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Abdelaziz MA, El-Aziz AMA, El-Sokkary MMA, Barwa R. Characterization and genetic analysis of extensively drug-resistant hospital acquired Pseudomonas aeruginosa isolates. BMC Microbiol 2024; 24:225. [PMID: 38926687 PMCID: PMC11201863 DOI: 10.1186/s12866-024-03321-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 05/06/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The incidence of hospital-acquired infections in extensively drug-resistant Pseudomonas aeruginosa (XDR-PA) has been increasing worldwide and is frequently associated with an increase in mortality and morbidity rates. The aim of this study was to characterize clinical XDR-PA isolates recovered during six months at three different hospitals in Egypt. RESULTS Seventy hospital-acquired clinical isolates of P. aeruginosa were classified into multidrug-resistant (MDR), extensively drug-resistant (XDR) and pandrug-resistant (PDR), according to their antimicrobial resistance profile. In addition, the possession of genes associated with mobile genetic elements and genes encoding antimicrobial resistance determinants among isolates were detected using polymerase chain reaction. As a result, a significant percentage of the isolates (75.7%) were XDR, while 18.5% were MDR, however only 5.7% of the isolates were non-MDR. The phenotypic detection of carbapenemases, extended-spectrum β-lactamases (ESBLs) and metallo β-lactamase (MBL) enzymes showed that 73.6% of XDR-PA isolates were carbapenemases producers, whereas 75.5% and 88.7% of XDR-PA isolates produced ESBLs and MBL respectively. In addition, PCR screening showed that oxa gene was the most frequently detected gene of carbapenemases (91.4%), while aac(6')-lb gene was mostly detected (84.3%) among the screened aminoglycosides-resistance genes. Furthermore, the molecular detection of the colistin resistance gene showed that 12.9% of isolates harbored mcr-1 gene. Concerning mobile genetic element markers (intI, traA, tnp513, and merA), intI was the highest detected gene as it was amplified in 67 isolates (95.7%). Finally, phylogenetic and molecular typing of the isolates via ERIC-PCR analysis revealed 10 different ERIC fingerprints. CONCLUSION The present study revealed a high prevalence of XDR-PA in hospital settings which were resistant to a variety of antibiotics due to several mechanisms. In addition, 98% of the XDR-PA clinical isolates contained at least one gene associated with movable genetic elements, which could have aided the evolution of these XDR-PA strains. To reduce spread of drug resistance, judicious use of antimicrobial agents and strict infection control measures are therefore essential.
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Affiliation(s)
- Mai A Abdelaziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Abeer M Abd El-Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mohamed M A El-Sokkary
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.
| | - Rasha Barwa
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
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2
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Healy HG, Ehde A, Bartholow A, Kantor RS, Nelson KL. Responses of drinking water bulk and biofilm microbiota to elevated water age in bench-scale simulated distribution systems. NPJ Biofilms Microbiomes 2024; 10:7. [PMID: 38253591 PMCID: PMC10803812 DOI: 10.1038/s41522-023-00473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 12/04/2023] [Indexed: 01/24/2024] Open
Abstract
Reductions in nonresidential water demand during the COVID-19 pandemic highlighted the importance of understanding how water age impacts drinking water quality and microbiota in piped distribution systems. Using benchtop model distribution systems, we aimed to characterize the impacts of elevated water age on microbiota in bulk water and pipe wall biofilms. Five replicate constant-flow reactors were fed with municipal chloraminated tap water for 6 months prior to building closures and 7 months after. After building closures, chloramine levels entering the reactors dropped; in the reactor bulk water and biofilms the mean cell counts and ATP concentrations increased over an order of magnitude while the detection of opportunistic pathogens remained low. Water age, and the corresponding physicochemical changes, strongly influenced microbial abundance and community composition. Differential initial microbial colonization also had a lasting influence on microbial communities in each reactor (i.e., historical contingency).
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Affiliation(s)
- Hannah Greenwald Healy
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Aliya Ehde
- Division of Environmental and Ecological Engineering, Purdue University, West Lafayette, IN, USA
| | - Alma Bartholow
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Rose S Kantor
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA.
| | - Kara L Nelson
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA.
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3
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Spencer-Williams I, Meyer M, DePas W, Elliott E, Haig SJ. Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking-Water-Associated Pathogens in a Full-Scale Drinking Water Distribution System. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:20360-20369. [PMID: 37970641 DOI: 10.1021/acs.est.3c05272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Increases in phosphate availability in drinking water distribution systems (DWDSs) from the use of phosphate-based corrosion control strategies may result in nutrient and microbial community composition shifts in the DWDS. This study assessed the year-long impacts of full-scale DWDS orthophosphate addition on both the microbial ecology and density of drinking-water-associated pathogens that infect the immunocompromised (DWPIs). Using 16S rRNA gene amplicon sequencing and droplet digital PCR, drinking water microbial community composition and DWPI density were examined. Microbial community composition analysis suggested significant compositional changes after the orthophosphate addition. Significant increases in total bacterial density were observed after orthophosphate addition, likely driven by a 2 log 10 increase in nontuberculous mycobacteria (NTM). Linear effect models confirmed the importance of phosphate addition with phosphorus concentration explaining 17% and 12% of the variance in NTM and L. pneumophila density, respectively. To elucidate the impact of phosphate on NTM aggregation, a comparison of planktonic and aggregate fractions of NTM cultures grown at varying phosphate concentrations was conducted. Aggregation assay results suggested that higher phosphate concentrations cause more disaggregation, and the interaction between phosphate and NTM is species specific. This work reveals new insight into the consequences of orthophosphate application on the DWDS microbiome and highlights the importance of proactively monitoring the DWDS for DWPIs.
