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Gavillet H, Hatfield L, Rivett D, Jones A, Maitra A, Horsley A, van der Gast C. Bacterial Culture Underestimates Lung Pathogen Detection and Infection Status in Cystic Fibrosis. Microbiol Spectr 2022; 10:e0041922. [PMID: 35972283 PMCID: PMC9602735 DOI: 10.1128/spectrum.00419-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/31/2022] [Indexed: 11/20/2022] Open
Abstract
Microbiological surveillance of airway secretions is central to clinical care in cystic fibrosis (CF). However, the efficacy of microbiological culture, the diagnostic gold standard for pathogen detection, has been increasingly questioned. Here we compared culture with targeted quantitative PCR (QPCR) for longitudinal detection of 2 key pathogens, Pseudomonas aeruginosa and Staphylococcus aureus. Prospectively collected respiratory samples taken from 20 pediatric and 20 adult CF patients over a period of 3-years were analyzed. Patients were eligible if considered free of chronic Pseudomonas infection within 12-months prior to start of study. QPCR revealed high levels of infection with both pathogens not apparent from culture alone. Pseudomonas and Staphylococcus were detected by culture on at least one sampling occasion in 12 and 29 of the patients, respectively. Conversely, both pathogens were detected in all 40 patients by QPCR. Classification of infection status also significantly altered in both pediatric and adult patients, where the number of patients deemed chronically infected with Pseudomonas and Staphylococcus increased from 1 to 28 and 9 to 34, respectively. Overall, Pseudomonas and Staphylococcus infection status classification changed respectively for 36 and 27 of all patients. In no cases did molecular identification lead to a patient being in a less clinically serious infection category. Pathogen detection and infection status classification significantly increased when assessed by QPCR in comparison to culture. This could have implications for clinical care of CF patients, including accuracy of infection diagnosis, relevant and timely antibiotic selection, antimicrobial resistance development, establishment of chronic infection, and cross-infection control. IMPORTANCE Chronic lung infection is the leading cause of morbidity and early mortality for people with cystic fibrosis (pwCF). Microbiological surveillance to detect lung pathogens is recommended as best practise in CF patient care. Here we studied pathogen detection in 40 pwCF over several years. We found that microbiological culture, the diagnostic gold standard, was significantly disparate to targeted culture-independent approaches for detection and determination of chronic infection status of two important pathogens in CF. Pathogen detection was significantly lower by culture and consequently infection status was also misclassified in most cases. In particular, the extent of chronic infection by both P. aeruginosa and S. aureus not realized with culture was striking. Our findings have implications for the development of infection and clinical care of pwCF. Future longitudinal studies with greater patient numbers will be needed to establish the full extent of the clinical implications indicated from this study.
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Affiliation(s)
- Helen Gavillet
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Lauren Hatfield
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Damian Rivett
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Andrew Jones
- Manchester Adult Cystic Fibrosis Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, United Kingdom
| | - Anirban Maitra
- Royal Manchester Children’s Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Alexander Horsley
- Manchester Adult Cystic Fibrosis Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, United Kingdom
| | - Christopher van der Gast
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
- Department of Respiratory Medicine, Northern Care Alliance NHS Foundation Trust, Salford, United Kingdom
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Garcia Gonzalez J, Hernandez FJ. Nuclease activity: an exploitable biomarker in bacterial infections. Expert Rev Mol Diagn 2022; 22:265-294. [PMID: 35240900 DOI: 10.1080/14737159.2022.2049249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION In the increasingly challenging field of clinical microbiology, diagnosis is a cornerstone whose accuracy and timing are crucial for the successful management, therapy, and outcome of infectious diseases. Currently employed biomarkers of infectious diseases define the scope and limitations of diagnostic techniques. As such, expanding the biomarker catalog is crucial to address unmet needs and bring about novel diagnostic functionalities and applications. AREAS COVERED This review describes the extracellular nucleases of 15 relevant bacterial pathogens and discusses the potential use of nuclease activity as a diagnostic biomarker. Articles were searched for in PubMed using terms: "nuclease", "bacteria", "nuclease activity" or "biomarker". For overview sections, original and review articles between 2000 and 2019 were searched for using terms: "infections", "diagnosis", "bacterial", "burden", "challenges". Informative articles were selected. EXPERT OPINION Using the catalytic activity of nucleases offers new possibilities compared to established biomarkers. Nucleic acid activatable reporters in combination with different transduction platforms and delivery methods can be used to detect disease-associated nuclease activity patterns in vitro and in vivo for prognostic and diagnostic applications. Even when these patterns are not obvious or of unknown etiology, screening platforms could be used to identify new disease reporters.
