qPCR) offers an opportunity to detect earlier the first acquisition of P. aeruginosa by CF patients. Given the lack of a validated protocol, our goal was to find an optimal molecular protocol for detection of P. aeruginosa in CF patients. Methods We compared two formerly described qPCR formats in early detection of P. aeruginosa in CF sputum samples: a qPCR targeting oprL gene, and a multiplex PCR targeting gyrB and ecfX genes. Results Tested in vitro on a large panel of P. aeruginosa isolates and others gram-negative bacilli, oprL qPCR exhibited a better sensitivity (threshold of 10 CFU/mL versus 730 CFU/mL), whereas the gyrB/ecfX qPCR exhibited a better specificity (90% versus 73%). These results were validated ex vivo on 46 CF sputum samples positive for P. aeruginosa in culture. Ex vivo assays revealed that qPCR detected 100 times more bacterial cells than culture-based method did. Conclusion Based on these results, we proposed a reference molecular protocol combining the two qPCRs, which offers a sensitivity of 100% with a threshold of 10 CFU/mL and a specificity of 100%. This combined qPCR-based protocol can be adapted and used for other future prospective studies.
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Affiliation(s)
- Florence Le Gall
- EA 3882-Laboratoire de Biodiversité et d'Ecologie Microbienne (LUBEM), SFR 148 ScInBioS, Faculté de Médecine, Université de Brest, Brest F-29200, France.
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Fothergill JL, Ledson MJ, Walshaw MJ, McNamara PS, Southern KW, Winstanley C. Comparison of real time diagnostic chemistries to detect Pseudomonas aeruginosa in respiratory samples from cystic fibrosis patients. J Cyst Fibros 2013; 12:675-81. [PMID: 23726365 DOI: 10.1016/j.jcf.2013.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/28/2013] [Accepted: 04/19/2013] [Indexed: 11/16/2022]
Abstract
BACKGROUND Early eradication therapy is key to keeping the airways Pseudomonas aeruginosa infection-free and rapid identification is essential. METHODS We used rapid DNA extraction and qPCR assays to detect bacterial, P. aeruginosa and strain-specific targets in samples using two qPCR chemistries. Using 459 respiratory samples from adult and children CF patients, we compared two qPCR methods to culture-based methods in terms of sensitivity and time to result. RESULTS For adult samples, there was 100% concordance between methods. There was no clear pattern in fluctuations in P. aeruginosa number during exacerbation. In child samples, qPCR methods identified additional P. aeruginosa positive samples. The time-to-result was reduced by over 24h and copy number and colony forming unit could differ dramatically in some samples. CONCLUSION If adopted, these methods could significantly improve early P. aeruginosa detection in diagnostic laboratories and therefore play a pivotal role in prolonging infection-free airways in CF patients.
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Affiliation(s)
- J L Fothergill
- NIHR Biomedical Research Centre in Microbial Disease, Royal Liverpool Hospital, Prescott Rd, Liverpool L7 8XP, UK; Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, West Derby St, Liverpool L69 7BE, UK.
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Tang Y, Zou J, Ma C, Ali Z, Li Z, Li X, Ma N, Mou X, Deng Y, Zhang L, Li K, Lu G, Yang H, He N. Highly sensitive and rapid detection of Pseudomonas aeruginosa based on magnetic enrichment and magnetic separation. Am J Cancer Res 2013; 3:85-92. [PMID: 23424183 PMCID: PMC3575588 DOI: 10.7150/thno.5588] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 01/04/2013] [Indexed: 12/25/2022] Open
Abstract
A method for highly sensitive and rapid detection of Pseudomonas aeruginosa, based on magnetic enrichment and magnetic separation, is described in this paper. The magnetic nanoparticles (MNPs) were applied to adsorb genome DNA after the sample was lysed. The DNA binding MNPs were directly subjected to polymerase chain reaction (PCR) to amplify gyrB specific sequence of Pseudomonas aeruginosa. The biotin labeled PCR products were detected by chemiluminescence when they were successively incubated with the probes-modified MNPs and alkaline phosphatase (ALP) labeled streptavidin (SA). Agarose gel electrophoresis analyses approved the method of in situ PCR to be highly reliable. The factors which could affect the chemiluminiscence were studied in detail. The results showed that the MNPs of 400 nm in diameter are beneficial to the detection. The sequence length and the binding site of the probe with a target sequence have obvious effects on the detection. The optimal concentration of the probes, hybridization temperature and hybridization time were 10 μM, 60 ºC and 60 mins, respectively. The method of in situ PCR based on MNPs can greatly improve the utilization rate of the DNA template ultimately enhancing the detection sensitivity. Experiment results proved that the primer and probe had high specificity, and Pseudomonas aeruginosa was successfully detected with detection limits as low as 10 cfu/mL by this method, while the detection of a single Pseudomonas aeruginosa can also be achieved.
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Logan C, Habington A, Lennon G, Grogan J, Byrne M, O'Leary J, O'Sullivan N. Genetic relatedness of Pseudomonas aeruginosa isolates among a paediatric cystic fibrosis patient cohort in Ireland. J Med Microbiol 2011; 61:64-70. [PMID: 21921114 DOI: 10.1099/jmm.0.035642-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosa is one of the primary pathogens in the cystic fibrosis (CF) lung and a significant cause of morbidity and mortality. Reports of the spread of epidemic or transmissible strains of P. aeruginosa within and across CF centres in Europe have raised concern regarding the possibility of clonal spread among and within CF centres in Ireland. P. aeruginosa isolates (313 isolates from 142 sputum samples and 53 throat swabs) from 68 CF patients were examined using PFGE to explore the diversity of P. aeruginosa isolates among CF patients in a Dublin paediatric hospital. Only 57 different P. aeruginosa genotypes were identified among the 313 isolates. Forty-three of the genotypes were observed only in individual patients (distinct genotypes) while 13 cluster strains (present in two to four patients) were observed. Typing of P. aeruginosa isolates identified one indistinguishable clonal isolate of P. aeruginosa present in 13 CF patients (13/68; 19.1 %) which displayed higher levels of antibiotic resistance than those displayed by P. aeruginosa isolates of distinct genotype.
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Affiliation(s)
- Catriona Logan
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Adele Habington
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Gráinne Lennon
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Juanita Grogan
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Margaret Byrne
- Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - John O'Leary
- Trinity College Dublin, Dublin, Ireland.,Department of Pathology, Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Niamh O'Sullivan
- Department of Pathology, Coombe Women and Infants University Hospital, Dublin, Ireland.,Department of Microbiology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
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Deschaght P, Van daele S, De Baets F, Vaneechoutte M. PCR and the detection of Pseudomonas aeruginosa in respiratory samples of CF patients. A literature review. J Cyst Fibros 2011; 10:293-7. [DOI: 10.1016/j.jcf.2011.05.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/23/2011] [Accepted: 05/25/2011] [Indexed: 10/18/2022]
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