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Affiliation(s)
- Isaiah Spencer-Williams
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Mitchell Meyer
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
| | - William DePas
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, United States
| | - Emily Elliott
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Geology and Environmental Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sarah-Jane Haig
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Environmental & Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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4
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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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5
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Khalaf EM, Hassan HM, El-Baz AM, Shata A, Khodir AE, Yousef ME, Elgharabawy RM, Nouh NA, Saleh S, Bin-Meferij MM, El-kott AF, El-Sokkary MM, Eissa H. A novel therapeutic combination of dapagliflozin, Lactobacillus and crocin attenuates diabetic cardiomyopathy in rats: Role of oxidative stress, gut microbiota, and PPARγ activation. Eur J Pharmacol 2022; 931:175172. [DOI: 10.1016/j.ejphar.2022.175172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/17/2022] [Accepted: 07/21/2022] [Indexed: 02/09/2023]
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6
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Dong K, Kang Z, Ji X, Zhang X, Cheng P, Sun B. A Loop-mediated Isothermal Amplification With a Nanoparticle-Based Lateral Flow Biosensor Assay to Detect Pseudomonas aeruginosa in Endophthalmitis. Transl Vis Sci Technol 2021; 10:26. [PMID: 34935909 PMCID: PMC8711014 DOI: 10.1167/tvst.10.14.26] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Pseudomonas aeruginosa is the most common bacteria causing endophthalmitis after cataract surgery. Vitreous fluid culture and molecular studies are commonly used in clinical diagnoses, but have disadvantages, such as a long culture cycle and low detection sensitivity. Here, we report a loop-mediated isothermal amplification (LAMP) method combined with the nanoparticles-lateral flow biosensor (LFB) method for rapid and specific detection of P. aeruginosa. Methods A set of six primers was designed to target the OprL gene of P. aeruginosa. Genomic DNA extracted from several gram-negative and gram-positive bacteria was used to determine the sensitivity and specificity of the analysis. LAMP reactions were conducted at 65 °C for 50 minutes, and results were reported using the LFB method. Results The DNA template of P. aeruginosa was specifically recognized by the P. aeruginosa-LAMP-LFB (PA-LAMP-LFB) method as no cross reactions were observed for non–P. aeruginosa templates. The analytical sensitivity of our assay was 100 fg per test for the pure cultured DNA template, and the result obtained using the LFB was consistent with that of colorimetric indicator detection. The whole test could be completed within 1h. This method was used to detect P. aeruginosa, Staphylococcus aureus, and Klebsiella pneumoniae; only P. aeruginosa was positive. The positive rates of P. aeruginosa detected by a traditional culture method, the LAMP-LFB method, and the fluorescence quantitative polymerase chain reaction method were 17.7%, 17.7%, and 13.3%, respectively. Conclusions The P. aeruginosa-LAMP-LFB method established here is a rapid, specific, and sensitive method for the detection of P. aeruginosa, which can be widely used.
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Affiliation(s)
- Kui Dong
- Shanxi Eye Hospital, Taiyuan, Shanxi, China
| | | | - Xuan Ji
- Shanxi Eye Hospital, Taiyuan, Shanxi, China
| | | | | | - Bin Sun
- Shanxi Eye Hospital, Taiyuan, Shanxi, China
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7
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El-Baz AM, Khodir AE, Adel El-Sokkary MM, Shata A. The protective effect of Lactobacillus versus 5-aminosalicylic acid in ulcerative colitis model by modulation of gut microbiota and Nrf2/Ho-1 pathway. Life Sci 2020; 256:117927. [PMID: 32526285 DOI: 10.1016/j.lfs.2020.117927] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023]
Abstract
AIMS Ulcerative colitis (UC) has many complications, from colonic damage to colorectal cancer. The mystery of both etiology and effective treatment of UC still challenging process. The role of gut microbiota in UC is still unclear. In the current study we compare the difference in gut microbiota abundance in both UC and normal colon besides the therapeutic effect of Lactobacillus spp. in treating UC versus the standard drug. MATERIALS AND METHODS The experimental panel included five group of rats; normal control, UC diseased rats, sterilizing rats, ASA treated and Lactobacillus treated. The change in the microbiota abundance was investigated using conventional and real time PCR. In parallel, clinical evaluation of UC and macroscopic examination scoring was also done. Colonic oxidants/antioxidant stress biomarkers; MDA, GSH, catalase, myeloperoxidase activity, and SOD activity were assessed. Colon Nrf2, HO-1 contents and TNF-α was evaluated. KEY FINDINGS The current study revealed a significant difference in the relative abundance of microbiota where, UC is associated with massive increase of E. coli and Fusobacterium spp., while enormous decrease in Bifidobacteria spp. in contrast with negative control. Both 5-ASA and Lactobacillus show a significant amelioration of all antioxidant enzymes and marked decline of inflammatory and oxidative stress markers. Both Lactobacillus and 5-ASA show significant increase of NrF2 and HO-1 and marked decrease of TNF-α. SIGNIFICANCE Lactobacillus spp. exerted a beneficial effect on the inflammation, oxidative stress and the symbiosis of gut microbiota that improve structural intestinal defect and promote healing in UC.