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Affiliation(s)
- Javier Garcia Gonzalez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
| | - Frank J Hernandez
- Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden.,Wallenberg Centre for Molecular Medicine (WCMM), Linköping, Sweden.,Nucleic Acids Technologies Laboratory (NAT-lab), Linköping University, Linköping, Sweden
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3
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Simultaneous detection of three foodborne pathogenic bacteria in food samples by microchip capillary electrophoresis in combination with polymerase chain reaction. J Chromatogr A 2018; 1555:100-105. [DOI: 10.1016/j.chroma.2018.04.058] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 11/22/2022]
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4
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Geng Y, Liu S, Wang J, Nan H, Liu L, Sun X, Li D, Liu M, Wang J, Tan K. Rapid Detection of Staphylococcus aureus in Food Using a Recombinase Polymerase Amplification-Based Assay. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1267-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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5
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Lin Q, Xu P, Li J, Chen Y, Feng J. Direct bacterial loop-mediated isothermal amplification detection on the pathogenic features of the nosocomial pathogen - Methicillin resistant Staphylococcus aureus strains with respiratory origins. Microb Pathog 2017; 109:183-188. [PMID: 28578093 DOI: 10.1016/j.micpath.2017.05.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 05/24/2017] [Accepted: 05/30/2017] [Indexed: 01/25/2023]
Abstract
Loop-mediated isothermal amplification based detection assays using bacterial culture or colony for direct detection of methicillin resistant Staphylococcus aureus(MRSA) had been developed and evaluated, followed by its extensive application on a large scale of clinical MRSA isolated from respiratory origins, including nasal swabs and sputums. Six primers, including outer primers, inner primers and loop primers, were specifically designed for recognizing eight distinct sequences on four targets: 16SrRNA, femA, mecA and orfX. Twenty-seven reference strains were used to develop, evaluate and optimize this assay. Then, a total of 532 clinical MRSA isolates were employed for each detected targets. And the results were determined through both visual observation of the color change by naked eye and electrophoresis. The specific of each primer had been confirmed, and the optimal amplification was obtained under 65 °C for 40 min. The limit of detections (LOD) of bacteria culture LAMP assays were determined to be 104 CFU/ml for 16S rRNA, femA, as well as orfX and 105 CFU/ml for mecA, respectively. The established novel assays on MRSA detection may provide new strategies for rapid detection of foodborne pathogens.
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Affiliation(s)
- Qun Lin
- Lecong Hospital Affiliated of Guangzhou Medical University, Shunde District, Foshan 528315, Guangdong province, China
| | - Pusheng Xu
- Lecong Hospital Affiliated of Guangzhou Medical University, Shunde District, Foshan 528315, Guangdong province, China.
| | - Jiaowu Li
- Lecong Hospital Affiliated of Guangzhou Medical University, Shunde District, Foshan 528315, Guangdong province, China
| | - Yin Chen
- Lecong Hospital Affiliated of Guangzhou Medical University, Shunde District, Foshan 528315, Guangdong province, China
| | - Jieyi Feng
- Lecong Hospital Affiliated of Guangzhou Medical University, Shunde District, Foshan 528315, Guangdong province, China
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6
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Usefulness of Multiplex Real-Time PCR for Simultaneous Pathogen Detection and Resistance Profiling of Staphylococcal Bacteremia. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6913860. [PMID: 27403436 PMCID: PMC4925937 DOI: 10.1155/2016/6913860] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/23/2016] [Indexed: 11/17/2022]
Abstract
Staphylococci are the leading cause of nosocomial blood stream infections. Fast and accurate identification of staphylococci and confirmation of their methicillin resistance are crucial for immediate treatment with effective antibiotics. A multiplex real-time PCR assay that targets mecA, femA specific for S. aureus, femA specific for S. epidermidis, 16S rRNA for universal bacteria, and 16S rRNA specific for staphylococci was developed and evaluated with 290 clinical blood culture samples containing Gram-positive cocci in clusters (GPCC). For the 262 blood cultures identified to the species level with the MicroScan WalkAway system (Siemens Healthcare Diagnostics, USA), the direct real-time PCR assay of positive blood cultures showed very good agreement for the categorization of staphylococci into methicillin-resistant S. aureus (MRSA), methicillin-susceptible S. aureus (MSSA), methicillin-resistant S. epidermidis (MRSE), methicillin-susceptible S. epidermidis (MSSE), methicillin-resistant non-S. epidermidis CoNS (MRCoNS), and methicillin-susceptible non-S. epidermidis CoNS (MSCoNS) (κ = 0.9313). The direct multiplex real-time PCR assay of positive blood cultures containing GPCC can provide essential information at the critical point of infection with a turnaround time of no more than 4 h. Further studies should evaluate the clinical outcome of using this rapid real-time PCR assay in glycopeptide antibiotic therapy in clinical settings.
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Nawattanapaiboon K, Prombun P, Santanirand P, Vongsakulyanon A, Srikhirin T, Sutapun B, Kiatpathomchai W. Hemoculture and Direct Sputum Detection of mecA-Mediated Methicillin-Resistant Staphylococcus aureus by Loop-Mediated Isothermal Amplification in Combination With a Lateral-Flow Dipstick. J Clin Lab Anal 2016; 30:760-7. [PMID: 26991017 DOI: 10.1002/jcla.21935] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 12/04/2015] [Accepted: 12/12/2015] [Indexed: 11/07/2022] Open
Abstract
This study reports loop-mediated isothermal amplification (LAMP) for rapid detection of methicillin-resistant Staphylococcus aureus from direct clinical specimens. Four primers including outer and inner primers were specifically designed on the two target sequences-femB to identify S. aureus and mecA to identify antibiotic-resistant gene. Reference strains including various species of gram-positive/gram-negative isolates were used to evaluate and optimize LAMP assays. The optimum LAMP condition was found at 63°C within 70 min assay time (include hybridization with FITC probe for 5 min and further 5 min for reading the results on the lateral flow dipstick). The detection limits of LAMP for mecA was 10 pg of total DNA or 100 CFU/ml. The LAMP assays were applied to a total of 155 samples of direct DNA extraction from sputum and hemoculture bottles. The sensitivity of LAMP for mecA detection in sputum and hemoculture bottles was 93.3% (28/30) and 100% (52/52), respectively. In conclusion, LAMP assay is an alternative technique for rapid detection of MRSA infection with a technical simplicity and cost-effective method in a routine diagnostic laboratory.
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Affiliation(s)
- Kawin Nawattanapaiboon
- Materials Science and Engineering Programme, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Photchanathorn Prombun
- Materials Science and Engineering Programme, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Apirom Vongsakulyanon
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Toemsak Srikhirin
- Materials Science and Engineering Programme, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Physics, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Boonsong Sutapun
- School of Electronic Engineering, Institute of Engineering, , Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Wansika Kiatpathomchai
- Bioengineering and Sensing Technology Laboratory, BIOTEC, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
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8
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Brandas V, Orrù G, Carraro V, Sanna A, Brajon G, Salati F, Sanna C, Ciusa ML, Meloni M, Coroneo V. Recovery of Staphylococcus aureus in Gray Mugil cephalus Roe (Bottarga): Investigation by an Integrated Cultural/Molecular Approach. J Food Sci 2015; 80:M1285-90. [PMID: 25944563 DOI: 10.1111/1750-3841.12891] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/23/2015] [Indexed: 11/30/2022]
Abstract
In the Mediterranean area, salted and dried roe from the gray Mugil cephalus "bottarga" represent a speciality food with great commercial value. Bottarga is currently produced by a traditional handmade process and, the risk of human bacterial contamination during its manufacturing is still unknown; in this perspective the foodborne pathogen Staphylococcus aureus could potentially contaminate this product due to poor sanitation or bad handling during processing. The aim of this work is: to evaluate the contamination level of foodborne pathogens at different product manufacturing stages and, in addition, to describe a fast and realizable method for the rapid detection of S. aureus in bottarga samples in the field. A cultural procedure was initially used to investigate the occurrence of S. aureus and the other main foodborne pathogens in bottarga samples at the different manufacturing stages (from roe to final product). In addition, a molecular approach was used to rapidly determine the presence of total bacteria, S. aureus, and its potential toxigenicity. Of the 194 specimens analyzed, we identified: Clostridium perfringens, Enterococcus spp. and Enterobacteriaceae. However, some samples resulted as being contaminated with S. aureus (4% in roe and 8.7% in the final product). During the bottarga manufacturing process, we observed an increase in pathogen levels (from 10(2) to 10(5) CFU/g) in contaminated samples, and entA and entB genotypes were identified. Reconstruction experiments suggest that the fresh roe and the bottarga (not completely dried) could represent a risk for the contamination and growth of pathogen bacteria.
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Affiliation(s)
| | - Germano Orrù
- IDNA Sequencing Service (DSS), Univ. di Cagliari, Cagliari, Italy
| | | | - Adriana Sanna
- Public Health Dept, Univ. di Cagliari, Cagliari, Italy
| | - Giovanni Brajon
- IZS of Lazio-Tuscany, State Veterinary Inst, Florence, Italy
| | - Fulvio Salati
- Fish Disease and Aquaculture Centre, IZS of Sardinia State Veterinary Inst., Oristano, Italy
| | - Clara Sanna
- Fish Disease and Aquaculture Centre, IZS of Sardinia State Veterinary Inst., Oristano, Italy
| | | | - Mauro Meloni
- Dipt. di Scienze degli Alimenti, Univ. degli Studi di Udine, Udine, Italy
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9
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da Costa Krewer C, Santos Amanso E, Veneroni Gouveia G, de Lima Souza R, da Costa MM, Aparecido Mota R. Resistance to antimicrobials and biofilm formation in Staphylococcus spp. isolated from bovine mastitis in the Northeast of Brazil. Trop Anim Health Prod 2014; 47:511-8. [DOI: 10.1007/s11250-014-0752-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 12/16/2014] [Indexed: 11/28/2022]
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10
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Jiang X, Jing W, Zheng L, Liu S, Wu W, Sui G. A continuous-flow high-throughput microfluidic device for airborne bacteria PCR detection. LAB ON A CHIP 2014; 14:671-6. [PMID: 24352365 DOI: 10.1039/c3lc50977j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rapid analysis of airborne pathogens plays a critical role in early warning of spreading infectious diseases, which is essential for public health and disease prevention. Herein we report an integrated microfluidic device that can perform airborne pathogen capture, enrichment and continuous-flow high-throughput gene analysis. The device was validated by six frequently encountered bacteria and shows great potential in environmental analysis and for public health protection.
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Affiliation(s)
- Xiran Jiang
- Shanghai Key laboratory of Atmospheric Particle Pollution Prevention (LAP3), Department of Environmental Science & Engineering, Institute of Biomedical Science, Fudan University, Shanghai 200433, PR China.
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11
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Arabestani MR, Fazzeli H, Bahram NE, Alikhani MY. Development and Assessment of a Single Tube Internally Controlled Multiplex PCR Assay to Detect Different Pathogenic Bacteria Involved in Blood Stream Infections. INTERNATIONAL JOURNAL OF ENTERIC PATHOGENS 2013. [DOI: 10.17795/ijep10601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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12
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Xu Z, Li L, Chu J, Peters BM, Harris ML, Li B, Shi L, Shirtliff ME. Development and application of loop-mediated isothermal amplification assays on rapid detection of various types of staphylococci strains. Food Res Int 2012; 47:166-173. [PMID: 22778501 PMCID: PMC3390935 DOI: 10.1016/j.foodres.2011.04.042] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) method for rapid detection of various Staphylococcus strains and associated antibiotic resistance determinant had been developed and evaluated in this study. Six primers, including outer primers, inner primers and loop primers, were specially designed for recognizing eight distinct sequences on three targets: 16SrRNA, femA and mecA.. Forty-one reference strains, including various species of gram-negative and -positive isolates, were included in this study to evaluate and optimize LAMP assays. The optimal reaction condition was found to be 65 °C for 45 min, with detection limits at 100 fg DNA/tube and 10 CFU/reaction for 16S rRNA, 100 fg DNA/tube and 10 CFU/reaction for femA, 1 pg DNA/tube and 100 CFU/reaction for mecA, respectively. Application of LAMP assays were performed on 118 various types of Staphylococcus isolates, the detection rate of LAMP assays for the 16SrRNA, femA and mecA was 100% (118/118), 98.5% (64/65) and 94.3% (66/70), and the negative predictive value (NPV) was 100%, 98.1% and 92.3% respectively; with a 100% positive predictive value (PPV) for all three targets. In conclusion, LAMP assays were demonstrated to be useful and powerful tools for rapid detection of various Staphylococcus strains, and undoubtedly, the rapidness, technical simplicity, and cost-effectiveness of LAMP assays will demonstrate broad application for bacteriological detection of food-borne Methicillin-resistant Staphylococcus (MRS) isolates.