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Affiliation(s)
- Ahmed M El-Baz
- Microbiology and Biotechnology Department, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa City, Mansoura, Dakhaliya, Egypt.
| | - Ahmed E Khodir
- Pharmacology and Biochemistry Department, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa City, Mansoura, Dakhaliya, Egypt
| | | | - Ahmed Shata
- Clinical Pharmacology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt; Clinical Pharmacy Department, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa City, Mansoura, Dakhaliya, Egypt
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8
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KrishnanNair Geetha D, Sivaraman B, Rammohan R, Venkatapathy N, Solai Ramatchandirane P. A SYBR Green based multiplex Real-Time PCR assay for rapid detection and differentiation of ocular bacterial pathogens. J Microbiol Methods 2020; 171:105875. [PMID: 32087185 DOI: 10.1016/j.mimet.2020.105875] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 11/26/2022]
Abstract
PURPOSE Ocular bacterial pathogenesis is a serious sight threatening infection due to several bacterial species like Staphylococcus aureus, Streptococcus pneumoniae and Pseudomonas aeruginosa which are predominant. It is necessary to expedite diagnosis of pathogens for early treatment. Hence, a SYBR Green based multiplex Real-Time PCR assay coupled with melting curve analysis has been developed for rapid detection and differentiation of Staphylococcus aureus, Streptococcus pneumoniae and Pseudomonas aeruginosa in a single reaction. METHODS The assay was designed for simultaneous detection and differentiation of pathogens based on their distinct melting curve. The analytical specificity, sensitivity and reproducibility of the assay were examined using various reference strains. Clinical validation was carried out with 100 ocular samples collected from patients suffering from ocular infections. RESULT Each reaction tested for the targets individually generated three non overlapping melting curves with well alienated peaks corresponding to each gene. Among 100 ocular samples tested, 40 samples diagnosed with positive results in RT-PCR. Thus assay showed 100% specificity with high sensitivity and reproducibility. CONCLUSION The developed assay consistently established as a rapid and accurate diagnosis of ocular bacterial pathogens compared to the conventional laboratory techniques. Such precise method would aid greatly in clinical management of devastating ocular infections.
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Affiliation(s)
| | - Balaji Sivaraman
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Ram Rammohan
- Aravind Eye Hospital and Postgraduate Institute of Ophthalmology, Coimbatore, Tamil Nadu, India
| | - Narendran Venkatapathy
- Aravind Eye Hospital and Postgraduate Institute of Ophthalmology, Coimbatore, Tamil Nadu, India
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9
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Alhogail S, Suaifan GA, Bikker FJ, Kaman WE, Weber K, Cialla-May D, Popp J, Zourob MM. Rapid Colorimetric Detection of Pseudomonas aeruginosa in Clinical Isolates Using a Magnetic Nanoparticle Biosensor. ACS OMEGA 2019; 4:21684-21688. [PMID: 31891046 PMCID: PMC6933554 DOI: 10.1021/acsomega.9b02080] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 11/08/2019] [Indexed: 05/21/2023]
Abstract
A rapid, sensitive, and specific colorimetric biosensor based on the use of magnetic nanoparticles (MNPs) was designed for the detection of Pseudomonas aeruginosa in clinical samples. The biosensing platform was based on the measurement of P. aeruginosa proteolytic activity using a specific protease substrate. At the N-terminus, this substrate was covalently bound to MNPs and was linked to a gold sensor surface via cystine at the C-terminus of the substrates. The golden sensor appears black to naked eyes because of the coverage of the MNPs. However, upon proteolysis, the cleaved peptide-MNP moieties will be attracted by an external magnet, revealing the golden color of the sensor surface, which can be observed by the naked eye. In vitro, the biosensor was able to detect specifically and quantitatively the presence of P. aeruginosa with a detection limit of 102 cfu/mL in less than 1 min. The colorimetric biosensor was used to test its ability to detect in situ P. aeruginosa in clinical isolates from patients. This biochip is anticipated to be useful as a rapid point-of-care device for the diagnosis of P. aeruginosa-related infections.
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Affiliation(s)
- Sahar Alhogail
- Department
of Clinical Laboratory Science, King Saud
University, Ad Diriyah District, 11433 Riyadh, Kingdom of Saudi
Arabia
- Department
of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al
Takhassusi Road, 11533 Riyadh, Saudi Arabia
| | - Ghadeer A.R.Y. Suaifan
- Department
of Pharmaceutical Sciences, Faculty of Pharmacy, The University of Jordan, 11942 Amman, Jordan
| | - Floris J. Bikker
- Department
of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
| | - Wendy E. Kaman
- Department
of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands
- Department
of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Wytemaweg 80, 3015 CE Rotterdam, The Netherlands
| | - Karina Weber
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Center for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Dana Cialla-May
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Center for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Jürgen Popp
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Center for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Mohammed M. Zourob
- Department
of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al
Takhassusi Road, 11533 Riyadh, Saudi Arabia
- King
Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh 12713, Saudi Arabia
- E-mail:
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Papanicolas LE, Wang Y, Choo JM, Gordon DL, Wesselingh SL, Rogers GB. Optimisation of a propidium monoazide based method to determine the viability of microbes in faecal slurries for transplantation. J Microbiol Methods 2018; 156:40-45. [PMID: 30529117 DOI: 10.1016/j.mimet.2018.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 12/01/2018] [Accepted: 12/03/2018] [Indexed: 02/02/2023]
Abstract
The efficacy of faecal microbiota transplantation (FMT) as a therapeutic intervention may depend on the viability of the microorganisms in faecal slurries (FS) prepared from donor stool. However, determining the viability of these organisms is challenging. Most microorganisms in stool are refractory to culture using standard techniques, and culture-independent PCR-based methods derive signal from both viable and non-viable cells. Propidium monoazide (PMA) treatment has been shown to be effective in preventing PCR amplification of DNA from non-viable bacteria in a range of contexts. However, this methodology can be sensitive to factors such as bacterial load and sample turbidity. We describe the optimisation of a PMA treatment methodology for FS that restricts quantitative PCR-based bacterial enumeration to viable cells. When applied to concentrated FS (10-25% stool content), PMA treatment at 100 μM concentration was ineffective in preventing DNA amplification from heat-killed cells. Efficacy was not significantly improved by doubling the PMA concentration. However, PMA treatment efficacy was improved markedly following 10-fold sample dilution, and was found to be optimal at 100-fold dilution. Substantial reductions in viable bacterial load could be observed following both freeze-thaw and heat-treatment of FS. This method successfully prevented DNA amplification of heat-killed Pseudomonas and Staphylococcus spiked into stool and could reliably determine the proportion of live bacteria and viable E. coli counts present in fresh and heat-treated stool. With appropriate sample dilution, PMA treatment excluded >97% of non-viable cells from amplification in all assays, without significantly affecting the amplification of DNA from viable cells. This method can be applied to optimise sample processing of FMT donor material, and to characterise bacterial viability within faecal samples more widely.