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Affiliation(s)
- Zhenbo Xu
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
- Department of Microbial Pathogenesis, Dental School, University of Maryland, Baltimore, Maryland, USA
| | - Lin Li
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Jin Chu
- School of Food Science and Nutrition, Faculty of Mathematics and Physical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Brian M. Peters
- Department of Microbial Pathogenesis, Dental School, University of Maryland, Baltimore, Maryland, USA
- Graduate Program in Life Sciences, Molecular Microbiology and Immunology Program, University of Maryland, Baltimore, Maryland, USA
| | - Megan L. Harris
- Department of Microbial Pathogenesis, Dental School, University of Maryland, Baltimore, Maryland, USA
| | - Bing Li
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Lei Shi
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, China
| | - Mark E. Shirtliff
- Department of Microbial Pathogenesis, Dental School, University of Maryland, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
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13
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Rapid detection of Staphylococcus aureus via a sensitive DNA hybridization assay based on a long-lifetime luminescent europium marker. Mikrochim Acta 2011. [DOI: 10.1007/s00604-011-0654-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Molecular Approaches to the Diagnosis of Sepsis. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Cattoir V, Merabet L, Djibo N, Rioux C, Legrand P, Girou E, Lesprit P. Clinical impact of a real-time PCR assay for rapid identification of Staphylococcus aureus and determination of methicillin resistance from positive blood cultures. Clin Microbiol Infect 2011; 17:425-31. [PMID: 20384710 DOI: 10.1111/j.1469-0691.2010.03233.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The full identification and susceptibility profile of staphylococci from positive blood cultures (BCs) generally takes 24-48 h using phenotypic methods. The aim of this prospective study was to evaluate the clinical impact of a real-time PCR strategy for rapid identification of staphylococci and determination of methicillin resistance directly from positive BCs. During a 12-month period, 250 episodes of positive BCs with organism morphology resembling staphylococci were enrolled. Two strategies were compared: conventional (n = 128) using standard phenotypic methods or rapid (n = 122) using a real-time PCR assay that is able to detect specific genes of Staphylococcus aureus (nuc and sa442) and the encoding gene for methicillin resistance (mecA). Overall, 97 episodes (39%) were clinical-significant bloodstream infections. The prevalence of methicillin resistance of S. aureus was 24%. A favorable outcome (defined as clinical cure with resolution of signs and no evidence of recurrence or relapse at 12 weeks follow-up) was observed in similar proportions of episodes with (58%) or without (60%) PCR testing (p 0.8). In multivariate analyses, age and infection due to methicillin-susceptible S. aureus (adjusted OR 0.96, 95% CI 0.93-0.99; and adjusted OR 3.11, 95% CI 1.12-8.65, respectively) were the unique factors independently associated with a favorable outcome. Among the 153 episodes of contaminated BCs, similar proportions received unjustified antibiotic therapy (PCR strategy: 17%, conventional testing: 10%; p 0.33). In a setting with a moderate level of methicillin-resistant S. aureus and relatively high contamination of BCs, real-time PCR testing was not beneficial compared to conventional methods.
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Affiliation(s)
- V Cattoir
- Department of Bacteriology-Virology Infection Control Unit, Hôpital Henri Mondor, Assistance Publique-Hôpitaux de Paris, Université Paris 12, Créteil, France
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16
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Jukes L, Mikhail J, Bome-Mannathoko N, Hadfield SJ, Harris LG, El-Bouri K, Davies AP, Mack D. Rapid differentiation of Staphylococcus aureus, Staphylococcus epidermidis and other coagulase-negative staphylococci and meticillin susceptibility testing directly from growth-positive blood cultures by multiplex real-time PCR. J Med Microbiol 2010; 59:1456-1461. [PMID: 20813851 DOI: 10.1099/jmm.0.023168-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study evaluated a multiplex real-time PCR method specific for the mecA, femA-SA and femA-SE genes for rapid identification of Staphylococcus aureus, Staphylococcus epidermidis and non-S. epidermidis coagulase-negative staphylococci (CoNS), and meticillin susceptibility testing directly in positive blood cultures that grew Gram-positive cocci in clusters. A total of 100 positive blood cultures produced: 39 S. aureus [12 meticillin-resistant S. aureus (MRSA), 31% of all the S. aureus]; 30 S. epidermidis (56.6% of the CoNS), 8 Staphylococcus capitis (15.1%), 3 Staphylococcus saprophyticus (5.7%), 4 Staphylococcus hominis (7.5%), 3 Staphylococcus haemolyticus (5.7%), 2 Staphylococcus warneri (3.8%), 1 Staphylococcus cohnii (1.9%) and 2 unidentified Staphylococcus spp. (3.8%); and 1 Micrococcus luteus in pure culture. Two blood cultures had no growth on subculture and five blood cultures grew mixed CoNS. For the 95 blood cultures with pure growth or no growth on subculture, there was very good agreement between real-time PCR and the BD Phoenix identification system for staphylococcal species categorization in S. aureus, S. epidermidis and non-S. epidermidis CoNS and meticillin-resistance determination (Cohen's unweighted kappa coefficient κ=0.882). All MRSA and meticillin-susceptible S. aureus were correctly identified by mecA amplification. PCR amplification of mecA was more sensitive for direct detection of meticillin-resistant CoNS in positive blood cultures than testing with the BD Phoenix system. There were no major errors when identifying staphylococcal isolates and their meticillin susceptibility within 2.5 h. Further studies are needed to evaluate the clinical benefit of using such a rapid test on the consumption of glycopeptide antibiotics and the alteration of empiric therapy in the situation of positive blood cultures growing staphylococci, and the respective clinical outcomes.
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Affiliation(s)
- Leanne Jukes
- Public Health Wales Microbiology ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, UK
| | - Jane Mikhail
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, UK
| | - Naledi Bome-Mannathoko
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, UK
| | - Stephen J Hadfield
- Public Health Wales Microbiology ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, UK
| | - Llinos G Harris
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, UK
| | - Khalid El-Bouri
- Public Health Wales Microbiology ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, UK
| | - Angharad P Davies
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, UK.,Public Health Wales Microbiology ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, UK
| | - Dietrich Mack
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea, UK.,Public Health Wales Microbiology ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea, UK
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Lee JH, Song KY, Hyeon JY, Hwang IG, Kwak HS, Han JA, Chung YH, Seo KH. Comparison of Standard Culture Method and Real-time PCR Assay for Detection of Staphylococcus aureus in Processed and Unprocessed Foods. Korean J Food Sci Anim Resour 2010. [DOI: 10.5851/kosfa.2010.30.3.410] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Kilic A, Muldrew KL, Tang YW, Basustaoglu AC. Triplex real-time polymerase chain reaction assay for simultaneous detection of Staphylococcus aureus and coagulase-negative staphylococci and determination of methicillin resistance directly from positive blood culture bottles. Diagn Microbiol Infect Dis 2010; 66:349-55. [DOI: 10.1016/j.diagmicrobio.2009.11.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 11/23/2009] [Accepted: 11/23/2009] [Indexed: 10/19/2022]
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19
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Quiel A, Jürgen B, Piechotta G, Le Foll AP, Ziebandt AK, Kohler C, Köster D, Engelmann S, Erck C, Hintsche R, Wehland J, Hecker M, Schweder T. Electrical protein array chips for the detection of staphylococcal virulence factors. Appl Microbiol Biotechnol 2009; 85:1619-27. [DOI: 10.1007/s00253-009-2347-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 11/05/2009] [Accepted: 11/07/2009] [Indexed: 10/20/2022]
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20
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Haas B, Nathens AB. Future diagnostic and therapeutic approaches in surgical infections. Surg Clin North Am 2009; 89:539-54, xi. [PMID: 19281899 DOI: 10.1016/j.suc.2008.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Despite ongoing efforts to standardize therapy and improve management, the morbidity and mortality associated with surgical infections remain high. Continued innovation is required to improve outcomes further, particularly in the face of the increasing prevalence of multidrug resistant organisms. Although they remain in the experimental stages, a number of recent advances have the potential to have significant impact on the management and outcomes of surgical infections. These include novel diagnostic strategies, antimicrobials targeting microbial virulence factors, novel vaccines, and risk stratification based on genetic profiling.
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Affiliation(s)
- Barbara Haas
- Department of Surgery, University of Toronto, Toronto, Ontario, M5G 1L5, Canada.
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21
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Development of a single-tube polymerase chain reaction assay for the simultaneous detection of Haemophilus influenzae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus spp. directly in clinical samples. Diagn Microbiol Infect Dis 2008; 63:121-6. [PMID: 19027257 DOI: 10.1016/j.diagmicrobio.2008.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Revised: 09/29/2008] [Accepted: 09/30/2008] [Indexed: 11/21/2022]
Abstract
This study describes the development and evaluation of a multiplex single-tube polymerase chain reaction assay for the simultaneous detection of Haemophilus influenzae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus spp. used as target species-specific or genus-specific genes. The assay enables the detection of 5 to 50 pg of bacterial DNA. The sensitivity of the assay was evaluated as 100% for P. aeruginosa, S. aureus, and Streptococcus spp., and 94.3% for H. influenzae; the specificity was 100% for all 4 microorganisms (positive predictive value, 100%; negative predictive value, 98.2%). The assay permits rapid and accurate detection of these 4 microorganisms in a wide range of clinical samples such as whole blood, cerebrospinal, ear, pleural and ophthalmic fluids, as well as bronchoalveolar lavage and bronchial secretions.
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22
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Stepán J, Pantůcek R, Doskar J. Molecular diagnostics of clinically important staphylococci. Folia Microbiol (Praha) 2008; 49:353-86. [PMID: 15530002 DOI: 10.1007/bf03354664] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bacterial species of the genus Staphylococcus known as important human and animal pathogens are the cause of a number of severe infectious diseases. Apart from the major pathogen Staphylococcus aureus, other species until recently considered to be nonpathogenic may also be involved in serious infections. Rapid and accurate identification of the disease-causing agent is therefore prerequisite for disease control and epidemiological surveillance. Modern methods for identification and typing of bacterial species are based on genome analysis and have many advantages compared to phenotypic methods. The genotypic methods currently used in molecular diagnostics of staphylococcal species, particularly of S. aureus, are reviewed. Attention is also paid to new molecular methods with the highest discriminatory power. Efforts made to achieve interlaboratory reproducibility of diagnostic methods are presented.