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Affiliation(s)
- Lito E Papanicolas
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia.
| | - Yanan Wang
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Jocelyn M Choo
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - David L Gordon
- Department of Microbiology and Infectious Diseases, Flinders University, Adelaide, South Australia, Australia
| | - Steve L Wesselingh
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Geraint B Rogers
- The South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
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11
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Specific type IV pili groups in clinical isolates of Pseudomonas aeruginosa. Int Microbiol 2018; 22:131-141. [PMID: 30810940 DOI: 10.1007/s10123-018-00035-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/21/2018] [Accepted: 10/04/2018] [Indexed: 01/09/2023]
Abstract
The relationships between specific type IV pili (TFP) groups and antibiotic resistance, biofilm formation, and bacterial motility were determined in 190 Pseudomonas aeruginosa clinical isolates. While motility and biofilm formation were determined by phenotypic assays, the presence of TFP was determined by PCR assay and antibiotic susceptibility by disk diffusion. The results showed a high ability to form biofilm (97.4%), multidrug resistance (44.7%), and the presence of a high number of motile isolates. We also found an association between strong biofilm production and multidrug resistance. Furthermore, TFP group III was associated with strong biofilm production. In contrast, the isolates with TFP group II and those without any TFP were associated with non-strong biofilm production. Regarding motility, TFP group II was associated with higher percentages of swarming, swimming, and twitching, while TFP group I showed lower percentages of swarming and twitching, and TFP group III showed lower levels of swarming and swimming. In conclusion, these findings highlight the differences in P. aeruginosa phenotypes related to the presence of specific TFP groups and their potential implications in clinical settings.
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12
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Prates MCM, Tamashiro E, Proenca-Modena JL, Criado MF, Saturno TH, Oliveira AS, Buzatto GP, Jesus BLS, Jacob MG, Carenzi LR, Demarco RC, Massuda ET, Aragon D, Valera FCP, Arruda E, Anselmo-Lima WT. The Relationship between Colonization by Moraxella catarrhalis and Tonsillar Hypertrophy. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2018; 2018:5406467. [PMID: 30515253 PMCID: PMC6236706 DOI: 10.1155/2018/5406467] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/11/2018] [Indexed: 11/30/2022]
Abstract
We sought to investigate the prevalence of potentially pathogenic bacteria in secretions and tonsillar tissues of children with chronic adenotonsillitis hypertrophy compared to controls. Prospective case-control study comparing patients between 2 and 12 years old who underwent adenotonsillectomy due to chronic adenotonsillar hypertrophy to children without disease. We compared detection of Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis by real-time PCR in palatine tonsils, adenoids, and nasopharyngeal washes obtained from 37 children with and 14 without adenotonsillar hypertrophy. We found high frequency (>50%) of Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, and Pseudomonas aeruginosa in both groups of patients. Although different sampling sites can be infected with more than one bacterium and some bacteria can be detected in different tissues in the same patient, adenoids, palatine tonsils, and nasopharyngeal washes were not uniformly infected by the same bacteria. Adenoids and palatine tonsils of patients with severe adenotonsillar hypertrophy had higher rates of bacterial coinfection. There was good correlation of detection of Moraxella catarrhalis in different sampling sites in patients with more severe tonsillar hypertrophy, suggesting that Moraxella catarrhalis may be associated with the development of more severe hypertrophy, that inflammatory conditions favor colonization by this agent. Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, and Moraxella catarrhalis are frequently detected in palatine tonsils, adenoids, and nasopharyngeal washes in children. Simultaneous detection of Moraxella catarrhalis in adenoids, palatine tonsils, and nasopharyngeal washes was correlated with more severe tonsillar hypertrophy.
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Affiliation(s)
- Mirela C. M. Prates
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Edwin Tamashiro
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - José L. Proenca-Modena
- Department of Cell Biology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
- Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP 13083-970, Brazil
| | - Miriã F. Criado
- Department of Cell Biology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Tamara H. Saturno
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Anibal S. Oliveira
- Department of Cell Biology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Guilherme P. Buzatto
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Bruna L. S. Jesus
- Department of Cell Biology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Marcos G. Jacob
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Lucas R. Carenzi
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Ricardo C. Demarco
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Eduardo T. Massuda
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Davi Aragon
- Department of Pediatrics, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Fabiana C. P. Valera
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Eurico Arruda
- Department of Cell Biology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
| | - Wilma T. Anselmo-Lima
- Department of Ophthalmology, Otorhinolaryngology, Head and Neck Surgery, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP 14049-900, Brazil
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Rapid Pseudomonas Species Identification from Chicken by Integrating Colorimetric Sensors with Near-Infrared Spectroscopy. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-1095-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Peleg AY, Choo JM, Langan KM, Edgeworth D, Keating D, Wilson J, Rogers GB, Kotsimbos T. Antibiotic exposure and interpersonal variance mask the effect of ivacaftor on respiratory microbiota composition. J Cyst Fibros 2017; 17:50-56. [PMID: 29042177 DOI: 10.1016/j.jcf.2017.08.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/03/2017] [Accepted: 08/02/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND G551D is a class III mutation of the cystic fibrosis transmembrane regulator (CFTR) that results in impaired chloride channel function in cystic fibrosis (CF). Ivacaftor, a CFTR-potentiating agent improves sweat chloride, weight, lung function, and pulmonary exacerbation rate in CF patients with G551D mutations, but its effect on the airway microbiome remains poorly characterised. METHODS Twenty CF patients with at least one G551D mutation from a single centre were recruited to a 4month double-blind, placebo-controlled, crossover study of ivacaftor with 28days of active treatment. Sputum microbiota composition was assessed by 16S rRNA gene amplicon sequencing and quantitative PCR at five key time points, along with regular clinical review, respiratory function assessment, and peripheral blood testing. RESULTS No significant difference in microbiota composition was observed in subjects following ivacaftor treatment or placebo (PERMANOVA P=0.95, square root ECV=-4.94, 9479 permutations). Microbiota composition variance was significantly greater between subjects, than within subjects over time (P<0.0001, Mann Whitney U test), and an additional within-patient paired assessment of microbiota similarity was therefore performed. Again, change in microbiota composition was not significantly greater during treatment with ivacaftor compared to placebo (Wilcoxon test, P=0.51). A significant change in microbiota composition was however associated with any change in antibiotic exposure, regardless of whether ivacaftor or placebo was administered (P=0.006). In a small, subgroup analysis of subjects whose antibiotic exposure did not change within the study period, a significant reduction in total bacterial load was observed during treatment with ivacaftor (P=0.004, two-tailed paired Student's t-test). CONCLUSIONS The short-term impact of ivacaftor therapy on sputum microbiota composition in patients with G551D mutations are modest compared to those resulting from antibiotic exposure, and may be masked by changes in antibiotic treatment regimen.