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Affiliation(s)
- J Stepán
- Department of Genetics and Molecular Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czechia
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23
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Ruimy R, Dos-Santos M, Raskine L, Bert F, Masson R, Elbaz S, Bonnal C, Lucet JC, Lefort A, Fantin B, Wolff M, Hornstein M, Andremont A. Accuracy and potential usefulness of triplex real-time PCR for improving antibiotic treatment of patients with blood cultures showing clustered gram-positive cocci on direct smears. J Clin Microbiol 2008; 46:2045-51. [PMID: 18417663 PMCID: PMC2446825 DOI: 10.1128/jcm.02250-07] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/24/2008] [Accepted: 04/09/2008] [Indexed: 11/20/2022] Open
Abstract
Bacterial identification and antibiotic susceptibility testing currently require 48 h when a first blood culture (BC) is positive for clustered gram-positive cocci on direct smear examination (DSE). Meanwhile, antibiotic treatment is often inadequate, reducing the chances of effective treatment or creating unnecessary selective pressure. A new real-time PCR (RT-PCR) technique that differentiates Staphylococcus aureus from coagulase-negative staphylococci (CoNS) and detects methicillin resistance in 90 min in BC bottles could help solve these problems. BC bottles from 410 patients with gram-positive cocci on DSE were processed by current methods, and patients' treatments were prospectively recorded. The RT-PCR assay was performed on aliquots of these BCs, which had been kept frozen. For the 121 patients who had true bacteremia, we established whether the faster availability of RT-PCR results could have led to the initiation of treatments different from those actually given. RT-PCR sensitivity and specificity were 100% for differentiating between S. aureus and CoNS and detecting methicillin resistance with two manufacturers' BC bottles. For 31/86 (36%) of the S. aureus-infected patients and for 8/35 (23%) of the CoNS-infected patients who either had suboptimal or nonoptimal treatment or were untreated 48 h after positivity was detected, the early availability of RT-PCR results could have allowed more effective treatment. Unnecessary glycopeptide treatments could have been avoided for 28 additional patients. The use of RT-PCR would increase treatment effectiveness in patients with staphylococcal bacteremia and reduce the selective pressure created by glycopeptides.
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Affiliation(s)
- Raymond Ruimy
- Hospital Group Bichat-Claude Bernard, Laboratoire de Bactériologie, 46, Rue Henri-Huchard, 75018 Paris, France.
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24
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Tang J, Zhou R, Shi X, Kang M, Wang H, Chen H. Two thermostable nucleases coexisted in Staphylococcus aureus: evidence from mutagenesis and in vitro expression. FEMS Microbiol Lett 2008; 284:176-83. [PMID: 18510563 DOI: 10.1111/j.1574-6968.2008.01194.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Thermostable nuclease is known to be an important pathogenic factor unique to Staphylococcus aureus and it is commonly presumed to have had the same genetic origin. However, two ORFs in S. aureus genomes were predicted to encode nucleases. One encoded an unnamed nuclease A (SNase) (termed nuc1), and the other encoded a thermonuclease (TNase) named nuc (termed nuc2). In order to verify whether the two thermostable nuclease proteins are coexpressed in S. aureus, the nuc1 and nuc2 genes were cloned and expressed in Escherichia coli, and both of the recombinant proteins showed thermostable nuclease activity in a toluidine blue-DNA assay. Furthermore, a nuc1-deleted mutant of S. aureus strain RN4220 (termed RNDeltanuc1) was successfully constructed by homologous recombination. Selection and characterization of this mutant strain revealed that it still exhibited thermostable nuclease activity, but at a relative lower level than that of the parent strain. The nucleases secreted by the parent strain and nuc1-deleted strain still showed functional activity after 30 min at 121 degrees C. The findings indicated that two types of thermostable nucleases, encoded by two different genes, coexisted in S. aureus.
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Affiliation(s)
- Junni Tang
- State Key Laboratory of Agricultural Microbiology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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Thomas LC, Gidding HF, Ginn AN, Olma T, Iredell J. Development of a real-time Staphylococcus aureus and MRSA (SAM-) PCR for routine blood culture. J Microbiol Methods 2006; 68:296-302. [PMID: 17046087 DOI: 10.1016/j.mimet.2006.09.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 08/28/2006] [Accepted: 09/05/2006] [Indexed: 11/24/2022]
Abstract
The notification of "Gram-positive cocci, possibly staphylococcus" in a blood culture drawn from a seriously ill patient is responsible for a large amount of vancomycin prescribing in institutions where methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of bacteraemia. A duplex real-time TaqMan polymerase chain reaction targeting the species-specific nuc gene, and the mecA gene encoding methicillin-resistance, was developed as a tool for rapid identification and detection of S. aureus and methicillin-resistance, and optimised for immediate as-needs testing. Three different DNA extraction methods achieved varying DNA quality, with PCR inhibition the main problem. Serial blood cultures (n=120) identified as possible staphylococci on Gram stain from our clinical laboratory were examined. There was one false negative result for a methicillin-resistant Staphylococcus epidermidis, which was positive on repeat testing, and one false negative result due to DNA extraction failure for MRSA from peritoneal dialysate inoculated into blood culture medium. Sensitivity and specificity of 97% and 100%, respectively, were obtained for mecA; and sensitivity and specificity of 98% and 100%, respectively, for nuc. Detection of slow-growing coagulase-negative staphylococci as co-infecting strains may be reduced. The assay quickly and reliably identified S. aureus in mixed infection, and identified methicillin resistance in both S. epidermidis and S. aureus strains.
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Affiliation(s)
- L C Thomas
- Centre for Infectious Diseases and Microbiology-Public Health, University of Sydney, Australia
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26
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Alarcón B, Vicedo B, Aznar R. PCR-based procedures for detection and quantification of Staphylococcus aureus and their application in food. J Appl Microbiol 2006; 100:352-64. [PMID: 16430512 DOI: 10.1111/j.1365-2672.2005.02768.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To evaluate the specificity of nuc targeted primers for PCR detection of Staphylococcus aureus in different food matrices and to establish a RTQ-PCR procedure suitable for the routine detection and quantification of this pathogen in food. METHODS AND RESULTS Specificity of nuc targeted primers (Pri1-Pri2 and the newly designed RTQ-PCR primers) was tested on a total of 157 strains of genetically confirmed identity, including reference and food isolates. PCR detection on artificially inoculated beef samples by DNA extraction using a DNeasy Tissue Kit (Qiagen GmhH, Hilden, Germany) showed a sensitivity value around 10(3) CFU g(-1). The two RTQ-PCR systems, incorporating SYBR-Green I and TaqMan, respectively, applied in the present work improved the sensitivity of conventional PCR by lowering the detection level to 10 and 100 cells, respectively. Out of 164 naturally contaminated foods tested for the presence of Staph. aureus, 74 were positive by conventional PCR and 69 by the traditional culture method with a high degree of result agreement between both methodologies (93.3%). CONCLUSIONS PCR approaches, using nuc targeted primers, have proved specific and combined with growth techniques may improve detection of Staph. aureus in different types of food. SIGNIFICANCE AND IMPACT OF THE STUDY The SYBR-Green I real-time PCR approach established allows the sensitive, automated and quantitative detection of Staph. aureus for routine analysis at a reasonable cost.
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Affiliation(s)
- B Alarcón
- Departamento de Microbiología y Ecología, Universitat de València, Spain
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TANG JUNNI, SHI XIANMING, SHI CHUNLEI, CHEN HUANCHUN. CHARACTERIZATION OF A DUPLEX POLYMERASE CHAIN REACTION ASSAY FOR THE DETECTION OF ENTEROTOXIGENIC STRAINS OF STAPHYLOCOCCUS AUREUS. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1745-4581.2006.00047.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Harakeh S, Yassine H, Hajjar S, El-Fadel M. Isolates of Staphylococcus aureus and saprophyticus resistant to antimicrobials isolated from the Lebanese aquatic environment. MARINE POLLUTION BULLETIN 2006; 52:912-9. [PMID: 16487984 DOI: 10.1016/j.marpolbul.2005.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 12/07/2005] [Accepted: 12/16/2005] [Indexed: 05/06/2023]
Abstract
The indiscriminate use of antimicrobials especially in developing countries has evoked serious bacterial resistance and led to the emergence of new and highly resistant strains of bacteria to commonly used antimicrobials. In Lebanon, pollution levels and bacterial infections are increasing at a high rate as a result of inadequate control measures to limit untreated effluent discharges into the sea or freshwater resources. The aim of this study was to isolate and molecularly characterize various Staphylococcus strains isolated from sea water, fresh water, sediments, and crab samples collected from representative communities along the coast of Lebanon. The results on the antimicrobial resistance indicated that the level of resistance of Staphylococcus aureus varied with various antimicrobials tested. The resistance patterns ranged between 45% in freshwater isolates and 54.8% in seawater ones. Fifty one percent of the tested isolates have shown resistance to at least one of the five tested antimicrobials; with seawater isolates exhibiting the highest rates of antimicrobial resistance.
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Affiliation(s)
- Steve Harakeh
- Department of Biology, American University of Beirut, P.O. Box 11-0236, Beirut, Lebanon.
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Shrestha NK, Tuohy MJ, Padmanabhan RA, Hall GS, Procop GW. Evaluation of the LightCycler Staphylococcus M GRADE kits on positive blood cultures that contained gram-positive cocci in clusters. J Clin Microbiol 2006; 43:6144-6. [PMID: 16333115 PMCID: PMC1317217 DOI: 10.1128/jcm.43.12.6144-6146.2005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated the Roche LightCycler Staphylococcus M(GRADE) kits to differentiate between Staphylococcus aureus and coagulase-negative staphylococci in blood cultures growing clusters of gram-positive cocci. Testing 100 bottles (36 containing S. aureus), the assay was 100% sensitive and 98.44% specific for S. aureus and 100% sensitive and specific for coagulase-negative staphylococci.
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Affiliation(s)
- Nabin K Shrestha
- Department of Infectious Diseases, The Cleveland Clinic Foundation, 9500 Euclid Avenue, S-32, Cleveland, OH 44195, USA.