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Affiliation(s)
- Anton Y Peleg
- Department of Infectious Disease, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia; Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Australia
| | - Jocelyn M Choo
- Department Infection & Immunity Theme, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Katherine M Langan
- Department of Infectious Disease, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | | | - Dominic Keating
- Department Respiratory Medicine, The Alfred, Melbourne, Australia; Department of Medicine, Monash University, Melbourne, Australia
| | - John Wilson
- Department Respiratory Medicine, The Alfred, Melbourne, Australia; Department of Medicine, Monash University, Melbourne, Australia
| | - Geraint B Rogers
- Department Infection & Immunity Theme, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Tom Kotsimbos
- Department Respiratory Medicine, The Alfred, Melbourne, Australia; Department of Medicine, Monash University, Melbourne, Australia.
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Vaccination with a recombinant OprL fragment induces a Th17 response and confers serotype-independent protection against Pseudomonas aeruginosa infection in mice. Clin Immunol 2017; 183:354-363. [PMID: 28970186 DOI: 10.1016/j.clim.2017.09.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/06/2017] [Accepted: 09/25/2017] [Indexed: 01/06/2023]
Abstract
Pseudomonas aeruginosa (PA) is the major causative agent of nosocomial infection. Despite of adequate use of antibiotics, it still represents a major challenge in controlling PA infection. The local pulmonary Th17 response plays an important protective role against PA infection. And the Th17-mediated protection is antibody independent, so we hypothesized that it would be an optimal strategy of a vaccine for PA control to induce an effective Th17 response. Herein we report the successful production of a recombinant fragment of the OprL (reOprL) of PA. Purified reOprL forms homogeneous monomers in solution and vaccination with reOprL elicited a remarkable Th17 response. In addition, reOprL vaccination conferred effective serotype-independent protection against PA infection, which relied on the Th17 response. Our data suggest that reOprL is a good candidate for the future development of Th17 immunity based PA vaccines.
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Tang Y, Ali Z, Zou J, Jin G, Zhu J, Yang J, Dai J. Detection methods for Pseudomonas aeruginosa: history and future perspective. RSC Adv 2017. [DOI: 10.1039/c7ra09064a] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The current review summarized and analyzed the development of detection techniques forPseudomonas aeruginosaover the past 50 years.
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Affiliation(s)
- Yongjun Tang
- School of Applied Chemistry and Biotechnology
- Shenzhen Polytechnic
- Shenzhen 518055
- China
| | - Zeeshan Ali
- School of Applied Chemistry and Biotechnology
- Shenzhen Polytechnic
- Shenzhen 518055
- China
| | - Jun Zou
- School of Chemistry and Chemical Engineering
- Hunan Institute of Engineering
- Xiangtan 411104
- China
| | - Gang Jin
- School of Applied Chemistry and Biotechnology
- Shenzhen Polytechnic
- Shenzhen 518055
- China
| | - Junchen Zhu
- School of Applied Chemistry and Biotechnology
- Shenzhen Polytechnic
- Shenzhen 518055
- China
| | - Jian Yang
- School of Applied Chemistry and Biotechnology
- Shenzhen Polytechnic
- Shenzhen 518055
- China
| | - Jianguo Dai
- School of Applied Chemistry and Biotechnology
- Shenzhen Polytechnic
- Shenzhen 518055
- China
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17
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Gadsby NJ, Russell CD, McHugh MP, Mark H, Conway Morris A, Laurenson IF, Hill AT, Templeton KE. Comprehensive Molecular Testing for Respiratory Pathogens in Community-Acquired Pneumonia. Clin Infect Dis 2016; 62:817-823. [PMID: 26747825 PMCID: PMC4787606 DOI: 10.1093/cid/civ1214] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/24/2015] [Indexed: 01/22/2023] Open
Abstract
Background. The frequent lack of a microbiological diagnosis in community-acquired pneumonia (CAP) impairs pathogen-directed antimicrobial therapy. This study assessed the use of comprehensive multibacterial, multiviral molecular testing, including quantification, in adults hospitalized with CAP. Methods. Clinical and laboratory data were collected for 323 adults with radiologically-confirmed CAP admitted to 2 UK tertiary care hospitals. Sputum (96%) or endotracheal aspirate (4%) specimens were cultured as per routine practice and also tested with fast multiplex real-time polymerase-chain reaction (PCR) assays for 26 respiratory bacteria and viruses. Bacterial loads were also calculated for 8 bacterial pathogens. Appropriate pathogen-directed therapy was retrospectively assessed using national guidelines adapted for local antimicrobial susceptibility patterns. Results. Comprehensive molecular testing of single lower respiratory tract (LRT) specimens achieved pathogen detection in 87% of CAP patients compared with 39% with culture-based methods. Haemophilus influenzae and Streptococcus pneumoniae were the main agents detected, along with a wide variety of typical and atypical pathogens. Viruses were present in 30% of cases; 82% of these were codetections with bacteria. Most (85%) patients had received antimicrobials in the 72 hours before admission. Of these, 78% had a bacterial pathogen detected by PCR but only 32% were culture-positive (P < .0001). Molecular testing had the potential to enable de-escalation in number and/or spectrum of antimicrobials in 77% of patients. Conclusions. Comprehensive molecular testing significantly improves pathogen detection in CAP, particularly in antimicrobial-exposed patients, and requires only a single LRT specimen. It also has the potential to enable early de-escalation from broad-spectrum empirical antimicrobials to pathogen-directed therapy.