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Shale K, Lues J, Venter P, Buys E. The distribution of Staphylococcus sp. on bovine meat from abattoir deboning rooms. Food Microbiol 2005. [DOI: 10.1016/j.fm.2004.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Pinto B, Chenoll E, Aznar R. Identification and typing of food-borne Staphylococcus aureus by PCR-based techniques. Syst Appl Microbiol 2005; 28:340-52. [PMID: 15997707 DOI: 10.1016/j.syapm.2005.01.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The possibility of using PCR for rapid identification of food-borne Staphylococcus aureus isolates was evaluated as an alternative to the API-Staph system. A total of 158 strains, 15 S. aureus, 12 other staphylococcal species, and 131 isolates recovered from 164 food samples were studied. They were phenotypically characterized by API-Staph profiles and tested for PCR amplification with specific primers directed to thermonuclease (nuc) and enterotoxin (sea to see) genes. Disagreement between the PCR results and API-Staph identification was further assessed by the analysis of randomly amplified polymorphic DNA (RAPD) profiles obtained with three universal primers (M13, T3, and T7) and 16S rDNA sequencing. Forty out of 131 isolates (31%) tested positive for PCR enterotoxin. Of these, 14 (11%) were positive for sea, 22 (17%) for sec, one (0.8%) for sed, and three (2.2%) for sea and sec. No amplification corresponding to seb nor see was obtained. Cluster analysis based on RAPD profiles revealed that most of the sec positive food isolates grouped together in three clusters. Cluster analysis combining the three RAPD fingerprints (M 13, T3, and T7), PCR-enterotoxin genotype and API-Staph profiles, grouped the nuc PCR positive isolates together with S. aureus reference strains and the nuc PCR negative isolates with reference strains of other staphylococcal species. The only nuc PCR positive food isolate that remained unclustered was a sed positive strain identified by 16S rDNA sequence as S. simulans. The high concordance between S. aureus and nuc PCR positive strains (99%) corroborates the specificity of the primers used and the suitability of nuc PCR for rapid identification of S. aureus in routine food analysis.
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Affiliation(s)
- Beatriz Pinto
- Departamento de Microbiologta y Ecologia, Universitat de Valencia, Spain
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Ruiz-Pérez de Pipaón M, Torres-Sánchez MJ, Arroyo-Pedrero LA, Prados-Blanco T, Palomares-Folía JC, Aznar-Martín J. [Detection of methicillin resistance and identification of Staphylococcus spp. from positive blood culture bottles using the mecA and nucA genes with the LightCycler System]. Enferm Infecc Microbiol Clin 2005; 23:208-12. [PMID: 15826545 DOI: 10.1157/13073146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
INTRODUCTION The aim of this study was to evaluate the feasibility of detecting Staphylococcus aureus and coagulase-negative staphylococci (CoNS) and of identifying methicillin resistance directly in positive BACTEC blood culture bottles using the LightCycler system. METHODS One hundred thirty-one positive blood culture bottles in which Gram-positive cocci in cluster were observed after Gram staining and 40 positive bottles with microorganisms other than staphylococci were studied. A molecular assay based on an automated DNA extraction protocol with a MagNA Pure LC instrument was used. Oligonucleotide primers and fluorescence-labeled hybridization probes were designed for amplification and sequence-specific detection of both a 408-pb fragment within the mecA gene and a 279-pb fragment within the S. aureus-specific nucA gene. RESULTS All the bottles that yielded methicillin-resistant S. aureus (MRSA), methicillin-sensitive S. aureus (MSSA) or methicillin-resistant CoNS (MRCoNS) strains were correctly identified by the nucA and mecA PCR assays. One bottle that yielded a mixed culture of MSSA and MRCoNS gave positive results for both genes. In the 21 bottles with methicillin-susceptible CoNS (MSCoNS), nucA PCR were negative, but two of these bottles gave positive results for the mecA gene. The sensitivity and specificity of the nucA gene assay were 100%. The sensitivity and specificity of the PCR assay for detection of methicillin resistance with the mecA gene were 100% and 97.5%, respectively. CONCLUSION This is a sensitive and highly specific method for identifying staphylococci in positive blood cultures, allowing discrimination between methicillin-susceptible and -resistant strains in less than 3 hours after Gram stain.
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Costa AM, Kay I, Palladino S. Rapid detection of mecA and nuc genes in staphylococci by real-time multiplex polymerase chain reaction. Diagn Microbiol Infect Dis 2005; 51:13-7. [PMID: 15629224 DOI: 10.1016/j.diagmicrobio.2004.08.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Accepted: 08/31/2004] [Indexed: 11/26/2022]
Abstract
A multiplex real-time polymerase chain reaction (RT-PCR) targeting the mecA and nuc genes was developed for the detection of methicillin resistance and identification of Staphylococcus aureus. Novel mecA and nuc primers and fluorescence resonance energy transfer hybridization probes specific for the mecA and nuc genes were evaluated. The assay was performed using the LightCycler system (Roche Molecular Biochemicals, Mannheim, Germany) and evaluated against the traditional gel-based multiplex PCR (PCR-gel) method currently used at Royal Perth Hospital. Clinical isolates (n = 222) and isolates from a culture collection library (n = 206) were tested by both assays in parallel. The RT-PCR assay was 100% sensitive and specific for the detection of methicillin resistance and for the identification of S. aureus when compared with the PCR-gel assay. Results from the RT-PCR assay showed 5 isolates with lower efficiency fluorescence curves for the nuc gene PCR fragment. DNA sequencing showed mutations within the region of the probe-binding sites compared with the reference strain. The results of the RT-PCR assay were available within 2 h. This rapid mecA/nuc RT-PCR assay is a suitable and practical tool for the routine detection of methicillin resistance and identification of S. aureus, which can be easily incorporated into the diagnostic molecular microbiology laboratory work flow.
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Affiliation(s)
- Anna-Maria Costa
- Department of Microbiology and Infectious Diseases, Royal Perth Hospital, Perth 6847, Western Australia, Australia.
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