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Affiliation(s)
- Naomi J Gadsby
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | - Clark D Russell
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh.,College of Medicine and Veterinary Medicine, University of Edinburgh
| | - Martin P McHugh
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | - Harriet Mark
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | | | - Ian F Laurenson
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
| | - Adam T Hill
- Respiratory Medicine, Royal Infirmary of Edinburgh, United Kingdom
| | - Kate E Templeton
- Medical Microbiology, Department of Laboratory Medicine, Royal Infirmary of Edinburgh
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Varposhti M, Entezari F, Feizabadi MM. Synergistic interactions in mixed-species biofilms of pathogenic bacteria from the respiratory tract. Rev Soc Bras Med Trop 2015; 47:649-52. [PMID: 25467269 DOI: 10.1590/0037-8682-0262-2013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/09/2014] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Mixed-species biofilms are involved in a wide variety of infections. We studied the synergistic interactions during dual-species biofilm formation among isolates of Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia. METHODS Isolates were cultured as single-species and all possible combinations of dual-species biofilms. RESULTS The 61 A. baumannii biofilms increased by 26-fold when cultured with S. maltophilia isolates; 62 A. baumannii biofilms increased by 20-fold when cultured with S. maltophilia isolates; and 31 P. aeruginosa biofilms increased by 102-fold when cultured with S. maltophilia 106. CONCLUSIONS Synergy was observed between two isolates, including those that inherently lacked biofilm formation ability.
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Affiliation(s)
- Maryam Varposhti
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Entezari
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Shen H, Zhu B, Wang S, Mo H, Wang J, Li J, Zhang C, Zeng H, Guan L, Shi W, Zhang Y, Ma X. Association of targeted multiplex PCR with resequencing microarray for the detection of multiple respiratory pathogens. Front Microbiol 2015; 6:532. [PMID: 26074910 PMCID: PMC4446546 DOI: 10.3389/fmicb.2015.00532] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/14/2015] [Indexed: 11/24/2022] Open
Abstract
A large number of viral and bacterial organisms are responsible for community-acquired pneumonia (CAP) which contributes to substantial burden on health management. A new resequencing microarray (RPM-IVDC1) associated with targeted multiplex PCR was recently developed and validated for multiple respiratory viruses detection and discrimination. In this study, we evaluated the capability of RPM-IVDC1 for simultaneous identification of multiple viral and bacterial organisms. The nasopharyngeal aspirates (NPAs) of 110 consecutive CAP patients, aged from 1 month to 96 years old, were collected from five distinct general hospitals in Beijing during 1-year period. The samples were subjected to the RPM-IVDC1 established protocol as compared to a real-time PCR (qRT-PCR), which was used as standard. The results of virus detection were consistent with those previously described. A total of 37 of Streptococcus pneumoniae, 14 of Haemophilus influenzae, 10 of Mycoplasma pneumoniae, two of Klebsiella pneumoniae and one of Moraxella catarrhalis were detected by RPM-IVDC1. The sensitivities and specificities were compared with those of qRT-PCR for S. pneumoniae (100, 100%, respectively), H. influenzae (92.3, 97.9%, respectively), M. pneumoniae (69.2, 99.0%, respectively), K. pneumoniae (100, 100%, respectively), and M. catarrhalis (100, 100%, respectively). Additional 22 of Streptococcus spp., 24 of Haemophilus spp. and 16 of Neisseria spp. were identified. In addition, methicillin-resistant and carbapenemases allele were also found in nine of Staphylococcus spp. and one of K. pneumoniae, respectively. These results demonstrated the capability of RPM-IVDC1 for simultaneous detection of broad-spectrum respiratory pathogens in complex backgrounds and the advantage of accessing to the actual sequences, showing great potential use of epidemic outbreak investigation. The detection results should be carefully interpreted when introducing this technique in the clinical diagnostics.
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Affiliation(s)
- Hongwei Shen
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China ; Futian District Center for Disease Control and Prevention Shenzhen, China
| | - Bingqing Zhu
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention Beijing, China
| | - Shulian Wang
- Third Hospital of Beijing Armed Police Corps Laboratory Beijing, China
| | - Haolian Mo
- Futian District Center for Disease Control and Prevention Shenzhen, China
| | - Ji Wang
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China
| | - Jin Li
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China
| | - Chen Zhang
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China
| | - Huashu Zeng
- Futian District Center for Disease Control and Prevention Shenzhen, China
| | - Li Guan
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China
| | - Weixian Shi
- Beijing Center for Disease Control and Prevention, Institute for Infectious Disease and Endemic Disease Control Beijing, China
| | - Yong Zhang
- Futian District Center for Disease Control and Prevention Shenzhen, China
| | - Xuejun Ma
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China
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The effect of long-term macrolide treatment on respiratory microbiota composition in non-cystic fibrosis bronchiectasis: an analysis from the randomised, double-blind, placebo-controlled BLESS trial. THE LANCET RESPIRATORY MEDICINE 2014; 2:988-96. [DOI: 10.1016/s2213-2600(14)70213-9] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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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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Kozlowska J, Rivett DW, Vermeer LS, Carroll MP, Bruce KD, Mason AJ, Rogers GB. A relationship between Pseudomonal growth behaviour and cystic fibrosis patient lung function identified in a metabolomic investigation. Metabolomics 2013; 9:10.1007/s11306-013-0538-5. [PMID: 24367285 PMCID: PMC3868936 DOI: 10.1007/s11306-013-0538-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chronic polymicrobial lung infections in adult cystic fibrosis patients are typically dominated by high levels of Pseudomonas aeruginosa. Determining the impact of P. aeruginosa growth on airway secretion composition is fundamental to understanding both the behaviour of this pathogen in vivo, and its relationship with other potential colonising species. We hypothesised that the marked differences in the phenotypes of clinical isolates would be reflected in the metabolite composition of spent culture media. 1H NMR spectroscopy was used to characterise the impact of P. aeruginosa growth on a synthetic medium as part of an in vitro CF lower airways model system. Comparisons of 15 CF clinical isolates were made and four distinct metabolomic clusters identified. Highly significant relationships between P. aeruginosa isolate cluster membership and both patient lung function (FEV1) and spent culture pH were identified. This link between clinical isolate growth behaviour and FEV1 indicates characterisation of P. aeruginosa growth may find application in predicting patient lung function while the significant divergence in metabolite production and consumption observed between CF clinical isolates suggests dominant isolate characteristics have the potential to play both a selective role in microbiota composition and influence pseudomonal behaviour in vivo.
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Affiliation(s)
- Justyna Kozlowska
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Damian W. Rivett
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Louic S. Vermeer
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Mary P. Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, SO16 6YD, UK
| | - Kenneth D. Bruce
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - A. James Mason
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Geraint B. Rogers
- Institute of Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
- For correspondence:
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Complexity, temporal stability, and clinical correlates of airway bacterial community composition in primary ciliary dyskinesia. J Clin Microbiol 2013; 51:4029-35. [PMID: 24068019 DOI: 10.1128/jcm.02164-13] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is a genetic disease characterized by abnormalities in ciliary function, leading to compromised airway clearance and chronic bacterial infection of the upper and lower airways. The compositions of these infections and the relationships between their characteristics and disease presentation are poorly defined. We describe here the first systematic culture-independent evaluation of lower airway bacteriology in PCD. Thirty-three airway samples (26 from sputum, 7 from bronchoalveolar lavage [BAL] fluid) were collected from 24 PCD patients aged 4 to 73 years. 16S rRNA quantitative PCR and pyrosequencing were used to determine the bacterial loads and community compositions of the samples. Bacterial loads, which ranged from 1.3 × 10(4) to 5.2 × 10(9) CFU/ml, were positively correlated with age (P = 0.002) but not lung function. An analysis of ∼7,000 16S rRNA sequences per sample identified bacterial species belonging to 128 genera. The concurrently collected paired samples showed high bacterial community similarity. The mean relative abundance of the dominant genera was 64.5% (standard deviation [SD], 24.5), including taxa reported through standard diagnostic microbiology (members of the genera Pseudomonas, Haemophilus, and Streptococcus) and those requiring specific ex vivo growth conditions (members of the genera Prevotella and Porphyromonas). The significant correlations observed included a positive relationship between Pseudomonas aeruginosa relative abundance and age and a negative relationship between P. aeruginosa relative abundance and lung function. Members of the genus Ralstonia were also found to contribute substantially to the bacterial communities in a number of patients. Follow-up samples from a subset of patients revealed high levels of bacterial community temporal stability. The detailed microbiological characterization presented here provides a basis for the reassessment of the clinical management of PCD airway infections.
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Robinson KM, Alcorn JF. T-Cell Immunotherapy in Cystic Fibrosis. Am J Respir Crit Care Med 2013; 187:564-6. [DOI: 10.1164/rccm.201212-2201ed] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Fard S, Nomanpour B, Fatolahzadeh B, Mobarez A, Darban-Sarokhalil D, Fooladi A, Leeuwen W, Feizabadi M. Hospital acquired pneumonia: comparison of culture and real-time PCR assays for detection of Legionella pneumophila from respiratory specimens at Tehran hospitals. Acta Microbiol Immunol Hung 2012; 59:355-65. [PMID: 22982639 DOI: 10.1556/amicr.59.2012.3.6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Legionella pneumophila is an important etiological agent in both hospital and community acquired pneumonia. The sensitivity of culture for isolation of L. pneumophila from clinical specimens is low and time consuming. Similar problem also exists when the method of direct immunofluorescence is used. To detect this organism quantitatively from respiratory specimens, a Taq Man based real-time PCR targeting the mip sequence was developed. Both real-time PCR and culture methods were applied on 262 respiratory specimens from 262 ICU patients with pneumonia admitted to 5 different hospitals in Tehran. The results of real-time PCR were compared with those obtained by culture. Real-time PCR and culture found 12 and 4 specimens, respectively, as positive for L. pneumophila. Its technical specificity (100%) was checked against a panel of microorganisms consisting of both Gram-positive and Gram-negative bacteria. Our real-time PCR assay showed high sensitivity (100%) and specificity (96.9%) and could detect 200 organisms per ml from respiratory specimens. Using real-time PCR as a screening method, the frequency of nosocomial pneumonia with L. pneumophila at Tehran hospitals was estimated as 4.58%.
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Affiliation(s)
- Somayeh Fard
- 1 Tehran University of Medical of Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Bizhan Nomanpour
- 1 Tehran University of Medical of Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Bahram Fatolahzadeh
- 1 Tehran University of Medical of Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Ashraf Mobarez
- 2 Tarbiat Modares University Department of Bacteriology, School of Medicine Tehran Iran
| | | | - Abbas Fooladi
- 4 Baqiyatallah University of Medical Sciences Applied Microbiology Research Center Tehran Iran
| | | | - Mohammad Feizabadi
- 1 Tehran University of Medical of Sciences Department of Microbiology, School of Medicine Tehran Iran
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Nomanpour B, Ghodousi A, Babaei T, Jafari S, Feizabadi M. Single tube real time PCR for detection of Streptococcus pneumoniae, Mycoplasma pneumoniae, Chlamydophila pneumoniae and Legionella pneumophila from clinical samples of CAP. Acta Microbiol Immunol Hung 2012; 59:171-84. [PMID: 22750778 DOI: 10.1556/amicr.59.2012.2.3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We designed a multiplex real time PCR for rapid, sensitive and specific detection of Streptococcus pneumoniae, Legionella pneumophila, Chlamydophila pneumoniae and Mycoplasma pneumoniae. The study cases consisted of 129 patients with community acquired pneumonia (CAP). Bacteriological techniques were implemented for detection of the cultivable organisms. DNA were extracted from sputa, throat swabs, bronchoalveolar lavages and tracheal aspirates and used as templates in real time PCR. The primers and probes were designed for cbpA (S. pneumoniae), p1adhesin (M. pneumoniae), mip (L. pneumophila) and ompA (C. pneumoniae). After optimization of real time PCR for every organism, the experiments were continued in multiplex in a single tube. Of 129 CAP specimens, the positive cultures included 14 (10.85%) for S. pneumoniae, 9 (6.98%) for L. pneumophila and 3 (2.33%) for M. pneumoniae. Four specimens (3.10%) were positive for C. pneumoniae by real time PCR. The sensitivity of our real time PCR was 100% for all selected bacteria. The specificity of the test was 98.26%, 98.34%, 100% and 100% for S. pneumoniae, L. pneumophila, M. pneumoniae and C. pneumoniae, respectively. This is the first report on the use of multiplex real time PCR for detection of CAP patients in the Middle East. The method covers more than 90% of the bacterial pathogens causing CAP.
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Affiliation(s)
- Bizhan Nomanpour
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Arash Ghodousi
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Toraj Babaei
- 2 Shaheed Rajaie Cardiovascular Medical & Research Center Department of Cardiac Anesthesiology Tehran Iran
| | - Siroos Jafari
- 3 Tehran University of Medical Sciences Department of Infectious Disease, School of Medicine Tehran Iran
| | - Mohammad Feizabadi
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
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Abstract
Evidenced-based-wound management continues to be a cornerstone for advancing patient care. The purpose of this article is to review the use of whirlpool as a wound treatment in light of evidence, outcomes, and potential harm. Whirlpool was initially harnessed as a means to impart biophysical energy to a wound or burn to enhance mechanical debridement and cleansing. Other credible single-patient-use technologies which provide an alternative to whirlpool in wound care are presented.
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Affiliation(s)
- Hanz Tao
- University of Colorado, Anschutz Medical Campus, Denver, CO, USA
| | - Jaime P Butler
- Littleton Adventist Hospital, Centura Health, Denver, CO, USA
| | - Tammy Luttrell
- National Jewish Health, Colorado University, Anschutz Medical Campus, Denver, CO, USA ; TCL Consulting Inc., USA
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Lee CS, Wetzel K, Buckley T, Wozniak D, Lee J. Rapid and sensitive detection of Pseudomonas aeruginosa in chlorinated water and aerosols targeting gyrB gene using real-time PCR. J Appl Microbiol 2011; 111:893-903. [PMID: 21794031 PMCID: PMC3173516 DOI: 10.1111/j.1365-2672.2011.05107.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
AIMS For the rapid detection of Pseudomonas aeruginosa from chlorinated water and aerosols, gyrB gene-based real-time PCR assay was developed and investigated. METHODS AND RESULTS Two novel primer sets (pa722F/746MGB/899R and pa722F/746MGB/788R) were designed using the most updated 611 Pseudomonas and 748 other bacterial gyrB genes for achieving high specificity. Their specificity showed 100% accuracy when tested with various strains including clinical isolates from cystic fibrosis patients. The assay was tested with Ps. aeruginosa-containing chlorinated water and aerosols to simulate the waterborne and airborne transmission routes (detection limit 3·3 × 10² CFU per PCR-2·3 × 10³ CFU per PCR). No chlorine interference in real-time PCR was observed at drinking water level (c. 1 mg l⁻¹), but high level of chorine (12 mg l⁻¹) interfered the assay, and thus neutralization was needed. Pseudomonas aeruginosa in aerosol was successfully detected after capturing with gelatin filters with minimum 2 min of sampling time when the initial concentration of 10⁴ CFU ml⁻¹ bacteria existed in the nebulizer. CONCLUSIONS A highly specific and rapid assay (2-3 h) was developed by targeting gyrB gene for the detection of Ps. aeruginosa in chlorinated water and aerosols, combined with optimized sample collection methods and sample processing, so the direct DNA extraction from either water or aerosol was possible while achieving the desired sensitivity of the method. SIGNIFICANCE AND IMPACT OF THE STUDY The new assay can provide timely and accurate risk assessment to prevent Ps. aeruginosa exposure from water and aerosol, resulting in reduced disease burden, especially among immune-compromised and susceptible individuals. This approach can be easily utilized as a platform technology for the detection of other types of micro-organisms, especially for those that are transmitted via water and aerosol routes, such as Legionella pneumophila.
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Affiliation(s)
- C S Lee
- College of Public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, OH 43210, USA.
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